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Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which to perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode Amplicon Sequence Variant (ASV) alpha diversity patterns, evolutionary distinctiveness (ED) and phylogenetic community structure at different depths and environments. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or environment-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each environment and/or depth zone; genetic diversity was thus highly localised. The intertidal and abyssal samples had the highest ED values, indicating that both a dynamic, fluctuating ecosystem, as well as a relatively stable yet very old one, can produce highly diversified assemblages. Overwhelmingly, nematode ASVs in all environments exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.

International audience; The increasing demand for metals is pushing forward the progress of deep-sea mining industry. The abyss between the Clarion and Clipperton Fracture Zones (CCFZ), a region holding a higher concentration of minerals than land deposits, is the most targeted area for the exploration of polymetallic nodules worldwide, which may likely disturb the seafloor across large areas and over many years. Effects from nodule extraction cause acute biodiversity loss of organisms inhabiting sediments and polymetallic nodules. Attention to deep-sea ecosystems and their services has to be considered before mining starts but the lack of basic scientific knowledge on the methodologies for the ecological surveys of fauna in the context of deep-sea mining impacts is still scarce. We review the methodology to sample, process and investigate metazoan infauna both inhabiting sediments and nodules dwelling on these polymetallic-nodule areas. We suggest effective procedures for sampling designs, devices and methods involving gear types, sediment processing, morphological and genetic identification including metabarcoding and proteomic fingerprinting, the assessment of biomass, functional traits, fatty acids, and stable isotope studies within the CCFZ based on both first-hand experiences and literature. We recommend multi- and boxcorers for the quantitative assessments of meio- and macrofauna, respectively. The assessment of biodiversity at species level should be focused and/or the combination of morphological with metabarcoding or proteomic fingerprinting techniques. We highlight that biomass, functional traits, and trophic markers may provide critical insights for biodiversity assessments and how statistical modeling facilitates predicting patterns spatially across point-source data and is essential for conservation management.

Mining of polymetallic nodules in abyssal seafloor sediments promises to address the growing worldwide demand for metallic minerals. Given that prospective mining operations are likely to have profound impacts on deep seafloor communities, industrial investment has been accompanied by scientific involvement for the assessment of baseline conditions and provision of guidelines for environmentally sustainable mining practices. Benthic meiofaunal communities were studied in four prospective mining areas of the Clarion–Clipperton Zone (CCZ) in the eastern Pacific Ocean, arranged in a southeast–northwest fashion coinciding with the productivity gradient in the area. Additionally, samples were collected from the Area of Particular Environmental Interest no. 3 (APEI-3) in the northwest of the CCZ, where mining will be prohibited and which should serve as a “source area” for the biota within the larger CCZ. Total densities in the 0–5 cm upper layer of the sediment were influenced by sedimentary characteristics, water depth and nodule density at the various sampling locations, indicating the importance of nodules for meiofaunal standing stock. Nematodes were the most abundant meiobenthic taxon, and their assemblages were typically dominated by a few genera (generally 2–6) accounting for 40 %–70 % of all individuals, which were also widely spread along the CCZ and shared among all sampled license areas. However, almost half of the communities consisted of rare genera, each contributing less than 5 % to the overall abundances and displaying a distribution which was usually restricted to a single license area. The same observations (dominant and widely spread versus rare and scattered) could be made for the species of one of the dominant genera, Halalaimus, implying that it might be mainly these rare genera and species that will be vulnerable to mining-induced changes in their habitat.

High‐throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species‐level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum‐specific species‐level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read‐merging and two clustering algorithms and the cluster‐free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus‐level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species‐level detections, which were, however, associated with higher error rates compared to ASVs. Genus‐level assignments using ASVs exhibited higher accuracy and lower error rates compared to species‐level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples.

Cold seeps occur globally in areas where gases escape from the seafloor, occasionally resulting in the formation of topographic depressions (pockmarks), characterised by unique physicochemical conditions such as anoxic and sulphuric sediments. Free-living marine nematodes tend to dominate the meiofaunal component in such environments, often occurring at extremely high densities and low richness; the mechanisms defining community assembly in areas of fluid seepage, however, have received little attention. Here we focus on a low-activity pockmark at 789 m in the Mozambique Channel (MC). We assessed the diversity, co-occurrence patterns and phylogenetic community structure of nematodes at this bathyal site to that of a nearby reference area as well as abyssal sediments using metabarcoding. In addition, we compared our molecularly-derived diversity estimates to replicate samples identified morphologically. Overall, nematode Amplicon Sequence Variants (ASVs) and generic richness were similar between Pockmark and Abyssal sediments, but lower compared to the Reference area. Although more than half the genera were shared, over 80% of ASVs were unique within each area and even within each replicate core. Even though both methodologies differentiated the Pockmark from the Reference and Abyssal sites, there was little overlap between the molecularly and morphologically identified taxa, highlighting the deficit of reference sequences for deep-sea nematodes in public databases. Phylogenetic community structure at higher taxonomic levels was clustered and did not differ between the three areas yet analysis within three shared and dominant genera (Acantholaimus, Desmoscolex, Halalaimus), revealed randomness with respect to phylogeny as well as co-occurrence which was exclusive to the Pockmark area. These patterns point to the influence of neutral dynamics at this locality resulting from the stochastic sampling of early colonizing taxa, the successional stage at sampling and/or the functional redundancy within the investigated genera.

Pockmarks are circular-shaped depressions that increase seabed heterogeneity and are characterized by discontinuous fluid emissions. To understand how environmental conditions of pockmarks affect the structure of macro- and meiofauna, we investigated two sites in a pockmark field in the northwestern Madagascar margin. In a comparative approach, we explored the community structure of the dominant taxa (Polychaeta, Nematoda and hyaline foraminifera) in each component (macro-, metazoan meiofauna and foraminifera, respectively). The investigated active pockmark showed approximately two times higher meiofauna abundance compared to in a site away from another pockmark field, but macrofauna showed the opposite trend, with almost half density at the pockmark site. However, at both sites, macro- and meiofauna showed higher richness and abundance values in the top well-oxygenated layers of the sediment than in the underlaying ones. Polychaeta and Nematoda showed lower richness in the pockmark, opposed to hyaline foraminiferans, but lower evenness in the pockmark was found for the three groups. The detection of gas flares in the water column attests of the recent activity within the pockmark. High amount of sulfur-bearing minerals (mainly pyrite) evidences a production of dissolved free sulfides (not detected at the time of sampling) by sulfate reduction process driven by organic matter degradation and anaerobic oxidation of methane. Furthermore, recent increase in sedimentation rates in the past 70 years and organic matter inputs could have led to higher organic matter degradation rates resulting in reduced conditions and a high oxygen consumption. All this together seem to act as key factors in the determination of variation in richness, abundance and community composition of macrofauna and meiofauna. Additionally, some taxa seem to be more tolerant to these extreme conditions, such as species belonging to the Nematoda genus Desmodora and the phylum Kinorhyncha, which are highly abundant in the pockmark, and hence, may be considered as potential bioindicators of pockmark activity in this area. Further studies are required for a better assessment.

This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel and Duse Bay. We compared five stations sampled at different water depths along the shelf and investigated their meiobenthic community structure. We approached nematode biodiversity combining traditional taxonomic identification and high throughput sequencing (HTS), with the use of Amplicon Sequence Variants (ASVs). Additionally, we characterized the environment by primary production proxies, grain size and seasonal ice conditions. Our results suggest that the availability of organic matter and its freshness are responsible for the high densities found at all depths. However, potential factors influencing the high local and regional variability of meiofauna density and biodiversity are less clear. A bathymetric transect consisting of three stations in Duse Bay (200 m, 500 m and 1000 m depth) showed increasing pigment concentrations in the first centimeters of the sediment vertical profile with increasing water depth, whereas the meiofauna densities showed the opposite trend. The deepest station of Duse Bay seems to function as a sink for fine material as supported by the higher silt fraction and higher organic matter concentrations. When comparing the two basins in the Prince Gustav Channel (1000 m and 1250 m) and the one in Duse Bay (1000 m), differences in terms of environmental variables, meiofaunal densities and composition were observed. The deepest basin in Prince Gustav Channel is located further South (closer to the highly unstable Larsen area), and marked differences with the other basins suggest that it might be experiencing different conditions as a result of its presence near the summer ice margin and its more elongated topography. Both, the shallowest and the deepest stations showed the highest number of unique sequences, suggesting a more biodiverse nematode assemblage. The morphological identification did not show significant differences in the biodiversity of all stations, differently from the ASVs approach. However the lack of reference sequences in online databases and the thickness of nematode’s cuticule are still important issues to consider as they potentially lead to underestimations of biodiversity and functional traits.

The deep sea (>200 m depth) encompasses >95% of the world’s ocean volume and represents the largest and least explored biome on Earth (

An understanding of the forces controlling community structure in the deep sea is essential at a time when its pristineness is threatened by polymetallic nodule mining. Because abiotically defined communities are more sensitive to environmental change, we applied occurrence- and phylogeny-based metrics to determine the importance of biotic versus abiotic structuring processes in nematodes, the most abundant invertebrate taxon of the Clarion–Clipperton Fracture Zone (CCFZ), an area targeted for mining. We investigated the prevalence of rarity and the explanatory power of environmental parameters with respect to phylogenetic diversity (PD). We found evidence for aggregation and phylogenetic clustering in nematode amplicon sequence variants (ASVs) and the dominant genus Acantholaimus , indicating the influence of environmental filtering, sympatric speciation, affinity for overlapping habitats and facilitation for community structure. PD was associated with abiotic variables such as total organic carbon, chloroplastic pigments equivalents and/or mud content, explaining up to 57% of the observed variability and providing further support of the prominence of environmental structuring forces. Rarity was high throughout, ranging from 64 to 75% unique ASVs. Communities defined by environmental filtering with a prevalence of rarity in the CCFZ suggest taxa of these nodule-bearing abyssal plains will be especially vulnerable to the risk of extinction brought about by the efforts to extract them.

Mining of polymetallic nodules in abyssal seafloor sediments promises to address the growing worldwide demand for metallic minerals. Given that prospective mining operations are likely to have profound impacts on deep seafloor communities, industrial investment has been accompanied by scientific involvement for the assessment of baseline conditions and provision of guidelines for environmentally sustainable mining practices. Benthic meiofaunal communities were studied in four prospective mining areas of the Clarion–Clipperton Zone (CCZ) in the east Pacific Ocean, arranged in a southeast-northwest fashion coinciding with the productivity gradient in the area. Additionally, samples were collected from an Area of Particular Environmental Interest (APEI-3) in the northwest of the CCZ where mining will be prohibited and which should serve as a source area for the biota within the larger CCZ. Total densities in the 0–5 upper cm layer of the sediment were influenced by sedimentary characteristics, water depth and nodule density at the various sampling locations, indicating the importance of nodules for meiofaunal standing stock. Nematodes were the most abundant meiobenthic taxon and displayed a relatively similar community composition for the different areas. Assemblages were typically dominated by a few genera (generally 2–6), accounting for 40–70 % of all individuals, as well as a large number of rare genera each contributing less than 5 % to the overall abundances. Dominant genera were widely spread within the CCZ and shared among all sampled license areas, whereas rare genera were usually limited to one. The same trend was present when looking at the species level of one of the dominant genera, Halalaimus, implying that it might be mainly these rare genera and species that will be affected by changes in their habitat due to mining activities.

Climate change has an impact on all levels of biodiversity: genes, species, populations and ecosystems. This effect is expected to be dependent on the rate of change. When faced with unfavorable environmental conditions, individuals have three non-exclusive options by which they can mitigate these changes: temporal alterations in phenology, spatial tracking of optimal conditions or in situ adaptation. For the latter to occur requires the existence of variability among conspecifics with respect to traits that directly or indirectly influence individual performance and fitness. One such “functional” trait is thermal stress tolerance. We investigated the presence of intraspecific functional trait variability of isofemale lineages of the free-living marine nematode Litoditis marina in monoculture, double and quadruple mixtures under thermal stress, which was applied in a gradient and a sudden treatment over 20 days, corresponding to at least four generations. We found a high degree of intraspecific functional trait variability relevant to thermal tolerance. This type of variability has traditionally been considered negligible compared to interspecific variation, but our results demonstrate the importance of its inclusion within trait-based eco-evolutionary studies as this will confer increased accuracy when inputting physiological parameters to relevant models (e.g. species distribution models). Additionally, we found a significant effect of the temperature treatments. In accordance with the majority of experimental evidence, our populations showed a stronger response to a sudden versus a gradient increase in temperature. Contrary to our expectations, no significant differences were observed between monocultures, double and quadruple lineage mixtures suggesting that increased intraspecific trait variability did not lead to higher fitness in L. marina populations exposed to thermal stress.

Recent years have seen a rapid increase in survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ) abyssal plain, a vast area of the central Pacific that is currently being actively explored for deep-sea minerals (ISA, 2016). Critical to the development of evidence-based environmental policy in the CCZ are data on the biogeography and connectivity of species at a CCZ-regional level. The London Workshop on the Biogeography and Connectivity of the CCZ was convened to support the integration and synthesis of data from European Union (EU) CCZ projects, supported by the EU Managing Impacts of Deep-Sea Resource Exploitation (MIDAS) and EU Joint Programming Initiative Healthy and Productive Seas and Oceans (JPI Oceans) projects. The London Workshop had three clear goals: (1) To explore, review and synthesise the latest molecular biogeography and connectivity data from across recent CCZ cruises from both contractor and academia-funded projects; (2) To develop complementary and collaborative institutional and program-based academic publication plans to avoid duplication of effort and ensure maximum collaborative impact; (3) To plan a joint synthetic data publication highlighting key results from a range of planned molecular biogeography/connectivity publications. 32 participants attended the workshop at the Natural History Museum in London from 10-12 May 2016. Presentations and discussions are summarised in this report covering (1) overviews of current CCZ environmental projects, (2) policy and industry perspectives, (3) synthesis of DNA taxonomy and biogeography studies, (4) summaries of the latest population genetic studies, (5) summaries of the latest broader morphological context, (6) an overview of publication and proposal plans to maximise collaborative opportunities and finally a series of workshop recommendations.