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.

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.

Erebusssau nom. nov. was originally described by Bussau, (1993) in his PhD thesis “Taxonomische und ökologische Untersuchungen an Nematoden des Peru-Beckens” but the name assigned was already in use, becoming an invalid name. Based on male specimens recovered from the Clarion-Clipperton Fracture Zone, we propose a new replacement nomen for the genus and describe a new species, also adding information about juveniles. Erebussau nom. nov. differs from all other Meyliidae genera by its peculiar offset head. Erebussau profundus sp. nov. differs from Erebussau tenebricosus nom. nov., comb. nov. by its larger size, the presence of pre- and post-cloacal supplements and the shape of the spicules. We also describe a new genus of the family Desmoscolecidae, Odetenema gesarae gen. nov., sp. nov. with an updated key to the genera of the subfamily Tricominae. Odetenema gen. nov. differs from the described Desmoscolecidae genera mainly in terms of the cuticle annulation pattern and the unique end ring with two tubular outlets. Erebussau tenebricosus, E. profundus sp. nov. and Odetenema gesarae gen. nov., sp. nov. have so far only been reported from deep-sea areas where polymetallic nodules are present.

Mangroves develop under environmental conditions and anthropogenic pressures whose impact on benthic meiofauna remains poorly understood. It is unclear how meiofauna communities are structured according to local sedimentary conditions. This study was designed to characterize the community structure of meiofauna and nematodes (dominant taxa) and the associated environmental forcings in intertidal mangrove sediments from Mayotte (Indo-West-Pacific), Martinique and Guadeloupe (Caribbean). Sediment cores were sampled at the end of the dry season at low tide on adult mangrove stands with similar immersion time. In each sediment layer, we analyzed redox potential, pH, porewater salinity, grain size, organic matter, metals, organic contaminants, prokaryotes and meiofauna. Our results show that sediments far from cities and agricultural fields trapped site-specific contaminants due to local water transport processes. Some metals, PAHs or pesticides exceeded toxicity thresholds in most of the studied stations, thus being harmful to benthic fauna. The sedimentary environment acts as a filter selecting specific meiofauna communities at station scale only in the Caribbean. In Mayotte, horizontal homogeneity contrasts with vertical heterogeneity of the sedimentary environment and the meiofauna. Nematode genera showed particular distribution patterns horizontally and vertically, suggesting the presence of sediment patches suitable for a restricted pool of genera on each island. Results in the Caribbean are consistent with nested diversity patterns due to environmental filtering. Conversely, horizontal homogeneity at Mayotte would reflect greater dispersal between stations or more spatially homogeneous anthropogenic pressures. The nematode genera present at depth may not be the most specialized, but the most versatile, capable of thriving in different conditions. Terschellingia and Daptonema showed contrasted responses to environmental forcing, likely due to their versatility, while Desmodora showed uniform responses between study areas, except when toxicity thresholds were exceeded. Our results emphasize that a given genus of nematode may respond differently to sedimentary conditions depending on sites.

Free-living aquatic nematodes are abundant, diverse and of general environmental importance. However, knowledge of species distributions of both marine and freshwater nematodes is sparse. Species distribution data are crucial for evaluating environmental impacts from human activities and to conduct integrated nematode community assessments. Basic knowledge on taxonomy and species descriptions is lacking for many regions due to decreasing taxonomic expertise, yet it is essential for biodiversity research and for building molecular sequence libraries for the application of methods such as environmental DNA. In order to encourage and facilitate taxonomic and descriptive work on this understudied group, we present here a framework for nematode species description. We begin by providing a brief overview of nematology history, then provide suggestions of microscopic methods that should be used and provide a list of characters essential for morphometric species descriptions. Finally, we briefly discuss common molecular sequencing approaches that are commonly used in nematode taxonomic literature.