Trawl impacts on the relative status of biotic communities of seabed sedimentary habitats in 24 regions worldwide.

Bottom trawling is widespread globally and impacts seabed habitats. However, risks from trawling remain unquantified at large scales in most regions. We address these issues by synthesizing evidence on the impacts of different trawl-gear types, seabed recovery rates, and spatial distributions of trawling intensity in a quantitative indicator of biotic status (relative amount of pretrawling biota) for sedimentary habitats, where most bottom-trawling occurs, in 24 regions worldwide. Regional average status relative to an untrawled state (=1) was high (>0.9) in 15 regions, but <0.7 in three (European) regions and only 0.25 in the Adriatic Sea. Across all regions, 66% of seabed area was not trawled (status = 1), 1.5% was depleted (status = 0), and 93% had status > 0.8. These assessments are first order, based on parameters estimated with uncertainty from meta-analyses; we recommend regional analyses to refine parameters for local specificity. Nevertheless, our results are sufficiently robust to highlight regions needing more effective management to reduce exploitation and improve stock sustainability and seabed environmental status-while also showing seabed status was high (>0.95) in regions where catches of trawled fish stocks meet accepted benchmarks for sustainable exploitation, demonstrating that environmental benefits accrue from effective fisheries management. Furthermore, regional seabed status was related to the proportional area swept by trawling, enabling preliminary predictions of regional status when only the total amount of trawling is known. This research advances seascape-scale understanding of trawl impacts in regions around the world, enables quantitative assessment of sustainability risks, and facilitates implementation of an ecosystem approach to trawl fisheries management globally.

Inter-reef Halimeda algal habitats within the Great Barrier Reef support a distinct biotic community and high biodiversity.

Tropical marine biodiversity studies have been biased towards more accessible coastal habitats and shallow coral reefs, while deeper inter-reef habitats are less studied due to different survey challenges. One such inter-reef habitat is the 'bioherms' dominated by the calcareous Halimeda macroalgae. In the northern section of Australia's Great Barrier Reef, Halimeda algal bioherms occupy >6,000 km2 of the inter-reef seabed, more than twice the area of adjacent shallow coral reefs. Here, we describe the biodiversity of the plant, vertebrate and invertebrate communities inhabiting Halimeda bioherms. By combining previous spatial mapping with legacy benthic biodiversity datasets, we find that Halimeda bioherms are a critically important complex habitat that hosts higher average species richness and diversity for both plants and invertebrates than the surrounding inter-reef (non-coral reef) seascape. Furthermore, at the community level, the structure of the bioherm-associated biotic assemblage is distinct from the non-bioherm community, with 40% of Halimeda bioherm-associated species not recorded at any non-bioherm sites. These findings improve estimates of the biodiversity of the Great Barrier Reef and elevate Halimeda bioherms as a critically important inter-reef habitat. Regular long-term monitoring is required to detect potential impacts to inter-reef biodiversity and ecosystem structure and function under future climate change scenarios.

Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences.

Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs.

First Measurement of the Total Neutron Cross Section on Argon between 100 and 800 MeV.

We report the first measurement of the neutron cross section on argon in the energy range of 100-800 MeV. The measurement was obtained with a 4.3-h exposure of the Mini-CAPTAIN detector to the WNR/LANSCE beam at LANL. The total cross section is measured from the attenuation coefficient of the neutron flux as it traverses the liquid argon volume. A set of 2631 candidate interactions is divided in bins of the neutron kinetic energy calculated from time-of-flight measurements. These interactions are reconstructed with custom-made algorithms specifically designed for the data in a time projection chamber the size of the Mini-CAPTAIN detector. The energy averaged cross section is 0.91±0.10(stat)±0.09(syst) b. A comparison of the measured cross section is made to the GEANT4 and FLUKA event generator packages, where the energy averaged cross sections in this range are 0.60 and 0.68 b, respectively.

Bottom trawl fishing footprints on the world's continental shelves.

Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Chile, and Gulf of Alaska to >50% in some European seas. Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when high-resolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, there was >95% probability that >90% of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.

Comment on "Tracking the global footprint of fisheries".

Kroodsma et al (Reports, 23 February 2018, p. 904) mapped the global footprint of fisheries. Their estimates of footprint and resulting contrasts between the scale of fishing and agriculture are an artifact of the spatial scale of analysis. Reanalyses of their global (all vessels) and regional (trawling) data at higher resolution reduced footprint estimates by factors of >10 and >5, respectively.

Global analysis of depletion and recovery of seabed biota after bottom trawling disturbance.

Bottom trawling is the most widespread human activity affecting seabed habitats. Here, we collate all available data for experimental and comparative studies of trawling impacts on whole communities of seabed macroinvertebrates on sedimentary habitats and develop widely applicable methods to estimate depletion and recovery rates of biota after trawling. Depletion of biota and trawl penetration into the seabed are highly correlated. Otter trawls caused the least depletion, removing 6% of biota per pass and penetrating the seabed on average down to 2.4 cm, whereas hydraulic dredges caused the most depletion, removing 41% of biota and penetrating the seabed on average 16.1 cm. Median recovery times posttrawling (from 50 to 95% of unimpacted biomass) ranged between 1.9 and 6.4 y. By accounting for the effects of penetration depth, environmental variation, and uncertainty, the models explained much of the variability of depletion and recovery estimates from single studies. Coupled with large-scale, high-resolution maps of trawling frequency and habitat, our estimates of depletion and recovery rates enable the assessment of trawling impacts on unprecedented spatial scales.

The effectiveness of marine reserve systems constructed using different surrogates of biodiversity.

Biological sampling in marine systems is often limited, and the cost of acquiring new data is high. We sought to assess whether systematic reserves designed using abiotic domains adequately conserve a comprehensive range of species in a tropical marine inter-reef system. We based our assessment on data from the Great Barrier Reef, Australia. We designed reserve systems aiming to conserve 30% of each species based on 4 abiotic surrogate types (abiotic domains; weighted abiotic domains; pre-defined bioregions; and random selection of areas). We evaluated each surrogate in scenarios with and without cost (cost to fishery) and clumping (size of conservation area) constraints. To measure the efficacy of each reserve system for conservation purposes, we evaluated how well 842 species collected at 1155 sites across the Great Barrier Reef seabed were represented in each reserve system. When reserve design included both cost and clumping constraints, the mean proportion of species reaching the conservation target was 20-27% higher for reserve systems that were biologically informed than reserves designed using unweighted environmental data. All domains performed substantially better than random, except when there were no spatial or economic constraints placed on the system design. Under the scenario with no constraints, the mean proportion of species reaching the conservation target ranged from 98.5% to 99.99% across all surrogate domains, whereas the range was 90-96% across all domains when both cost and clumping were considered. This proportion did not change considerably between scenarios where one constraint was imposed and scenarios where both cost and clumping constraints were considered. We conclude that representative reserve systems can be designed using abiotic domains; however, there are substantial benefits if some biological information is incorporated.

Congruence in demersal fish, macroinvertebrate, and macroalgal community turnover on shallow temperate reefs.

To support coastal planning through improved understanding of patterns of biotic and abiotic surrogacy at broad scales, we used gradient forest modeling (GFM) to analyze and predict spatial patterns of compositional turnover of demersal fishes, macroinvertebrates, and macroalgae on shallow, temperate Australian reefs. Predictive models were first developed using environmental surrogates with estimates of prediction uncertainty, and then the efficacy of the three assemblages as biosurrogates for each other was assessed. Data from underwater visual surveys of subtidal rocky reefs were collected from the southeastern coastline of continental Australia (including South Australia and Victoria) and the northern coastline of Tasmania. These data were combined with 0.01 degree-resolution gridded environmental variables to develop statistical models of compositional turnover (beta diversity) using GFM. GFM extends the machine learning, ensemble tree-based method of random forests (RF), to allow the simultaneous modeling of multiple taxa. The models were used to generate predictions of compositional turnover for each of the three assemblages within unsurveyed areas across the 6600 km of coastline in the region of interest. The most important predictor for all three assemblages was variability in sea surface temperature (measured as standard deviation from measures taken interannually). Spatial predictions of compositional turnover within unsurveyed areas across the region of interest were remarkably congruent across the three taxa. However, the greatest uncertainty in these predictions varied in location among the different assemblages. Pairwise congruency comparisons of observed and predicted turnover among the three assemblages showed that invertebrate and macroalgal biodiversity were most similar, followed by fishes and macroalgae, and lastly fishes and invertebrate biodiversity, suggesting that of the three assemblages, macroalgae would make the best biosurrogate for both invertebrate and fish compositional turnover.

Concept development for the ITER equatorial port visible∕infrared wide angle viewing system.

The ITER equatorial port visible∕infrared wide angle viewing system concept is developed from the measurement requirements. The proposed solution situates 4 viewing systems in the equatorial ports 3, 9, 12, and 17 with 4 views each (looking at the upper target, the inner divertor, and tangentially left and right). This gives sufficient coverage. The spatial resolution of the divertor system is 2 times higher than the other views. For compensation of vacuum-vessel movements, an optical hinge concept is proposed. Compactness and low neutron streaming is achieved by orienting port plug doglegs horizontally. Calibration methods, risks, and R&D topics are outlined.

Biological surrogacy in tropical seabed assemblages fails.

Surrogate taxa are used widely to represent attributes of other taxa for which data are sparse or absent. Because surveying and monitoring marine biodiversity is resource intensive, our understanding and management of marine systems will need to rely on the availability of effective surrogates. The ability of any marine taxon to adequately represent another, however, is largely unknown because there are rarely sufficient data for multiple taxa in the same region(s). Here, we defined a taxonomic group to be a surrogate for another taxonomic group if they possessed similar assemblage patterns. We investigated effects on surrogate performance of (1) grouping species by taxon at various levels of resolution, (2) selective removal of rare species from analysis, and (3) the number of clusters used to define assemblages, using samples for 11 phyla distributed across 1189 sites sampled from the seabed of Australia's Great Barrier Reef. This spatially and taxonomically comprehensive data set provided an opportunity for extensive testing of surrogate performance in a tropical marine system using these three approaches for the first time, as resource and data constraints were previously limiting. We measured surrogate performance as to how similarly sampling sites were divided into assemblages between taxa. For each taxonomic group independently, we grouped sites into assemblages using Hellinger distances and medoid clustering. We then used a similarity index to quantify the concordance of assemblages between all pairs of taxonomic groups. Surrogates performed better when taxa were grouped at a phylum level, compared to taxa grouped at a finer taxonomic resolution, and were unaffected by the exclusion of spatially rare species. Mean surrogate performance increased as the number of clusters decreased. Moreover, no taxonomic group was a particularly good surrogate for any other, suggesting that the use of any one (or few) group(s) for mapping seabed biodiversity patterns is imprudent; sampling several taxonomic groups appears to be essential for understanding tropical/subtropical seabed communities. Consequently, where resource constraints do not allow complete surveying of biodiversity, it may be preferable to exclude rare species to allow investment in a broader range of taxonomic groups.

Exploring the role of environmental variables in shaping patterns of seabed biodiversity composition in regional-scale ecosystems.

1. Environmental variables are often used as indirect surrogates for mapping biodiversity because species survey data are scant at regional scales, especially in the marine realm. However, environmental variables are measured on arbitrary scales unlikely to have simple, direct relationships with biological patterns. Instead, biodiversity may respond nonlinearly and to interactions between environmental variables.2. To investigate the role of the environment in driving patterns of biodiversity composition in large marine regions, we collated multiple biological survey and environmental data sets from tropical NE Australia, the deep Gulf of Mexico and the temperate Gulf of Maine. We then quantified the shape and magnitude of multispecies responses along >30 environmental gradients and the extent to which these variables predicted regional distributions. To do this, we applied a new statistical approach, Gradient Forest, an extension of Random Forest, capable of modelling nonlinear and threshold responses.3. The regional-scale environmental variables predicted an average of 13-35% (up to 50-85% for individual species) of the variation in species abundance distributions. Important predictors differed among regions and biota and included depth, salinity, temperature, sediment composition and current stress. The shapes of responses along gradients also differed and were nonlinear, often with thresholds indicative of step changes in composition. These differing regional responses were partly due to differing environmental indicators of bioregional boundaries and, given the results to date, may indicate limited scope for extrapolating bio-physical relationships beyond the region of source data sets.4.Synthesis and applications. Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms.Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms.

Gradient forests: calculating importance gradients on physical predictors.

In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called "gradient forest," which is an extension of the random forest approach. By synthesizing the cross-validated R2 and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25%, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys.

Defining the infrared systems for ITER.

The International Thermonuclear Experimental Reactor will have wide angle viewing systems and a divertor thermography diagnostic, which shall provide infrared coverage of the divertor and large parts of the first wall surfaces with spatial and temporal resolution adequate for operational purposes and higher resolved details of the divertor and other areas for physics investigations. We propose specifications for each system such that they jointly respond to the requirements. Risk analysis driven priorities for future work concern mirror degradation, interfaces with other diagnostics, radiation damage to refractive optics, reflections, and the development of calibration and measurement methods for varying optical and thermal target properties.

Adaptive management of the Great Barrier Reef: a globally significant demonstration of the benefits of networks of marine reserves.

The Great Barrier Reef (GBR) provides a globally significant demonstration of the effectiveness of large-scale networks of marine reserves in contributing to integrated, adaptive management. Comprehensive review of available evidence shows major, rapid benefits of no-take areas for targeted fish and sharks, in both reef and nonreef habitats, with potential benefits for fisheries as well as biodiversity conservation. Large, mobile species like sharks benefit less than smaller, site-attached fish. Critically, reserves also appear to benefit overall ecosystem health and resilience: outbreaks of coral-eating, crown-of-thorns starfish appear less frequent on no-take reefs, which consequently have higher abundance of coral, the very foundation of reef ecosystems. Effective marine reserves require regular review of compliance: fish abundances in no-entry zones suggest that even no-take zones may be significantly depleted due to poaching. Spatial analyses comparing zoning with seabed biodiversity or dugong distributions illustrate significant benefits from application of best-practice conservation principles in data-poor situations. Increases in the marine reserve network in 2004 affected fishers, but preliminary economic analysis suggests considerable net benefits, in terms of protecting environmental and tourism values. Relative to the revenue generated by reef tourism, current expenditure on protection is minor. Recent implementation of an Outlook Report provides regular, formal review of environmental condition and management and links to policy responses, key aspects of adaptive management. Given the major threat posed by climate change, the expanded network of marine reserves provides a critical and cost-effective contribution to enhancing the resilience of the Great Barrier Reef.

Global patterns and predictions of seafloor biomass using random forests.

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.

Use of overlapping peptide mixtures as antigens for cytokine flow cytometry.

Intracellular cytokine staining and flow cytometry can be used to measure T-cell responses to defined antigens. Although CD8+ T-cell responses to soluble proteins are inefficiently detected by this approach, peptides can be used as antigens. Using overlapping peptides spanning an entire protein sequence, CD8+ T-cell responses can be detected to multiple epitopes, regardless of HLA type. In this study, overlapping peptide mixes of various lengths were compared and 15 amino acid peptides with 11 amino acid overlaps were found to stimulate both CD4+ and CD8+ T-cell responses. Such peptide mixes stimulated CD4+ T-cell responses equivalent to those observed with whole recombinant protein, while simultaneously stimulating CD8+ T-cell responses much higher than those observed with whole protein. Although 8-12 amino acid peptides produced the highest level of CD8+ T-cell responses, 15 amino acid peptides were still very effective. Peptides that were 20 amino acids in length, however, did not stimulate strong CD8+ T-cell responses at the same peptide dose. The cytokine responses to individual epitopes added up approximately to the response to the entire mix, demonstrating that large mixes can detect responses in a quantitative fashion. Unlike whole protein antigens, peptide mixes were effective at stimulating responses in both cryopreserved PBMC and blood stored for 24 h at room temperature. Thus, overlapping 15 amino acid peptide mixes may facilitate the analysis of antigen-specific CD4+ and CD8+ T-cell responses by cytokine flow cytometry, using clinical specimens that include shipped blood or cryopreserved PBMC.

Clonotypic structure of the human CD4+ memory T cell response to cytomegalovirus.

High steady-state frequencies of CMV-specific CD4(+) memory T cells are maintained in CMV-exposed subjects, and these cells are thought to play a key role in the immunologic control of this permanent infection. However, the essential components of this response are poorly defined. Here, we report the use of a step-wise application of flow cytometric and molecular techniques to determine the number and size of the TCR Vbeta-defined clonotypes within freshly obtained CMV-specific CD4(+) memory T cell populations of four healthy, CMV-exposed human subjects. This analysis revealed a stable clonotypic hierarchy in which 1-3 dominant clonotypes are maintained in concert with more numerous subdominant and minor clonotypes. These dominant clonotypes accounted for 10-50% of the overall CMV response, and comprised from 0.3 to 4.0% of peripheral blood CD4(+) T cells. Two subjects displayed immunodominant responses to single epitopes within the CMV matrix phosphoprotein pp65; these single epitope responses were mediated by a single dominant clonotype in one subject, and by multiple subdominant and minor clonotypes in the other. Thus, the CMV-specific CD4(+) T cell memory repertoire in normal subjects is characterized by striking clonotypic dominance and the potential for epitope focusing, suggesting that primary responsibility for immunosurveillance against CMV reactivation rests with a handful of clones recognizing a limited array of CMV determinants. These data have important implications for the understanding of mechanisms by which a genetically stable chronic viral pathogen such as CMV is controlled, and offer possible insight into the failure of such control for a genetically flexible pathogen like HIV-1.

HIV-1-specific CD4+ T cells are detectable in most individuals with active HIV-1 infection, but decline with prolonged viral suppression.

The role of HIV-1-specific CD4+ T-cell responses in controlling HIV-1 infection remains unclear. Previous work has suggested that such cells are eliminated in the early stages of infection in most subjects, and thus cannot substantially contribute to host defense against HIV-1. Here, using flow cytometric detection of antigen-induced intracellular cytokines, we show that significant frequencies of gag specific, T-helper-1 CD4+ memory T cells are detectable in most subjects with active/progressive HIV-1 infection (median frequency, 0.12% of memory subset; range, 0-0.66%). Median frequencies of these cells were considerably higher in nonprogressive HIV-1 disease (0.40%), but there was substantial overlap between the two groups (range of nonprogressors, 0.10-1.7%). Continuous HIV-1 suppression with anti-retroviral therapy was associated with a time-dependent reduction in median frequencies of gag-specific CD4+ memory T cells: 0.08% in subjects treated for 4-24 weeks, and 0.03% in subjects treated for 47-112 weeks. Thus, functional HIV-1-specific CD4+ T cells are commonly available for support of anti-HIV-1 effector responses in active disease, but their decline with anti-retroviral therapy indicates that immunologic participation in long-term HIV-1 control will probably require effective vaccination strategies.