Productivity and environmental stress are major drivers of multiple biodiversity facets and faunal community structure. Little is known on their interacting effects on early community assembly processes in the deep sea (>200 m), the largest environment on Earth. However, at hydrothermal vents productivity correlates, at least partially, with environmental stress. Here, we studied the colonization of rock substrata deployed along a deep‐sea hydrothermal vent gradient at four sites with and without direct influence of vent fluids at 1,700‐m depth in the Lucky Strike vent field (Mid‐Atlantic Ridge [MAR]). We examined in detail the composition of faunal communities (>20 μm) established after 2 yr and evaluated species and functional patterns. We expected the stressful hydrothermal activity to (1) limit functional diversity and (2) filter for traits clustering functionally similar species. However, our observations did not support our hypotheses. On the contrary, our results show that hydrothermal activity enhanced functional diversity. Moreover, despite high species diversity, environmental conditions at surrounding sites appear to filter for specific traits, thereby reducing functional richness. In fact, diversity in ecological functions may relax the effect of competition, allowing several species to coexist in high densities in the reduced space of the highly productive vent habitats under direct fluid emissions. We suggest that the high productivity at fluid‐influenced sites supports higher functional diversity and traits that are more energetically expensive. The presence of exclusive species and functional entities led to a high turnover between surrounding sites. As a result, some of these sites contributed more than expected to the total species and functional β diversities. The observed faunal overlap and energy links (exported productivity) suggest that rather than operating as separate entities, habitats with and without influence of hydrothermal fluids may be considered as interconnected entities. Low functional richness and environmental filtering suggest that surrounding areas, with their very heterogeneous species and functional assemblages, may be especially vulnerable to environmental changes related to natural and anthropogenic impacts, including deep‐sea mining.

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<p><strong>Abstract.</strong> In the abyssal Equatorial Pacific Ocean, most of the seafloor of the Clarion-Clipperton Fracture Zone (CCFZ), a 6 million km<sup>2</sup> polymetallic nodule province, has been preempted for future mining. In light of the large footprint that mining would leave, and given the diversity and the vulnerability of the abyssal fauna, the International Seabed Authority has implemented a regional management plan that includes the creation of nine areas of particular environmental interest (APEIs) located at the periphery of the CCFZ. The APEIs were defined based on the best – albeit very limited – scientific knowledge for the area. The fauna and habitats in the APEIs are unknown, as are species' ranges and the extent of biodiversity across the CCFZ.</p> <p>As part of the Joint Programming Initiative Healthy and Productive Seas and Oceans (JPI Oceans) pilot action <q>Ecological aspects of deep-sea mining</q>, the SO239 cruise aimed at improving species inventories, determining species ranges, identifying the drivers of beta diversity patterns and assessing the representativeness of an APEI. Four exploration contract areas and an APEI (APEI#3) were sampled along a gradient of sea-surface primary productivity that spanned a distance of 1440 km in the eastern CCFZ. Between 3 and 8 quantitative box cores (0.25 m<sup>2</sup>; 0–10 cm) were sampled in each study area, resulting in a large collection of polychaetes that were morphologically and molecularly (COI and 16S genes) analyzed.</p> <p>A total of 275 polychaete morphotypes were identified. Only one morphotype was shared among all five study areas and 49 % were singletons. The patterns in community structure and composition were mainly attributed to variations in food fluxes at the regional scale and nodule density at the local scale. The four exploration contract areas belong to a mesotrophic province. The distance-decay of similarity among the four areas provides an estimated species turnover of 0.04 species km<sup>−1</sup> and an average species range of 25 km. The polychaete assemblage in APEI#3 showed the lowest densities, lowest diversity as well as very low, distant-independent similarity with the other four study areas. Given that APEI#3 is located in an oligotrophic province and separated from the CCFZ by the Clarion Fracture Zone, our results call into question the representativeness and the appropriateness of APEI#3 to meet its purpose of preserving the biodiversity of the CCFZ fauna. Two methods for estimating the total number of polychaete species gave estimates that ranged from 498 to 240 000 species. Both methods are biased by the high frequency of singletons in the dataset, which likely result from under-sampling; our estimates thereby merely reflect our level of uncertainty. The assessment of potential risks and scales of biodiversity loss due to nodule mining thus requires an appropriate inventory of species richness in the CCFZ.</p>

We analysed the robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species‐markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI‐TOF MS (matrix‐assisted laser desorption ionization time of flight mass spectrometry) data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to the species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity, that is identification was based on complex pattern‐differences rather than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species‐gap in proteome composition appeared at 0.7 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intraspecific variability increased, resulting in overlaps of intra and inter‐specific distance. Highest intraspecific distances (>0.7) were observed between specimens from brackish and marine habitats (i.e., salinity probably affects proteomic patterns). When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, the choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envisage high relevance of this time‐ and cost‐efficient method for future zooplankton monitoring as it provides not only in‐depth taxonomic resolution for counted specimens but also add‐on information, such as on developmental stage or environmental conditions.