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The recycling of scarce nutrient resources in the sunlit open ocean is crucial to ecosystem function. Nitrification directs ammonium (NH4+) derived from organic matter decomposition towards the regeneration of nitrate (NO3-), an important resource for photosynthetic primary producers. However, the technical challenge of making nitrification rate measurements in oligotrophic conditions combined with the remote nature of these environments means that data availability, and the understanding that provides, is limited. This study reports nitrite (NO2-) regeneration rate (RNO2 – the first product of nitrification derived from NH4+ oxidation) over a 13 000 km transect within the photic zone of the Atlantic Ocean. These measurements, at relatively high resolution (order 300 km), permit the examination of interactions between RNO2 and environmental conditions that may warrant explicit development in model descriptions. At all locations we report measurable RNO2 with significant variability between and within Atlantic provinces. Statistical analysis indicated significant correlative structure between RNO2 and ecosystem variables, explaining ∼65 % of the data variability. Differences between sampling depths were of the same magnitude as or greater than horizontally resolved differences, identifying distinct biogeochemical niches between depth horizons. The best overall match between RNO2 and environmental variables combined chlorophyll-a concentration, light-phase duration, and silicate concentration (representing a short-term tracer of water column physical instability). On this basis we hypothesize that RNO2 is related to the short-term autotrophic production and heterotrophic decomposition of dissolved organic nitrogen (DON), which regenerates NH4+ and supports NH4+ oxidation. However, this did not explain the observation that RNO2 in the deep euphotic zone was significantly greater in the Southern Hemisphere compared to the Northern Hemisphere. We present the complimentary hypothesis that observations reflect the difference in DON concentration supplied by lateral transport into the gyre interior from the Atlantic's eastern boundary upwelling ecosystems.

Background Many marine man-made structures (MMS), such as oil and gas platforms or offshore wind turbines, are nearing their ‘end-of-life’ and require decommissioning. Limited understanding of MMS decommissioning effects currently restricts the consideration of alternative management possibilities, often leaving complete removal as the only option in certain parts of the world. This evidence-base describes the ecosystem effects of marine MMS whilst in place and following cessation of operations, with a view to informing decision-making related to their potential decommissioning. Method The protocol used to create this map was published a priori. Systematic searches of published, literature in English were conducted using three bibliographic databases, ten specialist organisational websites or repositories, and one search engine, up to early 2021. A total of 15,697 unique articles were identified as potentially relevant to our research questions, of which 2,230 were screened at the full-text level. Of that subset, 860 articles met all pre-defined eligibility criteria. A further 119 articles were identified through “snowballing” of references from literature reviews. The final database consists of 979 articles. For each article included, metadata were extracted for key variables of interest and coded into a database. Review findings The vast majority of eligible articles related to the presence of MMS (96.2%), while just 5.8% considered decommissioning. Overall, articles mainly considered artificial reefs (51.5% of all articles) but increasingly oil and gas (22%), shipwrecks (15.1%) and offshore wind (13.1%). Studies were distributed globally, but the majority focused on the United States, single countries within Europe, Australia, Brazil, China, and Israel; 25 studies spanned multiple countries. Consequently, the bulk of the studies focused on the North Atlantic (incl. Gulf of Mexico, North Sea, and Mediterranean Sea) and North Pacific Oceans. A further 12 studies had a global scope. Studies in majority reported on fish (53%) and invertebrates (41%), and were disproportionately focused on biological (81%) and ecological (48%) impacts. Physico-chemical (13%), habitat (7%), socio-cultural (7%), economic (4%) and functional (8%) outcomes have received less attention. The number of decommissioning studies has been increasing since ca. 2012 but remains noticeably low. Studies mostly focus on oil and gas infrastructures in the USA (Gulf of Mexico) and Northern Europe (North Sea), covering 9 different decommissioning options. Conclusions This systematic map, the first of its kind, reveals a substantial body of peer-reviewed evidence relating to the presence of MMS in the sea and their impacts, but with considerable bias toward biological and ecological outcomes over abiotic and socio-economic outcomes. The map reveals extremely limited direct evidence of decommissioning effects, likely driven at least in part by international policy preventing consideration of a range of decommissioning options beyond complete removal. Despite evidence of MMS impacts continuing to grow exponentially since the early 1970s, this map reveals key gaps in evidence to support best practice in developing decommissioning options that consider environmental, social and economic effects. Relevant evidence is required to generate greater understanding in those areas and ensure decommissioning options deliver optimal ecosystem outcomes.

K. Robert Clarke is one of the most highly regarded and highly cited scientists in the field of ecology. Over the past 45+ years, He has inspired and empowered ecological researchers all across the globe by developing novel statistical methods, creating user-friendly PRIMER software, and presenting generous, spirited, personalised workshops in multivariate analysis for practicing scientists. We introduce this special issue in Austral Ecology by acknowledging his myriad contributions, including a brief biography of his professional career and details of his lasting positive legacy.

Harnessing natural solutions to mitigate climate change requires an understanding of carbon fixation, flux and sequestration across ocean habitats. Recent studies suggest that exported seaweed particulate organic carbon is stored within soft sediment systems. However, very little is known about how seaweed detritus disperses from coastlines, or where it may enter seabed carbon stores, where it could become the target of conservation efforts. Here, focusing on regionally dominant seaweed species, we surveyed environmental DNA (eDNA) of natural coastal sediments, and studied their connectivity to seaweed habitats using a particle tracking model parameterized to reproduce seaweed detritus dispersal behavior based on laboratory observation of seaweed fragment degradation and sinking. Experiments showed seaweed detritus density changing over time, differently across species. This, in turn, modified distances travelled by released fragments until they reached the seabed for the first time, during model simulations. Dispersal pathways connected detritus from the shore to the open ocean but, importantly, also to coastal sediments, and this was reflected by field eDNA evidence. Dispersion pathways were also affected by hydrodynamic conditions, varying in space and time. Both the properties and timing of released detritus, individual to each macroalgal population, and short-term near-seabed and medium-term water-column transport pathways, are thus seemingly important in determining the connectivity between seaweed habitats and potential sedimentary sinks. Studies such as this one, supported by further field verification of sedimentary carbon sequestration rates and source partitioning, are still needed to help quantify the role of seaweed in the ocean carbon cycle. Such studies will provide vital evidence to inform on the potential need to develop blue carbon conservation mechanisms, beyond wetlands. This article is protected by copyright. All rights reserved.

SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.

Zooplankton monitoring in shelf seas predominantly uses nets that miss the benthic boundary layer (BBL) just above the seabed. However, this boundary between pelagic and benthic assemblages can be faunistically rich, having its own distinct hyperbenthic fauna and acting as a low-light refuge for overwintering or dielly migrating zooplankton. To compare species richness and composition between pelagic and BBL habitats, we sampled a long-term monitoring site in the Western English Channel seasonally. Metabarcoding methods applied to vertical net samples (top 50 m in a ∼54-m water column) and those from a hyperbenthic sledge generated >100 000 sequences clustered into 294 operational taxonomic units. Of these, 215 were found in the BBL and 170 in the water column. Some key taxa (e.g. mysids) were native to the BBL; by contrast, other delicate taxa (e.g. ctenophores) seemed to avoid the BBL. The major contrasts in plankton composition related to the seasonal cycle rather than to pelagic-BBL differences, suggesting that the basic dynamics of the site are captured by our ongoing long-term weekly resolution monitoring. Overall, metabarcoding approaches, applied to both water column and BBL, provide an independent view of plankton dynamics, and augment existing traditional methods.

Understanding how different drivers shape relationships between abundance and body mass (size spectra) is important for understanding trophic and competitive interactions in food webs and for predicting the effects of human pressures. Here, we sample seabed communities from small polychaetes (1 kg) in the Celtic Sea and the western English Channel to examine how bottom trawling and primary production affect their size spectra and to compare these with predictions from a model that couples predator and detritivore communities. Size spectra were not well approximated by linear fits because of truncation of the size spectra of detritivores. Low primary production resulted in lower abundance of benthic fauna. Bottom trawling reduced the abundance of predators and large detritivores but allowed small detritivores to increase in abundance. These empirical size spectra were partly consistent with predictions from the size spectra model, showing that understanding the structuring of benthic communities requires a consideration of both size and functional group. The findings highlight the need for an ecosystem approach to understanding the effects of exploitation and climate change on marine ecosystems.

Size-spectral approaches quantify the efficiency of energy transfer through food webs, but theory and field studies disagree over how changes in temperature, nutrients, and extreme weather impact on this efficiency. We address this at two scales: via 6 years of weekly sampling of the plankton size spectrum at the Plymouth L4 shelf sea site, and via a new, global-scale, meta-analysis of aquatic size spectra. The time series showed that with summertime nutrient starvation, the energy transfer efficiency from picoplankton to macroplankton decreased (i.e., steepening slopes of the size spectra). This reflected increasing dominance by small cells and their microbial consumers. The extreme storms in winter 2013/2014 caused high metazoan mortality, steep size-spectral slopes, and reduced plankton biomass. However, recovery was within months, demonstrating an inbuilt resilience of the system. Both L4 and our meta-analysis showed steep slopes of normalized size spectra (median −1.11). This reflects much lower values, either of trophic transfer efficiency (3.5%) or predator–prey mass ratio (569), compared to commonly quoted values. Results from the meta-analysis further showed that to represent energy transfer faithfully, size spectra are best constructed in units of carbon mass and not biovolume, and span a mass range of > 107. When this range is covered, both the meta-analysis and time series show a dome-shaped relationship between spectral slopes and plankton biomass, with steepening slopes under increasingly oligotrophic and eutrophic conditions. This suggests that ocean warming could decrease the efficiency of energy transfer through pelagic food webs via indirect effects of increasing stratification and nutrient starvation.

The recycling of scarce nutrient resources in the sunlit open ocean is crucial to ecosystem function. Ammonium oxidation, the first stage of the nitrification process, directs ammonium derived from organic matter decomposition towards the regeneration nitrate, an important resource for photosynthetic primary producers. However, the technical challenge of making nitrification rate measurements in oligotrophic conditions combined with the remote nature of these marine systems means that data availability, and the understanding that provides, is limited. This study reports rate measurements of ammonium oxidation over a 13, 000 km transect within the photic zone of the Atlantic Ocean. These measurements, at relatively fine resolution (order 300 km), permit the examination of interactions with environmental conditions that may warrant explicit development and inclusion in model descriptions. At all locations we report measurable rates with significant variability between and within Atlantic provinces. This adds to evidence that nitrification is an important component of pelagic nitrogen cycling which modifies the inorganic nitrogen inventory of the sunlit ocean. Particular features of interest included a significant hemispheric difference in ammonium oxidation rate and elevated rates associated with mesoscale eddy features. Statistical analysis of potential links between ammonium oxidation rate and routinely measured ecosystem variables indicated significant correlative structure, explaining ~65 % of the data variability. Differences between sampling depths were of the same magnitude or greater than horizontally resolved differences along the transect length, identifying distinct biogeochemical niches between depth horizons. Principle component analysis demonstrated that the best overall match between ammonium oxidation rate and environmental variables involved a combination of chlorophyll-a concentration, the duration of the light phase and silicate concentration (which we argue to be a short-term tracer of physical instability). Results allude to an association between ammonium oxidation and potentially short-term product(s) of photosynthetic activity and subsequent degradation. Approximately 35 % of data variability was not explained, which may include descriptions of DOM pool dynamics.

While it is recognised that the nature of the sediment is a major driver of benthic macro-infaunal community structure, it is also true that diverse environmental factors determine the distribution and composition of sediments. Among those factors are depth, tidal stress and seasonal stratification of the water column. In the Celtic Sea an area of seabed approximately 20 km wide and 125 km long was selected in which variation in water depth, stratification, primary production and current velocity were minimised, but which contained sediments ranging from fine muds to coarse gravelly sands. 55 stations were sampled across the area using a box-corer. At each station a comprehensive suite of sediment and biogeochemical measurements were made. Macrofauna were identified and weighed. Of the stations sampled, four had been chosen as focal sites for a study of relationships between benthic biogeochemistry and sediment type. Relationships between variation in environmental and sediment variables and macrofaunal community structure were analysed using a range of non-parametric multivariate techniques. Environmental variables were discriminated into situational variables that broadly encapsulate potential drivers of spatial heterogeneity in the benthos such as depth and fishing effort, and in-situ variables that were measured at each site concurrently with the sampling of the macrobenthos, such as sediment properties and biogeochemical measurements. Among the former, analyses tended to identify the importance of average shear stress and depth in explaining observed variation in benthic community structure, even though the area had been chosen to minimise variation in those factors. Analyses using in-situ measurements of sedimentary conditions at each site identified very fine sand content (correlated with average shear stress) as the most important explanatory variable. Most of the measured biogeochemical variables varied with sediment structure, particularly reflecting differences between finer-grained sediments with higher organic content (generally from deeper areas) and coarser sediments with lower organic content. While clear spatial heterogeneity in sediments and associated biogeochemical variables could be demonstrated, spatial variation in benthic abundance and biomass was less clear. Benthic community structure varied significantly with sediment type, but did not vary closely with the in-situ environmental variables measured at the same sites. This may indicate that the samples collected were too small to accurately characterise the benthic assemblage at each site, or that most species inhabiting the area inhabit a range of sediment types, or that processes which are not reflected in sediment or biogeochemical measurements are also important determinants of benthic community structure.

Nitrous oxide (N2O) is important to the global radiative budget of the atmosphere and contributes to the depletion of stratospheric ozone. Globally the ocean represents a large net flux of N2O to the atmosphere but the direction of this flux varies regionally. Our understanding of N2O production and consumption processes in the ocean remains incomplete. Traditional understanding tells us that anaerobic denitrification, the reduction of NO3− to N2 with N2O as an intermediate step, is the sole biological means of reducing N2O, a process known to occur in anoxic environments only. Here we present experimental evidence of N2O removal under fully oxygenated conditions, coupled with observations of bacterial communities with novel, atypical gene sequences for N2O reduction. The focus of this work was on the high latitude Atlantic Ocean where we show bacterial consumption sufficient to account for oceanic N2O depletion and the occurrence of regional sinks for atmospheric N2O.

Background Numerous man-made structures (MMS) have been installed in various parts of the ocean (e.g. oil and gas structures, offshore wind installations). Many are now at, or nearing, the end of their intended life. Currently, we only have a limited understanding of decommissioning effects. In many locations, such as the North Sea, regulations restrict decommissioning options to complete removal, with little consideration of alternative management options might offer. To generate a reliable evidence-base to inform the decision-making processes pertaining to marine MMS management, we propose a wide-encompassing systematic map of published research on the ecosystem effects (including ecosystem services) of marine MMS while in place and following cessation of operations (i.e. including effects of alternative decommissioning options). This map is undertaken as part of the UKRI DREAMS project which aims to develop a system to show the relative effects of implementing different decommissioning strategies in the North Sea. Method For the purpose of this map, we will keep our focus global, in order to subsequently draw comparisons between marine regions. The proposed map will aim to answer the following two primary questions: 1. What published evidence exists for the effects of marine man-made structures while in place on the marine ecosystem? 2. What published evidence exists for the effects of the decommissioning of marine man-made structures on the marine ecosystem? The map will follow the Collaboration for Environmental Evidence Guidelines and Standards for Evidence Synthesis in Environmental Management. Searches will be run primarily in English in at least 13 databases and 4 websites. Returns will be screened at title/abstract level and at full-text against pre-defined criteria. Relevant meta-data will be extracted for each study included. Results will be used to build a database of evidence, which will be made freely available. This map, expected to be large, will improve our knowledge of the available evidence for the ecosystem effects of MMS in the global marine environment. It will subsequently inform the production of multiple systematic-reviews and meta-analyses.

Marine spatial planning that addresses ocean climate-driven change (‘climate-smart MSP’) is a global aspiration to support economic growth, food security and ecosystem sustainability. Ocean climate change (‘CC’) modelling may become a key decision-support tool for MSP, but traditional modelling analysis and communication challenges prevent their broad uptake. We employed MSP-specific ocean climate modelling analyses to inform a real-life MSP process; addressing how nature conservation and fisheries could be adapted to CC. We found that the currently planned distribution of these activities may become unsustainable during the policy's implementation due to CC, leading to a shortfall in its sustainability and blue growth targets. Significant, climate-driven ecosystem-level shifts in ocean components underpinning designated sites and fishing activity were estimated, reflecting different magnitudes of shifts in benthic versus pelagic, and inshore versus offshore habitats. Supporting adaptation, we then identified: CC refugia (areas where the ecosystem remains within the boundaries of its present state); CC hotspots (where climate drives the ecosystem towards a new state, inconsistent with each sectors’ present use distribution); and for the first time, identified bright spots (areas where oceanographic processes drive range expansion opportunities that may support sustainable growth in the medium term). We thus create the means to: identify where sector-relevant ecosystem change is attributable to CC; incorporate resilient delivery of conservation and sustainable ecosystem management aims into MSP; and to harness opportunities for blue growth where they exist. Capturing CC bright spots alongside refugia within protected areas may present important opportunities to meet sustainability targets while helping support the fishing sector in a changing climate. By capitalizing on the natural distribution of climate resilience within ocean ecosystems, such climate-adaptive spatial management strategies could be seen as nature-based solutions to limit the impact of CC on ocean ecosystems and dependent blue economy sectors, paving the way for climate-smart MSP.

The response of an ecological community to a disturbance event, and its capacity to recover, are of major interest to ecologists, especially at a time of increasing frequencies and intensities of environmental change brought about by humans. Meiofauna, a group of small-sized organisms, are an abundant and ubiquitous component of seafloor communities that respond rapidly to environmental change. We summarise the available research on the response of metazoan meiofauna to the most widespread anthropogenic disturbances in the marine environment, including bottom fishing, the introduction of invasive species and anthropogenic climate change. We show that disturbance effects on habitats interact critically with effects on resident meiofauna species. Their responses are consistent with competitive replacement, where disparate disturbance effects on competing species drive shifts in dominance and intra- and interspecific interactions. The widespread replacement of habitat-specific ecological specialists by broadly-adapted ecological generalists and opportunists results in biotic and functional homogenisation of once disparate biotas. Anthropogenic disturbances may facilitate novel interactions among meiofauna species, and between meiofauna and other benthic organisms, but the number and breadth of these interactions is likely to be limited. Knowledge about the dependence of meiofauna species on their environment and on other benthic species has been growing. Future studies will be most meaningful if this knowledge is expanded alongside understanding the potential of locally adapted species to respond to shifts in environmental conditions.

Although many studies have investigated the effects of disturbance and environmental drivers on marine ecosystems, comparatively few have studied their interactions. Using fuzzy coded biological traits, we compared the functional composition, diversity and evenness of benthic communities in the English Channel and in the Celtic and Irish Seas across interacting gradients of bottom trawling and primary production. Fuzzy correspondence analysis indicated greater similarity in trait composition at sites of high trawling pressure than at those of low trawling. In contrast, the analysis revealed no relationship between trait composition and primary production. Trawling and primary production had no effect on the traits ‘longevity’, ‘sediment position’, or ‘feeding mode’. However, trawling had negative effects on all modalities within the trait ‘living habit’, and these effects were strongest for attached and epifaunal organisms but weakest for burrow- and tube-dwelling species. Trawling also negatively affected most modalities within the trait ‘maximum weight’, with strongest effects for organisms weighing between 10 kg. For the trait ‘bioturbation’, upward conveyors were positively related with primary production, whilst other modalities exhibited no clear pattern. Because trawling affected some traits more than others, community biomass was less evenly distributed across traits in highly trawled areas, which resulted in lower levels of functional diversity and evenness. Overall, the effects of bottom trawling were greater in areas of high primary production.

International audience; In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods , such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecological studies, Artificial Substrate Units (ASUs) allow for standardized sampling. We deployed ASUs within five regional seas (Baltic Sea, Northeast Atlantic Ocean, Mediterranean Sea, Black Sea, and Red Sea) for 12-26 months to measure the diversity and community composition of macroinvertebrates. We identified invertebrates using a traditional approach based on morphological characters, and by metabarcoding of the mitochondrial cytochrome oxidase I (COI) gene. We compared community composition and diversity metrics obtained using the two methods. Diversity was significantly correlated between data types. Metabarcoding of ASUs allowed for robust comparisons of community composition and diversity, but not all groups were successfully sequenced. All locations were significantly different in taxonomic composition as measured with both kinds of data. We recovered previously known regional biogeographical patterns in both datasets (e.g., low species diversity in the Black and Baltic Seas, affinity between the Bay of Biscay and the Mediterranean). We conclude that the two approaches provide complementary information and that metabarcoding shows great promise for marine monitoring. However, until its pitfalls are addressed, the use of metabarcoding in monitoring of rocky benthic assemblages should be used in addition to classical approaches rather than instead of them.

Few studies consider meiofauna and macrofauna at the same time, even though both form parts of wider ecological networks, and fewer consider interactions between sample size, body size and spatial clustering. It has been suggested that the elements of the structure of the physical environment have fractal properties. If habitat complexity largely determines species diversity this leads to the prediction (for a single perfect fractal) that all organisms, regardless of size, will perceive the environment as equally complex and should have equivalent diversity and, as we move up the size spectrum, species composition should change in a regular and gradual fashion. This study examines the degree to which infaunal assemblage structure varies with mesh size, sample size and sample dispersion within two different areas of homogeneous intertidal sediment, a muddy sand and a coarse sand, in the Isles of Scilly, UK. In each area samples were extracted using a standard range of 5 mesh sizes (63, 125, 250, 500, 1000 μm), with the sample areas and distances between samples scaled to the mesh size. All metazoans were identified to species level. Diversity and species composition did not show a gradual and even degree of change over the size range at either site. Instead, they showed a dramatic stepwise change between the 250 μm and 500 μm mesh size samples, being relatively constant in the 500 μm categories, with diversity higher in the former. Higher proportions of species in the 500 μm categories. This suggests a fractal structure within but not between the 500 μm body size categories, which apparently is not driven by differences in sediment structure. The biology of marine metazoan benthos does not scale continuously across the full range of taxa and body size as has been recently suggested, but may do so for individual taxa and restricted size ranges.

This research was funded by the EU Seventh Framework Programme for research, technological development and demonstration (FP7/2007-2013) within the Ocean of Tomorrow call under Grant Agreement No.266445 for the project Vectors of Change in Oceans and Seas Marine Life (VECTORS). AMQ and PJS acknowledge support from the UK Natural Environment Research Council and Department for Environment, Food and Rural Affairs [grant number NE/L003279/1, Marine Ecosystems Research Programme]. HO and JK were partly funded by the Estonian Ministry of Education and Research (grant SF0180005s10) and the Estonian Research Council (IUT02-20). Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical-chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we used a global systematic review and meta-analysis to examine IEE effects on the abundance of individual species and communities, biodiversity (using several indices) and ecosystem functions, focusing on marine and estuarine environments. We found that IEE had a significant effect (positive and negative) in most studies testing impacts on individual species, but the overall (cumulative) effect size was small and negative. Many individual studies showed strong IEE effects on community abundance and diversity, but the direction of effects was variable, leading to statistically non-significant overall effects in most categories. In contrast, there was a strong overall effect on most ecosystem functions we examined. IEE negatively affected metabolic functions and primary production, but positively affected nutrient flux, sedimentation and decomposition. We use the results to develop a conceptual model by highlighting pathways whereby IEE impact communities and ecosystem functions, and identify several sources of research bias in the IEE-related invasion literature. Only a few of the studies simultaneously quantified IEE effects on community/diversity and ecosystem functions. Therefore, understanding how IEE may alter biodiversity-function relationships should be a primary focus of future studies of invasion biology. Moreover, the clear effects of IEE on ecosystem functions detected in our study suggest that scientists and environmental managers ought to examine how the effects of IEE might be manifested in the services that marine ecosystems provide to humans. Postprint

The ecosystem services approach is widely recognised as a concept, but more attention must be given to the development of tools to facilitate practical implementation if the approach is to become more widely used to support decision-making. A key component of natural resource management is understanding the implications of changing levels of pressures on ecosystem components, which is achieved through sensitivity assessment. This paper examines how sensitivity assessment could be applied to ecosystem services, as opposed to the underlying habitats and species, by considering the relationship between the sensitivity of a service to the sensitivity of the habitat responsible for its supply. The method is illustrated using a UK case study of supporting and regulating services provided by subtidal sedimentary habitats within the UNESCO Biosphere Reserve in North Devon.

Research Infrastructures (RIs) are facilities, resources and services used by scientists to perform research and support innovation. A number of EU research infrastructures [e.g. e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch) European Research Iinfrastructures Consortium (ERIC); The European life-sciences Infrastructure for biological Information (ELIXIR); the European Marine Biological Resource Centre (EMBRC ERIC); the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences (uroBioImaging ERIC)] have been building Virtual Research Environments (VREs), which include many virtual laboratories (vLabs) offering, one stop data access to scientists, high computational capacity and collaborative research platforms in support of the requirements of the digital science. This presentation gives examples on the use of the vLabs developed by LifeWatch ERIC which have subsequently been taken up as web services by other RIs. The RvLab operates on a high-performance computer cluster, and has been used in order to analyse various properties of taxon equality, with a focus on marine species. This taxonomic information on marine biota is organized and made publicly available through the World Register of Marine Species (WoRMS) that delivers more than 250,000 described valid species names. Although scientists consider an equal status (in terms of contribution to overall diversity) to each taxon used in taxonomy, biogeography, ecology and biodiversity, the question “are all taxa equal?” has never been tested at a global scale. We present evidence that this question can be addressed by applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree. The virtual micro-CT laboratory (Micro-CT vLab), which can be used by the members of the scientific community interested in the digitisation methods and biological collections, makes the micro-CT data exploration of natural history specimens freely available over the internet. Micro-CT vLab makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their very large size and a lack of dedicated online platforms supporting the interactive manipulation of 3D data. Examples of how these vLabs can be used by other RIs are provided.

Non-parametric multivariate analyses of complex ecological datasets are widely used. Following appropriate pre-treatment of the data inter-sample resemblances are calculated using appropriate measures. Ordination and clustering derived from these resemblances are used to visualise relationships among samples (or variables). Hierarchical agglomerative clustering with group-average (UPGMA) linkage is often the clustering method chosen. Using an example dataset of zooplankton densities from the Bristol Channel and Severn Estuary, UK, a range of existing and new clustering methods are applied and the results compared. Although the examples focus on analysis of samples, the methods may also be applied to species analysis. Dendrograms derived by hierarchical clustering are compared using cophenetic correlations, which are also used to determine optimum β in flexible beta clustering. A plot of cophenetic correlation against original dissimilarities reveals that a tree may be a poor representation of the full multivariate information. UNCTREE is an unconstrained binary divisive clustering algorithm in which values of the ANOSIM R statistic are used to determine (binary) splits in the data, to form a dendrogram. A form of flat clustering, k-R clustering, uses a combination of ANOSIM R and Similarity Profiles (SIMPROF) analyses to determine the optimum value of k , the number of groups into which samples should be clustered, and the sample membership of the groups. Robust outcomes from the application of such a range of differing techniques to the same resemblance matrix, as here, result in greater confidence in the validity of a clustering approach.

Despite increased research over the last decade, diversity patterns in Antarctic deep-sea benthic taxa and their driving forces are only marginally known. Depth-related patterns of diversity and distribution of isopods and bivalves collected in the Atlantic sector of the Southern Ocean are analysed. The data, sampled by epibenthic sledge at 40 deep-sea stations from the upper continental slope to the hadal zone (774–6348 m) over a wide area of the Southern Ocean, comprises 619 species of isopods and 81 species of bivalves. There were more species of isopods than bivalves in all samples, and species per station varied from 2 to 85 for isopods and from 0 to 18 for bivalves. Most species were rare, with 72% of isopod species restricted to one or two stations, and 45% of bivalves. Among less-rare species bivalves tended to have wider distributions than isopods. The species richness of isopods varied with depth, showing a weak unimodal curve with a peak at 2000–4000 m, while the richness of bivalves did not. Multivariate analyses indicate that there are two main assemblages in the Southern Ocean, one shallow and one deep. These overlap over a large depth-range (2000–4000 m). Comparing analyses based on the Sørensen resemblance measure and Γ+ (incorporating relatedness among species) indicates that rare species tend to have other closely related species within the same depth band. Analysis of relatedness among species indicates that the taxonomic variety of bivalves tends to decline at depth, whereas that of isopods is maintained. This, it is speculated, may indicate that the available energy at depth is insufficient to maintain a range of bivalve life-history strategies.

Lipids are key constituents of marine phytoplankton, and some fatty acids (key constituents of lipids) are essential dietary components for secondary producers. However, in natural marine ecosystems the interactions of factors affecting seasonal phytoplankton lipid composition are still poorly understood. The aim of this study was to assess the roles of seasonal succession in phytoplankton community composition and nutrient concentrations, on the lipid composition of the phytoplankton community. Fatty acid and polar lipid composition in seston was measured in surface waters at the time series station L4, an inshore station in the Western English Channel, from January to December 2013. Redundancy analyses (RDA) were used to identify factors (abiotic and biotic) that explained the seasonal variability in phytoplankton lipids. RDA demonstrated that nutrients (namely nitrogen) explained the majority of variation in phytoplankton lipid composition, as well as a smaller explanatory contribution from changes in phytoplankton community composition. The physiological adaptations of the phytoplankton community to nutrient deplete conditions during the summer season when the water column was stratified, was further supported by changes in the polar lipid to phytoplankton biomass ratios (also modelled with RDA) and increases in the lipid to chlorophyll a ratios, which are both indicative of nutrient stress. However, the association of key fatty acid markers with phytoplankton groups e.g. 22:6 n-3 and dinoflagellate biomass (predominant in summer), meant there were no clear seasonal differences in the overall degree of fatty acid saturation, as might have been expected from typical nutrient stress on phytoplankton. Based on the use of polyunsaturated fatty acids (PUFA) as markers of ‘food quality’ for grazers, our results suggest that in this environment high food quality is maintained throughout summer, due to seasonal succession towards flagellated phytoplankton species able to maintain PUFA synthesis under surface layer nutrient depletion.

Marine heatwaves have been observed worldwide and are expected to increase in both frequency and intensity due to climate change. Such events may cause ecosystem reconfigurations arising from species range contraction or redistribution, with ecological, economic and social implications. Macrophytes such as the brown seaweed Fucus vesiculosus and the seagrass Zostera marina are foundation species in many coastal ecosystems of the temperate northern hemisphere. Hence, their response to extreme events can potentially determine the fate of associated ecosystems. Macrophyte functioning is intimately linked to the maintenance of photosynthesis, growth and reproduction, and resistance against pathogens, epibionts and grazers. We investigated morphological, physiological, pathological and chemical defence responses of western Baltic Sea F. vesiculosus and Z. marina populations to simulated near-natural marine heatwaves. Along with (a) the control, which constituted no heatwave but natural stochastic temperature variability (0HW), two treatments were applied: (b) two late-spring heatwaves (June, July) followed by a summer heatwave (August; 3HW) and (c) a summer heatwave only (1HW). The 3HW treatment was applied to test whether preconditioning events can modulate the potential sensitivity to the summer heatwave. Despite the variety of responses measured in both species, only Z. marina growth was impaired by the accumulative heat stress imposed by the 3HW treatment. Photosynthetic rate, however, remained high after the last heatwave indicating potential for recovery. Only epibacterial abundance was significantly affected in F. vesiculosus. Hence both macrophytes, and in particular F. vesiculosus, seem to be fairly tolerant to short-term marine heatwaves at least at the intensities applied in this experiment (up to 5°C above mean temperature over a period of 9 days). This may partly be due to the fact that F. vesiculosus grows in a highly variable environment, and may have a high phenotypic plasticity.

In a warming climate, differential shifts in the seasonal timing of predators and prey have been suggested to lead to trophic “mismatches” that decouple primary, secondary and tertiary production. We tested this hypothesis using a 25-year time-series of weekly sampling at the Plymouth L4 site, comparing 57 plankton taxa spanning 4 trophic levels. During warm years, there was a weak tendency for earlier timings of spring taxa and later timings of autumn taxa. While this is in line with many previous findings, numerous exceptions existed and only a few taxa (e.g. Gyrodinium spp., Pseudocalanus elongatus, and Acartia clausi) showed consistent, strong evidence for temperature-related timing shifts, revealed by all 4 of the timing indices that we used. Also, the calculated offsets in timing (i.e. “mismatches”) between predator and prey were no greater in extreme warm or cold years than during more average years. Further, the magnitude of these offsets had no effect on the “success” of the predator, in terms of their annual mean abundance or egg production rates. Instead numerous other factors override, including: inter-annual variability in food quantity, high food baseline levels, turnover rates and prolonged seasonal availability, allowing extended periods of production. Furthermore many taxa, notably meroplankton, increased well before the spring bloom. While theoretically a chronic mismatch, this likely reflects trade-offs for example in predation avoidance. Various gelatinous taxa (Phaeocystis, Noctiluca, ctenophores, appendicularians, medusae) may have reduced these predation constraints, with variable, explosive population outbursts likely responding to improved conditions. The match–mismatch hypothesis may apply for highly seasonal, pulsed systems or specialist feeders, but we suggest that the concept is being over-extended to other marine systems where multiple factors compensate.

Disentangling the roles of environmental change and natural environmental variability on biologically mediated ecosystem processes is paramount to predict future marine ecosystem functioning. Bioturbation, the biogenic mixing of sediments, has a regulating role in marine biogeochemical processes. However, our understanding of bioturbation as a community level process and of its environmental drivers is still limited by loose use of terminology, and a lack of consensus about what bioturbation is. To help resolve these challenges, this empirical study investigated the links between four different attributes of bioturbation (bioturbation depth, activity and distance, and biodiffusive transport); the ability of an index of bioturbation (BPc) to predict each of them; and their relation to seasonality, in a shallow coastal system – the Western Channel Observatory, UK. Bioturbation distance depended on changes in benthic community structure, while the other three attributes were more directly influenced by seasonality in food availability. In parallel, BPc successfully predicted bioturbation distance but not the other attributes of bioturbation. This study therefore highlights that community bioturbation results from this combination of processes responding to environmental variability at different time-scales. However, community level measurements of bioturbation across environmental variability are still scarce, and BPc is calculated using commonly available data on benthic community structure and the functional classification of invertebrates. Therefore, BPc could be used to support the growth of landscape scale bioturbation research, but future uses of the index need to consider which bioturbation attributes the index actually predicts. As BPc predicts bioturbation distance, estimated here using a random-walk model applicable to community settings, studies using either of the metrics should be directly comparable and contribute to a more integrated future for bioturbation research.

A key challenge to progressing our understanding of biodiversity's role in the sustenance of ecosystem function is the extrapolation of the results of two decades of dedicated empirical research to regional, global and future landscapes. Ecosystem models provide a platform for this progression, potentially offering a holistic view of ecosystems where, guided by the mechanistic understanding of processes and their connection to the environment and biota, large-scale questions can be investigated. While the benefits of depicting biodiversity in such models are widely recognized, its application is limited by difficulties in the transfer of knowledge from small process oriented ecology into macro-scale modelling. Here, we build on previous work, breaking down key challenges of that knowledge transfer into a tangible framework, highlighting successful strategies that both modelling and ecology communities have developed to better interact with one another. We use a benthic and a pelagic case-study to illustrate how aspects of the links between biodiversity and ecosystem process have been depicted in marine ecosystem models (ERSEM and MIRO), from data, to conceptualisation and model development. We hope that this framework may help future interactions between biodiversity researchers and model developers by highlighting concrete solutions to common problems, and in this way contribute to the advance of the mechanistic understanding of the role of biodiversity in marine (and terrestrial) ecosystems.

Statutory monitoring of the fauna of the ‘mudflats and sandflats not covered by seawater at low tide’ biotope complex on St Martin's Flats, a part of the Isles of Scilly Complex Special Area of Conservation, was undertaken in 2000, 2004 and 2009. The targets set by Natural England for “characteristic biotopes” were that “composite species, abundance and diversity should not deviate significantly from an established baseline, subject to natural change”. The three specified biotopes could not be distinguished, and instead three assemblages were subjectively defined based on sediment surface features. There were statistically significant natural changes in diversity and species composition between years, especially in the association initially characterised by the razor-clam Ensis , and possible reasons for this are discussed. It is suggested that setting fixed local limits on natural variability is almost always impractical. Two possible approaches to distinguishing between natural and anthropogenic changes are suggested; a change in ecological condition as indicated by AMBI scores, and a significant change in average taxonomic distinctness (Δ + ) compared with expectation. The determination of species biomasses as well as abundances might also open more possibilities for assessment. The practice of setting objectives for a marine Special Area of Conservation (SAC) feature that include the range and number of biotopes cannot be supported, in view of the difficulty in ascribing assemblages to recognised biotopes. A more realistic definition of species assemblages might best be gained from examination of the species that consistently make a substantial contribution to the Bray–Curtis similarity among samples collected from specific sites.

Our understanding of ecological processes that lead to ecosystem services is still evolving but ecological research aims to understand the linkages between the ecosystem and services. These linkages can affect trade-offs between different ecosystem services. Understanding these linkages, by considering multiple ecosystem services simultaneously supports management of the environment and sustainable use of resources. The UK marine environment is relatively data rich, yet the links between ecosystem and several ecosystem services and linkages between services are poorly described. A workshop with 35 marine scientists was used to create a conceptual model that links ecosystem components and key processes to four services they provide and to highlight trade-offs between them. The model was subsequently further developed to include pressures and mitigating management measures. The models are discussed in terms of their application to marine data to facilitate evidence-based marine management and their usefulness to communicate management measures with managers and stakeholders.

Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programmes. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulphide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta-analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services.

Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (

Diverse assemblages of infauna in sediments provide important physical and biogeochemical services, but are under increasing pressure by anthropogenic activities, such as benthic trawling. It is known that trawling disturbance has a substantial effect on the larger benthic fauna, with reductions in density and diversity, and changes in community structure, benthic biomass, production, and bioturbation and biogeochemical processes. Largely unknown, however, are the mechanisms by which the trawling impacts on the large benthic macro- and megafauna may influence the smaller meiofauna. To investigate this, a mesocosm experiment was conducted whereby benthic nematode communities from a non-trawled area were exposed to three different densities (absent, low, normal) of 7 large (> 10 mm) naturally co-occurring, bioturbating species which are potentially vulnerable to trawling disturbance. The results showed that total abundances of nematodes were lower if these large macrofauna species were present, but no clear nematode abundance effects could be assigned to the macrofauna density differences. Nematode community structure changed in response to macrofauna presence and density, mainly as a result of the reduced abundance of a few dominant nematode species. Any detectable effects seemed similar for nearly all macrofauna species treatments, supporting the idea that there may be a general indirect, macrofauna-mediated trawling impact on nematode communities. Explanations for these results may be, firstly, competition for food resources, resulting in spatial segregation of the meio- and macrobenthic components. Secondly, different densities of large macrofauna organisms may affect the nematode community structure through different intensities of bioturbatory disturbance or resource competition. These results suggest that removal or reduced densities of larger macrofauna species as a result of trawling disturbance may lead to increased nematode abundance and hints at the validity of interference competition between large macrofauna organisms and the smaller meiofauna, and the energy equivalence hypothesis, where a trade-off is observed between groups of organisms that are dependent on a common source of energy.

For decades multivariate analysis has been recognised as being appropriate for the analysis and description of complex ecological datasets, such as are routinely generated in studies of biota along gradients in time or space. The main focus of analyses tends to be the description and analysis of patterns among samples and groups of samples. Early applications of multivariate analyses to ecological data also recognised the importance of, and gave equal weight to, understanding how variables (species or taxa, in biotic datasets) varied among samples and groups of samples, but such analyses have inherent difficulties. Among these are the facts that species do not vary independently of each other, that responses of species to gradients may not be monotonic, that there are generally many more species than samples, that abundances vary widely within and among species, and that some species are rare. Although some methods are routinely applied to explore species responses across and among samples to environmental gradients, few explicitly recognise that species do not vary independently. Within a very widely-used framework for the nonparametric multivariate analysis of ecological data we demonstrate how Similarity Profiles (SIMPROF) analysis and other approaches may be combined to analyse associations among species and to visualise those relationships. Type 2 SIMPROF determines whether observed associations could have arisen by chance. Type 3 SIMPROF detects statistically distinct subsets of species which respond to gradients in a coherent manner. How different groups respond is visualised using component line plots (coherent curves). We illustrate the method using a range of datasets. We show how the method discriminates groups of species which respond differently to a single gradient, or respond coherently to different environmental or anthropogenic pressure gradients. We demonstrate how these approaches extend naturally to analyses of other types of multivariate data where the identification of coherent groups of variables is of interest.

Under the Water Framework Directive (WFD) benthic Ecological Quality Ratios (EQRs) are important tools for assessing Ecological Status (ES) of coastal and transitional waters. Calculation of the Multivariate-AZTI Marine Biotic Index (M-AMBI) EQR is based on the proportions of sensitive and stress tolerant benthic invertebrate species, number of species and Shannon–Wiener diversity. The sensitivity of many tropical/sub-tropical taxa has not yet been determined, presenting a barrier to the direct transfer of WFD EQRs, and the ideas underpinning them, to the management of coastal waters beyond Europe. To overcome this we examine using higher taxonomic level data with M-AMBI. Before applying such approaches to assessing ES in new geographical regions it is essential to determine the effects of using higher taxonomic level data on M-AMBI in areas where the tool was developed. To this end, we use macrofaunal data from three well studied sites in north-western Europe to examine the effects of using taxonomic level data higher than species on M-AMBI. Using the European datasets M-AMBI ES classification was shown to be robust to changes in taxonomic level data. We test the suitability of family-level M-AMBI for assessing ES in subtropical Hong Kong waters. Family level M-AMBI was useful in detecting stress in Hong Kong, where it successfully detected temporal and spatial shifts in ES in response to seasonal hypoxia and salinity variability, and anthropogenic organic enrichment.

Physical and biological seabed impacts can persist long after the cessation of marine aggregate dredging. Whilst small-scale experimental studies have shown that it may be possible to mitigate such impacts, it is unclear whether the costs of restoration are justified on an industrial scale. Here we explore this question using a case study off the Thames Estuary, UK. By understanding the nature and scale of persistent impacts, we identify possible techniques to restore the physical properties of the seabed, and the costs and the likelihood of success. An analysis of the ecosystem services and goods/benefits produced by the site is used to determine whether intervention is justified. Whilst a comparison of costs and benefits at this site suggests restoration would not be warranted, the analysis is site-specific. We emphasise the need to better define what is, and is not, an acceptable seabed condition post-dredging.

Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 μatm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO(2) on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.

Mangroves are highly productive environments that play important ecological and socioeconomic roles; however, they have been impacted to different degrees in most countries worldwide. The knowledge of which organisms inhabit this environment and their ecological interactions is the first step towards its conservation. The natural variability of environmental factors in mangroves provides numerous niches available to different species. Meiofauna have patchy patterns of distribution that are related to the availability of resources. Hence, meiofauna are expected to present a high diversity of different taxa occupying the different microhabitats offered by mangroves. This work aims to test the hypothesis that the assemblage structure of Nematoda varies significantly among mangrove microhabitats and to contribute knowledge on the meiofauna diversity in mangrove environments. This work was carried out in a mangrove region at Pernambuco state, Northeastern Brazil. Qualitative samples were collected in nine microhabitats which show different characteristics mainly in terms of presence of vegetation or another organism and sediment grain size. Univariate and multivariate analysis were applied to Nematoda genera abundance data. Our results demonstrate the existence of significant differences among microhabitats regarding nematode assemblage structure corroborating the hypothesis. Different Nematoda assemblages are present in at least seven microhabitats. These assemblages are composed of nematode genera with different trophic and morphological features, demonstrating a strong relationship between morphological diversity and ecological plasticity. Furthermore, this study also demonstrates the importance of the conservation of this ecosystem and its attributes.

We consider quantification of biodiversity in the context of targets set by the Convention on Biological Diversity. Implicit in such targets is a requirement to monitor biodiversity at a regional level. Few monitoring schemes are designed with these targets in mind. Monitored sites are typically not selected to be representative of a wider region, and measures of biodiversity are often biased by a failure to account for varying detectability among species and across time. Precision is often not adequately quantified. We review methods for quantifying the biodiversity of regions, consider issues that should be addressed in designing and evaluating a regional monitoring scheme, and offer a practical guide to what types of survey are appropriate for addressing different objectives for biodiversity monitoring.

Initially described in 2000, AZTI's Marine Biotic Index (AMBI) aims to assess alterations in communities of soft-bottom marine benthic macroinvertebrates caused by anthropogenic impacts. Although it was designed to be used in European estuaries and coasts this index, based on Pearson and Rosenberg's model of responses to organic enrichment, is being used successfully worldwide. Taking into account statistical difficulties associated with the use of raw abundance data, modifications to the index were recently proposed. These included transforming abundances prior to its calculation, or to use data other than abundances which might be more functionally relevant (such as biomass or production data). Using data from the Basque coast and estuaries (northern Spain), collected between 1995 and 2009, where the evolution of human pressures and restoration actions in the area may be taken into account, the performance of AMBI is compared to that of the proposed modifications in order to assess their usefulness. Despite large variations in the form and nature of the input data, all variations of AMBI index are shown to be highly correlated, even when presence/absence data are used. New boundaries between disturbance categories were calculated, reflecting inter-relationships between different forms of the index. The disturbance classification obtained from all variations using the recalculated boundaries agreed closely with that derived from AMBI. The finding that AMBI values calculated with presence/absence data are potentially useful opens up many possibilities, such as determining the status of assemblages retrospectively using historical data.

Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well-documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance.

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

Sea level in the Indian Ocean is subject to considerable temporal and spatial variabilities. During the period 1960–2009 at Phuket, Thailand, in the NE Indian Ocean, mean sea level increased by 2.7 mm y−1. Regular monitoring of coral cover on fringing reef flats at Phuket since 1979 revealed a sensitive response of this habitat to both transient sea-level depressions and sea-level elevation. Since 1987 when more frequent sampling began, coral cover was positively correlated with the mean sea level experienced over the preceding months. Changing mean sea level explained a high proportion of the observed variation in cover, with overall increasing sea levels and a lack of negative sea-level anomalies promoting cover on the outer reef flats. Concomitantly, there have been no changes in reef community structure or any apparent shifts in zonation patterns across the reef. While future benefits of continued increases in mean sea level on reef flats in the region will be constrained by the frequency and intensity of sea-level depressions associated with the Indian Ocean Dipole, and bleaching events, the overall picture for these shallow reefs is a positive one as they respond to increasing sea level and show rapid recovery from environmental disturbances.

Soil organic matter (SOM) is known to increase with time as landscapes recover after a major disturbance; however, little is known about the evolution of the chemistry of SOM in reconstructed ecosystems. In this study, we assessed the development of SOM chemistry in a chronosequence (space for time substitution) of restored Jarrah forest sites in Western Australia. Replicated samples were taken at the surface of the mineral soil as well as deeper in the profile at sites of 1, 3, 6, 9, 12, and 17 years of age. A molecular approach was developed to distinguish and quantify numerous individual compounds in SOM. This used accelerated solvent extraction in conjunction with gas chromatography mass spectrometry. A novel multivariate statistical approach was used to assess changes in accelerated solvent extraction (ASE)-gas chromatography-mass spectrometry (GCMS) spectra. This enabled us to track SOM developmental trajectories with restoration time. Results showed total carbon concentrations approached that of native forests soils by 17 years of restoration. Using the relate protocol in PRIMER, we demonstrated an overall linear relationship with site age at both depths, indicating that changes in SOM chemistry were occurring. The surface soils were seen to approach native molecular compositions while the deeper soil retained a more stable chemical signature, suggesting litter from the developing diverse plant community has altered SOM near the surface. Our new approach for assessing SOM development, combining ASE-GCMS with illuminating multivariate statistical analysis, holds great promise to more fully develop ASE for the characterisation of SOM.

A large-scale database concerning benthic copepods from the Arctic, Baltic Sea, North Sea, British Isles, Adriatic Sea and Crete was compiled to assess species richness, biodiversity, communities, ecological range size and biogeographical patterns. The Adriatic showed the highest evenness and the most species-rich communities. Assemblages from the North Sea, British Isles, Baltic and Crete had a lower evenness. The British Isles were characterised by impoverished communities. The ecological specificity of copepod species showed two diverging trends: higher specificity of species in more diverse assemblages was observed in the Adriatic, North Sea and Baltic. A uniformly high species specificity disregarding sample diversity was found on Crete and in the British Isles. Benthic copepod communities showed distinct patterns that clearly fit the predefined geographical regions. Communities were distinguishable and β-diversity was found to be high around Europe, indicating a high species turnover on the scale of this investigation. The British Isles and the North Sea were found to be faunistic links to the Baltic and the Arctic.