1
|
Williams R, Cox KD, Amon D, Ashe E, Chapuis L, Erbe C, de Vos A, Nielsen KA, Collins MS, Smith C, Washburn T, Young KF, Clark CW. Noise from deep-sea mining in the Clarion-Clipperton Zone, Pacific Ocean will impact a broad range of marine taxa. MARINE POLLUTION BULLETIN 2025; 218:118135. [PMID: 40381439 DOI: 10.1016/j.marpolbul.2025.118135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Revised: 05/07/2025] [Accepted: 05/08/2025] [Indexed: 05/20/2025]
Abstract
Deep-sea mining activities in the Clarion-Clipperton Zone (CCZ), Pacific Ocean, are expected to generate continuous noise pollution across multiple depth zones, with potential impacts on biodiversity. Impact studies have primarily focused on sediment plumes and habitat destruction, leaving consequences of industrial-scale deep-sea mining noise largely unexplored. Many marine taxa, including invertebrates, fish, and mammals, rely on sound for communication, navigation, and predator avoidance. Our systematic literature review highlights that noise sensitivity is widespread across taxa, yet only 35 % of taxonomic classes known in the CCZ have been studied for noise impacts. Soniferous fish, which rely on acoustic communication, are particularly vulnerable to noise. Chronic exposure to mining noise may have cascading ecological consequences, disrupting key behaviors and physiological processes in an environment characterized by low anthropogenic stressors. By identifying knowledge gaps and quantifying taxa likely to be vulnerable to industrial noise, this review provides the foundation to guide evidence-based management required to safeguard deep-sea ecosystems. Given the uncertainty surrounding deep-sea biotic responses to prolonged noise exposure, we emphasize the urgent need for a transparent transfer of knowledge on noise characteristics of deep-sea mining. These data are essential for assessing risks from mining noise to species, communities, and ecosystem functions and services.
Collapse
Affiliation(s)
- Rob Williams
- Oceans Initiative, 117 E. Louisa St. #135, Seattle, WA 98102, USA.
| | - Kieran D Cox
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Diva Amon
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, USA; SpeSeas, D'Abadie, Trinidad and Tobago
| | - Erin Ashe
- Oceans Initiative, 117 E. Louisa St. #135, Seattle, WA 98102, USA
| | - Lucille Chapuis
- School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia
| | - Christine Erbe
- Centre for Marine Science and Technology, Curtin University, Perth, WA 6102, Australia
| | - Asha de Vos
- Oceanswell, Colombo 7, Sri Lanka and the University of Western Australia Oceans Institute, Crawley, WA 6009, Australia
| | | | | | - Craig Smith
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI 96822, United States of America
| | - Travis Washburn
- Department of Physical and Environmental Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA
| | - Kirsten F Young
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Devon, United Kingdom
| | - Christopher W Clark
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell University (Emeritus), Ithaca, NY 14850, USA
| |
Collapse
|
2
|
Bell KLC, Johannes KN, Kennedy BRC, Poulton SE. How little we've seen: A visual coverage estimate of the deep seafloor. SCIENCE ADVANCES 2025; 11:eadp8602. [PMID: 40333982 PMCID: PMC12057672 DOI: 10.1126/sciadv.adp8602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 03/18/2025] [Indexed: 05/09/2025]
Abstract
Despite the importance of visual observation in the ocean, we have imaged a minuscule fraction of the deep seafloor. Sixty-six percent of the entire planet is deep ocean (≥200 m), and our data show that we have visually observed less than 0.001%, a total area approximately a tenth of the size of Belgium. Data gathered from approximately 44,000 deep-sea dives indicate that we have also seen an incredibly biased sample. Sixty-five percent of all in situ visual seafloor observations in our dataset were within 200 nm of only three countries: the United States, Japan, and New Zealand. Ninety-seven percent of all dives we compiled have been conducted by just five countries: the United States, Japan, New Zealand, France, and Germany. This small and biased sample is problematic when attempting to characterize, understand, and manage a global ocean.
Collapse
Affiliation(s)
| | - Kristen N. Johannes
- Ocean Discovery League, Saunderstown, RI 02874, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92037, USA
| | - Brian R. C. Kennedy
- Ocean Discovery League, Saunderstown, RI 02874, USA
- Biology Department, Boston University, Boston, MA 02215 USA
| | | |
Collapse
|
3
|
Montoya L, Escobar-Briones E. Unveiling the significance of prokaryotic composition from ferromanganese crusts regarding the interlink between cobalt and vitamin B 12 in deep-sea ecosystems. Front Microbiol 2025; 16:1524057. [PMID: 40365069 PMCID: PMC12069332 DOI: 10.3389/fmicb.2025.1524057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 04/14/2025] [Indexed: 05/15/2025] Open
Abstract
The intricate relationship between prokaryotic vitamin B12 (cobalamin) producers and metazoans in deep-sea ecosystems, particularly within ferromanganese crusts and polymetallic nodules, is critical for understanding oceanic biogeochemical cycling of cobalt. Microbial communities are key regulators of essential biogeochemical cycles, with cobalt serving as a vital component in the synthesis of cobalamin, a metallocofactor indispensable for numerous metabolic processes. We analyzed the significance of cobalamin biosynthetic pathways confined to prokaryotes and emphasized the ecological importance of auxotrophic organisms that rely on exogenous sources of vitamin B12. Additionally, we recognize recent research regarding the spatial distribution of dissolved cobalt and its consequential effects on cobalamin production and bioavailability, indicating the scarcity of cobalt and cobalamin in marine environments. We propose that cobalt-rich environments may foster unique interactions between prokaryotic and eukaryotic organisms, potentially altering the food web dynamics owing to the localized abundance of this element. By investigating the roles of cobalt and cobalamin in nutrient cycling and interspecies interactions, we outlined key criteria for future research on deep-sea microbial communities and their contributions to the cobalt biogeochemical cycle.
Collapse
Affiliation(s)
- Lilia Montoya
- Consejo Nacional de Humanidades, Ciencias y Tecnologías, Mexico City, Mexico
| | - Elva Escobar-Briones
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| |
Collapse
|
4
|
Jones DOB, Arias MB, Van Audenhaege L, Blackbird S, Boolukos C, Bribiesca-Contreras G, Copley JT, Dale A, Evans S, Fleming BFM, Gates AR, Grant H, Hartl MGJ, Huvenne VAI, Jeffreys RM, Josso P, King LD, Simon-Lledó E, Le Bas T, Norman L, O'Malley B, Peacock T, Shimmield T, Stewart ECD, Sweetman AK, Wardell C, Aleynik D, Glover AG. Long-term impact and biological recovery in a deep-sea mining track. Nature 2025:10.1038/s41586-025-08921-3. [PMID: 40139245 DOI: 10.1038/s41586-025-08921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 03/20/2025] [Indexed: 03/29/2025]
Abstract
Deep-sea polymetallic nodule mining is in the exploration phase at present with some groups proposing a move towards extraction within years1. Management of this industry requires evidence of the long-term effects on deep-sea ecosystems2, but the ability of seafloor ecosystems to recover from impacts over decadal scales is poorly understood3. Here we show that, four decades after a test mining experiment that removed nodules, the biological impacts in many groups of organisms are persistent, although populations of several organisms, including sediment macrofauna, mobile deposit feeders and even large-sized sessile fauna, have begun to re-establish despite persistent physical changes at the seafloor. We also reveal that areas affected by plumes from this small-scale test have limited detectable residual sedimentation impacts with some biological assemblages similar in abundance compared to control areas after 44 years. Although some aspects of the modern collector design may cause reduced physical impact compared to this test mining experiment, our results show that mining impacts in the abyssal ocean will be persistent over at least decadal timeframes and communities will remain altered in directly disturbed areas, despite some recolonization. The long-term effects seen in our study provide critical data for effective management of mining activities, if they occur, including minimizing direct impacts and setting aside an effective network of protected areas4,5.
Collapse
Affiliation(s)
| | | | | | - Sabena Blackbird
- School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Corie Boolukos
- Natural History Museum, Cromwell Road, South Kensington, London, UK
| | - Guadalupe Bribiesca-Contreras
- National Oceanography Centre, European Way, Southampton, UK
- Natural History Museum, Cromwell Road, South Kensington, London, UK
| | - Jonathan T Copley
- Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, UK
| | - Andrew Dale
- Scottish Association for Marine Science, Oban, Argyll, UK
| | - Susan Evans
- National Oceanography Centre, European Way, Southampton, UK
| | - Bethany F M Fleming
- National Oceanography Centre, European Way, Southampton, UK
- Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, UK
| | - Andrew R Gates
- National Oceanography Centre, European Way, Southampton, UK
| | - Hannah Grant
- British Geological Survey, The Lyell Centre, Research Avenue South, Edinburgh, UK
| | | | | | - Rachel M Jeffreys
- School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Pierre Josso
- British Geological Survey, The Lyell Centre, Research Avenue South, Edinburgh, UK
| | - Lucas D King
- Natural History Museum, Cromwell Road, South Kensington, London, UK
| | - Erik Simon-Lledó
- National Oceanography Centre, European Way, Southampton, UK
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Tim Le Bas
- National Oceanography Centre, European Way, Southampton, UK
| | - Louisa Norman
- School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | | | - Thomas Peacock
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tracy Shimmield
- British Geological Survey, The Lyell Centre, Research Avenue South, Edinburgh, UK
- Heriot-Watt University, Riccarton, Edinburgh, UK
| | - Eva C D Stewart
- Natural History Museum, Cromwell Road, South Kensington, London, UK
- Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, UK
| | | | - Catherine Wardell
- National Oceanography Centre, European Way, Southampton, UK
- Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, UK
| | - Dmitry Aleynik
- Scottish Association for Marine Science, Oban, Argyll, UK
| | - Adrian G Glover
- Natural History Museum, Cromwell Road, South Kensington, London, UK
| |
Collapse
|
5
|
Gastineau R, Mianowicz K, Dąbek P, Otis C, Stoyanova V, Krawcewicz A, Abramowski T. Genomic investigation of benthic invertebrates from the Clarion-Clipperton fields of polymetallic nodules. Zookeys 2025; 1231:11-44. [PMID: 40109892 PMCID: PMC11915014 DOI: 10.3897/zookeys.1231.135347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 01/21/2025] [Indexed: 03/22/2025] Open
Abstract
The abyssal plains of the Clarion-Clipperton Zone (CCZ) are famous for their fields of polymetallic nodules, which are inhabited by benthic invertebrates. Ten specimens from the Interoceanmetal Joint Organisation (IOM) licence area in the CCZ were collected in 2014 and submitted to a short-read genome skimming sequencing. In total, mitochondrial genomes and nuclear ribosomal genes were retrieved for nine different organisms belonging to Ophiuroidea, Holothuroidea, Polychaeta, Bryozoa, Porifera, and Brachiopoda (assigned to these phyla immediately upon retrieval from the seafloor). As many of these samples were partial and physically deteriorated following their seven-year storage in IOM's collections, their morphology-based taxonomic identification could rarely be performed at the lowest possible level (species or genus) prior to preparing the samples for molecular or genomic investigations. Therefore, it was not possible to apply the reverse identification scheme recommended for such investigations. However, several of these specimens represent poorly studied groups for which few molecular references are available as of now. In two cases, the presence of introns in the mitochondrial genome questions the practicability of using the cox1 gene for further routine molecular barcoding of these organisms. These results might be useful in future DNA primers design, molecular barcoding, and phylogeny or population genetic studies when more samples are obtained.
Collapse
Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, ul. Mickiewicza 16a, Szczecin, 70-383, Poland University of Szczecin Szczecin Poland
| | - Kamila Mianowicz
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, Poland Interoceanmetal Joint Organization Szczecin Poland
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, ul. Mickiewicza 16a, Szczecin, 70-383, Poland University of Szczecin Szczecin Poland
| | - Christian Otis
- Plateforme d'Analyse Génomique, Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada Université Laval Québec Canada
| | - Valcana Stoyanova
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, Poland Interoceanmetal Joint Organization Szczecin Poland
| | - Artur Krawcewicz
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, Poland Interoceanmetal Joint Organization Szczecin Poland
| | - Tomasz Abramowski
- Maritime University of Szczecin, ul. Wały Chrobrego 1-2, Szczecin, 70-500, Poland Maritime University of Szczecin Szczecin Poland
| |
Collapse
|
6
|
Yan Y, Seim I, Guo Y, Chi X, Zhong Z, Wang D, Li M, Wang H, Zhang H, Wang M, Li C. Degenerated vision, altered lipid metabolism, and expanded chemoreceptor repertoires enable Lindaspio polybranchiata to thrive in deep-sea cold seeps. BMC Biol 2025; 23:13. [PMID: 39806408 PMCID: PMC11730519 DOI: 10.1186/s12915-025-02112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Lindaspio polybranchiata, a member of the Spionidae family, has been reported at the Lingshui Cold Seep, where it formed a dense population around this nascent methane vent. We sequenced and assembled the genome of L. polybranchiata and performed comparative genomic analyses to investigate the genetic basis of adaptation to the deep sea. Supporting this, transcriptomic and fatty acid data further corroborate our findings. RESULTS We report the first genome of a deep-sea spionid, L. polybranchiata. Over long-term adaptive evolution, genes associated with vision and biological rhythmicity were lost, which may indirectly benefit oligotrophy by eliminating energetically costly processes. Compared to its shallow-sea relatives, L. polybranchiata has a significantly higher proportion of polyunsaturated fatty acids (PUFAs) and expanded gene families involved in the biosynthesis of unsaturated fatty acids and chromatin stabilization, possibly in response to high hydrostatic pressure. Additionally, L. polybranchiata has broad digestive scope, allowing it to fully utilize the limited food resources in the deep sea to sustain a large population. As a pioneer species, L. polybranchiata has an expanded repertoire of genes encoding potential chemoreceptor proteins, including ionotropic receptors (IRs) and gustatory receptor-like receptors (GRLs). These proteins, characterized by their conserved 3D structures, may enhance the organism's ability to detect chemical cues in chemosynthetic ecosystems, facilitating rapid settlement in suitable environments. CONCLUSIONS Our results shed light on the adaptation of Lindaspio to the darkness, high hydrostatic pressure, and food deprivation in the deep sea, providing insights into the molecular basis for L. polybranchiata becoming a pioneer species.
Collapse
Affiliation(s)
- Yujie Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Yang Guo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xupeng Chi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | | | - Mengna Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Haining Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Huan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266071, China.
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266071, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| |
Collapse
|
7
|
Mikalsen SO, Í Hjøllum J, Salter I, Djurhuus A, Í Kongsstovu S. A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity. NPJ BIODIVERSITY 2024; 3:37. [PMID: 39632982 PMCID: PMC11618374 DOI: 10.1038/s44185-024-00068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024]
Abstract
Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference genomes gives the best basis for using genetics and genetic diversity towards the global aims of (1) the protection of species, biodiversity, and nature, and (2) the management of biodiversity for achieving sustainable harvesting of nature. Protecting biodiversity is a global responsibility, also resting on small nations, like the Faroe Islands. Being in the middle of the North Atlantic Ocean and having large fisheries activity, the nation has a particular responsibility towards maritime matters. We here provide the reasoning behind the Genome Atlas of Faroese Ecology (Gen@FarE), a project based on our participation in the European Reference Genome Atlas consortium (ERGA). Gen@FarE has three major aims: (1) To acquire high-quality genomes of all eukaryotic species in the Faroe Islands and Faroese waters. (2) To establish population genetics for species of commercial or ecological interest. (3) To establish an information databank for all Faroese species, combined with a citizen science registration database, making it possible for the public to participate in acquiring and maintaining the overview of Faroese species in both terrestrial and marine environments. Altogether, we believe that this will enhance the society's interest in and awareness of biodiversity, thereby protecting the foundations of our lives. Furthermore, the combination of a wide and highly competent ERGA umbrella and more targeted national projects will help fulfil the formal and moral responsibilities that all nations, also those with limited resources, have in protecting biodiversity and achieving sustainability in harvesting from nature.
Collapse
Affiliation(s)
- Svein-Ole Mikalsen
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands.
| | - Jari Í Hjøllum
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Ian Salter
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Anni Djurhuus
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Sunnvør Í Kongsstovu
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| |
Collapse
|
8
|
Guraieb M, Mendoza G, Mizell K, Rouse G, McCarthy RA, Pereira OS, Levin LA. Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland. PeerJ 2024; 12:e18290. [PMID: 39494296 PMCID: PMC11531752 DOI: 10.7717/peerj.18290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 09/20/2024] [Indexed: 11/05/2024] Open
Abstract
Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 μm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths above, within, and below the oxygen minimum zone (OMZ). A total of 3,555 macrofauna individuals were counted and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Average density for SCB macrofauna was 11.08 ± 0.87 ind. 200 cm-2 and mean Shannon-Wiener diversity per rock (H'[loge]) was 2.22 ± 0.07. A relationship was found between substrate type and macrofaunal communities. Phosphorite rocks had the highest H' of the four substrates compared on a per-rock basis. However, when samples were pooled by substrate, FeMn crusts had the highest H' and rarefaction diversity. Of all the environmental variables examined, water depth explained the largest variance in macrofaunal community composition. Macrofaunal density and diversity values were similar at sites within and outside the OMZ. This study is the first to analyze the macrofaunal communities of mineral-rich hardgrounds in the SCB, which support deep-ocean biodiversity by acting as specialized substrates for macrofaunal communities. Understanding the intricate relationships between macrofaunal assemblages and mineral-rich substrates may inform effects from environmental disruptions associated with deep-seabed mining or climate change. The findings contribute baseline information useful for effective conservation and management of the SCB and will support scientists in monitoring changes in these communities due to environmental disturbance or human impact in the future.
Collapse
Affiliation(s)
- Michelle Guraieb
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Guillermo Mendoza
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Kira Mizell
- USGS Pacific Coastal and Marine Science Center Santa Cruz, Santa Cruz, CA, USA, Santa Cruz, California, United States
| | - Greg Rouse
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Ryan A. McCarthy
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States
| | - Olívia S. Pereira
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Lisa A. Levin
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| |
Collapse
|
9
|
Hartop E, Lee L, Srivathsan A, Jones M, Peña-Aguilera P, Ovaskainen O, Roslin T, Meier R. Resolving biology's dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon. BMC Biol 2024; 22:215. [PMID: 39334308 PMCID: PMC11438253 DOI: 10.1186/s12915-024-02010-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Zoology's dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding ("megabarcoding"). We reveal the high abundance and diversity of scuttle flies (Diptera: Phoridae) in Sweden using 31,800 specimens from 37 sites across four seasonal periods. We investigate the number of scuttle fly species in Sweden and the environmental factors driving community changes across time and space. RESULTS Swedish scuttle fly diversity is much higher than previously known, with 549 putative specie) detected, compared to 374 previously recorded species. Hierarchical Modelling of Species Communities reveals that scuttle fly communities are highly structured by latitude and strongly driven by climatic factors. Large dissimilarities between sites and seasons are driven by turnover rather than nestedness. Climate change is predicted to significantly affect the 47% of species that show significant responses to mean annual temperature. Results were robust regardless of whether haplotype diversity or species-proxies were used as response variables. Additionally, species-level models of common taxa adequately predict overall species richness. CONCLUSIONS Understanding the bulk of the diversity around us is imperative during an era of biodiversity change. We show that dark insect taxa can be efficiently characterised and surveyed with megabarcoding. Undersampling of rare taxa and choice of operational taxonomic units do not alter the main ecological inferences, making it an opportune time to tackle zoology's dark matter.
Collapse
Affiliation(s)
- Emily Hartop
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway.
- Zoology Department, Stockholm University, Stockholm, 106 91, Sweden.
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore, 117558, Singapore
- National University of Singapore, Lee Kong Chian Natural History Museum, 2 Conservatory Dr, Singapore, 117377, Singapore
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore, 117558, Singapore
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum Für Naturkunde, Invalidenstraße 43, Berlin, 10115, Germany
| | - Mirkka Jones
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
- Institute of Biotechnology, HILIFE Helsinki Institute of Life Science, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
| | - Pablo Peña-Aguilera
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Ulls Väg 18B, Uppsala, 75651, Sweden
| | - Otso Ovaskainen
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, 40014, Finland
| | - Tomas Roslin
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Ulls Väg 18B, Uppsala, 75651, Sweden
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum Für Naturkunde, Invalidenstraße 43, Berlin, 10115, Germany.
- Institute for Biology, Humboldt University of Berlin, Unter Den Linden 6, Berlin, 10117, Germany.
| |
Collapse
|
10
|
Gallego R, Arias MB, Corral-Lou A, Díez-Vives C, Neave EF, Wang C, Cárdenas P, Steffen K, Taboada S, Villamor A, Kenchington E, Mariani S, Riesgo A. North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA. Commun Biol 2024; 7:1015. [PMID: 39160260 PMCID: PMC11333605 DOI: 10.1038/s42003-024-06695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.
Collapse
Affiliation(s)
- Ramón Gallego
- Department of Biology, Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, Cantoblanco, 28049, Madrid, Spain
| | - María Belén Arias
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK
| | - Andrea Corral-Lou
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Cristina Díez-Vives
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Calle Darwin 3, 28049, Madrid, Spain
| | - Erika F Neave
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Cai Wang
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Paco Cárdenas
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36, Uppsala, Sweden
| | - Karin Steffen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Sergio Taboada
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Adriana Villamor
- International Council for the Exploration of the Sea (ICES), H. C. Andersens Boulevard 44-46, DK, 1553, Copenhagen V, Denmark
| | - Ellen Kenchington
- Ocean and Ecosystem Sciences Division, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London, SW7 5BD, UK.
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| |
Collapse
|
11
|
Bezio N, Collins AG. Redescription of the deep-sea benthic ctenophore genus Tjalfiella from the North Atlantic (Class Tentaculata, Order Platyctenida, Family Tjalfiellidae). Zootaxa 2024; 5486:241-266. [PMID: 39646833 DOI: 10.11646/zootaxa.5486.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Indexed: 12/10/2024]
Abstract
Some of the most fascinating and poorly known animals on this planet are comb jellies of the phylum Ctenophora. About one-quarter of ctenophore richness is encompassed by the benthic species of the order Platyctenida, nearly all known from shallow waters. In this work, we integrate several systematic methods to elucidate an enigmatic genus, Tjalfiella, known previously only from deep waters near the western coastline of Greenland in the North Atlantic. For the first time, we employ microCT on museum specimens-one nearly 100 years old from the type locality of the only known species of the genus, T. tristoma-of extant ctenophores to visualize and compare their anatomy. With these data, we integrate in situ videography and genetic sequence data derived from newly collected deep sea specimens observed via NOAA Ship Okeanos Explorer in 2018 and 2022 at two distant localities in the North Atlantic, near North Carolina, USA, and the Azores, Portugal. The genetic data indicate that the newly collected specimens represent closely related but distinct species of Tjalfiella. However, neither can be named at this time because neither one could be definitively differentiated from T. tristoma, given that microCT and in situ imagery reveal striking morphological similarities and only variation in color and host preference. Despite the lack of new species descriptions, this work characterizes both the morphology and genetics of the benthic ctenophore genus Tjalfiella and specimens representing species within it, advancing our understanding of a rarely observed component of the deep-sea fauna.
Collapse
Affiliation(s)
- Nicholas Bezio
- The University of Maryland; Department of Biological Science; College Park; MD; 20742 USA; National Museum of Natural History; Smithsonian Institution; Department of Invertebrate Zoology; Washington; DC; 20560 USA.
| | - Allen G Collins
- National Museum of Natural History; Smithsonian Institution; Department of Invertebrate Zoology; Washington; DC; 20560 USA; NOAA Fisheries; Office of Science & Technology; National Systematics Laboratory; Washington; DC; 20560 USA.
| |
Collapse
|
12
|
Metaxas A, Anglin CD, Cross A, Drazen J, Haeckel M, Mudd G, Smith CR, Smith S, Weaver PPE, Sonter L, Amon DJ, Erskine PD, Levin LA, Lily H, Maest AS, Mestre NC, Ramirez-Llodra E, Sánchez LE, Sharma R, Vanreusel A, Wheston S, Tunnicliffe V. Comparing environmental impacts of deep-seabed and land-based mining: A defensible framework. GLOBAL CHANGE BIOLOGY 2024; 30:e17334. [PMID: 38780465 DOI: 10.1111/gcb.17334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 05/25/2024]
Abstract
The crises of climate change and biodiversity loss are interlinked and must be addressed jointly. A proposed solution for reducing reliance on fossil fuels, and thus mitigating climate change, is the transition from conventional combustion-engine to electric vehicles. This transition currently requires additional mineral resources, such as nickel and cobalt used in car batteries, presently obtained from land-based mines. Most options to meet this demand are associated with some biodiversity loss. One proposal is to mine the deep seabed, a vast, relatively pristine and mostly unexplored region of our planet. Few comparisons of environmental impacts of solely expanding land-based mining versus extending mining to the deep seabed for the additional resources exist and for biodiversity only qualitative. Here, we present a framework that facilitates a holistic comparison of relative ecosystem impacts by mining, using empirical data from relevant environmental metrics. This framework (Environmental Impact Wheel) includes a suite of physicochemical and biological components, rather than a few selected metrics, surrogates, or proxies. It is modified from the "recovery wheel" presented in the International Standards for the Practice of Ecological Restoration to address impacts rather than recovery. The wheel includes six attributes (physical condition, community composition, structural diversity, ecosystem function, external exchanges and absence of threats). Each has 3-5 sub attributes, in turn measured with several indicators. The framework includes five steps: (1) identifying geographic scope; (2) identifying relevant spatiotemporal scales; (3) selecting relevant indicators for each sub-attribute; (4) aggregating changes in indicators to scores; and (5) generating Environmental Impact Wheels for targeted comparisons. To move forward comparisons of land-based with deep seabed mining, thresholds of the indicators that reflect the range in severity of environmental impacts are needed. Indicators should be based on clearly articulated environmental goals, with objectives and targets that are specific, measurable, achievable, relevant, and time bound.
Collapse
Affiliation(s)
- A Metaxas
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - C D Anglin
- Anglin & Associates Consulting, North Vancouver, British Columbia, Canada
| | - A Cross
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- EcoHealth Network, Brookline, Massachusetts, USA
| | - J Drazen
- University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - M Haeckel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - G Mudd
- Environmental Engineering, RMIT University, Melbourne, Victoria, Australia
| | - C R Smith
- University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - S Smith
- Blue Globe Solutions Inc., Toronto, Ontario, Canada
| | | | - L Sonter
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - D J Amon
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California, USA
- SpeSeas, D'Abadie, Trinidad and Tobago
| | - P D Erskine
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - L A Levin
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - H Lily
- Independent Legal Consultant, Canterbury, Kent, UK
| | - A S Maest
- Buka Environmental, Telluride, Colorado, USA
| | - N C Mestre
- Centre for Marine and Environmental Research (CIMA)-Infrastructure Network in Aquatic Research (ARNET), Universidade do Algarve, Faro, Portugal
| | | | - L E Sánchez
- Department of Mining and Petroleum Engineering, University of São Paulo, São Paulo, Brazil
| | - R Sharma
- National Institute of Oceanography, Goa, India
| | - A Vanreusel
- Marine Biology Research Group Ghent University Krijgslaan, Ghent, Belgium
| | - S Wheston
- Tembusu-Sustainability & Risk Management, Cashel, County Tipperary, Ireland
| | - V Tunnicliffe
- Department of Biology/School Earth & Ocean Sciences, University of Victoria, Victoria, British Columbia, Canada
| |
Collapse
|
13
|
Grischenko AV, Gordon DP, Melnik VP. Bryozoa (Cheilostomata) from polymetallic nodules in the Russian exploration area, Clarion-Clipperton Fracture Zone, eastern Pacific Ocean-taxon novelty and characteristics as macro- and megafaunal elements. Zootaxa 2024; 5440:1-147. [PMID: 39646701 DOI: 10.11646/zootaxa.5440.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Indexed: 12/10/2024]
Abstract
This work describes Bryozoa of the order Cheilostomata associated with polymetallic nodules collected by box-coring in the eastern part of the Russian exploration area of the Clarion-Clipperton Fracture Zone (CCFZ or CCZ) under contract to Yuzhmorgeologiya. Study of 569 cheilostome specimens from 4510-5280 m depth yielded 32 species (22 new) in 20 genera (3 new) and 14 families (1 new). For six species, the nomenclature was left open (genus only) owing to the paucity of defining characters. One species with a costate frontal shield, possibly belonging to the otherwise monotypic Polliciporidae, clearly represents a new genus, but was not named, as it comprises only an ancestrula, one fully formed daughter zooid and a zooid bud. Four of the species we detected are known from the deep sea beyond the CCZ; Columnella magna and Acanthodesiomorpha problematica occur not only elsewhere in the Pacific Ocean but also the Atlantic Ocean, while Smithsonius quadratus was first described from the Kuril-Kamchatka Trench, and the authors have unpublished records of Smithsonius candelabrum n. sp. from the Magellan Seamounts and the Louisville Ridge. These records give hope that other CCZ bryozoan taxa may also occur elsewhere, offsetting local extirpation through nodule mining. Almost 63% (20 species) of CCZ Cheilostomata have a flexibly erect colony attached by one or several rhizoids (and/or the ancestrula has a proximal cuticular stalk-like portion). Ten other species have fixed-erect rigid colonies; only two species are encrusting. If a 50 mm height or spread is taken as the lower limit defining a megafaunal organism, then only C. magna qualifies as megafaunal. If 20 mm is taken as the lower size limit (definitions vary), then nine other species have the potential to be recognized in ROV-obtained images. The completion of this monograph allows a summary of all bryozoan data for the Russian sector of the CCZ. Altogether, 52 species are known from this area, totalling 1002 specimens from 437 stations. The most abundant and most ubiquitous species was the cyclostome Pandanipora helix, comprising 230 specimens from 137 stations and accounting for almost 23% of all specimens collected. The next most abundant and ubiquitous species were the cheilostomes Aulopocella polymorpha (124 specimens, 105 stations) and Fulgurella marina (104 specimens, 92 stations). These three species accounted for almost 46% of all specimens collected. All other species yielded fewer than 45 specimens each from 33 or fewer stations. Twelve species were represented by a single colony. Although some ROV images from eastern sectors of the CCZ have been recognized as bryozoans and published as such, few have been studied systematically. Bryozoans have also been reported from seamounts, level-bottom rock flats, ridges and troughs in the CCZ, but their identities remain unknown. It is imperative that institutions seek the collaboration of taxonomists rather than allow material to languish unidentified in collections.
Collapse
Affiliation(s)
- Andrei V Grischenko
- Department of Invertebrate Zoology and Aquatic Ecology; Biological Faculty; Perm State National Research University; Bukirev Street 15; GSP; Perm 614990; Russia; A.V. Zhirmunsky National Scientific Center of Marine Biology; Far East Branch; Russian Academy of Sciences; Palchevskogo Street 17; Vladivostok 690041; Russia.
| | - Dennis P Gordon
- National Institute of Water & Atmospheric Research; Private Bag 19401 Kilbirnie; Wellington; New Zealand.
| | - Viacheslav P Melnik
- Joint Stock Company Yuzhmorgeologiya; Federal Agency for State Property Management; Krymskaya Street 20; Gelendzhik; 353461; Russia.
| |
Collapse
|
14
|
Gilbert N. Complex deep-sea expeditions try to size up seabed mining impacts. Proc Natl Acad Sci U S A 2024; 121:e2404667121. [PMID: 38568965 PMCID: PMC11009680 DOI: 10.1073/pnas.2404667121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
|
15
|
Barrenechea Angeles I, Nguyen NL, Greco M, Tan KS, Pawlowski J. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity. PLoS One 2024; 19:e0298440. [PMID: 38422100 PMCID: PMC10903905 DOI: 10.1371/journal.pone.0298440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.
Collapse
Affiliation(s)
- Inès Barrenechea Angeles
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ngoc-Loi Nguyen
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| | - Koh Siang Tan
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- ID-Gene Ecodiagnostics Ltd., Plan-les-Ouates, Switzerland
| |
Collapse
|
16
|
Gastineau R, Dąbek P, Mianowicz K, Stoyanova V, Krawcewicz A, Abramowski T. Complete mitochondrial genome of the abyssal coral Abyssoprimnoagemina Cairns, 2015 (Octocorallia, Primnoidae) from the Clarion-Clipperton Zone, Pacific Ocean. Zookeys 2023; 1183:81-98. [PMID: 37953748 PMCID: PMC10632777 DOI: 10.3897/zookeys.1183.109000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
The Clarion-Clipperton Zone (CCZ) in the tropical East Pacific is a region of interest for deep-sea mining due to its underwater deposits of polymetallic nodules containing economically important metals such as nickel, copper, and cobalt. It is also a region of extensive baseline studies aiming to describe the state of the environment, including the biodiversity of the benthic fauna. An abundant component of the abyssal plain ecosystem consists of sessile fauna which encrusts polymetallic nodules and are vulnerable to potential impacts arising from exploitation activities, particularly removal of substrate. Therefore, this fauna is often considered to have key species whose genetic connectivity should be studied to assess their ecological resilience. One such species is Abyssoprimnoagemina Cairns, 2015, a deep-sea coral from the CCZ whose presence in the Interoceanmetal Joint Organization (IOM) claim area has been confirmed during samplings. In this study, we used next-generation sequencing (NGS) to obtain the 18S nuclear rRNA gene and the complete mitochondrial genome of A.gemina from IOM exploration area. The mitogenome is 18,825 bp long and encodes for 14 protein coding genes, 2 rRNAs, and a single tRNA. The two phylogeny reconstructions derived from these data confirm previous studies and display A.gemina within a highly supported cluster of seven species whose mitogenomes are all colinear and of comparable size. This study also demonstrates the suitability of NGS for DNA barcoding of the benthic megafauna of the CCZ, which could become part of the IOM protocol for the assessment of population diversity and genetic connectivity in its claim area.
Collapse
Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, ul. Mickiewicza 16a, Szczecin, 70-383, PolandUniversity of SzczecinSzczecinPoland
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, ul. Mickiewicza 16a, Szczecin, 70-383, PolandUniversity of SzczecinSzczecinPoland
| | - Kamila Mianowicz
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, PolandInteroceanmetal Joint OrganizationSzczecinPoland
| | - Valcana Stoyanova
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, PolandInteroceanmetal Joint OrganizationSzczecinPoland
| | - Artur Krawcewicz
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, PolandInteroceanmetal Joint OrganizationSzczecinPoland
| | - Tomasz Abramowski
- Interoceanmetal Joint Organization, ul. Cyryla i Metodego 9-9A, Szczecin, 71-541, PolandInteroceanmetal Joint OrganizationSzczecinPoland
| |
Collapse
|
17
|
Wiklund H, Rabone M, Glover AG, Bribiesca-Contreras G, Drennan R, Stewart ECD, Boolukos CM, King LD, Sherlock E, Smith CR, Dahlgren TG, Neal L. Checklist of newly-vouchered annelid taxa from the Clarion-Clipperton Zone, central Pacific Ocean, based on morphology and genetic delimitation. Biodivers Data J 2023; 11:e86921. [PMID: 38327336 PMCID: PMC10848496 DOI: 10.3897/bdj.11.e86921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/02/2023] [Indexed: 02/09/2024] Open
Abstract
Background We present a checklist of annelids from recent United Kingdom Seabed Resources (UKSR) expeditions (Abyssal Baseline - ABYSSLINE project) to the eastern abyssal Pacific Clarion-Clipperton Zone (CCZ) polymetallic nodule fields, based on DNA species delimitation, including imagery of voucher specimens, Darwin Core (DwC) data and links to vouchered specimen material and new GenBank sequence records. This paper includes genetic and imagery data for 129 species of annelids from 339 records and is restricted to material that is, in general, in too poor a condition to describe formally at this time, but likely contains many species new to science. We make these data available both to aid future taxonomic studies in the CCZ that will be able to link back to these genetic data and specimens and to better underpin ongoing ecological studies of potential deep-sea mining impacts using the principles of FAIR (Findable, Accessible, Interoperable, Reusuable) data and specimens that will be available for all. New information We include genetic, imagery and all associated metadata in Darwin Core format for 129 species of annelids from the Clarion-Clipperton Zone, eastern abyssal Pacific, with 339 records.
Collapse
Affiliation(s)
- Helena Wiklund
- Gothenburg Global Biodiversity Centre, Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
- University of Gothenburg, Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
| | - Muriel Rabone
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | - Adrian G Glover
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | | | - Regan Drennan
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
- University of Southampton, Southampton, United KingdomUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Eva C D Stewart
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
- University of Southampton, Southampton, United KingdomUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Corie M Boolukos
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | - Lucas D King
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | - Emma Sherlock
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| | - Craig R Smith
- University of Hawaii, Honolulu, United States of AmericaUniversity of HawaiiHonoluluUnited States of America
| | - Thomas G Dahlgren
- Gothenburg Global Biodiversity Centre, Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
- University of Gothenburg, Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
- NORCE Norwegian Research Centre, Bergen, NorwayNORCE Norwegian Research CentreBergenNorway
| | - Lenka Neal
- Natural History Museum, London, United KingdomNatural History MuseumLondonUnited Kingdom
| |
Collapse
|
18
|
Simon-Lledó E, Amon DJ, Bribiesca-Contreras G, Cuvelier D, Durden JM, Ramalho SP, Uhlenkott K, Arbizu PM, Benoist N, Copley J, Dahlgren TG, Glover AG, Fleming B, Horton T, Ju SJ, Mejía-Saenz A, McQuaid K, Pape E, Park C, Smith CR, Jones DOB. Carbonate compensation depth drives abyssal biogeography in the northeast Pacific. Nat Ecol Evol 2023; 7:1388-1397. [PMID: 37488225 PMCID: PMC10482686 DOI: 10.1038/s41559-023-02122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/08/2023] [Indexed: 07/26/2023]
Abstract
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.
Collapse
Affiliation(s)
| | - Diva J Amon
- SpeSeas, D'Abadie, Trinidad and Tobago
- Marine Science Institute, University of California, Santa Barbara, CA, USA
| | | | - Daphne Cuvelier
- Institute of Marine Sciences-Okeanos, University of the Azores, Horta, Portugal
| | | | - Sofia P Ramalho
- Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Katja Uhlenkott
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Germany
| | - Pedro Martinez Arbizu
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | | | - Jonathan Copley
- Ocean & Earth Science, University of Southampton, Southampton, UK
| | - Thomas G Dahlgren
- NORCE Climate and Environment, Bergen, Norway
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | | | - Bethany Fleming
- National Oceanography Centre, Southampton, UK
- Ocean & Earth Science, University of Southampton, Southampton, UK
| | | | - Se-Jong Ju
- Korea Institute of Ocean Science and Technology, Busan, South Korea
- Ocean Science Major, University of Science and Technology, Daejeon, South Korea
| | | | | | - Ellen Pape
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Chailinn Park
- Korea Institute of Ocean Science and Technology, Busan, South Korea
- Ocean Science Major, University of Science and Technology, Daejeon, South Korea
| | - Craig R Smith
- Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, USA
| | | |
Collapse
|
19
|
Sonne C, Ciesielski TM, Jenssen BM, Lam SS, Zhong H, Dietz R. Norway's mining plans threaten Arctic life. Science 2023; 381:843-844. [PMID: 37616344 DOI: 10.1126/science.adj4244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Affiliation(s)
- Christian Sonne
- Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
- University of Petroleum and Energy Studies, Uttarakhand, India
| | - Tomasz M Ciesielski
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Arctic Technology, The University Centre in Svalbard (UNIS), NO-9171 Longyearbyen, Norway
| | - Bjørn M Jenssen
- Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Arctic Technology, The University Centre in Svalbard (UNIS), NO-9171 Longyearbyen, Norway
| | - Su Shiung Lam
- Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Huan Zhong
- School of Environment, Nanjing University, Nanjing, China
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
| |
Collapse
|
20
|
Neal L, Abrahams E, Wiklund H, Rabone M, Bribiesca-Contreras G, Stewart ECD, Dahlgren TG, Glover AG. Taxonomy, phylogeny, and biodiversity of Lumbrineridae (Annelida, Polychaeta) from the Central Pacific Clarion-Clipperton Zone. Zookeys 2023; 1172:61-100. [PMID: 37538355 PMCID: PMC10394509 DOI: 10.3897/zookeys.1172.100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/02/2023] [Indexed: 08/05/2023] Open
Abstract
The DNA taxonomy of six species of the annelid family Lumbrineridae collected from the Clarion-Clipperton Zone (CCZ) in the Central Pacific, an area of potential mining interest for polymetallic nodules, is presented. Lumbrinerids are an ecologically important and understudied annelid family within the deep sea, with many species still undescribed. This study aims to document the taxonomy and biodiversity of the CCZ using specimens collected from the UK-1, OMS, and NORI-D exploration contract areas and Areas of Particular Environmental Interest. Species were identified through a combination of morphological and molecular phylogenetic analysis. We present informal species descriptions associated with voucher specimens, accessible through the Natural History Museum (London) collections, to improve future taxonomic and biodiversity studies of this region. Five taxa in this study had no morphological or genetic matches within the literature and therefore are possibly new to science, but their suboptimal morphological preservation prevented the formalisation of new species. The most abundant taxon Lumbrineridescf.laubieri (NHM_0020) was compared with the holotype of Lumbrinerideslaubieri Miura, 1980 from the deep Northeast Atlantic. Currently no reliable morphological characters separating the Pacific and Atlantic specimens have been found and molecular data from the Atlantic specimens was not available.
Collapse
Affiliation(s)
- Lenka Neal
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | - Emily Abrahams
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
- Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity Centre, Box 463, 40530 Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
| | - Muriel Rabone
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | | | - Eva C. D. Stewart
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
- School of Ocean and Earth Sciences, University of Southampton, Southampton, SO14 3ZH, UKUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Thomas G. Dahlgren
- Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity Centre, Box 463, 40530 Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
- NORCE Norwegian Research Centre, Bergen, NorwayNORCE Norwegian Research CentreBergenNorway
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| |
Collapse
|
21
|
Gilbert N. Deep-sea mining could soon be approved - how bad is it? Nature 2023; 619:684. [PMID: 37460685 DOI: 10.1038/d41586-023-02290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
|
22
|
Gilbert N. Major ocean database that will guide deep-sea mining has flaws, scientists warn. Nature 2023:10.1038/d41586-023-01303-7. [PMID: 37237121 DOI: 10.1038/d41586-023-01303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|