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.

To be able to adequately assess potential environmental impacts of deep-sea polymetallic nodule mining, the establishment of a proper environmental baseline, incorporating both spatial and temporal variability, is essential. The aim of the present study was to evaluate both spatial and intra-annual variability in meiofauna (higher taxa) and nematode communities (families and genera, and Halalaimus species) within the license area of Global Sea mineral Resources (GSR) in the northeastern Clarion Clipperton Fracture Zone (CCFZ), and to determine the efficiency of the current sampling of meiofauna and nematode diversity. In October 2015, three polymetallic nodule-bearing sites, about 60–270 km apart, located at similar depths (ca. 4,500 m) were sampled, of which one site was sampled in April in that same year. Despite the relatively large geographical distances and the statistically significant, but small, differences in sedimentary characteristics between sites, meiofauna and nematode communities were largely similar in terms of abundance, composition and diversity. Between-site differences in community composition were mainly driven by a set of rare and less abundant taxa. Moreover, although surface primary productivity in April exceeded that in October, no significant changes were observed in sedimentary characteristics or in meiofauna and nematode communities. At all sites and in both periods, Nematoda were the prevailing meiofaunal phylum, which was in turn dominated by Monhysterid genera and Acantholaimus. Our findings support the earlier purported notion of a low degree of endemism for nematode genera and meiofauna taxa in the deep sea, and hint at the possibility of large distribution ranges for at least some Halalaimus species. Taxon richness estimators revealed that the current sampling design was able to characterize the majority of the meiofauna and nematode taxa present. To conclude, implications of the present findings for environmental management and future research needs are provided

Abstract. 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.

We sampled the Darwin mud volcano (MV) for meiofaunal community and trophic structure in relation to pore-water geochemistry along a 10 m transect from a seep site on the rim of the crater towards the MV slope. Pore-water profiles indicated considerable variation in upward methane (CH 4 ) flow among sediment cores taken along the transect, with highest flux in the seep sediment core, gradually decreasing along the transect, to no CH 4 flux in the core taken at a 5 m distance. Low sulphate concentrations and high levels of total alkalinity and sulphide (H 2 S) suggested that anaerobic oxidation of methane (AOM) occurred close to the sediment surface in the seep sediment core. High H 2 S levels had a genus-and species-specific impact on meiofaunal densities. Nematode genus composition varied gradually between sediment cores, with the genus Sabatieria dominating almost all sediment cores. However, genus diversity increased with increasing distance from the seep site. These limited data suggest that the community structure of seep meiofauna is highly dependent on local (a)biotic habitat characteristics, and a typical seep meiofaunal community cannot be delineated. Stable isotope values suggested the nematode diet up to 10 m from the seep site included thiotrophic carbon. The thicker hemipelagic sediment layer (photosynthetic carbon), the increased trophic diversity, and the heavier nematode δ 13 C farther from the seep site suggest a decrease in thiotrophy and an increase in photosynthetic carbon in the nematode diet. KEY WORDS: Cold seep · Diversity · Stable isotope · Nematode · Diet Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 438: [71][72][73][74][75][76][77][78][79][80][81][82][83] 2011 There is no consistent meiofaunal response to seep conditions. Meiofaunal densities at different deepsea seeps are higher (Olu et al. 1997, Van Gaever et al. 2006 or similar (Shirayama & Ohta 1990) compared to non-seep sediments. In seep environments, nematodes usually are the predominant metazoans, although sometimes copepods dominate (Van Gaever et al. 2006). Generally, deep-sea nematodes are characterized by high local diversity (Lambshead & Boucher 2003). Cold seeps, however, exhibit substantially reduced species diversity, harbouring only a few dominant species (Levin 2005, Vanreusel et al. 2010. The low diversity in these habitats has been attributed to the harsh abiotic conditions, created by the high H 2 S and low oxygen levels (Levin 2005).Besides high biogeochemical and physical heterogeneity, seeps differ from most deep-sea environments in the local production of organic matter through chemosynthesis. Consequently, possible food sources for seep fauna, including meiobenthos are: (1) organic matter derived from symbiotic chemoautotrophic bacteria and (2) free-living chemoautotrophic bacteria, in addition to (3) the photosynthetic organic matter delivered to all deep-sea habitats. Studies on the diet of seep meiofauna are few. Both Van Gaever et al. (2006...

Alongside a primary productivity gradient between the Galicia Bank region in the Northeast Atlantic and the more oligotrophic eastern Mediterranean Basin, we investigated the bathymetric (1200–3000 m) and longitudinal variation in several measures for nematode taxon (Shannon–Wiener genus diversity, expected genus richness and generic evenness) and functional diversity (trophic diversity, diversity of life history strategies, biomass diversity and phylogenetic diversity). Our goals were to establish the form of the relation between diversity and productivity (measured as seafloor particulate organic carbon or POC flux), and to verify the positive and negative effect of sediment particle size diversity (SED) and the seasonality in POC flux (SVI), respectively, on diversity, as observed for other oceanographic regions and taxa. In addition, we hypothesised that higher taxon diversity is associated with higher functional diversity, which in turn stimulates nematode carbon mineralisation rates (determined from biomass-dependent respiration estimates). Taxon diversity related positively to seafloor POC flux. Phylogenetic diversity (measured as average taxonomic distinctness) was affected negatively by the magnitude and variability in POC flux, and positively by SED. The latter also showed an inverse relation with trophic diversity. Accounting for differences in total biomass between samples, we observed a positive linear relation between taxon diversity and carbon mineralisation in nematode communities. We could, however, not identify the potential mechanism through which taxon diversity may promote this ecosystem function since none of the functional diversity indices related to both diversity and nematode respiration. The present results suggest potential effects of climate change on deep-sea ecosystem functioning, but further also emphasise the need for a better understanding of nematode functions and their response to evolutionary processes

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 123Mar Biol DOI 10.1007/s00227-010-1454 patterns that clearly fit the predefined geographical regions. Communities were distinguishable and b-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.

Deep seabed mining is potentially imminent in the Clarion Clipperton Fracture Zone (CCFZ; northeast Pacific). Seabed collectors will remove polymetallic nodules and the surrounding surface sediments, both inhabited by meiofauna, along their path. To determine potential impacts of polymetallic nodule removal, we investigated the importance of nodule presence for the abundance, composition and diversity of sediment meiofauna, and evaluated the existence and composition of nodule crevice meiofauna in the Global Sea Mineral Resources (GSR) exploration contract area. Nodule-free and nodule-rich sediments displayed high biodiversity with many singletons and doubletons, potentially representing rare taxa. Nodule presence negatively influenced sediment meiofaunal abundances but did not markedly affect taxonomic composition or diversity. This is the first report on CCFZ nodule crevice meiofauna, whose abundance related positively to nodule dimensions. Though dominated by the same taxa, nodules and sediments differed regarding the taxonomic and trophic composition of the meio- and nematofauna. Nevertheless, there were no taxa endemic to the nodule crevices and nodule crevice meiofauna added only little to total small-scale (~ cm) meiofaunal abundance and diversity. We formulated environmental management recommendations at the contract area and regional (CCFZ) scale related to sampling effort, set-aside preservation and monitoring areas, and potential rehabilitation measures.

Nematode communities and relevant environmental variables were investigated to assess how the presence of a dam affects the Ba Lai estuary benthic ecosystem, in comparison to the adjacent dam-free estuary Ham Luong. Both estuaries are part of the Mekong delta system in Vietnam. This study has shown that the dam’s construction had an effect on the biochemical components of the Ba Lai estuary, as observed by the local increase in total suspended solids and heavy metal concentrations (Hg and Pb) and by a significant oxygen depletion compared to the natural river of Ham Luong. The nematode communities were also different between the two estuaries in terms of density, genus richness, Shannon–Wiener diversity, and dominant genera. The Ba Lai estuary exhibited lower nematode densities but a higher diversity, while the genus composition only slightly differed between estuaries. The results indicate that the present nematode communities may be well adapted to the natural organic load, to the heavy metal accumulation and to the oxygen stress in both estuaries, but the dam presence may potentially continue to drive the Ba Lai’s ecosystem to its tipping point.