New V. cholerae atypical El Tor variant emerged during the 2006 epidemic outbreak in Angola

<p>Abstract</p> <p>Background</p> <p><it>V. cholerae </it>is the etiological agent of cholera, a major public health concern in most developing countries. Virulence of <it>V. cholerae </it>relies on the powerful cholera toxin, encoded by the CTX prophage. The emergence of new pathogenic variants in the recent years has been mostly associated with new CTX prophage rearrangements.</p> <p>Results</p> <p>In this retrospective study, we show that the epidemic <it>V. cholerae </it>O1 El Tor strain responsible for the 2006 outbreak in Angola is clonally and genetically different from El Tor strains circulating in the 1990s in the same area. Strains from 2006 carry ICE<it>Vch</it>Ang3 of the SXT/R391 family. This ICE is associated with a narrower multidrug resistance profile compared to the one conferred by plasmid p3iANG to strains of the 1990s. The CTX prophage carried by 2006 El Tor strains is characterized by <it>rstR^ET</it>and <it>ctxB^Cla</it>alleles organized in a RS1-RS2-Core array on chromosome I. Interestingly, the newly emerging atypical strain belongs to a clade previously known to comprise only clinical isolates from the Indian subcontinent that also contain the same ICE of the SXT/R391 family.</p> <p>Conclusions</p> <p>Our findings remark the appearance of a novel <it>V. cholerae </it>epidemic variant in Africa with a new CTXΦ arrangement previously described only in the Indian Subcontinent.</p

How to meet new global targets in the offshore realms: biophysical guidelines for offshore networks of no-take marine protected areas

Networks of no-take marine protected areas (MPAs), where all extractive activities are prohibited, are the most effective tool to directly protect marine ecosystems from destructive and unsustainable human activities. No-take MPAs and MPA networks have been globally implemented in coastal seas, and their success has been significantly enhanced where science-based biophysical guidelines have informed their design. Increasingly, as human pressure on marine ecosystems is expanding further offshore, governments are establishing offshore MPAs—some very large—or MPA networks. Globally, there are growing calls from scientists, non-government organisations, and national governments to set global conservation targets upwards of 30%. Given that most of the ocean is found either in the high seas or offshore within national Exclusive Economic Zones, large offshore MPAs or networks of MPAs must be a major component of these global targets for ocean protection. However, without adequate design, these offshore MPAs risk being placed to minimise conflict with economic interests, rather than to maximise biodiversity protection. This paper describes detailed biophysical guidelines that managers can use to design effective networks of no-take MPAs in offshore environments. We conducted a systematic review of existing biophysical design guidelines for networks of MPAs in coastal seas, and found consistent elements relating to size, shape, connectivity, timeframes, and representation of biophysical features. However, few of the guidelines are tailored to offshore environments, and few of the large offshore MPAs currently in place were designed systematically. We discuss how the common inshore design guidelines should be revised to be responsive to the characteristics of offshore ecosystems, including giving consideration of issues of scale, data availability, and uncertainty. We propose 10 biophysical guidelines that can be used to systematically design offshore networks of MPAs which will also contribute to the global goal of at least 30% protection globally. Finally, we offer three priority guidelines that reflect the unique conservation needs of offshore ecosystems: emphasising the need for larger MPAs; maximising the inclusion of special features that are known and mapped; and representing minimum percentages of habitats, or, where mapped, bioregions. Ultimately, MPA guidelines need to be embedded within an adaptive management framework, and have the flexibility to respond to emerging knowledge and new challenges

Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+

<p>Abstract</p> <p>Background</p> <p>Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. <it>Leptospira interrogans </it>is a spirochaete parasitic bacterium capable of infecting humans and mammals in general. <it>Leptospira interrogans </it>FNR (LepFNR) displays low sequence identity with plant (34% with <it>Zea mays</it>) and bacterial (31% with <it>Escherichia coli</it>) FNRs. However, LepFNR contains all consensus sequences that define the plastidic class FNRs.</p> <p>Results</p> <p>The crystal structures of the FAD-containing LepFNR and the complex of the enzyme with NADP⁺, were solved and compared to known FNRs. The comparison reveals significant structural similarities of the enzyme with the plastidic type FNRs and differences with the bacterial enzymes. Our small angle X-ray scattering experiments show that LepFNR is a monomeric enzyme. Moreover, our biochemical data demonstrate that the LepFNR has an enzymatic activity similar to those reported for the plastidic enzymes and that is significantly different from bacterial flavoenzymes, which display lower turnover rates.</p> <p>Conclusion</p> <p>LepFNR is the first plastidic type FNR found in bacteria and, despite of its low sequence similarity with plastidic FNRs still displays high catalytic turnover rates. The typical structural and biochemical characteristics of plant FNRs unveiled for LepFNR support a notion of a putative lateral gene transfer which presumably offers <it>Leptospira interrogans </it>evolutionary advantages. The wealth of structural information about LepFNR provides a molecular basis for advanced drugs developments against leptospirosis.</p

Community management yields positive impacts for coastal fisheries resources and biodiversity conservation

Combining no-take marine reserves with exclusive access by communities to unreserved waters could provide the required incentives for community management to achieve positive impacts. However, few protected areas have been critically evaluated for their impact, which involves applying counterfactual thinking to predict conditions within protected areas if management had never occurred. Here, we use statistical matching to conduct a rigorous impact evaluation of dual management systems on coral reef fishes in Tonga, with communities having both full no-take areas and areas of exclusive fishing rights. No-take areas generally had positive impacts on the species richness, biomass, density, and size of target reef fish, while exclusive access areas were similar to predicted counterfactual conditions. The latter is likely because overall fishing pressure in exclusive access areas might not actually change, although more fish could be exploited by communities with access rights. Our findings suggest that dual management is effective at incentivizing effective community-based no-take areas for biodiversity conservation and resource management

Discriminating Catch Composition and Fishing Modes in an Artisanal Multispecies Fishery

Many small-scale fisheries are multi-species, and the catch composition can vary according to available habitats, fishing modes, and fisher groups. Here, we applied novel analyses for understanding the factors affecting differences in catch composition among fishers, which should be useful for planning regulatory measures and fishery development initiatives. Interviews with 235 artisanal fishers in Fiji were used to analyse how fishers' catch composition of 22 species of sea cucumbers varied across geographic scales (locations and villages within locations), genders, and fishing modes. Venn diagrams illustrated that gleaning and SCUBA diving were practiced to varying extents among locations and genders, whereas fishers used breath-hold diving more uniformly across the fishery. Segmented bubble plots revealed spatial variations in catch composition across the fishery. A PERMANOVA analysis found that species catch composition varied most across the two geographic scales and, secondarily, among fishing modes and between men and women. Gendered differences in catch composition were variable from one village to another, and so should not be generalized. SIMPER analyses showed that gleaners and SCUBA divers caught significantly different suites of sea cucumber species. Species threatened with extinction were among those typifying catches of SCUBA divers. Our novel graphical techniques are useful for visualizing fishing modes and catches across other fisheries. Artisanal fisheries may exhibit strong heterogeneity in catches at multiple spatial scales. Planning of regulatory measures that limit certain fishing modes or species should take into account the likely differential impacts on different fishing communities and genders

Coral restoration in a changing world - a global synthesis of methods and techniques

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades, due to increased nutrient outputs from agriculture, elevated levels of suspended sediment caused by deforestation and development, destructive fishing practices, over-harvesting of reef species, outbreaks of corallivorous crown-of-thorns starfish (COTS, Acanthaster planci), coral disease and tropical storms. However, in recent years climate change has emerged as the primary threat to coral reefs. While reefs have a natural capacity for recovery, recurring events like mass coral bleaching and extreme weather events is increasing in frequency, intensity and severity, and are eroding the time for recovery between catastrophic events. Marine conservation has primarily focused on passive habitat protection over active restoration, in contrast to terrestrial ecosystems where active restoration is common practice. Further, active restoration is well accepted for wetlands and shellfish reefs however coral reef restoration has remained controversial both in academia and amongst marine managers. This is despite recent research suggesting that optimal conservation outcomes include both habitat protection and restoration. Critics often argue that coral restoration detracts focus from mitigating climate change and other threats to the marine environment, while proponents of coral restoration counter that interventions can serve to protect coral biodiversity and endangered species in the short-term, while mitigation of large-scale threats such as climate change and water quality take effect. Despite this disconnect between coral restoration practitioners, coral reef managers and scientists, active coral restoration is increasingly used as a tool to attempt to restore coral populations. The field has largely developed through independent work of isolated groups, and has fallen victim to ‘growing pains’ associated with ecological restoration in many other ecosystems. Partly this is due to a reluctance to share outcomes of projects, and in some cases a lack of monitoring or appropriate reporting of project outcomes. To mitigate this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from a traditional literature search of the scientific literature, complemented with information gathered from online sources and through a survey of coral restoration practitioners. We identified 329 case studies on coral restoration, of which 195 were from the scientific literature, 79 were sourced from the grey literature (i.e. reports and online descriptions), and 55 were responses to our survey of restoration practitioners. We identified ten coral restoration intervention types: coral gardening - transplantation phase (23% of records), direct transplantation (21%), artificial reefs (19%), coral gardening - nursery phase (17%), coral gardening (both phases, 7%), substrate enhancement with electricity (4%), substrate stabilisation (4%), algae removal (2%), larval enhancement (1%) and microfragmentation (<1%). The majority of interventions involve coral fragmentation or transplantation of coral fragments (70%). While 52 countries are represented in the dataset, the majority of projects were conducted in the USA, Philippines, Thailand and Indonesia (together representing 40% of projects). Coral restoration case studies are dominated by short-term projects, with 66% of all projects reporting less than 18 months of monitoring of the restored sites. Overall, the median length of projects was 12 months. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 500 m2. A diverse range of species are represented in the dataset, with 221 different species from 89 coral genera. Overall, coral restoration projects focused primarily (65% of studies) on fast-growing branching corals. Among all the published documents, the top five species (22% of studies) were Acropora cervicornis, Pocillopora damicornis, Stylophora pistillata, Porites cylindrica and Acropora palmata. Over a quarter of projects (26%) involved the coral genus Acropora, while 9% of studies included a single species - Acropora cervicornis. Much of the focus on Acropora cervicornis and Acropora palmata is likely to have resulted from these important reef-forming species being listed as threatened on the United States Endangered Species List and as Endangered on the International Union for Conservation of Nature Red List of Endangered Species (IUCN 2018). We have dedicated a section to each intervention type covered in this review, and describe the potential and limitations of each intervention type in detail there. However, collating this information has highlighted the following main points which apply to coral restoration in general. 1. On average, survival in restored corals is relatively high. All coral genera with sufficient replication from which to draw conclusions (>10 studies listing that genus) report an average survival between 60-70%. 2. Differences in survival and growth are largely species and/or location specific, so the selection of specific methods should be tailored to the local conditions, costs, availability of materials, and to the specific objectives of each project. 3. Projects are overall small and short, however substantial scaling up is required for restoration to be a useful tool in supporting the persistence of reefs in the future. While there is ample evidence detailing how to successfully grow corals at smaller scales, few interventions demonstrate a capacity to be scaled up much beyond one hectare. Notable exceptions include methods which propagate sexually derived coral larvae. 4. To date, coral restoration has been plagued by the same common problems as ecological restoration in other ecosystems. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. a. Lack of clear objectives - There is a clear mismatch between the stated objectives of projects, and the design of projects and monitoring of outcomes. Poorly articulated or overinflated objectives risk alienating the general public and scientists, by over-promising and under-delivering. Social and economic objectives have inherent value and do not need to be disguised with ecological objectives. b. Lack of appropriate monitoring - A large proportion of projects do not monitor metrics relevant to their stated objectives, or do not continue monitoring for long enough to provide meaningful estimates of success. Further, there is a clear need for standardisation in the metrics that are used, to allow comparisons between projects. c. Lack of appropriate reporting - The outcomes of a large proportion of projects are not documented, which restricts knowledge-sharing and adaptive learning. While we attempted to access some of the unreported projects through our survey, it is clear we have only scratched the surface of existing knowledge. d. Poorly designed projects - An effect of inadequate monitoring and reporting is that projects are poorly suited to their specific area and conditions. Improved knowledge-sharing and development of best practice coral restoration guidelines aims to mitigate this problem

Best practice coral restoration for the Great Barrier Reef

As the Great Barrier Reef (GBR) continues to degrade through repeated mass bleaching events, crown-of-thorns starfish and major disease outbreaks, and the impacts of intense cyclones, pressure is growing for direct intervention to assist the recovery of reef-building corals. Decreasing coral cover on the GBR and other Australian reefs has been recognised as a serious problem relatively recently in Australia but follows a global trend, with many overseas reefs now highly degraded. Various types of coral restoration, rehabilitation and assisted recovery projects have been trialled overseas for decades and it makes sense to look at what has and hasn’t worked overseas to determine a range of options that may suit GBR conditions. Some direct interventions to assist coral recovery have been trialled in Australia such as transplanting corals, algae removal to promote coral recovery and larval enhancement promoting direct coral recruitment. In addition, after physical damage from cyclones, ship strikes or dragged anchors, local dive operators and dive clubs (permitted or unpermitted) often attempt to assist the recovery of corals by tipping over flipped tabular corals and reattaching broken branching corals or sea fans. These latter assisted recovery techniques are rarely underpinned by scientific data on coral recovery. A lack of best practice guidelines for these actions limits the chance of success and increases the health and safety risks of these activities

Thank You to Our 2018 Peer Reviewers

Public trust in science, effective science communication, and rapid and constructive response to authors about their submissions are of paramount importance to the scientific enterprise and indeed to society itself. This is really at the heart of peer review—providing thoughtful insights into both the scientific quality and importance of work, and also how it is communicated to other scientists and increasingly to a broader audience. Very few opportunities exist to acknowledge the mostly anonymous process of peer review, especially given the huge increase in review requests and the relatively mechanical nature of online reviewing platforms. We continue to be humbled by the time, effort, and careful insights that our colleagues share with each other through the process of peer review. In 2018, GeoHealth benefited from more than 83 reviews provided by 53 of our peers for papers submitted to the journal. Thank you all for your awesome efforts toward advancing geohealth now and for the future

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to many phages, these elements integrate into and replicate along with the host chromosome. Members of the SXT/R391 family of ICEs have been isolated from several species of gram-negative bacteria, including Vibrio cholerae, the cause of cholera, where they have been important vectors for disseminating genes conferring resistance to antibiotics. Here we developed a plasmid-based system to capture and isolate SXT/R391 ICEs for sequencing. Comparative analyses of the genomes of 13 SXT/R391 ICEs derived from diverse hosts and locations revealed that they contain 52 perfectly syntenic and nearly identical core genes that serve as a scaffold capable of mobilizing an array of variable DNA. Furthermore, selection pressure to maintain ICE mobility appears to have restricted insertions of variable DNA into intergenic sites that do not interrupt core functions. The variable genes confer diverse element-specific phenotypes, such as resistance to antibiotics. Functional analysis of a set of deletion mutants revealed that less than half of the conserved core genes are required for ICE mobility; the functions of most of the dispensable core genes are unknown. Several lines of evidence suggest that there has been extensive recombination between SXT/R391 ICEs, resulting in re-assortment of their respective variable gene content. Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements