The South African SDG Hub

Matching results: 100

Maximum Results:

Sort By:

SDG 14

Reef Sedimentary Accretion Model (ReefSAM): Understanding coral reef evolution on Holocene time scales using 3D stratigraphic forward modelling
03 December 2019
University of Sydney

Barrett, Samuel Jonathan;Webster, Jody Michael

A detailed understanding of the development of coral reefs and their internal structure has important applications for predicting future reef trajectories in light of climate changes, petroleum exploration and reconstructing past environmental changes such as sea level. Numerical computer modelling provides a quantitative means of testing and understanding reef processes and better predicting past and future reef development. However, most existing carbonate stratigraphic forward models (SFMs) focus on the platform scale and several limitations in their simulation of important reef processes and reef-scale features (e.g. patch reefs, sand aprons) have been previously identified. We present the Reef Sedimentary Accretion Model (ReefSAM) – a new carbonate SFM designed to test new approaches to modelling processes important at the reef scale, with the goal of better simulating reef features and evolution at higher temporal and spatial resolutions. Specific developments include a sediment transport model which calculates deposition based on a range of grain sizes, additional controls on coralgal growth including wave energy and surface substrate specificity, and model outputs showing categorized paleo-conditions (composition, paleo-depth and paleo-energy) along with numerous quantitative measures for objective comparison of model results to real-world observational data, which is often more abundant for modern/Holocene reefs than buried ancient reefs. Simulations of the well-studied Holocene One Tree Reef (OTR) in the southern Great Barrier Reef (GBR) showed improvements upon previous modelling attempts in both quantitative measures (e.g. lagoon size or reef sea level catch-up time), and the ability to produce more realistic reef-scale morphological features (e.g. lagoonal patch-reefs, mostly sand-filled lagoon) and reef development characteristics (e.g. transition from mostly vertical aggradation during sea level catch-up to horizontal progradation afterwards). Controls on reef maturity/lagoonal filling identified in previous modelling experiments were corroborated. Sensitivity testing also revealed a very high sensitivity to reef drowning. These results indicate the new modelling approaches are viable and provide a way forward for future Holocene reef evolution model development
Substrate range and enantioselectivity of epoxidation reactions mediated by the ethene-oxidising Mycobacterium strain NBB4
13 December 2019
University of Sydney

Cheung, Samantha;McCarl, Victoria;Holmes, Andrew;Coleman, Nicholas;Rutledge, Peter J

Mycobacterium strain NBB4 is an ethene-oxidizing micro-organism isolated from the estuarine sediments of Botany Bay. In pursuit of new systems for biocatalytic epoxidation, we report the capacity of strain NBB4 to convert a diverse range of alkene substrates to epoxides. A colorimetric assay based on 4-(4- nitrobenzyl)pyridine (NBP) has been developed to allow the rapid characterisation and quantification of biocatalytic epoxide synthesis. Using this assay we have demonstrated that ethene-grown NBB4 cells epoxidise a wide range of alkenes, including terminal (propene, 1-butene, 1-hexene, 1-octene and 1-decene), cyclic (cyclopentene, cyclohexene), aromatic (styrene, indene), and functionalised substrates (allyl alcohol, dihydropyran and isoprene). Apparent specific activities have been determined and range from 2.5 to 12.0 nmol min-1 per milligram of cell protein. The enantioselectivity of epoxidation by Mycobacterium strain NBB4 has been established using styrene as a test substrate; (R)-styrene oxide is produced in enantiomeric excesses greater than 95%. Thus the ethene monooxygenase of Mycobacterium NBB4 has a broad substrate range and promising enantioselectivity, confirming its potential as a biocatalyst for alkene epoxidation.
Total Synthesis of Polydiscamides B, C, and D via a Convergent Native Chemical Ligation–Oxidation Strategy
19 June 2020
University of Sydney

Santhakumar, Gajan;Payne, Richard J.

The first total syntheses of the marine sponge-derived cyclic depsipeptide natural products Polydiscamides B, C, and D are described. The molecules were constructed through the convergent fusion of cyclic and linear fragments via an unprecedented native chemical ligation–oxidation protocol.
Towards Adaptive Benthic Habitat Mapping
05 November 2020
University of Sydney

Shields, Jackson;Pizarro, Oscar;Williams, Stefan Bernard

Autonomous Underwater Vehicles (AUVs) are increasingly being used to support scientific research and monitoring studies. One such application is in benthic habitat mapping where these vehicles collect seafloor imagery that complements broadscale bathymetric data collected using sonar. Using these two data sources, the relationship between remotely-sensed acoustic data and the sampled imagery can be learned, creating a habitat model. As the areas to be mapped are often very large and AUV systems collecting seafloor imagery can only sample from a small portion of the survey area, the information gathered should be maximised for each deployment. This paper illustrates how the habitat models themselves can be used to plan more efficient AUV surveys by identifying where to collect further samples in order to most improve the habitat model. A Bayesian neural network is used to predict visually-derived habitat classes when given broad-scale bathymetric data. This network can also estimate the uncertainty associated with a prediction, which can be deconstructed into its aleatoric (data) and epistemic (model) components. We demonstrate how these structured uncertainty estimates can be utilised to improve the model with fewer samples. Such adaptive approaches to benthic surveys have the potential to reduce costs by prioritizing further sampling efforts. We illustrate the effectiveness of the proposed approach using data collected by an AUV on offshore reefs in Tasmania, Australia.
Multimodal learning and inference from visual and remotely sensed data
05 November 2020
University of Sydney

Rao, Dushyant;De Deuge, Mark;Nourani-Vatani, Navid;Williams, Stefan Bernard;Pizarro, Oscar

Autonomous vehicles are often tasked to explore unseen environments, aiming to acquire and understand large amounts of visual image data and other sensory information. In such scenarios, remote sensing data may be available a priori, and can help to build a semantic model of the environment and plan future autonomous missions. In this paper, we introduce two multimodal learning algorithms to model the relationship between visual images taken by an autonomous underwater vehicle during a survey and remotely sensed acoustic bathymetry (ocean depth) data that is available prior to the survey. We present a multi-layer architecture to capture the joint distribution between the bathymetry and visual modalities. We then propose an extension based on gated feature learning models, which allows the model to cluster the input data in an unsupervised fashion and predict visual image features using just the ocean depth information. Our experiments demonstrate that multimodal learning improves semantic classification accuracy regardless of which modalities are available at classification time, allows for unsupervised clustering of either or both modalities, and can facilitate mission planning by enabling class-based or image-based queries.
Virome composition in marine fish revealed by meta-transcriptomics
10 June 2021
University of Sydney

Geoghegan, J.L.;Di Giallonardo, F.;Wille, M.;Ortiz-Baez, A.S.;Costa, V.A.;Ghaly, T.;Mifsud, J.C.O.;Turnbull, O.M.H.;Bellwood, D.R.;Williamson, J.E.;Holmes, E.C.

Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, negative-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae, and Flaviviridae, and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition - viral richness, abundance, and diversity - can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi, and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
Antifouling Properties of Liquid-Infused Riblets Fabricated by Direct Contactless Microfabrication
22 November 2021
University of Sydney

Fenati, Renzo A.;Quinn, Mitchell S.;Bilinksy, Henry C.;Neto, Chiara

The fabrication of riblets and surfaces structured with aligned grooves, by direct contactless microfabrication (DCM), and the ability of the riblets to function as lubricant-infused surfaces, is reported. Three types of riblets are fabricated with features (width, height, and period) on the micrometric scale, and with two different UV-crosslinkable coatings. Riblets with width 10 μm, period 40 μm, and height 30 μm show high water repellence as prepared (water contact angle [WCA] 147 ) and, once infused with silicone oil 10 cSt, result in water droplets rolling off the surface at tilt angles of 10 . These riblets are effective at reducing the attachment of marine bacteria, both in the as-prepared and infused form. The DCM process produces structured surfaces over large areas (10 10 cm2) in a few minutes and using inexpensive materials, making mechanically robust surfaces. The DCM process is scalable to the large surface areas required for marine and other applications. The low roll-off angles and the bacterial inhibition results achieved on the riblets indicate that riblets are an up-scalable and nontoxic alternative to more complicated fabricated techniques, with potential as antifouling and drag-reducing coatings.
A review of environmental contamination and potential health impacts on aquatic life from the active chemicals in sunscreen formulations
15 March 2022
University of Sydney

Wheate, Nial

The active chemicals in sunscreen formulations are released into the environment from human skin, and found in recreational-use waters like seawater, but can also be washed into fresh water from bathing and showering. The level of sunscreen chemicals found in samples varies considerably between regions, time of year (higher in summer months), and time of day. Average typical concentrations are only in the nanograms per litre (ng L−1) range in marine and fresh water systems, and typically, the highest levels are in waste-water sludge because of a concentrating effect during the treatment process. From numerous studies, it is known that the active chemicals in sunscreens can have potential hormonal/oestrogenic activity and non-hormonal effects, including: acting as teratogens, altering gene regulation, inducing changes in antioxidant and free radical production, and inducing coral bleaching. However, the effects of sunscreens on aquatic life under laboratory conditions typically occur only at concentrations (µg or mg L−1) that far exceed (10–10 000-fold) levels found in the environment. As such, when damage does occur to reefs and animal life, there are often other causes that are more likely impacting the aquatic life including changes in water temperature, water turbidity, elevated nutrient levels, and the presence of pesticides and medicines used for human and animal health.
Marine Antifouling Behavior of Lubricant-Infused Nanowrinkled Polymeric Surfaces
25 March 2022
University of Sydney

Ware, Cameron S.;Smith-Palmer, Truis;Peppou-Chapman, Sam;Scarratt, Liam R.J.;Humphries, Erin M.;Balzer, D.;Neto, Chiara

A new family of polymeric, lubricant-infused, nanostructured wrinkled surfaces was designed that effectively retains inert non-toxic silicone oil, upon draining by spin-coating and vigorous shear for two weeks. The wrinkled surfaces were fabricated using three different polymers (Teflon AF, polystyrene, and poly(4-vinylpyridine)) and two shrinkable substrates (polyshrink and shrinkwrap), and Teflon on polyshrink was found to be the most effective system. The volume of trapped lubricant was quantified by adding Nile red to the silicone oil before infusion, then extracting the oil and Nile red from the surfaces in heptane and measuring by fluorimetry. Higher volumes of lubricant induced lower roll-off angles for water droplets, and in turn induced better antifouling performance. The infused surfaces displayed stability in seawater and inhibited growth of Pseudoalteromonas spp. bacteria up to 99%, with as little as 0.9 μL cm-2 of silicone oil infused. Field tests in the waters of Sydney Harbour over seven weeks showed that silicone oil infusion inhibited the attachment of algae, but as the silicone oil was slowly depleted over time algal attachment increased. The infused wrinkled surfaces have high transparency and are moldable, making them suited to protecting the windows of underwater sensors and cameras.
Parting the Waves: Claims to Maritime Jurisdiction and the Division of Ocean Space
13 April 2012
University of Pennsylvania

Schofield, Clive

This article casts aside traditional obsessions and examines the development and present state of coastal State claims to maritime jurisdiction, the overlapping claims to maritime space that have inevitably resulted from the significant extension of maritime claims in recent decades, and thus the delimitation of maritime boundaries.
The Opportunity Costs of Ignoring the Law of Sea Convention in the Arctic
01 January 2013
University of Pennsylvania

Houck, James W.

The paper begins by briefly surveying the extent to which the convention’s provisions intersect with United States interests in the Arctic. Not surprisingly, there is extensive overlap. The paper then reviews arguments that UNCLOS is irrelevant or even antithetical to achieving these important U.S. interests. After critiquing the anti-UNCLOS arguments, the paper examines the case for UNCLOS. The paper focuses in particular on U.S. interests on the Arctic seafloor, arguing that these interests are extensive and that accession would help avert a wide range of potential political, legal, and regulatory challenges from foreign governments and corporations. The possibility of such challenges creates political and legal uncertainty as long as the United States remains outside the convention and provides a bona fide disincentive for U.S.-licensed corporations to undertake the type of exploration and development activities necessary to realize a host of offshore benefits. Moreover, by staying outside UNCLOS, the United States is forfeiting an opportunity to reinforce a favorable Arctic legal regime that could face pressure from non-Arctic nations in the future. The paper concludes by recommending that the U.S. accede to UNCLOS at the soonest opportunity.
The Clash of the Acts: FEMA'sImplementation of the National FloodInsurance Program and its Collision with theEndangered Species Act and the NationalEnvironmental Policy Act
01 January 2019
University of Pennsylvania

Esenyan, Ani

The Federal Emergency Management Agency (FEMA) administers the National Flood Insurance Program (NFIP), a federal flood insurance program that also aims to prevent flooding in flood-prone areas. However, the structure and implementation of the NFIP has created mixed results. FEMA's implementation of the NFIP has been found to inadvertently incentivize unsustainable floodplain development, which in turn threatens species and their habitats protected by the Endangered Species Act (ESA). Over the years, FEMA has engaged in lawsuits and settlements regarding its implementation of the NFIP. As a result of these lawsuits, the National Marine Fisheries Service (NMFS) conducted scientific studies, known as biological opinions (BiOp), which found that three particular components of FEMA's implementation of the NFIP are at the root of FEMA's ESA-noncompliance issues. Additionally, one of these lawsuits resulted in a settlement which required FEMA to conduct a Nationwide Programmatic Environmental Impact Statement (NPEIS), a tool that comes from the National Environmental Policy Act (NEPA), evaluating the environmental impacts of the NFIP. The NPEIS was published in November 2017. In the NPEIS, FEMA asserts that its implementation of the NFIP does not impact floodplain development, and that the agency is compliant with the ESA. Accordingly, in the NPEIS, FEMA suggests four alternatives to the way the NFIP is currently implemented. Then, in May 2018, FEMA issued the Record of Decision (ROD), which finalizes FEMA's decision to implement the NPEIS's Preferred Alternative. The Preferred Alternative requires NFIP communities, meaning state and local governments, to "obtain and maintain documentation" of ESA compliance as a condition to issue floodplain development permits. This Comment provides an overview of the NFIP, the ESA, the litigation and consultation history, the NPEIS, the ROD, and makes three conclusions: (1) FEMA's imposition of ESA requirements on state and local governments is an impermissible shift of its own ESAresponsibilities onto parties who have no legal obligation to comply with the ESA; (2) FEMA lacks the authority to enforce its preferred alternative under the existing regulation; and (3) the ESA compliance requirement of the alternatives is a significant burden on NFIP communities. Based on these conclusions, FEMA's implementation of its Preferred Alternative is unwise.
Sustainable Ecolabelled Seafood from the East China Sea: Regional and General Regulatory Regimes
01 January 2020
University of Pennsylvania

Lin, Platinasoka

The aim of this work is to conduct a systematical review of fisheries management and to be an easy-understood guidebook for building an ecolabelling scheme of fisheries in the East China Sea, and also for Asian countries having plights of lacking good marine scientific research, advanced fisheries management, and public marine conservation awareness. For this purpose, details of ecolabelling mechanism and the definitions of sustainable seafood are explored and a scoring checklist for ecolabelled seafood is created as a check tool, together with a certification standard named "ProFish." This work examines multiple types of legal documents, among them international conventions related to fisheries and marine protected area, FAO agreements, WTO fisheries subsidies negotiation history and existing fisheries agreement sin the East China Sea, Landing Declaration and Sales Notes in the European Union and Norway, to seek legal tools and guidelines that can help Taiwan upgrade fisheries managements and marine health status better. Domestic fisheries regulations of East China Sea littoral countries, including Japan and China, are comprehensively compared. The ownership of and the legal transfer of property in marine life, capital-labor relations in fisheries, input and output controls over fishing capability, and fishery managers identity are illustrated in detail. Furthermore, sharks, crabs, mackerels, neritic squid, and mahi-mahi fishing regulations among Taiwan, Japan and China are reviewed thoroughly. Preliminary assessments of five fisheries in Taiwan are evaluated by ProFish checklist, and mackerel has the highest potential to become the first seafood certified as a sustainable ecolabel. This work concludes that a more centralized fisheries management competent authority can resolve most obstacles. A quasi-governmental-based accreditation organization is suggested for the government first in order to promote a seafood ecolabelling scheme smoothly in Taiwan. Establishing a Ministry of Oceans and Fisheries is important. It is vital to introduce AI technologies into fisheries management measures to meet the need of monitoring and surveillance fishing activities at any time. Setting up nanometer-sized marine protected areas first to form a netowrk is the best policy in politically-difficult regions. Reducing the fishboat fuel subsidy and introducing a higher subsidy for mandatory closed fishing seasons is necessary to develop a sustainable fishery industry.
From Lake Nyassa to Philadelphia: a geography of the Zambesi Expedition, 1858-64
14 February 2006
University of Edinburgh

Dritsas, Lawrence

This paper is about collecting, travel and the geographies of science. At one level it examines the circumstances that led to Isaac Lea’s description in Philadelphia of six freshwater mussel shells of the family Unionidae, originally collected by John Kirk during David Livingstone’s Zambesi Expedition, 1858–64. At another level it is about how travel is necessary in the making of scientific knowledge. Following these shells from south-eastern Africa to Philadelphia via London elucidates the journeys necessary for Kirk and Lea’s scientific work to progress and illustrates that the production of what was held to be malacological knowledge occurred through collaborative endeavours that required the travel of the specimens themselves. Intermediaries in London acted to link the expedition, Kirk’s efforts and Lea’s classification across three continents and to facilitate the novel description of six species of freshwater mussel. The paper demonstrates the role of travel in the making of mid-nineteenthcentury natural history and in developing the relationships and credibility necessary to perform the research on which classifications undertaken elsewhere were based.
Correlations in the chemical composition of rural background atmospheric aerosol in the UK determined in real time using time-of-flight mass spectrometry
05 October 2006
University of Edinburgh

Beddows, David C S;Donovan, Robert J;Harrison, Roy M;Heal, Mathew R;Kinnersley, Robert P;King, Martin;Nicholson, David;Thompson, Katherine

An aerosol time-of-flight mass spectrometer (ATOFMS) was used to determine, in real time, the size and chemical composition of individual particles in the atmosphere at the remote inland site of Eskdalemuir, Scotland. A total of 51980 particles, in the size range 0.3–7.4 µm, were detected between the 25th and 30th June 2001. Rapid changes in the number density, size and chemical composition of the atmospheric aerosol were observed. These changes are attributed to two distinct types of air mass; a polluted air mass that had passed over the British mainland before reaching Eskdalemuir, interposed between two cleaner air masses that had arrived directly from the sea. Such changes in the background aerosol could clearly be very important to studies of urban aerosols and attempts at source apportionment. The results of an objective method of data analysis are presented. Correlations were sought between the occurrence of: lithium, potassium, rubidium, caesium, beryllium, strontium, barium, ammonium, amines, nitrate, nitrite, boron, mercury, sulfate, phosphate, fluorine, chlorine, bromine, iodine and carbon (both elemental and organic hydrocarbon) in both fine (d 2.5 µm) particle fractions. Several previously unreported correlations were observed, for instance between the elements lithium, beryllium and boron. The results suggest that about 2 in 3 of all fine particles (by number rather than by mass), and 1 in 2 of all coarse particles containing carbon, consisted of elemental carbon rather than organic hydrocarbon (although a bias in the sensitivity of the ATOFMS could have affected these numbers). The ratio of the number of coarse particles containing nitrate anions to the number of particles containing chloride anions exceeded unity when the air mass had travelled over the British mainland. The analysis also illustrates that an air mass of marine origin that had travelled slowly over agricultural land can accumulate amines and ammonium.
Work-life balance across the lifecourse
15 June 2009
University of Edinburgh

Jamieson, Lynn;Morton, Sarah

In Summer 2004, CRFR held an international conference to explore work-life balance across the lifecourse. This briefing outlines some of the main issues from the conference, explores what we might learn from international comparisons, and makes recommendations for policy and for further research.
CRFR News 15 - Summer 2009
04 August 2009
University of Edinburgh

CRFR

New look to CRFR - Launch of new website and Research Network
Ethical considerations for field research on fishes
13 April 2017
University of the Witwatersrand

Bennett, R.H.;Ellender, B.R.;Miya, T.;Pattrick, P.;Wasserman, R.J.;Woodford, D.J.;Weyl, O.L.F.;Makinen, T.

Collection of data from animals for research purposes can negatively impact target or by-catch species if suitable animal ethics practices are not followed. This study aimed to assess the ethical requirements of peer-reviewed scientific journals that publish primary literature on fishes, and review the ethical considerations and animal care guidelines of national and international documents on the ethical treatment of animals for research, to provide an overview of the general ethical considerations for field research on fishes. A review of 250 peer-reviewed, ISI-rated journals publishing primary research on fishes revealed that nearly half (46%) had no mention of ethics, treatment of animals or ethical requirements for publication in their author guidelines or publication policies. However, 18% of the journals reviewed identify a specific set of ethical guidelines to be followed before publishing research involving animals. Ethical considerations for investigators undertaking field research on fishes, common to most animal care policies, legislation and guiding documents, include adhering to relevant legislation, minimising sample sizes, reducing or mitigating pain and distress, employing the most appropriate and least invasive techniques and accurately reporting methods and findings. This information will provide potential investigators with a useful starting point for designing and conducting ethical field research. Application of ethical best practices in field sampling studies will improve the welfare of study animals and the conservation of rare and endangered species. Conservation implications: This article provides a list of ethical considerations for designing and conducting field research on fishes. By reviewing sampling techniques and processes that are frequently used in field research on fishes and by highlighting the potential negative impacts of these sampling techniques, this article is intended to assist researchers in planning field research to minimise impacts on fish populations. It is envisaged that this review will be a useful resource for journal editorial committees intending to introduce ethical requirements for publication and for researchers, managers, conservation practitioners and research organisations when designing field studies on fishes, applying for ethical clearance and developing institutional ethical guidelines.
A review of biodiversity reporting by the South African seafood industry
14 July 2020
University of the Witwatersrand

Usher, K;Maroun, W

Background: Biodiversity reporting is an area of sustainability accounting research that has received comparatively little attention from the academic community. This is despite the growing scientific concern about climate change, habitat destruction and extinction of species and mounting evidence on the implications of these environmental issues for our current way of life. This necessitates additional research on biodiversity reporting, especially in a South African context given that the country is home to some of the richest biodiversity regions on earth. Aim: This research examines what information companies in the South African seafood industry are reporting on biodiversity. This includes the development and application of an easy-to-use disclosure scorecard to track the quality of biodiversity-related disclosures. Setting: The study focuses on South African biodiversity reporting. The choice of region is informed by the country’s significant marine resources and mature corporate reporting environment, where non-financial disclosures are expected to be well developed. Methods: Content analysis was used to collect data from a sample of companies’ integrated and sustainability reports. The data were analysed interpretively to determine what biodiversity disclosures companies provide and the quality of those disclosures. Conclusion: The study shows that while the quantum of biodiversity reporting is relatively low, some companies are starting to provide more detailed accounts of their biodiversity impact, pointing to higher levels of reporting quality. There is still room for improvement, but these findings suggest that reporting on non-financial sustainability issues is maturing and that companies are beginning to appreciate the importance of preserving biodiversity for ensuring long-term sustainability. © 2018. The Authors.
A practical exploration of the feasibility of integrative multidisciplinary research from a broad ecohealth perspective in South Africa.
19 January 2012
North West University

Van Eeden, Elize S

This discussion is a deliberation on the progress towards the possibility of carrying out feasible research according to an Integrative Multidisciplinary (IMD) research methodology (theoretically and practically). To explore the IMD research methodology, a group of researchers from several disciplines started discussions in early February 2011 to plan a pilot research process in the Bekkersdal Township of the municipal region of Westonaria (Gauteng, South Africa). It was decided that the focus of research would be on exploring a broad definition of ecohealth to accommodate several disciplines and to attempt to produce a “package” of research results from many disciplinary angles. These results will eventually be discussed and refined through interdisciplinary (ID) and transdisciplinary (TD) research phases to “contain” consolidated reflections of the status of the well-being of the Bekkersdal community. However, the primary research question remains: whether it is possible to do research using IMD methodology, and whether this proposed methodology is more promising and constructive as an aid to understanding and disseminating research from various disciplinary angles than other methodologies.
Interactive simulations for promoting transdisciplinary understanding: a case study of the Western Cape fisheries, South Africa
14 August 2012
North West University

Gerwel Proches, C N;Bodhanya, S

Simulations have proven beneficial in enabling participants from various backgrounds to meaningfully engage in learning from experience. The aim of this paper is to investigate how interactive simulations can play a role in navigating the changes faced in a multistakeholder setting, characterised by users dependent on marine resources and an authorising institution. Relevant literature in the areas of simulation and gaming, change management, systems thinking, and complexity theory was examined. A qualitative research approach and purposive sampling were employed. Interviews were first conducted with diverse stakeholders in the Western Cape fisheries of South Africa to determine the issues. A simulation was thereafter designed. The main findings from this study indicate that simulation use illustrates how the various stakeholders in a system interact, and how their actions and decisions influence each other. The simulation may be used in other areas of natural resource management, as well as in other kinds of multistakeholder scenarios.
Travel motivations of tourists to selected marine destinations
22 October 2012
North West University

Saayman, Melville;Slabbert, Elmarie;Van der Merwe, Petrus

South Africa is well known for its favourable climate, wildlife and golden beaches. Adding to this, its long summers make its coastline (over 3500 km) even more attractive to tourists around the world, and so are transforming the South African coast into a major marine tourism attraction. Along this lengthy coastline lie numerous marine destinations attracting thousands of tourists. These destinations offer various activities such as scuba diving, snorkelling, swimming, world class surfing and whale watching to tourists. When trying to capitalise on these assets, marketers clearly state that it is necessary to understand the market that uses them and the reasons people travel. Therefore, the purpose of this research is to determine the travel motives of tourists to selected marine destinations. Five surveys were conducted at marine resorts by means of a structured questionnaire. Two hundred and two (202) questionnaires were completed at Hartenbos, 210 at Jeffrey's Bay, 333 at Margate, 237 at Amanzimtoti and 153 at Plettenberg Bay. The statistical analysis entailed descriptive statistics and a factor analysis of the five surveys. The results revealed similarity regarding escape and relaxation as travel motives when compared to other research. However, time usage and personal attachment were unique motives identified by this study. A combination of psychological motives and of more tangible aspects should be used in tourism marketing strategies in order to attract a higher number of visitors to marine destinations. These results will, therefore, assist marketers and product developers of marine destinations, particularly with the marine tourism product being very similar.
Payment for ecosystem services
14 August 2013
North West University

Benjamin, Antonio Herman

This address focuses on the legislative design for payment or ecosystem services (PES) since most countries do not have specific legislation that addresses the subject. Brazil is in the process of drafting national legislation on ecosystem services and there are several important issues that can be learnt from this experience.
First report of chlorinated and brominated hydrocarbon pollutants in marine bird eggs from an oceanic Indian Ocean island
22 January 2014
North West University

Bouwman, Hindrik;Kylin, H.;Tatayah, Vikash;Choong Kwet Yive, Nee Sun;Løken, Katharina

We report for the first time levels of persistent organic pollutants in marine bird eggs from an oceanic island in the Indian Ocean, the world's third largest ocean. Ten eggs each of the Common Noddy, also known as the Brown Noddy (Anous stolidus), and Sooty Tern (Sterna fuscata) were collected from Ile Cocos off the coast of the island of Rodrigues, located 560 km east of the island of Mauritius. ΣPCBs had the highest levels (2.2 and 2.6 ng/g wm, wet mass; 20 and 19 ng/g lm, lipid mass) for common Noddy and Sooty Tern, respectively (and following), then ΣDDT (1.9 and 3.1 ng/g wm; 17 and 23 ng/g lm), and mirex (0.96 and 0.69 ng/g wm; 8.7 and 5.0 ng/g lm). ΣChlordanes (0.094 and 0.15 ng/g wm; 0.48 and 0.73 ng/g lm) and Σtoxaphenes (0.26 and 0.61 ng/g wm; 2.4 and 5.9 ng/g lm) are rare data for these compounds from this ocean. Brominated flame retardants were low (0.08 and 0.07 ng/g wm; 0.7 and 0.7 ng/g lm). Multivariate analyses indicated different contamination patterns in the prey items as Sooty Terns had significantly higher levels of mean Σchlordanes and Σtoxaphenes, as well as CB105, -108 and -157. p,p′-DDE had an association with thinner eggshells in the Sooty Tern. Although the contaminant levels were in all respects low, industrialisation, development on the periphery, commercial exploitation of the marine environment, and pollutants transferred over long distances by marine debris is likely to add to chemical pressure in this region. Monitoring changes in background levels of pollutants in remote regions will indicate such trends, and marine bird eggs from Rodrigues would be an excellent site.
Achieving equity in the fishing industry: the fate of informal fishers in the context of the policy for the small-scale fisheries sector in South Africa
12 March 2014
North West University

Young, Michaela

The implementation of the Marine Living Resources Act 18 of 1998 which governs fisheries management in South Africa is guided by a series of objectives. Chief amongst these are the need to ensure resource sustainability, promote economic growth and achieve equity in the fishing industry. Striking a balance among these competing imperatives is a necessary but also monumental task, one which South Africa has arguably failed to achieve to date. In particular, as far the equity objective is concerned, a group of fishers, including both subsistence and artisanal fishers, have continued to be marginalised and overlooked in the fishing rights allocation process. The Policy for the Small-Scale Fisheries Sector in South Africa aims to provide recognition and redress to this sector of the fishing industry. It seeks to achieve this objective by adopting a community-based, co-management approach. The Policy accordingly envisages that fishing rights will be allocated to small-scale fishing communities and that these communities will become involved in managing fisheries together with government. This contribution reviews and critically analyses the scope of application of the Small-Scale Policy and the management approach adopted by the Policy, with a view to assessing its potential to achieve the objective of providing redress to the formerly marginalised groups of fishers. This analysis takes place against the backdrop of the significant resource constraints in the fisheries arena and the country’s vision for its future economic development as described in the National Development Plan.
A customary right to fish when fish are sparse: managing conflicting claims between customary rights and environmental rights
12 March 2014
North West University

Feris, Loretta

This contribution considers the potential conflicts that may arise between customary rights and environmental rights in the face of dwindling marine resources. It sets the scene by reflecting on some of the common themes present in indigenous claims to marine resource by communities who were subjected to colonisation. In doing so it analyses the South African judgment, S v Gongqose Case No. E382/10 (unreported), which alluded to the existence of a customary right to fishing, a concept that has until now remained unexplored in South African law. This discussion is followed by a brief overview of the rapidly declining state of marine resources, worldwide and in South Africa. The note then considers the relationship between customary law and marine resources and some of the challenges in meeting rights-based customary claims to marine resources against the need to conserve a dwindling resource. It concludes by offering possibilities for reconciliation.
Determinants of visitor expenditure at the Tsitsikamma National Park
28 July 2014
North West University

Kruger, Martinette;Manners, Bianca;Saayman, Melville

The Tsitsikamma National Park is Africa's oldest and largest marine reserve. It has considerable importance for the community and the region. In the face of declining government funding, it needs to attract more high spenders if it is to be sustainable. This requires an understanding of expenditure patterns and the determinants of Park visitors' spending behaviour. This study investigated the socio-demographic and behavioural determinants of visitor expenditure, using visitor surveys at the Park in 2010/2011. Correlation analysis and regression analysis established the most significant determinants. The results indicated that a longer stay, a smaller travel group and obtaining information from magazines were the variables associated with higher spending. These findings provide strategic insights for marketing the Park, with the aim of achieving a greater economic impact and competitive advantage and ultimately aiding conservation efforts.
Perceived diving impacts and managment implications at a popular South African reef
11 May 2015
North West University

Lucrezi, Serena;Saayman, Melville;Van der Merwe, Peet

Coral reefs are threatened by impacts such as from scuba diving, and ongoing research is required to assess diving impacts, diver behavior and environmental knowledge. This study investigated perceived diving impacts, reef condition and norms among scuba divers at Sodwana Bay (South Africa). Divers viewed contact with coral as damaging, and perceived environmental degradation at dive sites. However, most divers saw activities such as photography as causing little or no damage to reefs. One meter or less was believed to be a safe distance from the reef or the wildlife to avoid contact or disturbance, and encounter norms were high. Age and experience influenced most perceptions, although cannot be accepted as reliable indicators of divers' perceptions or behavior, due to the heterogeneous conduct of divers of various experience and age as described in literature. The importance of human perceptions to understand what strategies need implementation in diving management is discussed.
Understanding visitor's image of the oldest marine park in Africa
11 May 2015
North West University

Cini, Francesca;Saayman, Melville

In successful tourism development and destination marketing, an important factor is individuals' tourist destination image (TDI). A review of the literature revealed a dearth of studies on the image of national parks as tourist destinations in less-developed countries (LDCs). To help alleviate this lack, visitors to the oldest marine park in Africa – the Tsitsikamma National Park (TNP) in South Africa – were surveyed to investigate their image of the TNP. A self-administered questionnaire was completed by 165 day visitors. Subsequently, independent t-tests and ANOVA were performed on the collected data. The contribution of this study to the literature on TDI was twofold. First, it analysed the image of a national park in an LDC as a tourist destination. Tourism in protected areas is an important and growing sector of the worldwide tourism industry, particularly in developing countries where a large portion of the world's biodiversity is concentrated and where tourism can really be a tool for poverty alleviation. Second, it contributed to the TDI-formation process by investigating the relationship between the respondents' TNP image – overall, cognitive and affective dimensions – and a set of their personal factors. This relationship is an issue that needs to be resolved by empirical studies, especially with regard to the cognitive but also the affective image components and its overall image.
Who is willing to pay to see the Big 7?
18 August 2016
North West University

Saayman, Melville;Saayman, Andrea

This article investigates the non-consumptive, or appreciative value of the 'Big 7' and identifies the variables that influence willingness to pay (WTP). Addo Elephant National Park in the Eastern Cape Province, South Africa, is one of few places in the world where tourists can view all seven species: lion, buffalo, rhinoceros, leopard, elephant, southern right whale and great white shark. Two surveys were conducted, using the same questionnaire, one during summer and one during winter. A total of 232 completed questionnaires were used in the Heckman model selection procedure. The findings revealed that, although a variety of socio-demographic, behavioural and motivational factors influence the amount respondents are willing to pay, there is a clear distinction between the determinants for land species compared to marine species. This poses challenges for the marketing of and establishment of the Big 7 as a brand.
Review of the fish-parasitic genus Ceratothoa Dana, 1852 (Crustacea: Isopoda: Cymothoidae) from Australia, with description of two new species
14 September 2016
North West University

Martin, Melissa B.;Bruce, Niel L.;Nowak, Barbara F.

The genus Ceratothoa Dana, 1852, is revised for Australian waters. Ceratothoa is represented in Australia by nine species, including two new species: Ceratothoa barracuda sp. nov. described from Cairns and Ceratothoa globulus sp. nov. described from Lord Howe Island. Ceratothoa imbricata Fabricius, 1775 is redescribed, with Ceratothoa trillesi (Avdeev, 1979) and Ceratothoa huttoni Filhol, 1885 placed into junior synonymy; the preferred hosts are species of the genus Trachurus (Carangidae). Ceratothoa banksii (Leach, 1818) is validated and brought out of synonymy with Ceratothoa imbricata; host species are from the families Kyphosidae, Scombridae, Latridae, Carangidae, Mugilidae, Salmonidae, Scatophagidae, Pomatomidae and Hemiramphidae. Species excluded from the Australian fauna are Ceratothoa trigonocephala (Leach, 1818) with an unknown host identity and type locality; and Ceratothoa lineata Miers, 1876a, that here is transferred to the genus Mothocya Costa, 1851, with Mothocya ihi Bruce, 1986 placed into junior synonymy. Ceratothoa contracta (Miers, 1880), the New Zealand Ceratothoa novaezelandiae Filhol, 1885 and the East Pacific Ceratothoa gaudichaudii (Milne Edwards, 1840) are regarded here as species inquirenda. A key to the Australian species of Ceratothoa is presented
Review of Mothocya Costa, in Hope, 1851 (Crustacea: Isopoda: Cymothoidae) from southern Africa, with the description of a new species
14 September 2016
North West University

Hadfield, Kerry A.;Bruce, Niel L.;Smit, Nico J.

Three species of Mothocya are reported from the east coast of southern Africa: Mothocya plagulophora (Haller, 1880) from Maputo, Mozambique, from the gills of Hemiramphus far (Forsskål, 1775); Mothocya renardi (Bleeker, 1857) from diverse localities in South Africa and Mozambique, from the hosts Strongylura leiura (Bleeker, 1850) and Tylosurus choram (Rüppell, 1837); and Mothocya affinis sp. nov. from Sodwana Bay, South Africa, from the gills of Hyporamphus affinis (Günther, 1866). Mothocya affinis sp. nov. is characterised by relatively small size (maximum 16 mm); large, wide coxae on pereonite 7 that overlap the pleon; uropods that do not extend past the pleotelson posterior margin; produced anterolateral margins on pereonite 1; and a twisted pleon and pleotelson. Mothocya katoi Nunomura, 1992 and Mothocya toyamaensis Nunomura, 1993 are both transferred to the genus Ceratothoa, with M. katoi being placed into junior synonymy with Ceratothoa guttata (Richardson, 1910). Irona ogcocephalus Avdeev & Avdeev, 1974 and I. callionymus Avdeev & Avdeev, 1974 are both transferred to Elthusa, and Irona trillesi Rokicki, 1986 is synonymised with Mothocya longicopa Bruce, 1986. A key to the south-western Indian Ocean species of Mothocya is given, and a table summarising recent and new nomenclatural acts in the genus is provided
Marine fish parasitology in South Africa: history of discovery and future direction
14 September 2016
North West University

Smit, Nico J.;Hadfield, Kerry A.

Almost 200 years have passed since the first description of a marine fish parasite from South Africa. It is therefore an opportune time to look back, take stock of and reflect on the history of discovery within this field and, based on what we know, propose the future direction for research. The aim of this paper is hence to provide some background information on the growth in our knowledge and understanding of the major groups of marine fish parasites and to give an account of how pioneers, such as Barnard, Stebbing, Fantham and Kensley, led the age of discovery and exploration in marine fish parasitology in South Africa. The paper also presents a brief overview of the contributions made by internationally acclaimed parasitologists, such as Rodney Bray and Angela Davies, to our knowledge of marine fish parasites from this region and also to acknowledge the role played by the South African parasitologists, especially over the past 30 years. A rich base of fundamental knowledge is available in South Africa and this research field continues to grow. The prognosis for the future of marine parasitology in South Africa is good; however, as we continue to acquire and record new information about species, it is proposed that future research should be more focused on the lesser studied groups, such as monogeneans, protists and Myxozoa, as these have received uneven attention to date. In addition, it is proposed that the scope of research on marine fish parasitology be broadened to include ecological and applied aspects, using modern techniques
Blood parasite biodiversity of reef-associated fishes of the eastern Caribbean
14 September 2016
North West University

Cook, Courtney A.;Sikkel, Paul C.;Renoux, Lance P.;Smit, Nico J.

Parasitic micro-organisms can influence multiple ecological processes, from growth, mortality, and behavior, to community structure and trophic interactions, yet are typically ignored components of marine biodiversity. We collected 1298 blood samples from reef fishes off 6 eastern Caribbean islands, representing 27 families, 57 genera and 103 species, in - cluding invasive Indo-Pacific lionfish. Members of 14 species from 8 families were infected, comprising damselfishes (Pomacentridae), parrotfishes (Scaridae), mullet (Mugilidae), jacks (Caranjidae), Blennies (Blen - neidae and Labrisomidae), snappers (Lutjanidae), and angelfishes (Pomacanthidae). None of the 8 distinct blood parasites found fit descriptions of other Ca - ribbean parasites, but resembled typical Haemo gre - garina-like intraerythrocytic parasites and Haemohormidium- like parasites collected from fishes on the Great Barrier Reef (GBR), Australia. No blood parasites were found in lionfish and there was surprisingly little overlap in the families of Caribbean and GBR fishes. Most infected species were strongly diurnal. The high incidence of infection in Stegastes damselfishes was particularly surprising and has potentially important ecological consequences, given that damselfishes influence benthic community structure and are prey for reef piscivores. Gnathiid isopods, an apparent vector of apicomplexan blood parasites in other systems, were common at sampling sites and collected for use in transmission experiments. Haemogregarinalike parasites were taken up by gnathiids that fed on infected blennies. By comparison, when gnathiids fed on Stegastes damselfish infected with a Hae mo - hormidium-like parasite, no parasites were found. This study reveals the high biodiversity of haemoparasites infecting eastern Caribbean reef fishes, and highlights the need for additional research throughout the Caribbean and in other tropical reef systems.
Morphological and molecular characterization of a marine fish trypanosome from South Africa, including its development in a leech vector
28 November 2016
North West University

Hayes, Polly M.;Lawton, Scott P.;Smit, Nico J.;Gibson, Wendy C.;Davies, Angela J.

Background Trypanosomes are ubiquitous blood parasites of marine and freshwater fishes, typically transmitted by aquatic leeches. Phylogenetic studies have been dominated by examples derived from freshwater fishes, with few marine representatives. Furthermore, life cycle studies on marine fish trypanosomes have focused on those of the northern hemisphere. In this investigation, we have examined the life cycle and molecular taxonomy of a marine fish trypanosome from South Africa. Methods To locate trypanosome stages, leeches were removed from fishes captured on the west and south coasts of South Africa, and fish blood films and leech squashes were Giemsa-stained and screened; leeches were also examined histologically. To determine whether trypanosome stages in fishes and leeches were of the same genotype, DNA was extracted from Giemsa-stained fish blood films and leech squashes, and from fish whole blood. Fragments of the 18S rRNA gene were amplified by PCR using trypanosome-specific primers and sequenced. Resulting sequence data were compared with each other and with published trypanosome 18S rDNA sequences, and used for phylogenetic analysis. Results Trypanosomes were detected in blood films from fishes of the families Clinidae, Blenniidae and Gobiidae. The flagellates ranged in size and staining properties within the films and across fish hosts. In squashes and histological sections of adult and juvenile leeches, identified as Zeylanicobdella arugamensis, trypanosome developmental stages were predominantly slender epimastigotes. Sequence data showed that trypanosomes derived from fishes were identical, irrespective of whether they were small or large forms; sequences derived largely from leech epimastigotes were also identical to those obtained from fish trypanosomes. Fish and leech trypanosome sequences fell into a marine fish aquatic clade, and aligned most closely with two trypanosome sequences from marine fishes off Norway. Conclusions Combined morphological and molecular methods indicate that the trypanosomes examined here represent a single pleomorphic species, rather than the three species described originally. This species is identified as Trypanosoma nudigobii Fantham, 1919 with the leech Z. arugamensis as its vector, and T. capigobii Fantham, 1919 and T. blenniclini Fantham, 1930 are regarded as junior synonyms of the species. Phylogenetic analysis establishes its affinity with marine fish trypanosomes off Norway.
Comparison of sampling methodologies and estimation of population parameters for a temporary fish ectoparasite
21 April 2017
North West University

Artim, J.M.;Sikkel, P.C.

Characterizing spatio-temporal variation in the density of organisms in a community is a crucial part of ecological study. However, doing so for small, motile, cryptic species presents multiple challenges, especially where multiple life history stages are involved. Gnathiid isopods are ecologically important marine ectoparasites, micropredators that live in substrate for most of their lives, emerging only once during each juvenile stage to feed on fish blood. Many gnathiid species are nocturnal and most have distinct substrate preferences. Studies of gnathiid use of habitat, exploitation of hosts, and population dynamics have used various trap designs to estimate rates of gnathiid emergence, study sensory ecology, and identify host susceptibility. In the studies reported here, we compare and contrast the performance of emergence, fish-baited and light trap designs, outline the key features of these traps, and determine some life cycle parameters derived from trap counts for the Eastern Caribbean coral-reef gnathiid, Gnathia marleyi. We also used counts from large emergence traps and light traps to estimate additional life cycle parameters, emergence rates, and total gnathiid density on substrate, and to calibrate the light trap design to provide estimates of rate of emergence and total gnathiid density in habitat not amenable to emergence trap deployment
Description of Citharodactylus gagei n. gen. et n. sp. (Monogenea: Gyrodactylidae) from the moon fish, Citharinus citharus (Geoffroy Saint-Hilaire), from Lake Turkana
08 May 2017
North West University

Prikrylová, Iva;Shinn, Andrew P.;Paladini, Giuseppe

A new genus and species of monogenean belonging to the Gyrodactylidae, Citharodactylus gagei n. gen. et n. sp. (Plathyhelminthes, Monogenea), is described from the gills of the moon fish, Citharinus citharus (Geoffroy Saint-Hilaire), a characiform fish collected from Lake Turkana in northern Kenya. The new viviparous genus can be readily distinguished from the six other gyrodactylid genera recorded from Africa and from the other viviparous genera within the Gyrodactylidae based on the morphology of the male copulatory organ (MCO), which consists of a muscular ovate organ with an opening onto the tegument through which the narrow tapered end of a sclerotised curved cone-shaped structure protrudes. The tegumental opening of the MCO is surrounded by a collar of short spines. Sequencing of the nuclear ribosomal DNA internal transcribed spacers 1 and 2, the 5.8S and the 18S rDNA genes and a comparison with the gyrodactylid species listed in GenBank confirmed the specimens are unique and do not match with any existing entry. When phylogenies for each genomic region were conducted (i.e. 0.064 gamma-corrected pairwise genetic distance based on a alignment of 1750 bp of the 1857 bp long 18S rDNA gene), the most similar match was that of Afrogyrodactylus sp. [= A. girgifae (Folia Parasitol 61:529–536, 2014)] from Brycinus nurse (Rüppell). The proposed name of the new parasite is Citharodactylus n. gen. which represents the seventh gyrodactylid genus to be found in Africa and the 25th viviparous genus and the 32nd genus to be added to the Gyrodactylidae
A revised description of Synodontella zambezensis Douëllou et Chishawa, 1995 (Monogenea: Ancyrocephalidae) from the gills of Synodontis zambezensis (Siluriformes: Mochokidae) from South Africa
11 May 2017
North West University

Raphahlelo, M.E.;Prikrylová, I.;Matla, M.M.;Theron, J.;Luus-Powell, W.J.

This study supplements the original description of Synodontella zambezensis Douëllou et Chishawa, 1995 and represents a new geographical record for this parasite from Synodontis zambezensis from South Africa. The revision is based on morphometric characteristics and molecular data. Characterisation of LSU, partial SSU and ITS1 rDNA represents a first record of DNA sequencing for Synodontella species
Contamination status and accumulation characteristics of heavy metals and arsenic in five seabird species from the central Bering Sea
06 June 2017
North West University

Ishii, Chihiro;Ikenaka, Yoshinori;Nakayama, Shouta M.M.;Mizukawa, Hazuki;Yohannes, Yared Beyene

Seabirds are marine top predators and accumulate high levels of metals and metalloids in their tissues. Contamination by metals in the highly productive offshore region has become a matter of public concern. It is home to 80% of the seabird population in the U.S.A., 95% of northern fur seals (Callorhinus ursinus), and major populations of Steller sea lions (Eumetopias jubatus), walruses (Odobenus rosmarus) and whales. Here, the concentrations of eight heavy metals (Hg, Cd, Cr, Co, Ni, Cu, Zn and Pb) and a metalloid (As) in the liver and kidneys of the northern fulmar (Fulmarus glacialis), thick-billed murre (Uria lomvia), short-tailed shearwater (Puffinus tenuirostris), tufted puffin (Fratercula cirrhata) and horned puffin (Fratercula corniculata) collected in the Bering Sea were measured. As proxies of trophic level and habitat, nitrogen (δ15N) and carbon (δ13C) stable isotope ratios of breast muscles were also measured. Hepatic Hg concentration was high in northern fulmar, whereas Cd level was high in tufted puffin and northern fulmar. The Hg concentration and δ15N value were positively correlated across individual birds, suggesting that Hg uptake was linked to the trophic status of consumed prey. Furthermore, Hg concentration in our study was higher than those of the same species of seabirds collected in 1990
Host-dependent differences in resource use associated with Anilocra spp. parasitism in two coral reef fishes, as revealed by stable carbon and nitrogen isotope analyses
09 June 2017
North West University

Welicky, Rachel L.;Sikkel, Paul C.;Demopoulos, Amanda W.J.

The role of parasites in trophic ecology is poorly understood in marine ecosystems. Stable isotope analyses (SIA) have been widely used in studies of trophic ecology, but have rarely been applied to study the role of parasites. Considering that some parasites are associated with altered host foraging patterns, SIA can help elucidate whether parasitism influences host trophic interactions. French grunt (Haemulon flavolineatum), an abundant Caribbean coral reef fish, contributes greatly to trophic connectivity. They typically depart the reef at dusk, feed overnight in seagrass beds, and return to the reef at dawn. The large parasitic isopod Anilocra haemuli commonly infects French grunt, and infected fish are less likely to complete their diel migration, and are in poorer condition than uninfected conspecifics. Brown chromis (Chromis multilineata) are diurnally feeding planktivores and infection by Anilocra chromis does not influence host condition. To determine if Anilocra infection influences host diet and foraging locality, we conducted stable carbon and nitrogen isotope analyses on scale, muscle, heart and gill tissues of infected and uninfected French grunt and brown chromis. We determined that all French grunt had δ13C values representative of seagrass habitats, but infected French grunt were significantly enriched in 13C and 15N compared to uninfected conspecifics. This suggests that compared to uninfected conspecifics, infected French grunt forage in seagrass, but on isotopically enriched prey, and/or are in poorer condition, which can elevate δ13C and δ15N values. For brown chromis, infection did not significantly influence any δ13C and δ15N values; hence they all foraged in the same environment and on similar prey. This is the first study to use SIA to examine differences in resource use by Caribbean coral reef fishes associated with parasitism and to evaluate how closely related parasites might have host-dependent effects on host trophic ecology
Bioaccumulation of persistent organic pollutants and their trophic transfer through the food web: human health risks to the rural communities reliant on fish from South Africa's largest floodplain
19 July 2019
North West University

Volschenk, C.M.;Gerber, R.;Ikenaka, Y.;Van Vuren, J.H.J.;Wepener, V.;Smit, N.J.

The Phongolo River Floodplain (PRF) is South Africa's largest floodplain, unique in being the only large floodplain able to sustain permanent waters throughout the dry season (Kyle, 2002). This highly productive region contains around 90 floodplain associated pans which are rich in biodiversity and is known to be of high ecological and socio-economic importance (Dube et al., 2017). The floodplain is surrounded by informal settlements and rural communities which are reliant on these aquatic resources, not only for domestic use or agricultural purposes such as watering livestock and subsistence farming, but also for subsistence fisheries as a source of protein (Coetzee et al., 2015). A recent study by Coetzee et al. (2015) indicated that several fish species in the study area are important sources of protein within artisanal fishery practices. Contamination due to the introduction of pesticides into aquatic ecosystems is of great concern, as many banned (World Health Organisation (WHO, 2002)) organochlorine pesticides (OCPs) are persistent in the environment and this is reflected by the fact that although many OCPs are no longer used, they still remain present in many, if not all aquatic ecosystems (Gerber et al., 2016). Implementation of effective long term management plans rely directly on fully understanding chemical compounds as well as their risks to both ecosystems and humans, where these aspects can be assessed using; (1) stable isotopes and trophic magnification factors (TMF's) and (2) human health risk assessments via exposure through consumption (Verhaert et al., 2013, Verhaert et al., 2017).
Biomarker responses in the freshwater shrimp Caridina nilotica as indicators of persistent pollutant exposure
06 February 2020
North West University

Jansen van Rensburg, Gregg;Smit, Nico J.;Wepener, Victor;Bervoets, Lieven;Van Vuren, Johan

Biomarkers are applied as early warning indicators of organisms’ exposure to pollutants. The aim of this study was to utilise a multi-biomarker approach in the freshwater shrimp Caridina nilotica (Decapoda: Atyidae) as indicators of persistent pollutant exposure. A suite of biomarkers was selected to cover oxidative stress and damage, and energetics of the organisms. Five sites, representing an agricultural and pesticide application gradient, were sampled during two flow related hydro-periods in rivers of the Phongolo floodplain, north-eastern South Africa. Cytochrome P450 (CYP) activity was significantly higher in shrimp at sites directly adjacent to regions of increased human activity. Increased oxidative responses, i.e. catalase (CAT; p < 0.01) and protein carbonyl (PC, p < 0.01) were also found at these sites. The energetics biomarker did not show any influence of increased contaminant exposure. We demonstrated that the biomarkers of exposure (CYP) and effect (CAT, PC) were suitable to detect effects of stressors, probably persistent pollutants
The effects of stakeholder education and capacity building in marine protected areas: a case study from southern Mozambique
02 March 2020
North West University

Lucrezi, Serena;Esfehani, Minoo Hassani;Ferretti, Eliana;Cerrano, Carlo

Stakeholder engagement is a critical component of marine protected area (MPA) management. Education and capacity-building initiatives, in particular, have the potential to empower stakeholders, promote collaboration, create a culture of marine stewardship and encourage alternative and sustainable livelihoods. Empirical evidence on the impacts of these initiatives on stakeholders and MPAs is however still lacking. This study tested the impact of an ocean literacy, marine education and environmental monitoring initiative on stakeholders' views of conservation, community and livelihood in the Ponta do Ouro Partial Marine Reserve (PPMR) in southern Mozambique. Data were collected via two focus groups, one before and one after participation in the initiative. Stakeholders who participated in this research included representatives from governance, tourism and education sectors in the PPMR. Participation in the initiative had a positive effect on stakeholders' views of conservation, community and livelihood. Following the initiative, some of these views became more aligned with the goals of the PPMR, while others highlighted important issues to be addressed by management. This study demonstrates the bilateral nature of stakeholder engagement in MPAs, including stakeholder empowerment and steering management strategies
Opportunities from citizen science for shark conservation, with a focus on the Mediterranean Sea
24 March 2020
North West University

Bargnesi, F.;Lucrezi, S.;Ferretti, F.

The Mediterranean Sea is a hotspot for shark conservation. A decline in large pelagic shark populations has been observed in this vast region over the last 50 years and a lack of data on the local population status of various species has been pointed out. Throughout history, the relation between people and sharks has been revolving around a mixture of mystery, fear, and attraction. Recently, however, a remunerative ecotourism industry has been growing in areas of shark aggregation globally. This growth has been accompanied by the establishment of a citizen science (CS) movement aimed to engage and recruit ecotourists in data collection for shark research. Several CS projects have generated interesting results in terms of scientific findings and public engagement. In the Mediterranean Sea, shark aggregations are not as relevant to support locally-focused CS actions on shark diving sites as in other parts of the world. However, a series of other initiatives are taking place and CS could offer an excellent opportunity for shark conservation in the Mediterranean Sea. The dramatic decline of shark populations shown in the region calls for alternative ways to collect data on species distributions and abundance. Obtaining such data to set proper conservation and management plans for sharks in the Mediterranean Sea will be possible if existing CS initiatives collaborate and coordinate, and CS is widely acknowledged and deployed as a valuable tool for public education, engagement, and scientific discovery. After providing an overview of multiple facets of the relationship between humans and sharks, we focus on the possibility of exploiting new technologies and attitudes toward sharks among some groups of ocean users to boost participatory research. CS is a great opportunity for shark science, especially for areas such as the Mediterranean Sea and for large pelagic sharks whose populations are highly impacted
Impacts of a shallow shipwreck on a coral reef: a case study from St. Brandon's Atoll, Mauritius, Indian Ocean
25 March 2020
North West University

Van der Schyff, Veronica;Du Preez, Marinus;Blom, Karin;Kylin, Henrik;Bouwman, Hindrik

Shallow shipwrecks, can have severe ecological and toxicological impacts on coral atolls. In 2012, a tuna longliner ran aground on the reef crest of St Brandon's Atoll, Mauritius, broke up into three pieces which was moved by currents and storms into the lagoon. In the months following the grounding, the coral around the wreck became dead and black. Down-current from the wreck, a dense bloom of filamentous algae (Ulva sp.) attached to coral occurred. To determine the ecological effects of the wreck on the system, the marine biota around the wreck, in the algal bloom, and fish reference zones were counted in 2014. Metal concentrations in reference and affected coral was determined using inductively coupled plasma mass spectrometry (ICP/MS). A pronounced difference was seen in the metal concentration pattern between coral from the wreck- and algal zones, and the coral reference zone. While the wreck zone contained the highest abundance of fish, the fish reference zone had the highest species diversity but with fewer fish. We also counted eleven Critically Endangered hawksbill sea turtles Eretmochelys imbricata and significantly more sea cucumbers in the algal zone than the reference zones. The effects of shipwrecks on coral reefs must be considered a threat over periods of years and should be studied further
Concentrations and relative compositions of metallic elements differ between predatory squid and filter-feeding sardine from the Indian and South Atlantic oceans
25 March 2020
North West University

Uren, Ryan C.;Kylin, Henrik;Bouwman, Hindrik;Van der Lingen, Carl D.

Although metallic elements occur naturally, they can occur or accumulate in organisms at levels toxic to the organism and/or their consumers. Concentrations of twenty-nine metallic elements in muscle tissue from sardine Sardinops sagax and chokka squid Loligo reynaudii from South Atlantic and Indian Ocean waters off South Africa were established, for the first time, using inductively-coupled plasma mass spectrometry. Chokka showed significantly higher (p < 0.05) concentrations of B, Cr, Zn, As, Se, Rb, Sr, Cd, and Tl and significantly lower concentrations of V, Mn, Ti, and Mo compared to sardine. There were also significant differences in some metallic elements between the two oceans. Multivariate analyses indicated possible population structure of both species, suggesting that these analyses may be useful as a stock discrimination tool. Only two sardine samples contained quantifiable Hg. Based on South African estimated daily intake, total hazard quotient, and European Union limits for Hg, Cd, and Pb, we consider tissues from sardine and chokka in South African waters to be safe for human consumption
Perfluoroalkyl substances (PFAS) in tern eggs from St. Brandon's Atoll, Indian Ocean
31 March 2020
North West University

Van der Schyff, Veronica;Polder, Anuschka;Cole, Nik C.;Bouwman, Hindrik;Kwet Yive, Nee Sun Choong

Per- and polyfluoroalkyl substances (PFAS) are anthropogenic fluorinated compounds of concern for human and environmental health. There is no data on PFAS concentrations in marine bird eggs from the Western Indian Ocean. We analysed eight PFAS in eggs of fairy terns (Gygis alba), sooty terns (Onychoprion fuscatus), and common noddies (Anous stolidus) from St. Brandon's Atoll. Fairy tern eggs contained the highest concentrations, followed by sooty terns and common noddies. Perfluoroundecanoic acid (PFUdA) had the highest mean concentration (2.3 ng/g wm), followed by perfluorooctane sulfonic acid (PFOS) (2.0 ng/g wm), and perfluorononanoic acid (PFNA) (0.93 ng/g wm) in fairy tern eggs. Concentrations of all PFAS were lower than values found in literature. PFOS and PFOA concentrations were three orders of magnitude lower than toxicity reference values and levels of lowest-observed-adverse-effect-level concentrations. Eggs from St. Brandon's would be useful to monitor background changes on a regional and perhaps global scale
Polyhalogenated compounds (Halogenated natural products and POPs) in sardine (Sardinops sagax) from the South Atlantic and Indian Oceans
26 June 2020
North West University

Wu, Qiong;Uren, Ryan;Bouwman, Hindrik;Schlag, Sarah;Van der Lingen, Carl D.

Halogenated natural products (HNPs) and persistent organic pollutants (POPs) were quantified in South African sardines (Sardinops sagax) from one site in the South Atlantic Ocean and one in the Indian Ocean. At both sites, HNPs [2,3,3′,4,4′,5,5′-heptachloro-1′-methyl-1,2′-bipyrrole (Q1), mixed halogenated compound 1 (MHC-1), 2,4,6-tribromoanisole (2,4,6-TBA), 2′-MeO-BDE 68 (BC-2), and 6-MeO-BDE 47 (BC-3)] were 1 order of magnitude higher concentrated than anthropogenic POPs [mainly polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), ∼3 ng/g lipids]. MHC-1 and Q1 were the major HNPs in the samples from both sites, contributing with up to 49 and 52 ng/g lipids, respectively. The same 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane (p,p′-DDE)/PCB ratio suggested that the major POPs were evenly distributed at both sites. Different ratios of Q1/MHC-1 in the samples from the Indian (∼2:1) and South Atlantic (∼1:1) Oceans indicated that the occurrence of HNPs in seafood is difficult to predict and should be investigated more in detail. The PCB levels in sardines were found to pose no risk to human consumers, whereas HNPs could not be evaluated because of the lack of toxicological data
The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea
02 July 2020
North West University

Xavier, Raquel;Sikkel, Paul C.;Pereira, Ana;Pagan, Andres;Hendrick, Gina C.

Damselfishes of the genus Stegastes are some of the most abundant fish inhabiting shallow reef habitats. Although Stegastes play an important role in promoting primary production in reef ecosystems, their territories are known to favor the occurrence of bacterial pathogens. However, no studies so far have examined the microbiome composition of Caribbean Stegastes species. Here, we characterized the skin bacterial microbiome of juveniles and adults of Stegastes leucostictus and Stegastes adustus collected from La Parguera, Puerto Rico, and St. Thomas, US Virgin Islands. Our results showed that bacterial communities residing on the skin of Stegastes were related to taxonomy, environment and ontogeny. These results are in line with previous knowledge on the dynamics of fish skin microbiomes
Into the future: Donkergat Military Training Area and the Langebaan Ramsar site
28 July 2020
North West University

Marx, Jan T.;Liebenberg, Ian

Militaries need natural areas for offensive and defensive combat-readiness programmes. Here soldiers, war machinery and munitions are employed to prepare forces to execute warfighting tactics. Integration of environmental considerations into military activities is a growing global challenge. This study is based on a qualitative approach underpinned by an extensive literature review. The potential for the contribution of the military to a sensitive and diminishing wetland on the West Coast of South Africa (SA) is addressed. Donkergat Military Training Area (DMTA) in the Western Cape province, SA, provides diverse, seaborne training and warfighting facilities for the South African Special Forces (SASF), a specialist branch of the South African National Defence Force (SANDF). This facility borders the Atlantic Ocean and Langebaan Lagoon, a Ramsar site (no. 398). One of only 15 island ecosystems on the southern African coastline, lies within the boundaries of the area. Saldanha Bay was identified as an economic development node by the national government. The 4 Special Forces Regiment (4 SFR) is thus obliged to contribute to the conservation of these environmental assets. Industrial development includes Operation Phakisa by the Department of Agriculture, Forestry and Fisheries (DAFF) that envisages expanded aquaculture practices in Saldanha Bay. Developers of fish and bivalve farms are allowed up-scaling aquaculture operations. These result in the loss of ecological attributes of the Langebaan Lagoon Wetland system. In the study, we recommend that parts of DMTA should be incorporated in the Ramsar definition for the Langebaan Lagoon Wetland system. Ecosystem indicators monitoring bird life, water and sediment quality, fish and rocky intertidal macrofauna in the DMTA waters should be intensified. The DMTA as a benchmark ecosystem in the Saldanha Bay area will facilitate environmentally sound planning amidst recent developments. Integrating sections of the Langebaan Lagoon that is part of the DMTA into the existing internationally recognised wetland area, the military can contribute significantly to wetland conservation. Management of these areas should be formulated in a Military Integrated Environmental Management (MIEM) plan by incorporating international guidelines.
The role of fish helminth parasites in monitoring metal pollution in aquatic ecosystems: a case study in the world's most productive platinum mining region
31 July 2020
North West University

Erasmus, Johannes H.;Wepener, Victor;Zimmermann, Sonja;Malherbe, Wynand;Smit, Nico J.

Due to the increasing consumption of platinum (Pt), especially in automobile exhaust catalysts, environmental concentrations of Pt are of emerging concern worldwide. Limited information exists on environmental concentrations, particularly in Pt mining regions, while South Africa is the world’s main supplier of Pt. Moreover, other metals are also released as by-products of Pt mining, which might also cause environmental concern. Certain fish parasite taxa have the ability to accumulate metals orders of magnitude higher than their hosts and can be used to reliably detect metals with naturally low abundance. Studies on Pt accumulation in parasite-host systems are limited. Therefore, the aims of the present study were (1) to determine the accumulation of a variety of metals (cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), platinum (Pt), and zinc (Zn)) in helminth fish parasites compared with their hosts from a reference site and an impoundment impacted by Pt mining activities; (2) to assess whether there is a difference between bioaccumulation of metals in infected and uninfected hosts, as well as between hosts with different infection intensities; and (3) to compare the biomarker responses (acetylcholine esterase activity (AChE), metallothionein content (MT), catalase activity (CAT), reduced glutathione content (GSH), malondialdehyde content (MDA), protein carbonyls induction (PC), superoxide dismutase activity (SOD), and cellular energy allocation (CEA)) between infected and uninfected hosts. The cestode Atractolytocestus huronensis accumulated significantly higher concentrations of Cr, Ni, and Pt than their host Cyprinus carpio, while the nematode Contracaecum sp. accumulated significantly higher concentrations of Pt and Zn than their host Clarias gariepinus. Infected fish showed lower metal concentrations compared to uninfected fish, while the parasites had no significant effects on their hosts’ biomarker responses. The parasites demonstrated the bioavailability of metals derived from Pt mining activities and their ability to resist its toxic effects. Thus, these parasites are promising sensitive accumulation indicators for Cr, Ni, Pb, and Pt contaminations from Pt mining activities
Aegiochus gracilipes (Hansen, 1895) a senior synonym of Aegiochus tara Bruce, 2009 (Crustacea: Isopoda: Aegidae)
31 July 2020
North West University

Hughes, Lauren E.;Bruce, Niel L.;Osborn, Karen

Aegiochus gracilipes Hansen, 1895 was described from a single immature specimen accompanied by three figures (Hansen 1895). Hansen (1916) subsequently reported the species without figures. Over the next 100 years A. gracilipes only appeared in the literature as a citation in larger review and cataloguing studies. Most significantly, Bruce (2009) transferred A. gracilipes from Aega Leach, 1815 to Aegiochus Bovallius, 1885, as part of a broader study redefining the morphological characters used to distinguish Aegiochus. To the present day A. gracilipes, described from the north-eastern Atlantic off the Outer Hebrides, Scotland, is known only from the original figures and its limited primary description
Comparison of the dietary bioavailability of copper sulphate and copper oxide nanomaterials inex vivogut sacs of rainbow trout: effects of low pH and amino acids in the lumen
07 August 2020
North West University

Boyle, David;Botha, Tarryn L.;Clark, Nathaniel J.;Handy, Richard D.

Diet is an important exposure pathway of engineered nanomaterials (ENMs) in fish, but the long duration of in vivo toxicity tests is a barrier to hazard assessment. This study used ex vivo gut sacs from rainbow trout (Oncorhynchus mykiss) to compare the bioaccumulation of Cu from CuO ENMs with CuSO4 in the tissue layers of the gut after short-term (4 h) exposure. The effect of gut lumen conditions such as pH and the presence of amino acids on the behaviour and dissolution of the CuO ENMs was explored and how amino acids (cysteine, histidine) altered bioaccumulation in the gut sacs. Exposure to either CuSO4 or CuO ENMs at pH 7.8 resulted in Cu accumulation in the mucosa of gut sacs prepared from the stomach, anterior-, mid- and posterior-regions of the gut when compared to saline only controls. In contrast, only CuSO4 accumulated in the underlying muscularis which suggests transepithelial transport of CuO ENMs may be limited. Dialysis experiments showed that at pH 2, typical of the stomach, more than 90% of the Cu from the CuO ENMs became dissolved suggesting that the particulate is transformed to dissolved metal for most of the gastrointestinal tract. Amino acids greatly increased ENM dissolution, and in the gut sacs, L-cysteine caused elevated Cu accumulation in the muscularis after exposure to CuO ENMs at pH 7.8. In conclusion, CuO ENMs have lower bioavailability than CuSO4 in gut sacs, but dissolution of ENMs in the gut can lead to dissolved Cu accumulation in fish
Statement from world aquatic scientific societies on the need to take urgent action against human-caused climate change, based on scientific evidence
01 October 2020
North West University

Wepener, Victor

The Southern African Society of Aquatic Scientists (SASAqS) has a membership of 250, representing individuals and organisations involved in all aspects of aquatic sciences in academia, the private sector (e.g. environmental consultancies and environmental practioners in industry) and government (local, provincial and national government). On 14 September 2020, SASAqS joined forces with 110 aquatic scientific societies, representing more than 80 000 scientists across the world to sound a climate change alarm. This initiative, led by the American Fisheries Society (AFS), calls for drastically curtailed global greenhouse gas emissions to avoid the worst impacts of human-made climate change to fish and aquatic ecosystems. Unless urgent action is taken to reduce emissions, scientists predict catastrophic impacts to commercial, recreational, and subsistence fisheries, as well as human health and global economies
The challenges experienced by small-scale fishing communities of Lake Kariba, Zimbabwe
09 November 2020
North West University

Muringai, Rodney T.;Naidoo, Denver;Mafongoya, Paramu

Small-scale fisheries play a significant role in enhancing livelihoods, creating employment and contributing to food security especially in developing countries. Rural fishing communities are highly dependent on natural resources, which are climate sensitive. Many research efforts have been made to understand the impacts of climate change on fisheries and fishing economies. However, little attention has been given to understand the challenges experienced by small-scale fishing communities in developing countries in Africa. This article assesses non-climate change and climate change-induced challenges according to the experiences of the gillnet small-scale fishers of Sanyathi fishing basin of Lake Kariba, Zimbabwe. The study used a qualitative research design, and data were collected using semi-structured in-depth interviews with fishers. Thematic content analysis was used to analyse interview transcripts. The study results showed that declining fish catches is one of the major challenges experienced by fishers. The main themes that emanated as the challenges faced by fishers are food insecurity, wildlife attacks, lack of access to information systems, lack of fishing equipment, the existence of the predator crayfish, poor lake co-management and shrinking fishing boundaries. Overall, the study found that fish production is negatively affected by several political, economic and environmental factors; therefore, development through the public and private organisations should incorporate small-scale fishers in policy formulation to positively enhance livelihoods and food security.
Monitoring metals in South African harbours between 2008 and 2009, using resident mussels as indicator organisms
16 November 2020
North West University

Wepener, V.;Degger, N.

More than 65% of the South African coastline is threatened as a result of pollution, a large proportion of which is land derived. To date the majority of published data on metal monitoring has been on limited regions or once-off sampling events. In this paper, we present the first data on metal exposure at sites along the eastern seaboard of South Africa in resident brown mussels (Perna perna) from six harbour sites (Cape Town, Durban, East London, Mossel Bay, Port Elizabeth and Richards Bay Harbours) over a two-year period (2008 and 2009). These data do not represent historical or the current metal exposure levels, but rather an indication of the degree of metal exposure fluctuations over two years at the same site. Metal accumulation of aluminium, arsenic, cadmium, cobalt, chromium, copper, iron, manganese, molybdenum, nickel, lead, selenium, strontium, uranium and zinc was determined by thermo-inductive coupled plasma mass spectrophotometry. The results showed marked fluctuations in metal concentrations between years and identified Cape Town, Mossel Bay and Port Elizabeth Harbours as those sites where mussels had the highest metal levels. Statistically significant variations in metal concentrations were observed between the two sampling periods and the six harbours. Metal concentrations decreased from 2008 to 2009, which was largely attributed to changes in ambient metal concentrations, as a result of variable non-point discharges of metals into the harbours and larger-scale oceanographic changes in upwelling events. The results further emphasise the necessity for annual monitoring of the South African marine environment
Nature's enduring patterns: a path to systems literacy
26 November 2020
North West University

Goede, Roelien

The theme of this special issue, Nature's Enduring Patterns: A Path to Systems Literacy, was celebrated at the 63rd Meeting of the International Society for the Systems Sciences in Corvallis in July 2019. In a world dominated by the artificial, 2019 ISSS President Peter Tuddenham in his presidential address, took conference attendees on a journey, going back to nature, its patterns and the identification of our individual spiritual purpose, towards fulfilment of our joint responsibility to manage natural resources for future generations. In making sense of our world and our purpose, we use specific literacies. We use ocean literacies to make sense of the ocean, climate literacies to make sense of climate change and many more literacies including earth science literacy, data literacy and network literacy
Stable isotope dynamics of herbivorous reef fishes and their ectoparasites
26 November 2020
North West University

Jenkins, William G.;Sikkel, Paul C.;Demopoulos, Amanda W. J.;Nicholson, Matthew D.

Acanthurids (surgeonfishes) are an abundant and diverse group of herbivorous fishes on coral reefs. While their contribution to trophic linkages and dynamics in coral reef systems has received considerable attention, the role of linkages involving their parasites has not. As both consumers of fish tissue and prey to microcarnivores, external parasites may play a significant role in trophic transfer between primary consumers (and hence their predominantly algae-based diet) and the broader coral reef community. Stable isotope analysis is a common tool for studying trophic linkages which can be used for studies involving parasites. We examined the stable isotope ecology (13C and 15N) of copepod (Caligus atromaculatus) and monogenean (Neobenedenia sp.) ectoparasites collected from two species of Caribbean acanthurids (Acanthurus coeruleus and Acanthurus bahianus). There were significant intraspecific differences in isotope discrimination factors between parasites collected from the two different host species as well as interspecific differences between parasites collected from the same host species. Discrimination factors for 15N were consistently positive but varied in magnitude depending on host and parasite species and were slightly lower than what would be expected for consumers. The 13C discrimination factors for both monogeneans and copepods collected from A. coeruleus were consistently positive but were negative for copepods collected from A. bahianus. These findings emphasize the complexity of the stable isotope trophic interactions occurring between parasites and their hosts, highlighting the value of these types of host-parasite isotopic studies
Ten research questions to support South Africa’s Inland Fisheries Policy
03 December 2020
North West University

Weyl, O.L.F.;Smit, N.J.;Wepener, V.;Barkhuizen, L.;Christison, K.

South Africa is in the process of developing a National Freshwater (Inland) Wild Capture Fisheries Policy. A properly focused research strategy is essential to guide the policy development process, and thus a dedicated ‘Inland Fisheries’ workshop was convened by the South African Society for Aquatic Scientists in June 2018 to update and further develop a list of priority knowledge requirements for inland fisheries in the country. The main themes that emerged during the workshop were developed and contextualised as ten research questions. These were: (1) What is the exploitation potential of inland fisheries? (2) What are the health risks from consuming freshwater fishes? (3) Who currently uses inland fisheries and what are their harvests? (4) What can we learn from historical constraints to inland fisheries development? (5) How will governance of fisheries have to change in an evolving sectoral environment? (6) What are the options for fisheries enhancement? (7) What are the most appropriate fisheries technologies? (8) What value chains and employment opportunities are associated with inland fisheries? (9) What is the impact of water level fluctuations on fish production? (10) What are the impacts of pathogenic diseases on fish populations?
Profiles of tourists participating in shark cage diving in Gansbaai, South Africa
06 December 2021
North West University

Mabaleka, Nolwazi;Ntloko, Ncedo J.;Swart, Kamilla

Coastal and marine tourism is a sector that draws visitors from around the globe to South Africa. This is largely because of an array of marine wildlife resources found in the country. Despite this strong pull factor, there is limited information on the economic value of the marine environment. This article focuses on establishing the profiles of visitors taking part in shark cage diving in Gansbaai. Such profiling will facilitate the understanding of the potential target market of CMT visitors to Gansbaai, whilst contributing towards targeted developments in the area aimed at capturing the economic value of such visitors through the provision of a range of visitor-specific activities to make the destination more appealing. It will also contribute to further developments in the area, in providing a wide range of activities to make the destination more appealing. In ascertaining the profile of visitors, a quantitative research design was adopted. A total of n = 378 self-administered questionnaires were collected from visitors taking part in shark cage diving using a face-to-face proportionate sampling technique. The results revealed that a majority of visitors were drawn to Gansbaai because of shark cage diving and that a large portion travelled to Gansbaai for holiday purposes. There was a challenge in the ability of the destination to attract overnight visitors because of a limited product offering in the area. As a result, minimal spending occurs in Gansbaai as an overwhelming majority of the visitors are day visitors. These results have implications for tourists, tourism destination planners, tour operators and tourism establishments in Gansbaai.
Gongqose v Minister of Agriculture, Forestry and Fisheries–a tale of customary rituals and practices in Marine Protected Areas
16 February 2022
North West University

Monyamane, Lesetja;Bapela, Mpho P.

The correct application of customary law post constitutionalism continues to be the subject of much judicial and academic deliberation. This is especially true where the existence and/or scope of customary rights and cultural practices are not well defined in a specific case. Gongqose v Minister of Agriculture, Forestry and Fisheries 2018 5 SA 104 (SCA) presents a perfect example of the dissonance between the recognition of customary law by the Constitution of the Republic of South Africa, 1996 and the regulation of rights and cultural practices emanating from customary law. The case grapples with the meeting point of customary rights and customs and the need to preserve the environment. This intersection is considered in view of earth jurisprudence as an emerging legal thought topic in environmental law. On the whole, the decision of the SCA demonstrates encouraging signs of an appreciation of customary law as deserving of an equal place on the legal podium.
Creating win-wins from trade-offs? Ecosystem services for human well-being: A meta-analysis of ecosystem service trade-offs and synergies in the real world
01 October 2014
Cambridge University

Howe, C;Suich, H;Vira, B;Mace, GM

Ecosystem services can provide a wide range of benefits for human well-being, including provisioning, regulating and cultural services and benefitting both private and public interests in different sectors of society. Biophysical, economic and social factors all make it unlikely that multiple needs will be met simultaneously without deliberate efforts, yet while there is still much interest in developing win-win outcomes there is little understanding of what is required for them to be achieved. We analysed outcomes in a wide range of case studies where ecosystem services had been used for human well-being. Using systematic mapping of the literature from 2000 to 2013, we identified 1324 potentially relevant reports, 92 of which were selected for the review, creating a database of 231 actual or potential recorded trade-offs and synergies. The analysis of these case studies highlighted significant gaps in the literature, including: a limited geographic distribution of case studies, a focus on provisioning as opposed to non-provisioning services and a lack of studies exploring the link between ecosystem service trade-offs or synergies and the ultimate impact on human well-being. Trade-offs are recorded almost three times as often as synergies and the analysis indicates that there are three significant indicators that a trade-off will occur: at least one of the stakeholders having a private interest in the natural resources available, the involvement of provisioning ecosystem services and at least one of the stakeholders acting at the local scale. There is not, however, a generalisable context for a win-win, indicating that these trade-off indicators, although highlighting where a trade-off may occur do not indicate that it is inevitable. Taking account of why trade-offs occur (e.g. from failures in management or a lack of accounting for all stakeholders) is more likely to create win-win situations than planning for a win-win from the outset. Consequently, taking a trade-offs as opposed to a win-win approach, by having an awareness of and accounting for factors that predict a trade-off (private interest, provisioning versus other ES, local stakeholder) and the reasons why trade-offs are often the outcome, it may be possible to create the synergies we seek to achieve.
Total synthesis of the antimitotic marine macrolide (-)-leiodermatolide.
17 October 2014
Cambridge University

Paterson, Ian;Ng, Kenneth K-H;Williams, Simon;Millican, David C;Dalby, Stephen M

Leiodermatolide is an antimitotic macrolide isolated from the marine sponge Leiodermatium sp. whose potentially novel tubulin-targeting mechanism of action makes it an exciting lead for anticancer drug discovery. In pursuit of a sustainable supply, we report a highly stereocontrolled total synthesis (3.2% yield) based on a convergent sequence of palladium-mediated fragment assembly and macrolactonization. Boron-mediated aldol reactions were used to configure the three key fragments 2, 5, and 6 by employing the appropriate enantiomer of the lactate-derived ketone 7.
An Engineered Community Approach for Industrial Cultivation of Microalgae.
24 November 2014
Cambridge University

Kazamia, Elena;Riseley, Anthony S;Howe, Christopher J;Smith, Alison G

Although no species lives in isolation in nature, efforts to grow organisms for use in biotechnology have generally focused on a single-species approach, particularly where a product is required at high purity. In such scenarios, preventing the establishment of contaminants requires considerable effort that is economically justified. However, for some applications in biotechnology where the focus is on lower-margin biofuel production, axenic culture is not necessary, provided yields of the desired strain are unaffected by contaminants. In this article, we review what is known about interspecific interactions of natural algal communities, the dynamics of which are likely to parallel contamination in industrial systems. Furthermore, we discuss the opportunities to improve both yields and the stability of cultures by growing algae in multi-species consortia.
Mep72, a metzincin protease that is preferentially secreted by biofilms of Pseudomonas aeruginosa.
16 February 2015
Cambridge University

Passmore, Ian J;Nishikawa, Kahoko;Lilley, Kathryn S;Bowden, Steven D;Chung, Jade CS;Welch, Martin

In this work, we compared the profile of proteins secreted by planktonic and biofilm cultures of Pseudomonas aeruginosa using two-dimensional difference gel electrophoresis (2D-DiGE). This revealed that a novel metzincin protease, Mep72, was secreted during biofilm growth. Subsequent Western blotting and reverse transcription-PCR (RT-PCR) analyses demonstrated that Mep72 was expressed only during biofilm growth. Mep72 has a tridomain structure comprised of a metzincin protease-like domain and two tandem carbohydrate-binding domains. Unlike the only other metzincin (alkaline protease; AprA) in P. aeruginosa, Mep72 is secreted through the type II pathway and undergoes processing during export. During this processing, the metzincin domain is liberated from the carbohydrate-binding domains. This processing may be self-catalyzed, since purified Mep72 autodegraded in vitro. This autodegradation was retarded in the presence of alginate (an extracellular matrix component of many P. aeruginosa biofilms). The expression of full-length mep72 in Escherichia coli was toxic. However, this toxicity could be alleviated by coexpression of mep72 with the adjacent gene, bamI. Mep72 and BamI were found to form a protein-protein complex in vitro. 2D-DiGE revealed that the electrophoretic mobility of several discrete protein spots was altered in the biofilm secretome of an mep72 mutant, including type III secretion proteins (PopD, PcrV, and ExoS) and a flagellum-associated protein (FliD). Mep72 was found to bind directly to ExoS and PcrV and to affect the processing of these proteins in the biofilm secretome. We conclude that Mep72 is a secreted biofilm-specific regulator that affects the processing of a very specific subset of virulence factors.
Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations
19 March 2015
Cambridge University

Miller, LA;Fripiat, F;Else, BGT;Bowman, JS;Brown, KA;Collins, RE;Ewert, M;Fransson, A;Gosselin, M;Lannuzel, D;Meiners, KM;Michel, C;Nishioka, J;Nomura, D;Papadimitriou, S;Russell, LM;Sørensen, LL;Thomas, DN;Tison, JL;Van Leeuwe, MA;Vancoppenolle, M;Wolff, EW;Zhou, J

AbstractOver the past two decades, with recognition that the ocean’s sea-ice cover is neither insensitive to climate change nor a barrier to light and matter, research in sea-ice biogeochemistry has accelerated significantly, bringing together a multi-disciplinary community from a variety of fields. This disciplinary diversity has contributed a wide range of methodological techniques and approaches to sea-ice studies, complicating comparisons of the results and the development of conceptual and numerical models to describe the important biogeochemical processes occurring in sea ice. Almost all chemical elements, compounds, and biogeochemical processes relevant to Earth system science are measured in sea ice, with published methods available for determining biomass, pigments, net community production, primary production, bacterial activity, macronutrients, numerous natural and anthropogenic organic compounds, trace elements, reactive and inert gases, sulfur species, the carbon dioxide system parameters, stable isotopes, and water-ice-atmosphere fluxes of gases, liquids, and solids. For most of these measurements, multiple sampling and processing techniques are available, but to date there has been little intercomparison or intercalibration between methods. In addition, researchers collect different types of ancillary data and document their samples differently, further confounding comparisons between studies. These problems are compounded by the heterogeneity of sea ice, in which even adjacent cores can have dramatically different biogeochemical compositions. We recommend that, in future investigations, researchers design their programs based on nested sampling patterns, collect a core suite of ancillary measurements, and employ a standard approach for sample identification and documentation. In addition, intercalibration exercises are most critically needed for measurements of biomass, primary production, nutrients, dissolved and particulate organic matter (including exopolymers), the CO2 system, air-ice gas fluxes, and aerosol production. We also encourage the development of in situ probes robust enough for long-term deployment in sea ice, particularly for biological parameters, the CO2 system, and other gases.
Shortfalls and Solutions for Meeting National and Global Conservation Area Targets
20 May 2015
Cambridge University

Butchart, SHM;Clarke, M;Smith, RJ;Sykes, RE;Scharlemann, JPW;Harfoot, M;Buchanan, GM;Angulo, A;Balmford, A;Bertzky, B;Brooks, TM;Carpenter, KE;Comeros-Raynal, MT;Cornell, J;Ficetola, GF;Fishpool, LDC;Fuller, RA;Geldmann, J;Harwell, H;Hilton-Taylor, C;Hoffmann, M;Joolia, A;Joppa, L;Kingston, N;May, I;Milam, A;Polidoro, B;Ralph, G;Richman, N;Rondinini, C;Segan, DB;Skolnik, B;Spalding, MD;Stuart, SN;Symes, A;Taylor, J;Visconti, P;Watson, JEM;Wood, L;Burgess, ND

Governments have committed to conserving 17% of terrestrial and 10% of marine environments globally, especially “areas of particular importance for biodiversity” through “ecologically representative” Protected Area (PA) systems or other “area-based conservation measures”, while individual countries have committed to conserve 3–50% of their land area. We estimate that PAs currently cover 14.6% of terrestrial and 2.8% of marine extent, but 59–68% of ecoregions, 77–78% of important sites for biodiversity, and 57% of 25,380 species have inadequate coverage. The existing 19.7 million km2 terrestrial PA network needs only 3.3 million km2 to be added to achieve 17% terrestrial coverage. However, it would require nearly doubling to achieve, costefficiently, coverage targets for all countries, ecoregions, important sites, and species. Poorer countries have the largest relative shortfalls. Such extensive and rapid expansion of formal PAs is unlikely to be achievable. Greater focus is therefore needed on alternative approaches, including community- and privately managed sites and other effective area-based conservation measures.
Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.
08 July 2015
Cambridge University

Arif, Chatchanit;Daniels, Camille;Bayer, Till;Banguera-Hinestroza, Eulalia;Barbrook, Adrian;Howe, Christopher J;LaJeunesse, Todd C;Voolstra, Christian R

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.
A concise and scalable strategy for the total synthesis of dictyodendrin B based on sequential C-H functionalization.
14 July 2015
Cambridge University

Pitts, Andrew K;O'Hara, Fionn;Snell, Robert H;Gaunt, Matthew J

A sequential CH functionalization strategy for the synthesis of the marine alkaloid dictyodendrin B is reported. Our synthesis begins from commercially available 4-bromoindole and involves six direct functionalizations around the heteroarene core as part of a gram-scale strategy towards the natural product.
Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels.
18 August 2015
Cambridge University

Fraïsse, Christelle;Belkhir, Khalid;Welch, John J;Bierne, Nicolas

Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genomewide patterns of introgression in Mytilus and that gene flow between different species, with contiguous ranges, explained up to half of the intraspecific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, for example Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganization of genetic backgrounds, needs to be more widely considered to make better sense of genome scans.
Biotechnological exploitation of microalgae.
07 September 2015
Cambridge University

Gangl, Doris;Zedler, Julie AZ;Rajakumar, Priscilla D;Martinez, Erick M Ramos;Riseley, Anthony;Włodarczyk, Artur;Purton, Saul;Sakuragi, Yumiko;Howe, Christopher J;Jensen, Poul Erik;Robinson, Colin

Microalgae are a diverse group of single-cell photosynthetic organisms that include cyanobacteria and a wide range of eukaryotic algae. A number of microalgae contain high-value compounds such as oils, colorants, and polysaccharides, which are used by the food additive, oil, and cosmetic industries, among others. They offer the potential for rapid growth under photoautotrophic conditions, and they can grow in a wide range of habitats. More recently, the development of genetic tools means that a number of species can be transformed and hence used as cell factories for the production of high-value chemicals or recombinant proteins. In this article, we review exploitation use of microalgae with a special emphasis on genetic engineering approaches to develop cell factories, and the use of synthetic ecology approaches to maximize productivity. We discuss the success stories in these areas, the hurdles that need to be overcome, and the potential for expanding the industry in general.
Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle.
21 September 2015
Cambridge University

Lea-Smith, David J;Biller, Steven J;Davey, Matthew P;Cotton, Charles AR;Perez Sepulveda, Blanca M;Turchyn, Alexandra V;Scanlan, David J;Smith, Alison G;Chisholm, Sallie W;Howe, Christopher J

Hydrocarbons are ubiquitous in the ocean, where alkanes such as pentadecane and heptadecane can be found even in waters minimally polluted with crude oil. Populations of hydrocarbon-degrading bacteria, which are responsible for the turnover of these compounds, are also found throughout marine systems, including in unpolluted waters. These observations suggest the existence of an unknown and widespread source of hydrocarbons in the oceans. Here, we report that strains of the two most abundant marine cyanobacteria, Prochlorococcus and Synechococcus, produce and accumulate hydrocarbons, predominantly C15 and C17 alkanes, between 0.022 and 0.368% of dry cell weight. Based on global population sizes and turnover rates, we estimate that these species have the capacity to produce 2-540 pg alkanes per mL per day, which translates into a global ocean yield of ∼ 308-771 million tons of hydrocarbons annually. We also demonstrate that both obligate and facultative marine hydrocarbon-degrading bacteria can consume cyanobacterial alkanes, which likely prevents these hydrocarbons from accumulating in the environment. Our findings implicate cyanobacteria and hydrocarbon degraders as key players in a notable internal hydrocarbon cycle within the upper ocean, where alkanes are continually produced and subsequently consumed within days. Furthermore we show that cyanobacterial alkane production is likely sufficient to sustain populations of hydrocarbon-degrading bacteria, whose abundances can rapidly expand upon localized release of crude oil from natural seepage and human activities.
Exploring mutualistic interactions between microalgae and bacteria in the omics age.
21 October 2015
Cambridge University

Cooper, Matthew B;Smith, Alison G

Microalgae undertake a wide range of mutualistic interactions with bacteria. Here we consider how transcriptomic, metagenomic and metabolomic approaches have been combined with microbiological and biochemical analyses to expand our understanding of algal-bacterial interactions. Identification of the major bacterial species associated with algae indicates that specific bacterial groups, particularly the alpha-Proteobacteria, are found more frequently, suggesting that these may have the means to initiate and maintain symbiotic relationships. Nutrient exchange is frequently the basis of algal-bacterial mutualism, and as the compounds involved are characterised, evidence is accumulating that these are complex and specific molecules, offering opportunities for signalling processes and regulation rather than merely passive diffusion. At the same time, it is clear that the interactions are not static, but can be initiated and broken in response to environmental and developmental cues.
Quantifying fish and mobile invertebrate production from a threatened nursery habitat
11 November 2015
Cambridge University

zu Ermgassen, PSE;Grabowski, JH;Gair, JR;Powers, SP

1. Quantification of ecosystem services is increasingly valuable for conservation and restoration decision making. Structured habitats serve as nursery grounds by enhancing juvenile fish and mobile crustacean survival and abundance. This service is challenging to quantify due to ontogenetic shifts in habitat use by many species. 2. We reviewed available literature on the increased abundance of juvenile fish and mobile crustaceans in a key nursery habitat – Crassostrea virginica reefs in the USA. We modelled the growth and mortality of the enhanced species using three different natural mortality (M) estimates to provide estimates of the gross and net lifetime production and uncertainty that can be attributed to the habitat. 3. Recruitment of nineteen and twelve species were found to be enhanced by the addition of C. virginica reefs to previously unstructured habitat in the Gulf of Mexico and the South and Mid Atlantic USA, respectively. This increased recruitment is estimated to result in a mean lifetime enhancement in production of 397 ± 115 (1 SD) g m-2 y-1 in the Gulf of Mexico and 281 ± 56 g m-2 y-1 in the South and Mid Atlantic. 4. The two regions differed with regards to the identity of the enhanced species and their degree of augmentation. Thus, our results highlight the inadequacy of applying regional estimates of ecosystem services to global scales. Furthermore, estimates of total enhancement varied by up to a factor of 2.8 across the three methods of M estimation. 5. Our estimates are quantitative predictions of the ecological benefits derived from the restoration or conservation of a threatened habitat, and advance the field of restoration science beyond qualitative statements that just predict direction of benefit (e.g. increased or decreased). Quantification of the uncertainty in the production estimates further increases their utility for decision makers. 6. Synthesis and applications. Our results can be applied to the restoration or conservation of nursery habitats where habitat is limiting the recruitment of fish species. Quantitative estimates of fisheries productivity enhancement by habitats can be used by managers to determine the expected return on investment in restoration activities, provide testable predictions for monitoring programs, and communicate the value of restoring or conserving habitat.
Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi.
24 November 2015
Cambridge University

Dorrell, Richard G;Hinksman, George A;Howe, Christopher J

Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.
Dynamic modelling of Haematococcus pluvialis photoinduction for astaxanthin production in both attached and suspended photobioreactors
27 November 2015
Cambridge University

Zhang, D;Wan, M;del Rio-Chanona, EA;Huang, J;Wang, W;Li, Y;Vassiliadis, VS

Haematococcus pluvialis is a green algae with the great potential to generate natural astaxanthin. In the current study, dynamic models have been proposed to simulate effects of light intensity, light attenuation, temperature and nitrogen quota on cell growth and astaxanthin production in both suspended and attached photobioreactors, which to the best of our knowledge has not been addressed before. Based on the current models, optimal temperature s for algal growth and astaxanthin accumulation are identified. Cell absorption is found to be the primary factor causing light attenuation in the suspended reactor. In this reactor, astaxanthin accumulation is limited by the low local light intensity due to light attenuation during the initial operation period, but almost independent from that once it is close to the maximum value. Compared to the suspended reactor, light attenuation in the attached reactor is much reduced and biomass growth is remarkably enhanced, which suggests the attached reactor is a better choice if the process aims for biomass cultivation. However, the well-mixed culture in the suspended reactor can push most cells toward astaxanthin production; while the attached reactor has the potential to prevent the accumulation of astaxanthin in the bottom algae. Therefore, the suspended photobioreactor should be selected if the process target is astaxanthin production.
Identification of Sequences Encoding Symbiodinium minutum Mitochondrial Proteins.
14 January 2016
Cambridge University

Butterfield, Erin R;Howe, Christopher J;Nisbet, R Ellen R

The dinoflagellates are an extremely diverse group of algae closely related to the Apicomplexa and the ciliates. Much work has previously been undertaken to determine the presence of various biochemical pathways within dinoflagellate mitochondria. However, these studies were unable to identify several key transcripts including those encoding proteins involved in the pyruvate dehydrogenase complex, iron-sulfur cluster biosynthesis, and protein import. Here, we analyze the draft nuclear genome of the dinoflagellate Symbiodinium minutum, as well as RNAseq data to identify nuclear genes encoding mitochondrial proteins. The results confirm the presence of a complete tricarboxylic acid cycle in the dinoflagellates. Results also demonstrate the difficulties in using the genome sequence for the identification of genes due to the large number of introns, but show that it is highly useful for the determination of gene duplication events.
Cyanobacteria and Eukaryotic Algae Use Different Chemical Variants of Vitamin B12.
19 February 2016
Cambridge University

Helliwell, Katherine Emma;Lawrence, Andrew David;Holzer, Andre;Kudahl, Ulrich Johan;Sasso, Severin;Kräutler, Bernhard;Scanlan, David John;Warren, Martin James;Smith, Alison Gail

Eukaryotic microalgae and prokaryotic cyanobacteria are the major components of the phytoplankton. Determining factors that govern growth of these primary producers, and how they interact, is therefore essential to understanding aquatic ecosystem productivity. Over half of microalgal species representing marine and freshwater habitats require for growth the corrinoid cofactor B12, which is synthesized de novo only by certain prokaryotes, including the majority of cyanobacteria. There are several chemical variants of B12, which are not necessarily functionally interchangeable. Cobalamin, the form bioavailable to humans, has as its lower axial ligand 5,6-dimethylbenzimidazole (DMB). Here, we show that the abundant marine cyanobacterium Synechococcus synthesizes only pseudocobalamin, in which the lower axial ligand is adenine. Moreover, bioinformatic searches of over 100 sequenced cyanobacterial genomes for B12 biosynthesis genes, including those involved in nucleotide loop assembly, suggest this is the form synthesized by cyanobacteria more broadly. We further demonstrate that pseudocobalamin is several orders of magnitude less bioavailable than cobalamin to several B12-dependent microalgae representing diverse lineages. This indicates that the two major phytoplankton groups use a different B12 currency. However, in an intriguing twist, some microalgal species can use pseudocobalamin if DMB is provided, suggesting that they are able to remodel the cofactor, whereas Synechococcus cannot. This species-specific attribute implicates algal remodelers as novel and keystone players of the B12 cycle, transforming our perception of the dynamics and complexity of the flux of this nutrient in aquatic ecosystems.
A shared role for sonic hedgehog signalling in patterning chondrichthyan gill arch appendages and tetrapod limbs.
03 March 2016
Cambridge University

Gillis, J Andrew;Hall, Brian K

Chondrichthyans (sharks, skates, rays and holocephalans) possess paired appendages that project laterally from their gill arches, known as branchial rays. This led Carl Gegenbaur to propose that paired fins (and hence tetrapod limbs) originally evolved via transformation of gill arches. Tetrapod limbs are patterned by asonic hedgehog(Shh)-expressing signalling centre known as the zone of polarising activity, which establishes the anteroposterior axis of the limb bud and maintains proliferative expansion of limb endoskeletal progenitors. Here, we use loss-of-function, label-retention and fate-mapping approaches in the little skate to demonstrate that Shh secretion from a signalling centre in the developing gill arches establishes gill arch anteroposterior polarity and maintains the proliferative expansion of branchial ray endoskeletal progenitor cells. These findings highlight striking parallels in the axial patterning mechanisms employed by chondrichthyan branchial rays and paired fins/limbs, and provide mechanistic insight into the anatomical foundation of Gegenbaur's gill arch hypothesis.
Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome.
08 April 2016
Cambridge University

Juhas, Mario;Ajioka, James W

Bacillus subtilis is a well-characterized model bacterium frequently used for a number of biotechnology and synthetic biology applications. Novel strategies combining the advantages of B. subtilis with the DNA assembly and editing tools of Escherichia coli are crucial for B. subtilis engineering efforts. We combined Gibson Assembly and λ red recombineering in E. coli with RecA-mediated homologous recombination in B. subtilis for bacterial artificial chromosome-mediated DNA integration into the well-characterized amyE target locus of the B. subtilis chromosome. The engineered integrative bacterial artificial chromosome iBAC(cav) can accept any DNA fragment for integration into B. subtilis chromosome and allows rapid selection of transformants by B. subtilis-specific antibiotic resistance and the yellow fluorescent protein (mVenus) expression. We used the developed iBAC(cav)-mediated system to integrate 10kb DNA fragment from E. coli K12 MG1655 into B. subtilis chromosome. iBAC(cav)-mediated chromosomal integration approach will facilitate rational design of synthetic biology applications in B. subtilis.
Coordinated beating of algal flagella is mediated by basal coupling.
20 April 2016
Cambridge University

Wan, Kirsty Y;Goldstein, Raymond E

Cilia and flagella often exhibit synchronized behavior; this includes phase locking, as seen in Chlamydomonas, and metachronal wave formation in the respiratory cilia of higher organisms. Since the observations by Gray and Rothschild of phase synchrony of nearby swimming spermatozoa, it has been a working hypothesis that synchrony arises from hydrodynamic interactions between beating filaments. Recent work on the dynamics of physically separated pairs of flagella isolated from the multicellular alga Volvox has shown that hydrodynamic coupling alone is sufficient to produce synchrony. However, the situation is more complex in unicellular organisms bearing few flagella. We show that flagella of Chlamydomonas mutants deficient in filamentary connections between basal bodies display markedly different synchronization from the wild type. We perform micromanipulation on configurations of flagella and conclude that a mechanism, internal to the cell, must provide an additional flagellar coupling. In naturally occurring species with 4, 8, or even 16 flagella, we find diverse symmetries of basal body positioning and of the flagellar apparatus that are coincident with specific gaits of flagellar actuation, suggesting that it is a competition between intracellular coupling and hydrodynamic interactions that ultimately determines the precise form of flagellar coordination in unicellular algae.
Ultraviolet absorbing compounds provide a rapid response mechanism for UV protection in some reef fish.
28 April 2016
Cambridge University

Braun, C;Reef, R;Siebeck, UE

The external mucus surface of reef fish contains ultraviolet absorbing compounds (UVAC), most prominently Mycosporine-like Amino Acids (MAAs). MAAs in the external mucus of reef fish are thought to act as sunscreens by preventing the damaging effects of ultraviolet radiation (UVR), however, direct evidence for their protective role has been missing. We tested the protective function of UVAC's by exposing fish with naturally low, Pomacentrus amboinensis, and high, Thalassoma lunare, mucus absorption properties to a high dose of UVR (UVB: 13.4W∗m(-2), UVA: 6.1W∗m(-2)) and measuring the resulting DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). For both species, the amount of UV induced DNA damage sustained following the exposure to a 1h pulse of high UVR was negatively correlated with mucus absorbance, a proxy for MAA concentration. Furthermore, a rapid and significant increase in UVAC concentration was observed in P. amboinensis following UV exposure, directly after capture and after ten days in captivity. No such increase was observed in T. lunare, which maintained relatively high levels of UV absorbance at all times. P. amboinensis, in contrast to T. lunare, uses UV communication and thus must maintain UV transparent mucus to be able to display its UV patterns. The ability to rapidly alter the transparency of mucus could be an important adaptation in the trade off between protection from harmful UVR and UV communication.
Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics.
06 July 2016
Cambridge University

Crone, William JK;Vior, Natalia M;Santos-Aberturas, Javier;Schmitz, Lukas G;Leeper, Finian J;Truman, Andrew W

Bottromycin A2 is a structurally unique ribosomally synthesized and post-translationally modified peptide (RiPP) that possesses potent antibacterial activity towards multidrug-resistant bacteria. The structural novelty of bottromycin stems from its unprecedented macrocyclic amidine and rare β-methylated amino acid residues. The N-terminus of a precursor peptide (BtmD) is converted into bottromycin A2 by tailoring enzymes encoded in the btm gene cluster. However, little was known about key transformations in this pathway, including the unprecedented macrocyclization. To understand the pathway in detail, an untargeted metabolomic approach that harnesses mass spectral networking was used to assess the metabolomes of a series of pathway mutants. This analysis has yielded key information on the function of a variety of previously uncharacterized biosynthetic enzymes, including a YcaO domain protein and a partner protein that together catalyze the macrocyclization.
Connection: The port of Colombo, the geographical "Circuit," and the visual politics of new imperialism, ca. 1880-1914
15 July 2016
Cambridge University

Sivasundaram, S

AbstractConnections, circuits, webs, and networks: these are concepts that are overused in today's world histories. Working from a commitment to reflexive historicization, this paper points to one moment in the consolidation of these terms: the late nineteenth- and early twentieth-century visual politics of “new imperialism.” Utilizing photographs, engravings, postcards, letters, and colonial documents, the paper argues that connection was mesmerizing and can still mesmerize the historian. Being connected became possible because of visual and infrastructural projects that allowed the production and consumption of lines that literally cut sea and land. At a time of high empire, and in accordance with the dictates of Imperial Geography, particular locales or “nodes” were thus positioned in the “global.” To mount this critique of our language, the paper focuses on the infrastructural development of the port of Colombo, alongside the thinking of Halford Mackinder, the building of breakwaters in Colombo, the arrival of mass tourism, projections of capitalist improvement for the business of transshipment, and the use of the port by Indian laborers on their way to Ceylon's highland plantations. By attending to the place where connection is wrought, its material workings, and its traces in the visual, intellectual, and capitalist archive, it is argued that connectivity's forgettings and displacements come more forcefully into view. If connection had an evacuating character and could be so imperialist, what of its status in our writings?
Transcripts in the Plasmodium Apicoplast Undergo Cleavage at tRNAs and Editing, and Include Antisense Sequences.
03 August 2016
Cambridge University

Nisbet, R Ellen R;Kurniawan, Davy P;Bowers, Harrison D;Howe, Christopher J

The apicoplast, an organelle found in Plasmodium and many other parasitic apicomplexan species, is a remnant chloroplast that is no longer able to carry out photosynthesis. Very little is known about primary transcripts and RNA processing in the Plasmodium apicoplast, although processing in chloroplasts of some related organisms (chromerids and dinoflagellate algae) shows a number of unusual features, including RNA editing and the addition of 3' poly(U) tails. Here, we show that many apicoplast transcripts are polycistronic and that there is extensive RNA processing, often involving the excision of tRNA molecules. We have identified major RNA processing sites, and have shown that these are associated with a conserved sequence motif. We provide the first evidence for the presence of RNA editing in the Plasmodium apicoplast, which has evolved independently from editing in dinoflagellates. We also present evidence for long, polycistronic antisense transcripts, and show that in some cases these are processed at the same sites as sense transcripts. Together, this research has significantly enhanced our understanding of the evolution of chloroplast RNA processing in the Apicomplexa and dinoflagellate algae.
Structural Color in Marine Algae
09 November 2016
Cambridge University

Chandler, CJ;Wilts, BD;Brodie, J;Vignolini, S

Structural colouration is widespread in the marine environment. Within the large variety of marine organisms, macroalgae represent a diverse group of more than 24,700 species. Some macroalgae have developed complex optical responses using different nanostructures and material compositions. In this review, we describe the mechanisms that are employed to produce structural colour in algae and provide a discussion on the functional relevance by analysing the geographical distribution and ecology in detail. In contrast to what is observed in the animal kingdom, we hypothesise that structural colour in algae predominantly functions for a non-communicative purpose, most likely protection from radiation damage, e.g. by harmful UV light. We suggest that the presence of structural colour in algae is likely influenced by local factors such as radiation intensity and turbidity of the water.
The Evolution of Silicon Transport in Eukaryotes.
17 November 2016
Cambridge University

Marron, Alan O;Ratcliffe, Sarah;Wheeler, Glen L;Goldstein, Raymond E;King, Nicole;Not, Fabrice;de Vargas, Colomban;Richter, Daniel J

Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, including major silicified lineages (radiolarians and chrysophytes) and also bacterial SIT-Ls. Our evidence suggests that the symmetrical 10-transmembrane-domain SIT structure has independently evolved multiple times via duplication and fusion of 5-transmembrane-domain SIT-Ls. We also identify a second gene family, similar to the active Si transporter Lsi2, that is broadly distributed amongst siliceous and nonsiliceous eukaryotes. Our analyses resolve a distinct group of Lsi2-like genes, including plant and diatom Si-responsive genes, and sequences unique to siliceous sponges and choanoflagellates. The SIT/SIT-L and Lsi2 transporter families likely contribute to biosilicification in diverse lineages, indicating an ancient role for Si transport in eukaryotes. We propose that these Si transporters may have arisen initially to prevent Si toxicity in the high Si Precambrian oceans, with subsequent biologically induced reductions in Si concentrations of Phanerozoic seas leading to widespread losses of SIT, SIT-L, and Lsi2-like genes in diverse lineages. Thus, the origin and diversification of two independent Si transporter families both drove and were driven by ancient ocean Si levels.
Strategy Evolution in the Total Synthesis of (-)-Leiodermatolide
06 December 2016
Cambridge University

Paterson, Ian;Williams, Simon

This review highlights the various challenges overcome during our recent synthetic campaign towards (−)-leiodermatolide, a potent cytotoxic and antimitotic macrolide isolated from the marine sponge $\textit{Leiodermatium}$ sp. This structurally unprecedented macrocyclic chemotype represents a promising lead for anticancer drug discovery, provided a sustainable supply can be realised by an efficient chemical synthesis. Faced with the stereochemical ambiguities arising from our structural assignment work, a flexible and modular synthetic strategy was adopted for the construction of various key fragments, as a prelude to the controlled assembly of the two diene moieties. Installation of the nine stereocentres was achieved by the strategic use of boron-mediated aldol reactions of chiral ketone building blocks. Following the exploratory construction of the macrocyclic core, we revised our strategy to circumvent some problematic steps, enabling a highly convergent total synthesis of (−)-leiodermatolide.
Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches.
04 January 2017
Cambridge University

Yousef Kalafi, Elham;Tan, Wooi Boon;Town, Christopher;Dhillon, Sarinder Kaur

BACKGROUND: Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods. RESULT: Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%. CONCLUSIONS: The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented.
Combining Genes from Multiple Phages for Improved Cell Lysis and DNA Transfer from $\textit{Escherichia coli}$ to $\textit{Bacillus subtilis}$
13 January 2017
Cambridge University

Juhas, M;Wong, C;Ajioka, JW

The ability to efficiently and reliably transfer genetic circuits between the key synthetic biology chassis, such as $\textit{Escherichia coli}$ and $\textit{Bacillus subtilis}$, constitutes one of the major hurdles of the rational genome engineering. Using lambda Red recombineering we integrated the thermosensitive lambda repressor and the lysis genes of several bacteriophages into the $\textit{E. coli}$ chromosome. The lysis of the engineered autolytic cells is inducible by a simple temperature shift. We improved the lysis efficiency by introducing different combinations of lysis genes from bacteriophages lambda, ΦX174 and MS2 under the control of the thermosensitive lambda repressor into the $\textit{E. coli}$ chromosome. We tested the engineered autolytic cells by transferring plasmid and bacterial artificial chromosome (BAC)-borne genetic circuits from $\textit{E. coli}$ to $\textit{B. subtilis}$. Our engineered system combines benefits of the two main synthetic biology chassis, $\textit{E. coli}$ and B. subtilis, and allows reliable and efficient transfer of DNA edited in $\textit{E. coli}$ into $\textit{B. subtilis}$.
A 2017 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity
27 January 2017
Cambridge University

Sutherland, WJ;Barnard, P;Broad, S;Clout, M;Connor, B;Côté, IM;Dicks, LV;Doran, H;Entwistle, AC;Fleishman, E;Fox, M;Gaston, KJ;Gibbons, DW;Jiang, Z;Keim, B;Lickorish, FA;Markillie, P;Monk, KA;Pearce-Higgins, JW;Peck, LS;Pretty, J;Spalding, MD;Tonneijck, FH;Wintle, BC;Ockendon, N

We present the results of our eighth annual horizon scan of emerging issues likely to affect global biological diversity, the environment, and conservation efforts in the future. The potential effects of these novel issues might not yet be fully recognized or understood by the global conservation community, and the issues can be regarded as both opportunities and risks. A diverse international team with collective expertise in horizon scanning, science communication, and conservation research, practice, and policy reviewed 100 potential issues and identified 15 that qualified as emerging, with potential substantial global effects. These issues include new developments in energy storage and fuel production, sand extraction, potential solutions to combat coral bleaching and invasive marine species, and blockchain technology.
Bayesian Nonparametric Ordination for the Analysis of Microbial Communities.
10 April 2017
Cambridge University

Ren, Boyu;Bacallado, Sergio;Favaro, Stefano;Holmes, Susan;Trippa, Lorenzo

Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample's microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior, the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets.
Transcription of the apicoplast genome
31 May 2017
Cambridge University

Nisbet, RER;McKenzie, JL

Many members of the Apicomplexa contain a remnant chloroplast, known as an apicoplast. The apicoplast encodes numerous genes, and loss of the organelle is lethal. Here, we present a summary of what is known about apicoplast transcription. Unlike plant chloroplasts, there is a single RNA polymerase, and initial transcription is polycistronic. RNA is then cleaved into tRNA, mRNA and rRNA molecules. Significant levels of antisense transcription have been reported, together with a single case of RNA editing. Polycistronic transcription is also observed in the related algae Chromera and Vitrella, which retain a photosynthetic chloroplast. Surprisingly, a polyU tail is added to Chromera and Vitrella transcripts which encode proteins involved in photosynthesis. No such tail is added to Plasmodium transcripts. Transcription in the Apicomplexa is remarkably similar to that seen in the chloroplast of the related peridinin dinoflagellate algae, reflecting the common evolutionary origins of the organelle.
Blueprints of Effective Biodiversity and Conservation Knowledge Products That Support Marine Policy
05 July 2017
Cambridge University

Weatherdon, LV;Appeltans, W;Bowles-Newark, N;Brooks, TM;Davis, FE;Despot-Belmonte, K;Fletcher, S;Garilao, C;Hilton-Taylor, C;Hirsch, T;Juffe-Bignoli, D;Kaschner, K;Kingston, N;Malsch, K;Regan, EC;Kesner-Reyes, K;Rose, DC;Wetzel, FT;Wilkinson, T;Martin, CS

Biodiversity and conservation data are generally costly to collect, particularly in the marine realm. Hence, data collected for a given—often scientific—purpose are occasionally contributed toward secondary needs, such as policy implementation or other types of decision-making. However, while the quality and accessibility of marine biodiversity and conservation data have improved over the past decade, the ways in which these data can be used to develop and implement relevant management and conservation measures and actions are not always explicit. For this reason, there are a number of scientifically-sound datasets that are not used systematically to inform policy and decisions. Transforming these marine biodiversity and conservation datasets into knowledge products that convey the information required by policy- and decision-makers is an important step in strengthening knowledge exchange across the science-policy interface. Here, we identify seven characteristics of a selection of online biodiversity and conservation knowledge products that contribute to their ability to support policy- and decision-making in the marine realm (as measured by e.g., mentions in policy resolutions/decisions, or use for reporting under selected policy instruments; use in high-level screening for areas of biodiversity importance). These characteristics include: a clear policy mandate; established networks of collaborators; iterative co-design of a user-friendly interface; standardized, comprehensive and documented methods with quality assurance; consistent capacity and succession planning; accessible data and value-added products that are fit-for-purpose; and metrics of use collated and reported. The outcomes of this review are intended to: (a) support data creators/owners/providers in designing and curating biodiversity and conservation knowledge products that have greater influence, and hence impact, in policy- and decision-making, and (b) provide recommendations for how decision- and policy-makers can support the development, implementation, and sustainability of robust biodiversity and conservation knowledge products through the framing of marine policy and decision-making frameworks.
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
16 July 2017
Cambridge University

Akay, A;Di Domenico, T;Suen, KM;Nabih, A;Parada, GE;Larance, M;Medhi, R;Berkyurek;Zhang, X;Wedeles, CJ;Rudolph;Engelhardt, J;Hemberg, M;Ma, P;Lamond, AI;Claycomb, JM;Miska

Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in $\textit{Caenorhabditis elegans}$. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
ClientEarth (No 2): A Case of Three Legal Dimensions
17 July 2017
Cambridge University

Bell, J

This analysis has two main aims. The first is to explore in some detail the recent decision of the Administrative Court in ClientEarth (No 2). Here the central focus will be on drawing out three legal dimensions which it is argued played a significant role in the court’s judgment: an environmental modelling, an EU law and a domestic judicial review dimension. The second aim is then to offer some reflections on the environmental and judicial review dimensions of the case. Here, two main arguments will be developed. Firstly, that while ClientEarth (No 2) does not mark a sea-change in the judicial approach to the scrutiny of environmental modelling processes, it does show that the courts are willing to engage in a higher degree of scrutiny when the legislative background requires it. Secondly, that there are important insights to be gained, both from an administrative and an environmental law perspective, from reflecting on the role that domestic grounds of judicial review played in the court’s legal reasoning this case.
Synoptic-to-planetary scale wind variability enhances phytoplankton biomass at ocean fronts
08 August 2017
Cambridge University

Whitt, DB;Taylor, JR;Lévy, M

In nutrient-limited conditions, phytoplankton growth at fronts is enhanced by winds, which drive upward nutrient fluxes via enhanced turbulent mixing and upwelling. Hence, depth-integrated phytoplankton biomass can be 10 times greater at isolated fronts. Using theory and two-dimensional simulations with a coupled physical-biogeochemical ocean model, this paper builds conceptual understanding of the physical processes driving upward nutrient fluxes at fronts forced by unsteady winds with timescales of 4–16 days. The largest vertical nutrient fluxes occur when the surface mixing layer penetrates the nutricline, which fuels phytoplankton in the mixed layer. At a front, mixed layer deepening depends on the magnitude and direction of the wind stress, cross-front variations in buoyancy and velocity at the surface, and potential vorticity at the base of the mixed layer, which itself depends on past wind events. Consequently, mixing layers are deeper and more intermittent in time at fronts than outside fronts. Moreover, mixing can decouple in time from the wind stress, even without other sources of physical variability. Wind-driven upwelling also enhances depth-integrated phytoplankton biomass at fronts; when the mixed layer remains shallower than the nutricline, this results in enhanced subsurface phytoplankton. Oscillatory along-front winds induce both oscillatory and mean upwelling. The mean effect of oscillatory vertical motion is to transiently increase subsurface phytoplankton over days to weeks, whereas slower mean upwelling sustains this increase over weeks to months. Taken together, these results emphasize that wind-driven phytoplankton growth is both spatially and temporally intermittent and depends on a diverse combination of physical processes.
Correction to: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
21 October 2018
Cambridge University

Lager, Susanne;de Goffau, Marcus C;Sovio, Ulla;Peacock, Sharon J;Parkhill, Julian;Stephen Charnock-Jones, D.;Smith, Gordon C S

The author reported an error in an equation in the article [1].
Fish tank granuloma: An emerging skin disease in Iran mimicking Cutaneous Leishmaniasis.
27 September 2019
Cambridge University

Fata, Abdolmajid;Bojdy, Amin;Maleki, Masoud;Hosseini Farash, Bibi Razieh;Ghazvini, Kiarash;Tajzadeh, Parastoo;Vakili, Vida;Moghaddas, Elham;Mastroeni, Pietro;Rahmani, Shadi

OBJECTIVE: Mycobacterium marinum causes a rare cutaneous disease known as fish tank granuloma (FTG). The disease manifestations resemble those associated with Cutaneous Leishmaniasis (CL). The aim of this study was to determine whether FTG was the cause of cutaneous lesions in patients who were referred to the Parasitology laboratory of Imam Reza Hospital in Mashhad to be investigated for CL. MATERIALS/METHODS: One hundered patients, clinically diagnosed with CL between April 2014 and March 2015, were included in this study. Ziehl-Neelsen staining was performed to identify acid-fast Mycobacterium in addition to bacterial cultures using Löwenstein-Jensen medium. Skin lesion samples were also collected and kept on DNA banking cards for PCR testing. RESULTS: Twenty-nine of the 100 individuals with skin lesions, and therefore suspected of suffering from CL, tested positive for Mycobacterium marinum by PCR. Of these, 21 (72.4%) were male and 8(27.6%) were female. In 97% of these cases the lesions were located on hands and fingers. These patients had a history of manipulating fish and had been in contact with aquarium water. A sporotrichoid appearance was observed in 58.6% of the patients with mycobacterial lesions; 67% of patients had multiple head appearance. CONCLUSION: Patients suspected to have CL and who test negative for CL could be affected by FTG. Therefore, after obtaining an accurate case history, molecular diagnosis is recommended for cases that give a negative result by conventional methods.
Biomineralization plasticity and environmental heterogeneity predict geographical resilience patterns of foundation species to future change.
16 October 2019
Cambridge University

Telesca, Luca;Peck, Lloyd S;Sanders, Trystan;Thyrring, Jakob;Sejr, Mikael K;Harper, Elizabeth M

Although geographical patterns of species' sensitivity to environmental changes are defined by interacting multiple stressors, little is known about compensatory processes shaping regional differences in organismal vulnerability. Here, we examine large-scale spatial variations in biomineralization under heterogeneous environmental gradients of temperature, salinity and food availability across a 30° latitudinal range (3,334 km), to test whether plasticity in calcareous shell production and composition, from juveniles to large adults, mediates geographical patterns of resilience to climate change in critical foundation species, the mussels Mytilus edulis and M. trossulus. We find shell calcification decreased towards high latitude, with mussels producing thinner shells with a higher organic content in polar than temperate regions. Salinity was the best predictor of within-region differences in mussel shell deposition, mineral and organic composition. In polar, subpolar, and Baltic low-salinity environments, mussels produced thin shells with a thicker external organic layer (periostracum), and an increased proportion of calcite (prismatic layer, as opposed to aragonite) and organic matrix, providing potentially higher resistance against dissolution in more corrosive waters. Conversely, in temperate, higher salinity regimes, thicker, more calcified shells with a higher aragonite (nacreous layer) proportion were deposited, which suggests enhanced protection under increased predation pressure. Interacting effects of salinity and food availability on mussel shell composition predict the deposition of a thicker periostracum and organic-enriched prismatic layer under forecasted future environmental conditions, suggesting a capacity for increased protection of high-latitude populations from ocean acidification. These findings support biomineralization plasticity as a potentially advantageous compensatory mechanism conferring Mytilus species a protective capacity for quantitative and qualitative trade-offs in shell deposition as a response to regional alterations of abiotic and biotic conditions in future environments. Our work illustrates that compensatory mechanisms, driving plastic responses to the spatial structure of multiple stressors, can define geographical patterns of unanticipated species resilience to global environmental change.

Search

Filter by SDG

Filter by Institutions

Matching results: 100