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Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:md20100617. [DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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Canuti M, Large G, Verhoeven JTP, Dufour SC. A Novel Iridovirus Discovered in Deep-Sea Carnivorous Sponges. Viruses 2022; 14:v14081595. [PMID: 35893660 PMCID: PMC9330688 DOI: 10.3390/v14081595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Carnivorous sponges (family Cladorhizidae) use small invertebrates as their main source of nutrients. We discovered a novel iridovirus (carnivorous sponge-associated iridovirus, CaSpA-IV) in Chondrocladia grandis and Cladorhiza oxeata specimens collected in the Arctic and Atlantic oceans at depths of 537–852 m. The sequenced viral genome (~190,000 bp) comprised 185 predicted ORFs, including those encoding 26 iridoviral core proteins, and phylogenetic analyses showed that CaSpA-IV is a close relative to members of the genus Decapodiridovirus and highly identical to a partially sequenced virus pathogenic to decapod shrimps. CaSpA-IV was found in various anatomical regions of six C. grandis (sphere, stem, root) from the Gulf of Maine and Baffin Bay and of two C. oxeata (sphere, secondary axis) from Baffin Bay. Partial MCP sequencing revealed a divergent virus (CaSpA-IV-2) in one C. oxeata. The analysis of a 10 nt long tandem repeat showed a number of repeats consistent across sub-sections of the same sponges but different between animals, suggesting the presence of different strains. As the genetic material of crustaceans, particularly from the zooplanktonic copepod order Calanoida, was identified in the investigated samples, further studies are required to elucidate whether CaSpA-IV infects the carnivorous sponges, their crustacean prey, or both.
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Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
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Taboada S, Serra Silva A, Díez-Vives C, Neal L, Cristobo J, Ríos P, Hestetun JT, Clark B, Rossi ME, Junoy J, Navarro J, Riesgo A. Sleeping with the enemy: unravelling the symbiotic relationships between the scale worm Neopolynoe chondrocladiae (Annelida: Polynoidae) and its carnivorous sponge hosts. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
The North Atlantic deep-water polynoid worm Neopolynoe chondrocladiae is involved in an exceptional symbiotic relationship with two hosts: the carnivorous sponges Chondrocladia robertballardi and Chondrocladia virgata. While this is an obligate symbiotic relationship, its real nature is unclear. We used a multidisciplinary approach to narrow down the type of symbiotic relationship between symbiont and hosts. Molecular connectivity analyses using COI and 16S suggest that N. chondrocladiae has high potential for dispersal, connecting sites hundreds of kilometres apart, likely aided by oceanographic currents. Microbial analyses on different anatomical parts of five Chondrocladia species suggest that the presence of the worm in C. robertballardi does not affect the microbiome of the sponge. MicroCT analysis on N. chondrocladiae show that it has dorsally oriented parapodia, which might prevent the worm from getting trapped in the sponge. A faecal pellet recovered from the worm suggests that the polynoid feeds on the crustacean prey captured by the sponge, something corroborated by our stable isotope analysis. Light and confocal microscopy images suggest that N. chondrocladiae elytra produce bioluminescence. We propose that the worm might use bioluminescence as a lure for prey (increasing the food available for both the sponge and the polynoid) and thus fuelling a mutualistic relationship.
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Affiliation(s)
- Sergi Taboada
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
- Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Facultad de Ciencias, Cantoblanco, Madrid, Spain
| | - Ana Serra Silva
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
- Division of Biosciences, University College London, Gower Street, London, UK
- School of Earth Sciences, University of Bristol, Queens Road, Bristol, UK
| | - Cristina Díez-Vives
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | - Lenka Neal
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | - Javier Cristobo
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, C/ Príncipe de Asturias 70 bis, Gijón, Asturias, Spain
| | - Pilar Ríos
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Instituto Español de Oceanografía, Centro Oceanográfico de Santander, Promontorio San Martín s/n, Apdo. 240, Santander, Spain
| | - Jon Thomassen Hestetun
- NORCE Environment, NORCE Norwegian Research Centre, Nygårdsgaten 112 NO-5838 Bergen, Norway
| | - Brett Clark
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | | | - Juan Junoy
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Joan Navarro
- Instituto de Ciencias del Mar CSIC, Passeig Marítim de la Barceloneta 37–49, Barcelona, Spain
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
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Georgieva MN, Taboada S, Riesgo A, Díez-Vives C, De Leo FC, Jeffreys RM, Copley JT, Little CTS, Ríos P, Cristobo J, Hestetun JT, Glover AG. Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications. Front Microbiol 2020; 11:1636. [PMID: 32793148 PMCID: PMC7393317 DOI: 10.3389/fmicb.2020.01636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The peripheral areas of deep-sea hydrothermal vents are often inhabited by an assemblage of animals distinct to those living close to vent chimneys. For many such taxa, it is considered that peak abundances in the vent periphery relate to the availability of hard substrate as well as the increased concentrations of organic matter generated at vents, compared to background areas. However, the peripheries of vents are less well-studied than the assemblages of vent-endemic taxa, and the mechanisms through which peripheral fauna may benefit from vent environments are generally unknown. Understanding this is crucial for evaluating the sphere of influence of hydrothermal vents and managing the impacts of future human activity within these environments, as well as offering insights into the processes of metazoan adaptation to vents. In this study, we explored the evolutionary histories, microbiomes and nutritional sources of two distantly-related sponge types living at the periphery of active hydrothermal vents in two different geological settings (Cladorhiza from the E2 vent site on the East Scotia Ridge, Southern Ocean, and Spinularia from the Endeavour vent site on the Juan de Fuca Ridge, North-East Pacific) to examine their relationship to nearby venting. Our results uncovered a close sister relationship between the majority of our E2 Cladorhiza specimens and the species Cladorhiza methanophila, known to harbor and obtain nutrition from methanotrophic symbionts at cold seeps. Our microbiome analyses demonstrated that both E2 Cladorhiza and Endeavour Spinularia sp. are associated with putative chemosynthetic Gammaproteobacteria, including Thioglobaceae (present in both sponge types) and Methylomonaceae (present in Spinularia sp.). These bacteria are closely related to chemoautotrophic symbionts of bathymodiolin mussels. Both vent-peripheral sponges demonstrate carbon and nitrogen isotopic signatures consistent with contributions to nutrition from chemosynthesis. This study expands the number of known associations between metazoans and potentially chemosynthetic Gammaproteobacteria, indicating that they can be incredibly widespread and also occur away from the immediate vicinity of chemosynthetic environments in the vent-periphery, where these sponges may be adapted to benefit from dispersed vent fluids.
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Affiliation(s)
| | - Sergi Taboada
- Life Sciences Department, Natural History Museum, London, United Kingdom
- Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
| | - Ana Riesgo
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | | | - Fabio C. De Leo
- Ocean Networks Canada, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Rachel M. Jeffreys
- School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan T. Copley
- School of Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | - Crispin T. S. Little
- Life Sciences Department, Natural History Museum, London, United Kingdom
- School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Pilar Ríos
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Santander, Instituto Español de Oceanografía, Santander, Spain
| | - Javier Cristobo
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| | - Jon T. Hestetun
- NORCE Environment, Norwegian Research Centre (NORCE), Bergen, Norway
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, London, United Kingdom
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Godefroy N, Le Goff E, Martinand-Mari C, Belkhir K, Vacelet J, Baghdiguian S. Sponge digestive system diversity and evolution: filter feeding to carnivory. Cell Tissue Res 2019; 377:341-351. [PMID: 31053892 DOI: 10.1007/s00441-019-03032-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/09/2019] [Indexed: 12/28/2022]
Abstract
Sponges are an ancient basal life form, so understanding their evolution is key to understanding all metazoan evolution. Sponges have very unusual feeding mechanisms, with an intricate network of progressively optimized filtration units: from the simple choanocyte lining of a central cavity, or spongocoel, to more complex chambers and canals. Furthermore, in a single evolutionary event, a group of sponges transitioned to carnivory. This major evolutionary transition involved replacing the filter-feeding apparatus with mobile phagocytic cells that migrate collectively towards the trapped prey. Here, we focus on the diversity and evolution of sponge nutrition systems and the amazing adaptation to carnivory.
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Affiliation(s)
- Nelly Godefroy
- ISEM, CNRS, EPHE, IRD, Univ Montpellier, Montpellier, France
| | - Emilie Le Goff
- ISEM, CNRS, EPHE, IRD, Univ Montpellier, Montpellier, France
| | | | - Khalid Belkhir
- ISEM, CNRS, EPHE, IRD, Univ Montpellier, Montpellier, France
| | - Jean Vacelet
- IMBE, CNRS, IRD, Station Marine d'Endoume, Aix Marseille Univ, Univ Avignon, 13007, Marseille, France.
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Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. ISME JOURNAL 2019; 13:1209-1225. [PMID: 30647460 PMCID: PMC6474228 DOI: 10.1038/s41396-019-0346-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 01/26/2023]
Abstract
Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host–symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.
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Chen See JR, Ulrich N, Nwanosike H, McLimans CJ, Tokarev V, Wright JR, Campa MF, Grant CJ, Hazen TC, Niles JM, Ressler D, Lamendella R. Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania. Front Microbiol 2018; 9:1697. [PMID: 30116227 PMCID: PMC6083035 DOI: 10.3389/fmicb.2018.01697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/09/2018] [Indexed: 01/24/2023] Open
Abstract
Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds. One stream was located in a watershed that previously had UOG extraction activities but was recently abandoned. We utilized high-throughput sequencing of the 16S rRNA gene to infer differences in sediment aquatic bacterial community structure between UOG+ and UOG- streams, as well as correlate bacterial community structure to physicochemical water parameters. Although overall alpha and beta diversity differences were not observed, there were a plethora of significantly enriched operational taxonomic units (OTUs) within UOG+ and UOG- samples. Our biomarker analysis revealed many of the bacterial taxa enriched in UOG+ streams can live in saline conditions, such as Rubrobacteraceae. In addition, several bacterial taxa capable of hydrocarbon degradation were also enriched in UOG+ samples, including Oceanospirillaceae. Methanotrophic taxa, such as Methylococcales, were significantly enriched as well. Several taxa that were identified as enriched in these samples were enriched in samples taken from different streams in 2014; moreover, partial least squares discriminant analysis (PLS-DA) revealed clustering between streams from the different studies based on the presence of hydraulic fracturing along the second axis. This study revealed significant differences between bacterial assemblages within stream sediments of UOG+ and UOG- streams and identified several potential biomarkers for evaluating and monitoring the response of autochthonous bacterial communities to potential hydraulic fracturing impacts.
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Affiliation(s)
- Jeremy R Chen See
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Nikea Ulrich
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | | | | | - Vasily Tokarev
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Justin R Wright
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Maria F Campa
- The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Terry C Hazen
- The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jonathan M Niles
- Freshwater Research Initiative, Susquehanna University, Selinsgrove, PA, United States
| | - Daniel Ressler
- Department of Earth and Environmental Sciences, Susquehanna University, Selinsgrove, PA, United States
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, United States
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Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. MICROBIOME 2018; 6:46. [PMID: 29523192 PMCID: PMC5845141 DOI: 10.1186/s40168-018-0428-1] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
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Affiliation(s)
- L. Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - L. Rix
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - B. M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A. Franke
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - U. Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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