Paul J. Somerfield

Marine reserves: size and age do matter

Marine reserves are widely used throughout the world to prevent overfishing and conserve biodiversity, but uncertainties remain about their optimal design. The effects of marine reserves are heterogeneous. Despite theoretical findings, empirical studies have previously found no effect of size on the effectiveness of marine reserves in protecting commercial fish stocks. Using 58 datasets from 19 European marine reserves, we show that reserve size and age do matter: Increasing the size of the no-take zone increases the density of commercial fishes within the reserve compared with outside; whereas the size of the buffer zone has the opposite effect. Moreover, positive effects of marine reserve on commercial fish species and species richness are linked to the time elapsed since the establishment of the protection scheme. The reserve size-dependency of the response to protection has strong implications for the spatial management of coastal areas because marine reserves are used for spatial zoning.

Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time

The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change. We also discuss methodological issues, such as false alerts and modifications in design, of which users of these data sets need to be aware.

The seasonal structure of microbial communities in the Western English Channel

Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and approximately 12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.

Marine reserves: fish life history and ecological traits matter.

Marine reserves are assumed to protect a wide range of species from deleterious effects stemming from exploitation. However, some species, due to their ecological characteristics, may not respond positively to protection. Very little is known about the effects of life history and ecological traits (e.g., mobility, growth, and habitat) on responses of fish species to marine reserves. Using 40 data sets from 12 European marine reserves, we show that there is significant variation in the response of different species of fish to protection and that this heterogeneity can be explained, in part, by differences in their traits. Densities of targeted size-classes of commercial species were greater in protected than unprotected areas. This effect of protection increased as the maximum body size of the targeted species increased, and it was greater for species that were not obligate schoolers. However, contrary to previous theoretical findings, even mobile species with wide home ranges benefited from protection: the effect of protection was at least as strong for mobile species as it was for sedentary ones. Noncommercial bycatch and unexploited species rarely responded to protection, and when they did (in the case of unexploited bentho-pelagic species), they exhibited the opposite response: their densities were lower inside reserves. The use of marine reserves for marine conservation and fisheries management implies that they should ensure protection for a wide range of species with different life-history and ecological traits. Our results suggest this is not the case, and instead that effects vary with economic value, body size, habitat, depth range, and schooling behavior.

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.

Surrogates in marine benthic investigations ‐ which taxonomic unit to target?

Although the identification of organisms to the levelof species is the ideal in studies of marinemacrobenthos, there are situations where such a finelevel of taxonomic discrimination may be eitherimpossible or unwarranted, for example when much thefauna is undescribed, or if the task for which samplesare collected does not require them to be identifiedto the species level. The idea that abundances ofhigher taxa, or particular groups of organisms, may beused as surrogates for the total fauna in such studiesis explored in this paper using data from theNorwegian sector of the North Sea. The generalconclusion is that, in surveys of soft sedimentmacrofauna in disturbed areas of the North Sea wherepollution imposes simple spatial gradients on thebenthic communities, little information aboutinter-sample relationships is lost using data based onfamily, polychaete species, or polychaete familyabundances, rather than species abundances. In morepristine areas where spatial patterns are determinedby a number of processes, correlations betweencalculated diversity indices and similarity in faunalpatterns between species and family abundances arestill very high, but less so for polychaete species orpolychaete family abundances. This suggests thatidentification to the level of family may besatisfactory in many routine monitoring surveys,andidentification of only the polychaetes, either to thelevel of species or family, may also be a possiblealternative if there are clear disturbance gradientsin the survey area. Polychaetes are of importance indisturbed areas because the group contains tolerantand intolerant species, and in undisturbed areasbecause within the taxon species have a greater rangeof trophic and reproductive strategies than withinother taxa. Ultimately it is the distribution ofspecies, their identities, and their interactions witheach other and with the environment, that are ofinterest. The use of surrogates is likely to be mostadvantageous if it is only the extent of pollutioneffects from a discrete source that matters, andspecies level baseline studies have already beencompleted.

A Comparison of Some Methods Commonly Used for the Collection of Sublittoral Sediments and Their Associated Fauna

Abstract Five replicate samples were collected using each of four different collection methods, at two sites with contrasting sediment types, namely soft mud and hard muddy sand. The four methods were: 1. direct collection by divers; 2. collection using a Craib corer; 3. subsampling from an USNEL pattern box corer; and 4. subsampling from a van Veen grab. As far as possible, biasing factors, other than the actual sampling operation at the sediment surface, were controlled. Nematodes in the samples were identified and the resulting data analysed using a range of techniques. Univariate measures of community structure, such as diversity indices, did not reveal any significant difference between sampling methods, neither was any significant difference detected in diversity profiles ( k -dominance curves). The conclusion which might be drawn from these experiments is that it makes little difference which method of sampling is chosen for a particular study. Such a conclusion would be erroneous, as multivariate analyses did reveal significant differences in community structure between samples retrieved by different methods. The patterns of differences at the two sites were dependent, in detail, on the transformations used in the analyses, but in general there was a smooth shift in community structure from cores collected by divers, through Craib cores and box-core subsamples, to subsamples from grabs. The detected differences, although significant, were small, and did not suggest a strong, or ecologically meaningful, explanation. A modified index of multivariate dispersion is described, and this is used to examine differences between sampling methods in intra-sample variability. This showed that differences in variability contribute to, but do not fully explain, the observed differences. It should also be borne in mind that factors which might not be expected to affect different samplers in the same way, such as water depth, weather conditions and sample size, were controlled. It is likely that these have biasing effects as important as the actual operation of sampling gear on the seabed, where explanations of the differences between sample quality from different methods, such as bow-wave effects, have been focused.

A bioturbation classification of European marine infaunal invertebrates

Bioturbation, the biogenic modification of sediments through particle reworking and burrow ventilation, is a key mediator of many important geochemical processes in marine systems. In situ quantification of bioturbation can be achieved in a myriad of ways, requiring expert knowledge, technology, and resources not always available, and not feasible in some settings. Where dedicated research programmes do not exist, a practical alternative is the adoption of a trait-based approach to estimate community bioturbation potential (BPc). This index can be calculated from inventories of species, abundance and biomass data (routinely available for many systems), and a functional classification of organism traits associated with sediment mixing (less available). Presently, however, there is no agreed standard categorization for the reworking mode and mobility of benthic species. Based on information from the literature and expert opinion, we provide a functional classification for 1033 benthic invertebrate species from the northwest European continental shelf, as a tool to enable the standardized calculation of BPc in the region. Future uses of this classification table will increase the comparability and utility of large-scale assessments of ecosystem processes and functioning influenced by bioturbation (e.g., to support legislation). The key strengths, assumptions, and limitations of BPc as a metric are critically reviewed, offering guidelines for its calculation and application.

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Background Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

A community level sediment bioassay applied to an estuarine heavy metal gradient

Abstract A simple laboratory microcosm system, previously used as a community level sediment bioassay for laboratory contaminated sediments, has been used for testing contaminated field sediments. Meiobenthic communities from the Lynher Estuary were incubated with defaunated sediment collected from the Fal Estuary system where a gradient of heavy metal concentrations is reflected in meiofaunal community structure. In the microcosms changes in nematode community structure were related to sediment metal concentrations. These changes in community structure were similar to those previously observed between creeks in the Fal Estuary system indicating that an experimental microcosm approach can be useful both as a sediment bioassay and in the validation of conclusions drawn from field surveys.