Challenging the paradigms of deep-sea ecology

Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis

BACKGROUND

The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.

RESULTS

The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.

CONCLUSIONS

These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

Comparative study of integrated bio-responses in deep-sea and nearshore mussels upon abiotic condition changes: Insight into distinct regulation and adaptation

Deep-sea mussels, one of the dominant species in most deep-sea ecosystems, have long been used as model organisms to investigate the adaptations and symbiotic relationships of deep-sea macrofauna under laboratory conditions due to their ability to survive under atmospheric pressure. However, the impact of additional abiotic conditions beyond pressure, such as temperature and light, on their physiological characteristics remains unknown. In this study, deep-sea mussels (Gigantidas platifrons) from cold seep of the South China Sea, along with nearshore mussels (Mytilus coruscus) from the East China Sea, were reared in unfavorable abiotic conditions for up to 8 days. Integrated biochemical indexes including antioxidant defense, immune ability and energy metabolism were investigated in the gill and digestive gland, while cytotoxicity was determined in hemocytes of both types of mussels. The results revealed mild bio-responses in two types of mussels in the laboratory, represented by the effective antioxidant defense with constant total antioxidant capability level and malondialdehyde content. There were also disparate adaptations in deep-sea and nearshore mussels. In deep-sea mussels, significantly increased immune response and energy reservation were observed in gills, together with the elevated cytotoxicity in hemocytes, implying the more severe biological adaptation was required, mainly due to the symbiotic bacteria loss under laboratory conditions. On the contrary, insignificant biological responses were exhibited in nearshore mussels except for the increased energy consumption, indicating the trade-off strategy to use more energy to deal with potential stress. Overall, this comparative study highlights the basal bio-responses of deep-sea and nearshore mussels out of their native environments, providing evidence that short-term culture of both mussels under easily achievable laboratory conditions would not dramatically alter their biological status. This finding will assist in broadening the application of deep-sea mussels as model organism in future research regardless of the specialized research equipment.

Marine macro-litter mass outweighs biomass in trawl catches along abyssal seafloors of Sardinia channel (Italy)

This study provides new insights onto spatial and temporal trends of seafloor macro-litter in the abyssal seafloor of Sardinian channel, in central western Mediterranean (Italy). Trawl surveys were conducted at depths between 884 and 1528 m, thus focusing on one of the least investigated marine environments. None of the considered sites was litter free, with plastics being numerically dominant (57% of items), followed by metal (11%) and glass (16%). Recorded densities and weight ranged between 49.9 and 499 items km-2 and 1.4 and 1052 kg km-2. In the most contaminated sites, the weight of the litter collected in nets represented up to nine times the biomass of benthic megafauna, and, overall, in 60% of hauls macro-litter mass outweighed the biomass collected. Moreover, we report that megafauna was observed to be more abundant in sites where macro-litter presence was more severe. More studies are needed to elucidate the nature of this correlation, with biota being more abundant in hotspots of accumulation of seafloor macro-litter.

Marine Science Can Contribute to the Search for Extra-Terrestrial Life

Life on our planet likely evolved in the ocean, and thus exo-oceans are key habitats to search for extraterrestrial life. We conducted a data-driven bibliographic survey on the astrobiology literature to identify emerging research trends with marine science for future synergies in the exploration for extraterrestrial life in exo-oceans. Based on search queries, we identified 2592 published items since 1963. The current literature falls into three major groups of terms focusing on (1) the search for life on Mars, (2) astrobiology within our Solar System with reference to icy moons and their exo-oceans, and (3) astronomical and biological parameters for planetary habitability. We also identified that the most prominent research keywords form three key-groups focusing on (1) using terrestrial environments as proxies for Martian environments, centred on extremophiles and biosignatures, (2) habitable zones outside of "Goldilocks" orbital ranges, centred on ice planets, and (3) the atmosphere, magnetic field, and geology in relation to planets' habitable conditions, centred on water-based oceans.

3D ocean assessments reveal that fisheries reach deep but marine protection remains shallow

The wave of new global conservation targets, the conclusion of the High Seas Treaty negotiations, and the expansion of extractive use into the deep sea call for a paradigm shift in ocean conservation. The current reductionist 2D representation of the ocean to set targets and measure impacts will fail at achieving effective biodiversity conservation. Here, we develop a framework that overlays depth realms onto marine ecoregions to conduct the first three-dimensional spatial analysis of global marine conservation achievements and fisheries footprint. Our novel approach reveals conservation gaps of mesophotic, rariphotic, and abyssal depths and an underrepresentation of high protection levels across all depths. In contrast, the 3D footprint of fisheries covers all depths, with benthic fishing occurring down to the lower bathyal and mesopelagic fishing peaking in areas overlying abyssal depths. Additionally, conservation efforts are biased towards areas where the lowest fishing pressures occur, compromising the effectiveness of the marine conservation network. These spatial mismatches emphasize the need to shift towards 3D thinking to achieve ocean sustainability.

Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes

The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.

Fungal Abundance and Diversity in the Mariana Trench, the Deepest Ecosystem on Earth

Hadal trenches host abundant and diversified benthic prokaryotic assemblages, but information on benthic fungi is still extremely limited. We investigated the fungal abundance and diversity in the Challenger Deep (at ca. 11,000 m depth) and the slope of the Mariana Trench in comparison with three sites of the adjacent abyssal plain. Our results indicate that trench sediments are a hotspot of fungal abundance in terms of the 18S rRNA gene copy number. The fungal diversity (as the number of amplicon sequence variants, ASVs) was relatively low at all sites (10-31 ASVs) but showed a high turnover diversity among stations due to the presence of exclusive fungal taxa belonging to Aspergillaceae, Trichosphaeriaceae, and Nectriaceae. Fungal abundance and diversity were closely linked to sediment organic matter content and composition (i.e., phytopigments and carbohydrates), suggesting a specialization of different fungal taxa for the exploitation of available resources. Overall, these findings provide new insights into the diversity of deep-sea fungi and the potential ecological role in trench sediments and pave the way for a better understanding of their relevance in one of the most extreme ecosystems on Earth.

Microbiomes respond predictably to built habitats on the seafloor

The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.

Predicting the distribution and abundance of abandoned, lost or discarded fishing gear (ALDFG) in the deep sea of the Azores (North Atlantic)

Abandoned, lost, or discarded fishing gear (ALDFG), represents a significant percentage of the global plastic pollution, currently considered one of the major sources from sea-based activities. However, there is still limited understanding of the quantities of ALDFG present on the seafloor and their impacts. In this study, data on the presence of ALDFG was obtained from a large archive of seafloor video footage (351 dives) collected by different imaging platforms in the Azores region over 15 years (2006-2020). Most ALDFG items observed in the images relate to the local bottom longline fishery operating in the region, and include longlines but also anchors, weights, cables and buoys. A generalized additive mixed model (GAMM) was used to predict the distribution and abundance of ALDFG over the seafloor within the limits of the Azores Exclusive Economic Zone (EEZ) using a suite of environmental and anthropogenic variables. We estimated an average of 113 ± 310 items km-2 (597 ± 756 per km-2 above 1000 m depth), which could imply that over 20 million ALDFG items are present on the deep seafloor of the Azores EEZ. The resulting model identified potential hotspots of ALDFG along the seabed, some of them located over sensitive benthic habitats, such as specific seamounts. In addition, the interactions between ALDFG and benthic organisms were also analysed. Numerous entanglements were observed with several species of large anthozoans and sponges. The use of predictive distribution modelling for ALDFG should be regarded as a useful tool to support ecosystem-based management, which can provide indirect information about fishing pressure and allow the identification of potential high-risk areas. Additional knowledge about the sources, amounts, fates and impacts of ALDFG will be key to address the global issue of plastic pollution and the effects of fishing on marine ecosystems.

Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts

Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.

Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment

The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.

High Microeukaryotic Diversity in the Cold-Seep Sediment

Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.

Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes)

To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507-16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.

A 104-Ma record of deep-sea Atelostomata (Holasterioda, Spatangoida, irregular echinoids) - a story of persistence, food availability and a big bang

Deep-sea macrobenthic body fossils are scarce due to the lack of deep-sea sedimentary archives in onshore settings. Therefore, hypothesized migrations of shallow shelf taxa into the deep-sea after phases of mass extinction (onshore-offshore pattern in the literature) due to anoxic events is not constrained by the fossil record. To resolve this conundrum, we investigated 1,475 deep-sea sediment samples from the Atlantic, Pacific and Southern oceans (water depth ranging from 200 to 4,700 m), providing 41,460 spine fragments of the crown group Atelostomata (Holasteroida, Spatangoida). We show that the scarce fossil record of deep-sea echinoids is in fact a methodological artefact because it is limited by the almost exclusive use of onshore fossil archives. Our data advocate for a continuous record of deep-sea Atelostomata back to at least 104 Ma (late early Cretaceous), and literature records suggest even an older age (115 Ma). A gradual increase of different spine tip morphologies from the Albian to the Maastrichtian is observed. A subsequent, abrupt reduction in spine size and the loss of morphological inventory in the lowermost Paleogene is interpreted to be an expression of the "Lilliput Effect", related to nourishment depletion on the sea floor in the course of the Cretaceous-Paleogene (K-Pg) Boundary Event. The recovery from this event lasted at least 5 Ma, and post-K-Pg Boundary Event assemblages progress-without any further morphological breaks-towards the assemblages observed in modern deep-sea environments. Because atelostomate spine morphology is often species-specific, the variations in spine tip morphology trough time would indicate species changes taking place in the deep-sea. This observation is, therefore, interpreted to result from in-situ evolution in the deep-sea and not from onshore-offshore migrations. The calculation of the "atelostomate spine accumulation rate" (ASAR) reveals low values in pre-Campanian times, possibly related to high remineralization rates of organic matter in the water column in the course of the mid-Cretaceous Thermal Maximum and its aftermath. A Maastrichtian cooling pulse marks the irreversible onset of fluctuating but generally higher atelostomate biomass that continues throughout the Cenozoic.

A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis)

Understanding of adaptation and evolution of organisms in the deep sea requires more genomic resources. Zoroaster cf. ophiactis is a sea star in the family Zoroasteridae occurring exclusively in the deep sea. In this study, a chromosome-level genome assembly for Z. cf. ophiactis was generated by combining Nanopore long-read, Illumina short-read, and Hi-C sequencing data. The final assembly was 1,002.0 Mb in length, with a contig N50 of 376 Kb and a scaffold N50 of 40.4 Mb, and included 22 pseudo-chromosomes, covering 92.3% of the assembly. Completeness analysis evaluated with BUSCO revealed that 95.91% of the metazoan conserved genes were complete. Additionally, 39,426 protein-coding genes were annotated for this assembly. This chromosome-level genome assembly represents the first high-quality genome for the deep-sea Asteroidea, and will provide a valuable resource for future studies on evolution and adaptation of deep-sea echinoderms.

Stressors of emerging concern in deep-sea environments: microplastics, pharmaceuticals, personal care products and deep-sea mining

Although most deep-sea areas are remote in comparison to coastal zones, a growing body of literature indicates that many sensitive ecosystems could be under increased stress from anthropogenic sources. Among the multiple potential stressors, microplastics (MPs), pharmaceuticals and personal care products (PPCPs/PCPs) and the imminent start of commercial deep-sea mining have received increased attention. Here we review recent literature on these emerging stressors in deep-sea environments and discuss cumulative effects with climate change associated variables. Importantly, MPs and PPCPs have been detected in deep-sea waters, organisms and sediments, in some locations in comparable levels to coastal areas. The Atlantic Ocean and the Mediterranean Sea are the most studied areas and where higher levels of MPs and PPCPs have been detected. The paucity of data for most other deep-sea ecosystems indicates that many more locations are likely to be contaminated by these emerging stressors, but the absence of studies hampers a better assessment of the potential risk. The main knowledge gaps in the field are identified and discussed, and future research priorities are highlighted to improve hazard and risk assessment.

Intra- and Interspecific Foraging and Feeding Interactions in Three Sea Stars and a Gastropod from the Deep Sea

Competitive interactions come in a variety of forms and may be modulated by the size and number of individuals involved, and/or the resources available. Here, intra- and interspecific competitive behaviours for food (i.e., foraging/food search and feeding/food ingestion) were experimentally characterized and quantified in four co-existing deep-sea benthic species. Three sea stars (Ceramaster granularis, Hippasteria phrygiana, and Henricia lisa) and one gastropod (Buccinum scalariforme) from the bathyal Northwest Atlantic were investigated using video trials in darkened laboratory conditions. A range of competitive or cooperative behaviours occurred, depending on species (conspecific or heterospecific), comparative body size, and the number of individuals involved. Contrary to expectations, small individuals (or smaller species) were not always outcompeted by larger individuals (or larger species) when foraging and feeding. Moreover, faster species did not always outcompete slower ones while scavenging. Overall, this study sheds new light on scavenging strategies of co-existing deep-sea benthic species in food-limited bathyal environments, based on complex behavioural inter- and intraspecific relationships.

Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

Hadal trenches are perceived as a unique deep-sea ecosystem with fundamentally different communities compared to the nearby abyss. So far, however, scarce information exists about how populations are genetically linked within a trench and about mechanisms for species divergence. The present study presents the morphological and molecular-genetic characterization and description of a new nannoniscid species within the genus Austroniscus Vanhöffen, 1914 obtained from abyssal and hadal depths of the Puerto Rico Trench, NW Atlantic. Samples were collected as part of the Vema-TRANSIT expedition onboard RV Sonne in January 2015. Because of the large depth differences between sampling locations (4,552-8,338 m), we expected to find different species within the genus inhabiting abyssal and hadal sites. Initial morphological examination using traditional light microscopy and Confocal Laser Scanning Microscopy was paired with subsequent molecular analysis based on mtDNA (COI and 16S). Contrary to our assumptions, combined morphological and molecular species delimitation analyses (sGMYC, mPTP, ABGD) revealed the presence of only one species spanning the abyssal and hadal seafloor of the Puerto Rico Trench. In addition, comparison with type material could show that this species belongs to a new species, Austroniscus brandtae n. sp., which is described herein. Incongruence between some species delimitation methods suggesting the presence of multiple species is interpreted as strong genetic population structuring within the trench, which is also supported by the analysis of the haplotype networks. The geographic and bathymetric distribution of Austroniscus species is discussed. The species described herein represents the first in the genus Austroniscus from the Atlantic Ocean and the deepest record of the genus to date, and hence significantly expanding previously known limits of its geographic and bathymetric range.

Reduced efficiency of pelagic-benthic coupling in the Arctic deep sea during lower ice cover

Pelagic-benthic coupling describes the connection between surface-water production and seafloor habitats via energy, nutrient and mass exchange. Massive ice loss and warming in the poorly studied Arctic Chukchi Borderland are hypothesized to affect this coupling. The strength of pelagic-benthic coupling was compared between 2 years varying in climate settings, 2005 and 2016, based on δ¹³C and δ¹⁵N stable isotopes of food-web end-members and pelagic and deep-sea benthic consumers. Considerably higher isotopic niche overlap and generally shorter isotopic distance were found between pelagic and benthic food web components in 2005 than in 2016, suggesting weaker coupling in the latter, low-ice year. δ¹⁵N values indicated more refractory food consumed by benthos in 2016 and fresher food reaching the seafloor in 2005. Higher δ¹³C values of zooplankton indirectly suggested a higher contribution of ice algae in 2005 than 2016. The difference in pelagic-benthic coupling between these years is consistent with higher energy retention within the pelagic system, perhaps due to strong stratification in the Amerasian Basin in the recent decade. Weaker coupling to the benthos can be expected to continue with ice loss in the study area, perhaps reducing benthic biomass and remineralization capacity; monitoring of the area is needed to confirm this prediction.

Selection in coral mitogenomes, with insights into adaptations in the deep sea

Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean's surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject to selection pressures at greater depths to meet the metabolic demands of that environment. Here, we use a phylogenomic framework combined with codon-based models to evaluate whether mt protein-coding genes (PCGs) associated with cellular energy functions are under positive selection across depth in three groups of corals: Octocorallia, Scleractinia, and Antipatharia. The results demonstrated that mt PCGs of deep- and shallow-water species of all three groups were primarily under strong purifying selection (0.0474 < ω < 0.3123), with the exception of positive selection in atp6 (ω = 1.3263) of deep-sea antipatharians. We also found evidence for positive selection at fifteen sites across cox1, mtMutS, and nad1 in deep-sea octocorals and nad3 of deep-sea antipatharians. These results contribute to our limited understanding of mt adaptations as a function of depth and provide insight into the molecular response of corals to the extreme deep-sea environment.

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.

Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding

Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.

Deep-sea organisms research oriented by deep-sea technologies development

Deep-sea environment, characterized by high pressures, extremely high/low temperatures, limited photosynthesis-generated organic matter, darkness, and high levels of corrosion, is home to flourishing special ecosystems in the world. Here, we illustrate how the deep-sea equipment offers insights into the study of life in the deep sea based on the work in the past five decades. We first describe how organisms in the deep sea are studied, even though it is highly difficult to get access to such extreme environments. We then explain the role of deep-sea technologies in advancing research on the evolution of organisms in hydrothermal vents, cold seeps, seamounts, oceanic trenches, and whale falls from the following perspectives: biological diversity, mechanisms of environmental adaptation, biological evolution, and ecosystem connectivity. Finally, to better understand the function and service of deep-sea organisms, and further conserve the special creatures under anthropologic activity and climate change, we highlight the importance of innovative deep-sea technologies to promote cutting-edge research on deep-sea organisms, and note the remaining challenges and developing directions for deep-sea equipment.

Habitat variability and faunal zonation at the Ægir Ridge, a canyon-like structure in the deep Norwegian Sea

The Ægir Ridge System (ARS) is an ancient extinct spreading axis in the Nordic seas extending from the upper slope east of Iceland (∼550 m depth), as part of its Exclusive Economic Zone (EEZ), to a depth of ∼3,800 m in the Norwegian basin. Geomorphologically a rift valley, the ARS has a canyon-like structure that may promote increased diversity and faunal density. The main objective of this study was to characterize benthic habitats and related macro- and megabenthic communities along the ARS, and the influence of water mass variables and depth on them. During the IceAGE3 expedition (Icelandic marine Animals: Genetics and Ecology) on RV Sonne in June 2020, benthic communities of the ARS were surveyed by means of a remotely-operated vehicle (ROV) and epibenthic sledge (EBS). For this purpose, two working areas were selected, including abyssal stations in the northeast and bathyal stations in the southwest of the ARS. Video and still images of the seabed were usedtoqualitatively describebenthic habitats based on the presence of habitat-forming taxa and the physical environment. Patterns of diversity and community composition of the soft-sediment macrofauna, retrieved from the EBS, were analyzed in a semiquantitative manner. These biological data were complemented by producing high-resolution bathymetric maps using the vessel's multi-beam echosounder system. As suspected, we were able to identify differences in species composition and number of macro- and megafaunal communities associated with a depth gradient. A biological canyon effect became evident in dense aggregates of megafaunal filter feeders and elevated macrofaunal densities. Analysis of videos and still images from the ROV transects also led to the discovery of a number ofVulnerable Marine Ecosystems (VMEs) dominated by sponges and soft corals characteristic of the Arctic region. Directions for future research encompass a more detailed, quantitative study of the megafauna and more coherent sampling over the entire depth range in order to fully capture the diversity of the habitats and biota of the region. The presence of sensitive biogenic habitats, alongside seemingly high biodiversity and naturalness are supportive of ongoing considerations of designating part of the ARS as an "Ecologically and Biologically Significant Area" (EBSA).

Sixth sense in the deep-sea: the electrosensory system in ghost shark Chimaera monstrosa

Animals that continually live in deep sea habitats face unique challenges and require adaptive specializations solutions in order to locate and identify food, predators, and conspecifics. The Ampullae of Lorenzini are specialized electroreceptors used by chondrichthyans for important biological functions. Ampullary organs of the ghost shark Chimaera monstrosa, a deep-sea species commonly captured as by-catch in the bottom trawl fishery, are here described for the first time using macroscopic, ultrastructural and histological approaches. The number of ampullary pores in C. monstrosa is about 700, distributed into the whole cephalic section of C. monstrosa, and organized in12 pore clusters and they are arranged into different configurations and form a distinct morphological pattern for this species, showing some anatomical peculiarities never described before in others cartilaginous fishes and may constitute an evolutionary adaptation of this ancient chondrichthyan species to the extreme environmental conditions of its deep sea niche.

Deep seabed mining and communities: A transdisciplinary approach to ecological risk assessment in the South Pacific

Deep-sea mineral extraction is a fledgling industry whose guiding principles, legislation, protocols, and regulations are still evolving. Responsible management of the industry is difficult when it is not clearly understood what biological and environmental diversity or ecosystem services may be at risk. But the industry's infancy provides an opportunity to address this challenge by stakeholder-led development and implementation of a multidisciplinary risk assessment framework. This article aims to present the findings of a workshop held in New Zealand that hosted stakeholders from a broad range of interests and regions in the South Pacific associated with the deep-sea mineral activity. The outputs provide stakeholder-informed ecological risk assessment approaches for deep-sea mining activities, identifying tools and techniques to improve the relevance of risk assessment of deep seabed mining projects to communities in the South Pacific. Discussions highlighted the importance of trust or respect among stakeholders, valuing the "life force" of the ocean, the importance of scientific data, and the complications associated with defining acceptable change. This research highlighted the need for a holistic transdisciplinary approach that connects science, management, industry, and community, an approach most likely to provide a "social license" to operate. There is also a need to revise traditional risk assessment methods to make them more relevant to stakeholders. The development of ecotoxicological tools and approaches is an example of how existing practices could be improved to better support deep-sea mineral management. A case study is provided that highlights the current challenges within the legislative framework of New Zealand. Integr Environ Assess Manag 2022;18:664-673. © 2021 SETAC.

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

Simple Summary

SAR324, newly proposed as its own candidate phylum, is a diverse and globally abundant bacterial group living in a wide range of environments, from deep-sea hydrothermal vents and brine pools to the epipelagic regions of the global oceans and terrestrial aquifers. The different SAR324 clades harbor a diverse array of genes and pathways well adapted to their respective environments. This metabolic flexibility explains the ubiquitous presence and the importance of SAR324 in global biogeochemical cycles.

Abstract

The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin–Benson–Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.

Oxygen gradients shape the unique structure of picoeukaryotic communities in the Bay of Bengal

Picoeukaryotic communities respond rapidly to global climate change and play an important role in marine biological food webs and ecosystems. The formation of oxygen minimum zones (OMZ) is facilitated by the stratification of seawater and higher primary production in the surface layer, and the marine picoeukaryotic community this low-oxygen environment is topic of interest. To better understand the picoeukaryotic community assembly mechanisms in an OMZ, we collected samples from the Bay of Bengal (BOB) in October and November 2020 and used 18S rDNA to study the picoeukaryotic communities and their community assembly mechanisms that they are controlled by in deep-sea and hypoxic zones. The results show that deterministic and stochastic processes combine to shape picoeukaryotic communities in the BOB. We divided the water column into three vertical layers: the upper oxycline (UO), the OMZ, and the lower oxycline (LO), based on dissolved oxygen concentrations (dissolved oxygen: UO > LO > OMZ) at vertical depths (from 5 m to 2000 m). Deterministic processes controlled the picoeukaryotic community in the UO, while the picoeukaryotic communities in the OMZ and LO were dominated by stochastic processes. The OMZ had a stronger diffusional limitation and the habitat niche breadth in the UO was wider than that in OMZ and LO. We classified the picoeukaryotic community into three functional composition types (phototrophic, mixotrophic, and heterotrophic); heterotrophs were most abundant in the surveyed area, and the proportion of decreased significantly with increasing depth and decreasing dissolved oxygen. The picoeukaryotes in the investigated area also correlated with temperature, salinity, and nutrients (phosphate, silicate, nitrate, nitrite, and ammonium). These findings contribute to a better understanding of picoeukaryotic communities in deep-sea and low-oxygen environments, their functional structuring, as well as the effects of environmental changes on their community structure.

The First Deep-Sea Stylasterid (Hydrozoa, Stylasteridae) of the Red Sea

The Stylasteridae, commonly known as lace corals, is a family of colonial calcifying hydrozoans mostly inhabiting deep waters. Stylasterids show a cosmopolitan distribution but, in some areas, they are characterized by low species diversity, such as in the Red Sea, where only a shallow-water species has been reported so far. With this work, we provide the first evidence of a deep-sea stylasterid inhabiting the NEOM region in the northern Saudi Arabian Red Sea, at depths ranging between 166 and 492 m. Morphological examinations revealed that this species was previously unknown and belonging to the genus Stylaster. We, therefore, describe Stylaster tritoni sp. nov., representing the first record of the genus in the Red Sea. Lastly, the phylogenetic position of the species within the Stylasteridae was evaluated, revealing a close relationship with shallow-water Indo-Pacific and Western Atlantic Stylaster species and confirming the polyphyletic nature of the genus Stylaster.

Challenges in eDNA detection of the invasive European green crab, Carcinus maenas

The early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.

Intra- and inter-spatial variability of meiofauna in hadal trenches is linked to microbial activity and food availability

Hadal trenches are depocenters for organic material, and host intensified benthic microbial activity. The enhanced deposition is presumed to be reflected in elevated meiofaunal standing-stock, but available studies are ambiguous. Here, we investigate the distribution of meiofauna along the Atacama Trench axis and adjacent abyssal and bathyal settings in order to relate the meiofauna densities to proxies for food availability. Meiofauna densities peaked at the sediment surface and attenuated steeply with increasing sediment depth. The distribution mirrored the vertical profile of the microbial-driven oxygen consumption rate demonstrating a close linkage between microbial activity and meiofauna density. Meiofaunal standing-stock along the trench axis varied by a factor of two, but were markedly higher than values from the abyssal site at the oceanic plate. Overall, meiofaunal densities poorly correlated with common proxies for food availability such as total organic carbon and phytopigments, but strongly correlated with the microbial benthic O₂ consumption rate. We argue that microbial biomass likely represents an important meiofaunal food source for hadal meiofauna. Observations from three trench systems underlying surface water of highly different productivity confirmed elevated meiofaunal densities at the trench axis as compared to abyssal sites on oceanic plates. Food availability appear to drive elevated abundance and variations in meiofauna densities in hadal sediments.

Management and Sustainable Exploitation of Marine Environments through Smart Monitoring and Automation

Monitoring of aquatic ecosystems has been historically accomplished by intensive campaigns of direct measurements (by probes and other boat instruments) and indirect extensive methods such as aero-photogrammetry and satellite detection. These measurements characterized the research in the last century, with significant but limited improvements within those technological boundaries. The newest advances in the field of smart devices and increased networking capabilities provided by emerging tools, such as the Internet of Things (IoT), offer increasing opportunities to provide accurate and precise measurements over larger areas. These perspectives also correspond to an increasing need to promptly respond to frequent catastrophic impacts produced by drilling stations and intense transportation activities of dangerous materials over ocean routes. The shape of coastal ecosystems continuously varies due to increasing anthropic activities and climatic changes, aside from touristic activities, industrial impacts, and conservation practices. Smart buoy networks (SBNs), autonomous underwater vehicles (AUVs), and multi-sensor microsystems (MSMs) such as smart cable water (SCW) are able to learn specific patterns of ecological conditions, along with electronic “noses”, permitting them to set innovative low-cost monitoring stations reacting in real time to the signals of marine environments by autonomously adapting their monitoring programs and eventually sending alarm messages to prompt human intervention. These opportunities, according to multimodal scenarios, are dramatically changing both the coastal monitoring operations and the investigations over large oceanic areas by yielding huge amounts of information and partially computing them in order to provide intelligent responses. However, the major effects of these tools on the management of marine environments are still to be realized, and they are likely to become evident in the next decade. In this review, we examined from an ecological perspective the most striking innovations applied by various research groups around the world and analyzed their advantages and limits to depict scenarios of monitoring activities made possible for the next decade.

Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation

The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.

Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica)

Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g−1) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants−ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes.

Role of deep-sea equipment in promoting the forefront of studies on life in extreme environments

The deep-sea environment creates the largest ecosystem in the world with the largest biological community and extensive undiscovered biodiversity. Nevertheless, these ecosystems are far from well known. Deep-sea equipment is an indispensable approach to research life in extreme environments in the deep-sea environment because of the difficulty in obtaining access to these unique habitats. This work reviewed the historical development and the state-of-the-art of deep-sea equipment suitable for researching extreme ecosystems, to clarify the role of this equipment as a promoter for the progress of life in extreme environmental studies. Linkages of the developed deep-sea equipment and the discovered species are analyzed in this study. In addition, Equipment associated with researching the deep-sea ecosystems of hydrothermal vents, cold seeps, whale falls, seamounts, and oceanic trenches are introduced and analyzed in detail. To clarify the thrust and key points of the future promotion of life in extreme environmental studies, prospects and challenges related to observing equipment, samplers, laboratory simulation systems, and submersibles are proposed. Furthermore, a blueprint for the integration of in situ observations, sampling, controllable culture, manned experiments in underwater environments, and laboratory simulations is depicted for future studies.

A Treasure of Bioactive Compounds from the Deep Sea

The deep-sea environment is a unique, challenging extreme habitat where species have had to adapt to the absence of light, low levels of oxygen, high pressure and little food. In order to survive such harsh conditions, these organisms have evolved different biochemical and physiological features that often have no other equivalent in terrestrial habitats. Recent analyses have highlighted how the deep sea is one of the most diverse and species-rich habitats on the planet but less explored compared to more accessible sites. Because of their adaptation to this extreme environment, deep-sea species have the potential to produce novel secondary metabolites with potent biological activities. Recent advances in sampling and novel techniques in microorganism culturing and chemical isolation have promoted the discovery of bioactive agents from deep-sea organisms. However, reports of natural products derived from deep-sea species are still scarce, probably because of the difficulty in accessing deep-sea samples, sampling costs and the difficulty in culturing deep-sea organisms. In this review, we give an overview of the potential treasure represented by metabolites produced by deep marine species and their bioactivities for the treatment and prevention of various human pathologies.

Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu

The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.

Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.

Biological and Ecological Aspects of the Blackmouth Catshark (Galeus melastomus Rafinesque, 1810) in the Southern Tyrrhenian Sea

Data on the biology and ecology of Galeus melastomus are old/absent for the Southern Tyrrhenian Sea, despite there being numerous studies in the wider area. A total of 127 specimens of G. melastomus from the southern Tyrrhenian Sea, collected in 2018–2019 using trawling nets, were analyzed to investigate size at sexual maturity, sex ratio, length–weight relationships, and feeding habits. To our best knowledge, this is the first time in which all these features were investigated in the Southern Tyrrhenian Sea for G. melastomus. The stomach content analysis showed that G. melastomus had intermediate feeding habits, preying on a great variety of species, especially Cephalopoda, Osteichthyes, and Crustacea. The Levin’s index value (Bi) was 0.53. Sex ratio was 0.92:1, with females slightly more abundant and bigger than males. The results also showed a decrease (33.7 cm for females, 31.1 cm for males) in length at 50% maturity (L50). This could be a result of anthropogenic stressors, such as overfishing and/or and environmental changes, which can induce physiological responses in several species. Our results highlighted the differences related to sexual maturity, growth, and feeding habits of the blackmouth catshark in the studied area, providing reference data to allow comparison with future studies on this species adaptations to this and other deep-sea areas in the Mediterranean Sea.

Underwater Hyperspectral Imaging (UHI): A Review of Systems and Applications for Proximal Seafloor Ecosystem Studies

Marine ecosystem monitoring requires observations of its attributes at different spatial and temporal scales that traditional sampling methods (e.g., RGB imaging, sediment cores) struggle to efficiently provide. Proximal optical sensing methods can fill this observational gap by providing observations of, and tracking changes in, the functional features of marine ecosystems non-invasively. Underwater hyperspectral imaging (UHI) employed in proximity to the seafloor has shown a further potential to monitor pigmentation in benthic and sympagic phototrophic organisms at small spatial scales (mm–cm) and for the identification of minerals and taxa through their finely resolved spectral signatures. Despite the increasing number of studies applying UHI, a review of its applications, capabilities, and challenges for seafloor ecosystem research is overdue. In this review, we first detail how the limited band availability inherent to standard underwater cameras has led to a data analysis “bottleneck” in seafloor ecosystem research, in part due to the widespread implementation of underwater imaging platforms (e.g., remotely operated vehicles, time-lapse stations, towed cameras) that can acquire large image datasets. We discuss how hyperspectral technology brings unique opportunities to address the known limitations of RGB cameras for surveying marine environments. The review concludes by comparing how different studies harness the capacities of hyperspectral imaging, the types of methods required to validate observations, and the current challenges for accurate and replicable UHI research.

Abyssal deposit feeders are secondary consumers of detritus and rely on nutrition derived from microbial communities in their guts

Trophic ecology of detrital-based food webs is still poorly understood. Abyssal plains depend entirely on detritus and are among the most understudied ecosystems, with deposit feeders dominating megafaunal communities. We used compound-specific stable isotope ratios of amino acids (CSIA-AA) to estimate the trophic position of three abundant species of deposit feeders collected from the abyssal plain of the Northeast Pacific (Station M; ~ 4000 m depth), and compared it to the trophic position of their gut contents and the surrounding sediments. Our results suggest that detritus forms the base of the food web and gut contents of deposit feeders have a trophic position consistent with primary consumers and are largely composed of a living biomass of heterotrophic prokaryotes. Subsequently, deposit feeders are a trophic level above their gut contents making them secondary consumers of detritus on the abyssal plain. Based on δ¹³C values of essential amino acids, we found that gut contents of deposit feeders are distinct from the surrounding surface detritus and form a unique food source, which was assimilated by the deposit feeders primarily in periods of low food supply. Overall, our results show that the guts of deposit feeders constitute hotspots of organic matter on the abyssal plain that occupy one trophic level above detritus, increasing the food-chain length in this detritus-based ecosystem.

The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers

The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

An integrated approach of Ecological Footprint (EF) and Analytical Hierarchy Process (AHP) in human ecology: A base for planning toward sustainability

Environmental challenges to natural resources have been attributed to human behavior and traditional agricultural production techniques. Natural resource degradation in agriculture has always been a prime concern in agro ecological research and sustainability analysis. There are many techniques for assessing environmental performance; one of which, ecological footprint (EF), assesses human pressure on the environment and natural resources. The main purpose of this study was calculation of ecological indices including biocapacity (BC) and EF of rural areas of Fars province of Iran. The study was accomplished using survey and structured interviews consisting of three main questionnaires in two different steps. Different agricultural stakeholders, including farmers (for the first step) as well as the policymakers, extension managers and authorities (for the second step) were interviewed. Based on multi-stage stratified random sampling, 50 villages and 423 farmers were selected. Face validity and reliability of the questionnaires were assessed by a panel of specialists as well as conducting a pilot study, respectively. The paradigmatic perspectives of agricultural policy makers and managers (22 individuals) were also analyzed using another specific questionnaire by Analytical Hierarchy Process (AHP). Findings revealed that most of the studied villages faced a critical environmental condition due to the results of ecological indicator which was calculated in the study. According to the four main components of human ecology (POET model) including Population, Organization, Environment and Technology, village groups that differed in terms of sustainability level also showed significantly differences due to population, social participation, use of green technologies and attitude towards diverse environmental management paradigms. The causal model also revealed that population, green technology, social participation and attitude toward frontier economics, which were in accordance with the elements of human ecology model, were the main factors affecting the ecological index. Finally, AHP results determined the dominant economic perspectives of agricultural authorities. A paradigm shift toward the comprehensive paradigm of eco-development plus consideration of the results of the ecological indicator calculation as the base of agricultural planning at the local level were recommended.

A glimpse of deep-sea adaptation in chemosynthetic holobionts: Depressurization causes DNA fragmentation and cell death of methanotrophic endosymbionts rather than their deep-sea Bathymodiolinae host

Bathymodiolinae mussels are typical species in deep-sea cold seeps and hydrothermal vents and an ideal model for investigating chemosynthetic symbiosis and the influence of high hydrostatic pressure on deep-sea organisms. Herein, the potential influence of depressurization on DNA fragmentation and cell death in Bathymodiolinae hosts and their methanotrophic symbionts were surveyed using isobaric and unpressurized samples. As a hallmark of cell death, massive DNA fragmentation was observed in methanotrophic symbionts from unpressurized Bathymodiolinae while several endonucleases and restriction enzymes were upregulated. Additionally, genes involved in DNA repair, glucose/methane metabolism as well as two-component regulatory system were also differentially expressed in depressurized symbionts. DNA fragmentation and programmed cell death, however, were rarely detected in the host bacteriocytes owing to the orchestrated upregulation of inhibitor of apoptosis genes and downregulation of caspase genes. Meanwhile, diverse host immune recognition receptors were promoted during depressurization, probably enabling the regain of symbionts. When the holobionts were subjected to a prolonged acclimation at atmospheric pressure, alternations in both the DNA fragmentation and the expression atlas of aforesaid genes were continuously observed in symbionts, demonstrating the persistent influence of depressurization. Contrarily, the host cells demonstrated certain tolerance against depressurization stress as expression level of some immune-related genes returned to the basal level in isobaric samples. Altogether, the present study illustrates the distinct stress responses of Bathymodiolinae hosts and their methanotrophic symbionts against depressurization, which could provide further insight into the deep-sea adaptation of Bathymodiolinae holobionts while highlighting the necessity of using isobaric sampling methods in deep-sea research.

Governing deep sea mining in the face of uncertainty

Progress towards deep sea mining (DSM) is driven by projected demands for metals and the desire for economic development. DSM remains controversial, with some political leaders calling for a moratorium on DSM pending further research into its impacts. This paper highlights the need for governance architectures that are tailored to DSM. We conceptualise DSM as a type of complex orebody, which encompasses the breadth of environmental, social and governance (ESG) risks that make a mineral source complex. Applying a spatial overlay approach, we show that there are significant data gaps in understanding the ESG risks of DSM. Such uncertainties are compounded by fact that there are no extant commercial DSM projects to function as a precedent - either in terms of project design, or the impacts of design on environment and people. Examining the legislation of the Cook Islands and International Seabed Authority, we demonstrate how regulators are defaulting to terrestrial mining governance architectures, which cannot be meaningfully implemented until a fuller understanding of the ESG risk landscape is developed. We argue that DSM be approached as a distinct extractive industry type, and governed with its unique features in frame.