Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments

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

Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

peer reviewedThe 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

Description and distribution of Erebussau nom. nov. pro Erebus Bussau, 1993 nec Erebus Latreille, 1810 with description of a new specie, and of Odetenema gesarae gen. nov., sp. nov. (Nematoda: Desmoscolecida) from nodule-bearing abyssal sediments in the Pacific (vol 4903, pg 542, 2021)

Bezerra, Tania Nara, Pape, Ellen, Hauquier, Freija, Vanreusel, Ann (2021): TANIA NARA BEZERRA, ELLEN PAPE, FREIJA HAUQUIER & ANN VANREUSEL (2021) Description and distribution of Erebussau nom. nov. pro Erebus Bussau, 1993 nec Erebus Latreille, 1810 with description of a new specie, and of Odetenema gesarae gen. nov., sp. nov. (Nematoda: Desmoscolecida) from nodule-bearing abyssal sediments in the Pacific. Zootaxa, 4903: 542-562. Zootaxa 4948 (4): 600-600, DOI: https://doi.org/10.11646/zootaxa.4948.4.

Description and distribution of Erebussau nom. nov. pro Erebus Bussau, 1993 nec Erebus Latreille, 1810 with description of a new specie, and of Odetenema gesarae gen. nov., sp. nov. (Nematoda: Desmoscolecida) from nodule-bearing abyssal sediments in the Pacific

Bezerra, Tania Nara, Pape, Ellen, Hauquier, Freija, Vanreusel, Ann (2021): Description and distribution of Erebussau nom. nov. pro Erebus Bussau, 1993 nec Erebus Latreille, 1810 with description of a new specie, and of Odetenema gesarae gen. nov., sp. nov. (Nematoda: Desmoscolecida) from nodule-bearing abyssal sediments in the Pacific. Zootaxa 4903 (4): 542-562, DOI: https://doi.org/10.11646/zootaxa.4903.4.

Meiofauna response to physical disturbance at the DEA: the importance of scale to identify long-term effects

Polymetallic nodules in deep-sea habitats of the Pacific Ocean will be subject to commercial exploitation in the near future but the potential effects of such mining activities on benthic life are difficult to assess. Here we present results from a recent revisit onboard RV SONNE (leg SO242/2) to the site of the “DISturbance and reCOLonization experiment” (DISCOL), a large scale benthic impact study initiated in 1989 in a polymetallic nodule area in the Peru Basin (tropical south-eastern Pacific). The area was artificially disturbed by a plow harrow to simulate manganese nodule extraction. In 2015, Meiofauna samples were collected and analysed at two different spatial scales in the framework of the JPI Oceans' programme ‘Ecological Aspects of Deep-Sea Mining’ to study the response and recovery rate of benthic faunal communities. At a macroscale, meiofauna densities and community composition were compared between two stations within the DISCOL experimental area (DEA) and three undisturbed reference stations. No long-term disturbance effects could be identified, most likely because high sediment heterogeneity in the disturbed and reference sites resulted in large variation in meiofauna communities. However, additional ROV push core sampling at selected microhabitats within the disturbance tracks (white patches, ripple crests and ripple valleys) revealed significant differences at a microscale for two out of three tracks. Meiofauna abundances were significantly reduced at all sites compared to outside track control samples with the exception of ripple valleys. Lowest densities were found at the white spot habitats where disturbances in 1989 exposed deeper sediment layers and where lowest pigment and organic matter contents were found. The study demonstrates that physical disturbances as they will be associated with mining will most likely result in long-term impacts on meiofauna communities in nodule areas. However, the results also show that detailed investigations at small spatial scales may be required to discriminate disturbance effects on meiofauna communities from natural variability

Longitudinal and bathymetrical trends in the relative abundance of nematode feeding types.

<p>The basins sampled are displayed on the x-axis (GB: Galicia Bank region, A: Algerian basin, AP: Algero-Provençal basin, I: Ionian basin, L: Levantine basin) and are ordered from west to east. The colour of the bars indicates approximate water depth (1200 m: white, 1900 m: grey, 3000 m: dark grey). Bars represent average values; error bars denote standard errors. 1A: selective deposit feeder, 1B: non-selective deposit feeder, 2A: epistrate feeder, 2B: predator/scavenger).</p

Non-metric multi-dimensional scaling (nMDS) plot of fourth-root transformed relative nematode genus abundances per station.

<p>The dashed line separates the seamount station from the non-seamount stations. Station codes are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059954#pone-0059954-t001" target="_blank">Table 1</a>.</p

Longitudinal and bathymetric trends in densities, total and individual biomass of nematodes.

<p>The basins sampled are displayed on the x-axis (GB: Galicia Bank region, A: Algerian basin, AP: Algero-Provençal basin, I: Ionian basin, L: Levantine basin) and are ordered from west to east. The colour of the bars indicates approximate water depth (1200 m: white, 1900 m: grey, 3000 m: dark grey). Bars represent average values; error bars denote standard errors.</p

Within-station variability in nematode genus composition in function of sedimentary phytopigment concentrations.

<p>Top: chlorophyll a (chl-a) concentrations. Bottom: chloroplastic pigment equivalents (CPE). Pigment data were missing for station A1900. Only one sample was collected at L3000, prohibiting the assessment of within-station variability in community structure.</p