Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling.

Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.

Mixtophyes toothlessi sp. n., a new Kinorhyncha species (Anomoirhaga: Neocentrophyidae) from the Clarion-Clipperton Zone, with a revision of terminology and taxonomic features of the family.

A new species of Mixtophyes Sánchez et al. 2014 is described from the Clarion-Clipperton Fracture Zone (north-eastern Pacific Ocean). The new species is characterised by the presence of spinose processes on segments 1-11 in middorsal position and on segments 1-10 in midlateral position, paired paradorsal setae on segments 2, 4-6 and 8-9, and unpaired ones on segments 3 and 7, paired setae in paralateral and ventrolateral positions on segments 2-9. In addition, some morphological characteristics of the family Neocentrophyidae and the genus Mixtophyes are discussed, and the diagnoses of both taxa are updated. Lastly, the taxonomic nomenclature of Neocentrophyidae and the sexual characters of the genus are accordingly emended.

Carbonate compensation depth drives abyssal biogeography in the northeast Pacific.

Abyssal seafloor communities cover more than 60% of Earth's surface. Despite their great size, abyssal plains extend across modest environmental gradients compared to other marine ecosystems. However, little is known about the patterns and processes regulating biodiversity or potentially delimiting biogeographical boundaries at regional scales in the abyss. Improved macroecological understanding of remote abyssal environments is urgent as threats of widespread anthropogenic disturbance grow in the deep ocean. Here, we use a new, basin-scale dataset to show the existence of clear regional zonation in abyssal communities across the 5,000 km span of the Clarion-Clipperton Zone (northeast Pacific), an area targeted for deep-sea mining. We found two pronounced biogeographic provinces, deep and shallow-abyssal, separated by a transition zone between 4,300 and 4,800 m depth. Surprisingly, species richness was maintained across this boundary by phylum-level taxonomic replacements. These regional transitions are probably related to calcium carbonate saturation boundaries as taxa dependent on calcium carbonate structures, such as shelled molluscs, appear restricted to the shallower province. Our results suggest geochemical and climatic forcing on distributions of abyssal populations over large spatial scales and provide a potential paradigm for deep-sea macroecology, opening a new basis for regional-scale biodiversity research and conservation strategies in Earth's largest biome.

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean.

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1-C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment.

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.

Tigriopus iranicus sp. nov., a new species of Harpacticidae (Copepoda, Crustacea) from Iran, with a redescription of T. raki Bradford, 1967.

The first representative of Tigriopus Norman, 1869 from the north-western Indian Ocean is described from rock pools on the Iranian coast. Tigriopus iranicus sp. nov. is distinguishable from its congeners by i) the possession of two maxillary endites, each with two setae; ii) a two-segmented mandibular endopod; iii) P1enp-3 with one pinnate claw, a well-developed geniculate spine and a small seta; and iv) female P6 with two setae. Additionally, we present a complete redescription of Tigriopus raki Bradford, 1967 on the basis of paratype material and a key to the species of the genus.

A new species of Psammonitocrella Huys, 2009 (Copepoda, Harpacticoida, Ameiridae) from California (USA), with a discussion of the relationship between Psammonitocrella and Parastenocarididae.

The freshwater harpacticoid Psammonitocrella kumeyaayi sp. nov. from the Nearctic Region (California; USA) is proposed. The position of the genus within Harpacticoida and its relationship with the Parastenocarididae is discussed. The new species can be included within Psammonitocrella on account of a) the cylindrical furca, longer than the telson, b) the unmodified inner spine on the basis of the male first leg, c) loss of the outer spine on the second exopodal segment of the first leg, d) loss of the outer spine of the third exopodal segment of the second, third, and fourth legs, e) loss of the inner apical seta on the third exopodal segment of the second and third legs, f) transformation of the inner apical seta of the third exopodal segment of the fourth leg into a spine, and g) loss of the endopodite of the fourth leg. The new species differs remarkably from P. boultoni, and P. longifurcata in the loss of the outer spine of the second exopodal segment of the fourth leg, in the presence of a one-segmented fifth leg exopodite, and in the presence of an outer seta on the basis of the first and second legs. Both Psammonitocrella and the known species of Parastenocarididae have a one-segmented endopod on the fourth leg, and the endopods of the second and third legs are reduced to one or two segments. Psammonitocrella is currently allocated into the Ameiridae, and evidence suggesting a sister-group relationship with Parastenocarididae-both share the loss of the inner seta on the first endopodal segment of the first leg-indicates that the Parastenocarididae should be included into the Ameiridae. In an evolutionary context, Parastenocarididae could have evolved from a lineage of freshwater ameirids that became interstitial in continental waters and colonized aquifers and groundwaters.

Retraction Note: Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda).

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72330-x.

Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida).

In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.

Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field.

The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain.

Publisher Correction: Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Traditional and confocal descriptions of a new genus and two new species of deep water Cerviniinae Sars, 1903 from the Southern Atlantic and the Norwegian Sea: with a discussion on the use of digital media in taxonomy (Copepoda, Harpacticoida, Aegisthidae).

Aegisthidae is one of the most abundant and diverse families of harpacticoid copepods living in deep-sea benthos, and the phylogenetic relationships within the family are in state of flux. Females of two new deep-water species of harpacticoid copepods belonging to the Hasegen. n. (Aegisthidae: Cerviniinae) are described. The first taxonomic description of marine copepod species based on the combined use of interference and confocal microscopy for the study of the habitus and dissected appendages is presented here. CLSM (Confocal Laser Scanning Microscopy) is a non-destructive method, comparable in quality to SEM (scanning electron microscopy) at the same magnifications. To observe and reconstruct in detail the habitus and dissected appendages, whole specimens and dissected parts were stained with Congo Red, mounted on slides with glycerine for CLSM and scanned under three visible-light lasers. Hase lagomorphicusgen. et sp. n. and Hase talpamorphicusgen. et sp. n. were collected from the sediments of the Southern Atlantic and the Norwegian Sea, from 2270 m and 5468 m depths, respectively. Hasegen. n. is included within Cerviniinae based on the caudal rami which are relatively divergent. Hasegen. n. is the sister taxon of Cerviniella based on the following synapomorphies: sturdy body, exopodites 1-3 of pereopods 1-3 heavily built, transformed into digging limbs, with strong outer and distal spines/setae, two-segmented endopod on the pereopods 2 and 3, and a reduced pereopod 5. Compared to Cerviniella, Hasegen. n. exhibits a more developed armature on the pereopod 1, which has outer and distal elements transformed into strong and long spines vs. stiff setae on Cerviniella.Hasegen. n. has one or two strong and long spines on the inner margin of the exopodite 3 of pereopod 4 and pereopod 5 is fused to the somite, ornamented with three distal setae. The telson of Hasegen. n. is subquadratic, and the furca is among the shortest yet described for Aegisthidae. The new species differ in a number of diagnostic characters, three of which are: a) the somite bearing pereopods 3 and 4 with latero-distal spiniform processes in H. talpamorphicusgen. et sp. n. but smooth in H. lagomorphicusgen. et sp. n., b) antenna is armed with three stout spines on the lateral inner margin of the exopod in H. talpamorphicusgen. et sp. n. and two proximal setae in H. lagomorphicusgen. et sp. n., and c) pereopod 4 exopodite 3 has two long and strong spines on the inner margin in H. lagomorphicusgen. et sp. n. and one spine in H. talpamorphicusgen. et sp. n. The high quality of CLSM images should foster discussion about the use of high quality digital images as type or as part of the type series in zoological studies, especially when studying rare and small macrofaunal and meiofaunal taxa.

Revision of the Remaneicaris argentina-group (Copepoda, Harpacticoida, Parastenocarididae): supplementary description of species, and description of the first semi-terrestrial Remaneicaris from the tropical forest of Southeast Mexico.

Remaneicaris is a species-rich Neotropical monophyletic group, easily recognized by the synapomorphic position of the outer seta of the third exopodite of leg 4, localized at 2/3 of the outer margin. The genus, comprising 35 species in five monophyletic groups, plus R. ignotus and R. meyerabichi, retains an unusual set of plesiomorphic characters. Herein we supplement the descriptions of the species belonging to the Remaneicaris argentina-group, and describe a new species from the tropical forest of Southeast Mexico. The present study extends the geographic distribution of the genus, with the northernmost record until now being from El Salvador. The genus having hitherto been known from interstitial groundwater habitats, this is its first record in epigean semi-terrestrial habitats. Remaneicaris siankaan sp. nov. was found in phytotelmata (bromeliads), leaf litter, moist soil, permanent ponds (known locally as "aguadas"), and temporal and permanent wetlands (savannahs). The new species can be easily characterized by its finely pitted cuticle, the ε (epsilon)-shaped thumb of the male P3 and the bifid accessory spine with distal hyaline inner tip, which precedes the thumb. A new method for the 3D reconstruction of microcrustaceans is described.

Biological responses to disturbance from simulated deep-sea polymetallic nodule mining.

Commercial-scale mining for polymetallic nodules could have a major impact on the deep-sea environment, but the effects of these mining activities on deep-sea ecosystems are very poorly known. The first commercial test mining for polymetallic nodules was carried out in 1970. Since then a number of small-scale commercial test mining or scientific disturbance studies have been carried out. Here we evaluate changes in faunal densities and diversity of benthic communities measured in response to these 11 simulated or test nodule mining disturbances using meta-analysis techniques. We find that impacts are often severe immediately after mining, with major negative changes in density and diversity of most groups occurring. However, in some cases, the mobile fauna and small-sized fauna experienced less negative impacts over the longer term. At seven sites in the Pacific, multiple surveys assessed recovery in fauna over periods of up to 26 years. Almost all studies show some recovery in faunal density and diversity for meiofauna and mobile megafauna, often within one year. However, very few faunal groups return to baseline or control conditions after two decades. The effects of polymetallic nodule mining are likely to be long term. Our analyses show considerable negative biological effects of seafloor nodule mining, even at the small scale of test mining experiments, although there is variation in sensitivity amongst organisms of different sizes and functional groups, which have important implications for ecosystem responses. Unfortunately, many past studies have limitations that reduce their effectiveness in determining responses. We provide recommendations to improve future mining impact test studies. Further research to assess the effects of test-mining activities will inform ways to improve mining practices and guide effective environmental management of mining activities.

Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna.

Polymetallic nodule mining at abyssal depths in the Clarion Clipperton Fracture Zone (Eastern Central Pacific) will impact one of the most remote and least known environments on Earth. Since vast areas are being targeted by concession holders for future mining, large-scale effects of these activities are expected. Hence, insight into the fauna associated with nodules is crucial to support effective environmental management. In this study video surveys were used to compare the epifauna from sites with contrasting nodule coverage in four license areas. Results showed that epifaunal densities are more than two times higher at dense nodule coverage (>25 versus ≤10 individuals per 100 m(2)), and that taxa such as alcyonacean and antipatharian corals are virtually absent from nodule-free areas. Furthermore, surveys conducted along tracks from trawling or experimental mining simulations up to 37 years old, suggest that the removal of epifauna is almost complete and that its full recovery is slow. By highlighting the importance of nodules for the epifaunal biodiversity of this abyssal area, we urge for cautious consideration of the criteria for determining future preservation zones.

Bryozoans from RV Sonne deep-sea cruises SO 167 'Louisville' and SO 205 'Mangan'.

The German research vessel Sonne is operating in the Pacific, Southern and Indian Oceans. In the current stage of development in Pacific deep-sea mining projects, prior understanding of biodiversity patterns in the affected regions is one of the major research goals of the RV Sonne cruises. In the present study, nine bryozoan species are reported from the Equatorial East Pacific and the Kermadec-Tonga Ridge, collected during RV Sonne cruises SO 167 "Louisville" and SO 205 "Mangan", from 356-4007 m. Two new species, Raxifabia oligopora n. sp. and Opaeophora triangula n. sp., are described.

Ancient DNA complements microfossil record in deep-sea subsurface sediments.

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

Tantulocarida (Crustacea) from the Southern Ocean deep sea, and the description of three new species of Tantulacus Huys, Andersen & Kristensen, 1992.

During the expedition ANT XIX/3 meiofauna samples were collected from the German research vessel Polarstern near the Shackleton Fracture Zone. During sorting of the samples 86 tantulus larvae were found. Extensive examination of the larvae revealed a high diversity of tantulocaridans in the Southern Ocean deep sea (33 species). A remarkable proportion of these were new species of Tantulacus Huys, Andersen & Kristensen, 1992. The present paper reports the discovery of three new Antarctic tantulocarids which are referred to Tantulacus. The affiliation of T. longispinosus n. sp., T. karolae n. sp. and T. dieteri n. sp. to Tantulacus is straightforward: all representatives of the Tantulocarida are characterised by the presence of 1-2 slender setae on the endopod of the second to fifth thoracopods, but in none of the hitherto described genera, other than Tantulacus, are these elements modified. Tantulacus hoegi Huys, Andersen & Kristensen, 1992 and the three new species share the possession of a distal rigid spine on the endopod of the second to fifth thoracopods as a synapomorphy and thus can be readily distinguished from other tantulocaridans. This is the first record of free-living sediment-inhabiting tantulus larvae from this area, although this probably reflects the degree of undersampling.

Advances in taxonomy, ecology, and biogeography of Dirivultidae (copepoda) associated with chemosynthetic environments in the deep sea.

BACKGROUND: Copepoda is one of the most prominent higher taxa with almost 80 described species at deep-sea hydrothermal vents. The unique copepod family Dirivultidae with currently 50 described species is the most species rich invertebrate family at hydrothermal vents. METHODOLOGY/PRINCIPAL FINDINGS: We reviewed the literature of Dirivultidae and provide a complete key to species, and map geographical and habitat specific distribution. In addition we discuss the ecology and origin of this family. CONCLUSIONS/SIGNIFICANCE: Dirivultidae are only present at deep-sea hydrothermal vents and along the axial summit trough of midocean ridges, with the exception of Dirivultus dentaneus found associated with Lamellibrachia species at 1125 m depth off southern California. To our current knowledge Dirivultidae are unknown from shallow-water vents, seeps, whale falls, and wood falls. They are a prominent part of all communities at vents and in certain habitat types (like sulfide chimneys colonized by pompei worms) they are the most abundant animals. They are free-living on hard substrate, mostly found in aggregations of various foundation species (e.g. alvinellids, vestimentiferans, and bivalves). Most dirivultid species colonize more than one habitat type. Dirivultids have a world-wide distribution, but most genera and species are endemic to a single biogeographic region. Their origin is unclear yet, but immigration from other deep-sea chemosynthetic habitats (stepping stone hypothesis) or from the deep-sea sediments seems unlikely, since Dirivultidae are unknown from these environments. Dirivultidae is the most species rich family and thus can be considered the most successful taxon at deep-sea vents.