Phylogenetic clustering and rarity imply risk of local species extinction in prospective deep-sea mining areas of the Clarion-Clipperton Fracture Zone

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

Distribution of free-living marine nematodes in the Clarion–Clipperton Zone: implications for future deep-sea mining scenarios

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

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

A threefold perspective on the role of a pockmark in benthic faunal communities and biodiversity patterns

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 macroand 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, macroand 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

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

Combining traditional taxonomy and metabarcoding : assemblage structure of nematodes in the shelf sediments of the Eastern Antarctic Peninsula

This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel (PGC) and Duse Bay (DB). 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 DB (200, 500, and 1,000 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 DB 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 PGC (1,000 and 1,250 m) and the one in DB (1,000 m), differences in terms of environmental variables, meiofaunal densities, and composition were observed. The deepest basin in PGC 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

Total organic carbon and total nitrogen measured on MUC and ROV samples during SONNE cruises SO268/1 and SO268/2 to the BGR and GSR license areas in the Clarion Clipperton Fracture Zone

This dataset contains sedimentary parameters total nitrogen (TN) and total organic carbon (TOC) measured from Multicorer (MUC) and Remotely Operated Vehicle (ROV) samples from the Bundesanstalt für Geowissenschaften und Rohstoffe (BGR, Germany) and Global Sea Mineral Resources (GSR, Belgium) license areas in the Clarion Clipperton Fracture Zone collected on onboard the RV Sonne during expeditions SO268 (Leg1 and Leg2) in 2019. Values are given in their respective units (SI) and have been collected and measured by the Marine Biology Research Group of Ghent University (Belgium)