1
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Cadena LR, Edgcomb V, Lukeš J. Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor. Environ Microbiol 2024; 26:e16598. [PMID: 38444221 DOI: 10.1111/1462-2920.16598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.
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Affiliation(s)
- Lawrence Rudy Cadena
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Virginia Edgcomb
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
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2
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Emil Ruff S, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. bioRxiv 2023:2023.11.27.568837. [PMID: 38076927 PMCID: PMC10705294 DOI: 10.1101/2023.11.27.568837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Zackary J. Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - S. Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543
| | | | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
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3
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Mara P, Geller-McGrath D, Edgcomb V, Beaudoin D, Morono Y, Teske A. Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface. Nat Commun 2023; 14:7768. [PMID: 38012208 PMCID: PMC10681998 DOI: 10.1038/s41467-023-43296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Geller-McGrath
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Beaudoin
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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4
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Mara P, Zhou YL, Teske A, Morono Y, Beaudoin D, Edgcomb V. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. ISME J 2023; 17:1907-1919. [PMID: 37658181 PMCID: PMC10579382 DOI: 10.1038/s41396-023-01492-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Ying-Li Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - David Beaudoin
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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5
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Wang M, Mara P, Burgaud G, Edgcomb V, Long X, Yang H, Cai L, Li W. Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters. Mol Ecol 2023; 32:2750-2765. [PMID: 36852430 DOI: 10.1111/mec.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.
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Affiliation(s)
- Mengmeng Wang
- College of Science, Shantou University, Shantou, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gaëtan Burgaud
- University of Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Xuedan Long
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haiping Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Science, Shantou University, Shantou, China
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6
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Geller-McGrath D, Mara P, Taylor GT, Suter E, Edgcomb V, Pachiadaki M. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin. Nat Commun 2023; 14:656. [PMID: 36746960 PMCID: PMC9902471 DOI: 10.1038/s41467-023-36026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023] Open
Abstract
Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
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Affiliation(s)
| | - Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,Biology, Chemistry and Environmental Studies Department, Molloy College, Rockville Centre, NY, USA
| | - Virginia Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Keeler E, Burgaud G, Teske A, Beaudoin D, Mehiri M, Dayras M, Cassand J, Edgcomb V. Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities. FEMS Microbiol Ecol 2021; 97:6318858. [PMID: 34245561 DOI: 10.1093/femsec/fiab103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.
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Affiliation(s)
- Emma Keeler
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, 220 McLean, Mail Stop 08, Woods Hole, MA 02543, USA
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, EA 3882, Technopôle Brest-Iroise, Plouzané, France
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Murray Hall 3117B, Chapel Hill, NC 27599, USA
| | - David Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, 220 McLean, Mail Stop 08, Woods Hole, MA 02543, USA
| | - Mohamed Mehiri
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, Marine Natural Products Team, 06108 Nice, France
| | - Marie Dayras
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, Marine Natural Products Team, 06108 Nice, France
| | - Jacquelin Cassand
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, Marine Natural Products Team, 06108 Nice, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, 220 McLean, Mail Stop 08, Woods Hole, MA 02543, USA
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8
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Quemener M, Dayras M, Frotté N, Debaets S, Le Meur C, Barbier G, Edgcomb V, Mehiri M, Burgaud G. Highlighting the Biotechnological Potential of Deep Oceanic Crust Fungi through the Prism of Their Antimicrobial Activity. Mar Drugs 2021; 19:md19080411. [PMID: 34436250 PMCID: PMC8399467 DOI: 10.3390/md19080411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Among the different tools to address the antibiotic resistance crisis, bioprospecting in complex uncharted habitats to detect novel microorganisms putatively producing original antimicrobial compounds can definitely increase the current therapeutic arsenal of antibiotics. Fungi from numerous habitats have been widely screened for their ability to express specific biosynthetic gene clusters (BGCs) involved in the synthesis of antimicrobial compounds. Here, a collection of unique 75 deep oceanic crust fungi was screened to evaluate their biotechnological potential through the prism of their antimicrobial activity using a polyphasic approach. After a first genetic screening to detect specific BGCs, a second step consisted of an antimicrobial screening that tested the most promising isolates against 11 microbial targets. Here, 12 fungal isolates showed at least one antibacterial and/or antifungal activity (static or lytic) against human pathogens. This analysis also revealed that Staphylococcus aureus ATCC 25923 and Enterococcus faecalis CIP A 186 were the most impacted, followed by Pseudomonas aeruginosa ATCC 27853. A specific focus on three fungal isolates allowed us to detect interesting activity of crude extracts against multidrug-resistant Staphylococcus aureus. Finally, complementary mass spectrometry (MS)-based molecular networking analyses were performed to putatively assign the fungal metabolites and raise hypotheses to link them to the observed antimicrobial activities.
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Affiliation(s)
- Maxence Quemener
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Marie Dayras
- Marine Natural Products Team, Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France; (M.D.); (M.M.)
| | - Nicolas Frotté
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Stella Debaets
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Christophe Le Meur
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Georges Barbier
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Virginia Edgcomb
- Departments of Geology and Geophysics and Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
| | - Mohamed Mehiri
- Marine Natural Products Team, Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France; (M.D.); (M.M.)
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
- Correspondence: ; Tel.: +33-290915148
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9
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Quemener M, Mara P, Schubotz F, Beaudoin D, Li W, Pachiadaki M, Sehein TR, Sylvan JB, Li J, Barbier G, Edgcomb V, Burgaud G. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ Microbiol 2020; 22:3950-3967. [PMID: 32743889 DOI: 10.1111/1462-2920.15181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023]
Abstract
The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low-biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the diversity, activity and adaptations of fungal communities in the deep oceanic crust from ~10 to 780 mbsf by combining metabarcoding analyses with mid/high-throughput culturing approaches. Metabarcoding along with culturing indicate a low diversity of viable fungi, mostly affiliated to ubiquitous (terrestrial and aquatic environments) taxa. Ecophysiological analyses coupled with metatranscriptomics point to viable and transcriptionally active fungal populations engaged in cell division, translation, protein modifications and other vital cellular processes. Transcript data suggest possible adaptations for surviving in the nutrient-poor, lithified deep biosphere that include the recycling of organic matter. These active communities appear strongly influenced by the presence of cracks and veins in the rocks where fluids and resulting rock alteration create micro-niches.
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Affiliation(s)
- Maxence Quemener
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florence Schubotz
- MARUM-Center for Marine Environmental Sciences, University Bremen, Leobener Strasse 8, Bremen, 28359, Germany
| | - David Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Maria Pachiadaki
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Taylor R Sehein
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, 77845, USA
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Georges Barbier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Gaëtan Burgaud
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:551. [PMID: 32296171 PMCID: PMC7200595 DOI: 10.1038/s41592-020-0828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | | | - Elena Casacuberta
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Aresté
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Cecilia Balestreri
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | | | - Patrick Beardslee
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Sara Bender
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - François-Yves Bouget
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Susana A Breglia
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Colin Brownlee
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Rachele Cesaroni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Thomas Clemente
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Duncan B Coles
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Coyne
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pía A Elustondo
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,AGADA Biosciences Inc., Halifax, Nova Scotia, Canada
| | - Fernan Federici
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Veronica Freire-Beneitez
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | | | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Paulo A García
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Yutaka Hanawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Esteban R Haro-Contreras
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Highfield
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jorge Ibañez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Natalia Ewa Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Konomi Fujimura-Kamada
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Eleanna Kazana
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Noelia Lander
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Zhuhong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Fulei Luan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Tamara Matute
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Mark Moosburner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Sebastián R Najle
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Deepak Nanjappa
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Isabel C Nimmo
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luke Noble
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Institute de Biologie de l'ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Isaac Nuñez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jan Pyrih
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mariana Rius
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | | | - Albane Ruaud
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Departament de Genètica Microbiologia i Estadıśtica, Universitat de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Monika A Sigg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G Jason Smith
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | | | - Rowena Stern
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anastasios D Tsaousis
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Lev Tsypin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Aaron Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jernej Turnšek
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Valérie Vergé
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Peter von Dassow
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Instituto Milenio de Oceanografia de Chile, Concepción, Chile
| | | | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lu Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoxue Wen
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Glen Wheeler
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - April Woods
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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Waller RF, Cleves PA, Rubio-Brotons M, Woods A, Bender SJ, Edgcomb V, Gann ER, Jones AC, Teytelman L, von Dassow P, Wilhelm SW, Collier JL. Strength in numbers: Collaborative science for new experimental model systems. PLoS Biol 2018; 16:e2006333. [PMID: 29965960 PMCID: PMC6044537 DOI: 10.1371/journal.pbio.2006333] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/13/2018] [Indexed: 11/18/2022] Open
Abstract
Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.
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Affiliation(s)
- Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (RFW); (JLC)
| | - Phillip A. Cleves
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Maria Rubio-Brotons
- Institut de Biologia Evolutiva, Spanish National Research Council (CSIC)–Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - April Woods
- Environmental Biotechnology Lab, Moss Landing Marine Laboratories, California, United States of America
| | - Sara J. Bender
- Gordon and Betty Moore Foundation, Palo Alto, California, United States of America
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Adam C. Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, United States of America
| | | | - Peter von Dassow
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía, Concepción, Chile
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail: (RFW); (JLC)
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13
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Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. UniEuk: Time to Speak a Common Language in Protistology! J Eukaryot Microbiol 2017; 64:407-411. [PMID: 28337822 PMCID: PMC5435949 DOI: 10.1111/jeu.12414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
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Affiliation(s)
- Cédric Berney
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Andreea Ciuprina
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany
| | - Sara Bender
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA
| | - Jeena Rajan
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Laura Wegener Parfrey
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada
| | - Stéphane Audic
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Lucas Czech
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Frank Oliver Glöckner
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | | | - Christian Quast
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Jonathan Z Kaye
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.,Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany
| | - Javier Del Campo
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Colomban de Vargas
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
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Rédou V, Ciobanu MC, Pachiadaki MG, Edgcomb V, Alain K, Barbier G, Burgaud G. In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths. FEMS Microbiol Ecol 2014; 90:908-21. [DOI: 10.1111/1574-6941.12447] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/15/2014] [Accepted: 10/18/2014] [Indexed: 10/24/2022] Open
Affiliation(s)
- Vanessa Rédou
- EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne; Université de Brest; Plouzané France
| | - Maria Cristina Ciobanu
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Plouzané France
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); CNRS; IUEM - UMR 6197; Plouzané France
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Ifremer; UMR 6197; Plouzané France
| | - Maria G. Pachiadaki
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole MA USA
| | - Virginia Edgcomb
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole MA USA
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Plouzané France
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); CNRS; IUEM - UMR 6197; Plouzané France
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Ifremer; UMR 6197; Plouzané France
| | - Georges Barbier
- EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne; Université de Brest; Plouzané France
| | - Gaëtan Burgaud
- EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne; Université de Brest; Plouzané France
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Pachiadaki MG, Yakimov MM, LaCono V, Leadbetter E, Edgcomb V. Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin. ISME J 2014; 8:2478-89. [PMID: 24950109 DOI: 10.1038/ismej.2014.100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/30/2014] [Accepted: 05/11/2014] [Indexed: 11/09/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most hostile environments on Earth. Little is known about the biochemical adaptations of microorganisms living in these habitats. This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine. The analysis of Thetis DHAB interface indicates that sulfate reduction occurs in both the upper (7.0-16.3% salinity) and lower (21.4-27.6%) halocline, but that expression of dissimilatory sulfate reductase is reduced in the more hypersaline lower halocline. High dark-carbon assimilation rates in the upper interface coincided with high abundance of transcripts for ribulose 1,5-bisphosphate carboxylase affiliated to sulfur-oxidizing bacteria. In the lower interface, increased expression of genes associated with methane metabolism and osmoregulation is noted. In addition, in this layer, nitrogenase transcripts affiliated to uncultivated putative methanotrophic archaea were detected, implying nitrogen fixation in this anoxic habitat, and providing evidence of linked carbon, nitrogen and sulfur cycles.
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Affiliation(s)
| | | | - Violetta LaCono
- CNR-Institute for Coastal Marine Environment, Messina, Italy
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Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 2013. [PMID: 23834625 DOI: 10.1186/1471‐2180‐13‐150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. RESULTS Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. CONCLUSIONS Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The "isolated island character" of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).
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Affiliation(s)
- Alexandra Stock
- University of Kaiserslautern, School of Biology, Erwin-Schroedinger-Str, 14, D-67663 Kaiserslautern, Germany
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Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T. Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 2013; 13:150. [PMID: 23834625 PMCID: PMC3707832 DOI: 10.1186/1471-2180-13-150] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 05/15/2013] [Indexed: 12/01/2022] Open
Abstract
Background Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. Results Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. Conclusions Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The “isolated island character” of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).
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Affiliation(s)
- Alexandra Stock
- University of Kaiserslautern, School of Biology, Erwin-Schroedinger-Str, 14, D-67663 Kaiserslautern, Germany
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Orsi W, Biddle JF, Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces. PLoS One 2013; 8:e56335. [PMID: 23418556 PMCID: PMC3572030 DOI: 10.1371/journal.pone.0056335] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/08/2013] [Indexed: 02/01/2023] Open
Abstract
The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America.
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Filker S, Stock A, Breiner HW, Edgcomb V, Orsi W, Yakimov MM, Stoeck T. Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. Microbiologyopen 2012; 2:54-63. [PMID: 23239531 PMCID: PMC3584213 DOI: 10.1002/mbo3.56] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 10/31/2012] [Accepted: 11/12/2012] [Indexed: 11/25/2022] Open
Abstract
High salt concentrations, absence of light, anoxia, and high hydrostatic pressure make deep hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea one of the most polyextreme habitats on Earth. Taking advantage of the unique chemical characteristics of these basins, we tested the effect of environmental selection and geographic distance on the structure of protistan communities. Terminal restriction fragment length polymorphism (T-RFLP) analyses were performed on water samples from the brines and seawater/brine interfaces of five basins: Discovery, Urania, Thetis, Tyro, and Medee. Using statistical analyses, we calculated the partitioning of diversity among the ten individual terminal restriction fragment (T-RF) profiles, based on peak abundance and peak incidence. While a significant distance effect on spatial protistan patterns was not detected, hydrochemical gradients emerged as strong dispersal barriers that likely lead to environmental selection in the DHAB protistan plankton communities. We identified sodium, magnesium, sulfate, and oxygen playing in concerto as dominant environmental drivers for the structuring of protistan plankton communities in the Eastern Mediterranean DHABs.
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Affiliation(s)
- Sabine Filker
- School of Biology, University of Kaiserslautern, Erwin-Schroedinger-Str. 14, D-67663, Kaiserslautern, Germany
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Kormas KA, Smith DC, Edgcomb V, Teske A. Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 2012; 45:115-25. [PMID: 19719622 DOI: 10.1016/s0168-6496(03)00128-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract The prokaryotic community inhabiting the deep subsurface sediments in the Forearc Basin of the Nankai Trough southeast of Japan (ODP Site 1176) was analyzed by 16S rDNA sequencing. Sediment samples from 1.15, 51.05, 98.50 and 193.96 m below sea floor (mbsf) harbored highly diverse bacterial communities. The most frequently retrieved clones included members of the Green non-sulfur bacteria whose closest relatives come from deep subsurface environments, a new epsilon-proteobacterial phylotype, and representatives of a cluster of closely related bacterial sequences from hydrocarbon- and methane-rich sediments around the world. Archaeal clones were limited to members of the genus Thermococcus, and were only obtained from the two deepest samples.
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Orsi W, Edgcomb V, Faria J, Foissner W, Fowle WH, Hohmann T, Suarez P, Taylor C, Taylor GT, Vd'ačný P, Epstein SS. Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela. Int J Syst Evol Microbiol 2012; 62:1425-1433. [PMID: 21841005 DOI: 10.1099/ijs.0.034710-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
The majority of environmental micro-organisms identified with the rRNA approach have never been visualized. Thus, their reliable classification and taxonomic assignment is often difficult or even impossible. In our preliminary 18S rRNA gene sequencing work from the world's largest anoxic marine environment, the Cariaco Basin (Caribbean Sea, Venezuela), we detected a ciliate clade, designated previously as CAR_H [Stoeck, S., Taylor, G. T. & Epstein, S. S. (2003). Appl Environ Microbiol 63, 5656-5663]. Here, we combine the traditional rRNA detection method of fluorescent in situ hybridization (FISH) with scanning electron microscopy (SEM) and confirm the phylogenetic separation of the CAR_H sequences from all other ciliate classes by showing an outstanding morphological feature of this group: a unique, archway-shaped kinety surrounding the oral apparatus and extending to the posterior body end in CAR_H cells. Based on this specific feature and the molecular phylogenies, we propose a novel ciliate class, Cariacotrichea nov. cl.
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Affiliation(s)
- William Orsi
- Department of Biology, Northeastern University, 313 Mugar Building, Boston, MA 02115, USA
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Jose Faria
- Departamento de Biología de Organismos, Universidad Simón Bolívar, Sartenejas, Baruta, Estado Miranda, Venezuela
| | - Wilhelm Foissner
- Department of Organismal Biology, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, A 5020, Austria
| | - William H Fowle
- Department of Biology, Northeastern University, 313 Mugar Building, Boston, MA 02115, USA
| | - Tine Hohmann
- Department of Biology, Northeastern University, 313 Mugar Building, Boston, MA 02115, USA
| | - Paula Suarez
- Departamento de Biología de Organismos, Universidad Simón Bolívar, Sartenejas, Baruta, Estado Miranda, Venezuela
| | - Craig Taylor
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Gordon T Taylor
- Marine Sciences Research Center, State University of New York, Stony Brook, NY 11794, USA
| | - Peter Vd'ačný
- Department of Zoology, Comenius University, Mlynská dolina B-1, Bratislava, SK 84215, Slovak Republic
| | - Slava S Epstein
- Department of Biology, Northeastern University, 313 Mugar Building, Boston, MA 02115, USA
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Abstract
Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs. Eukaryotic 18S rRNA gene sequences recovered from the Saanich Inlet water column on were deposited in Genbank under accession numbers HQ864863–HQ871151.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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Stock A, Breiner HW, Pachiadaki M, Edgcomb V, Filker S, La Cono V, Yakimov MM, Stoeck T. Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 2011; 16:21-34. [DOI: 10.1007/s00792-011-0401-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 09/27/2011] [Indexed: 02/03/2023]
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Orsi W, Edgcomb V, Jeon S, Leslin C, Bunge J, Taylor GT, Varela R, Epstein S. Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. ISME J 2011; 5:1357-73. [PMID: 21390077 DOI: 10.1038/ismej.2011.7] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This is the second paper in a series of three that investigates eukaryotic microbial diversity and taxon distribution in the Cariaco Basin, Venezuela, the ocean's largest anoxic marine basin. Here, we use phylogenetic information, multivariate community analyses and statistical richness predictions to test whether protists exhibit habitat specialization within defined geochemical layers of the water column. We also analyze spatio-temporal distributions of protists across two seasons and two geographic sites within the basin. Non-metric multidimensional scaling indicates that these two basin sites are inhabited by distinct protistan assemblages, an observation that is supported by the minimal overlap in observed and predicted richness of sampled sites. A comparison of parametric richness estimations indicates that protistan communities in closely spaced-but geochemically different-habitats are very dissimilar, and may share as few as 5% of total operational taxonomic units (OTUs). This is supported by a canonical correspondence analysis, indicating that the empirically observed OTUs are organized along opposing gradients in oxidants and reductants. Our phylogenetic analyses identify many new clades at species to class levels, some of which appear restricted to specific layers of the water column and have a significantly nonrandom distribution. These findings suggest many pelagic protists are restricted to specific habitats, and likely diversify, at least in part due to separation by geochemical barriers.
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Affiliation(s)
- William Orsi
- Department of Biology, Northeastern University, Boston, MA, USA
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Edgcomb V, Orsi W, Taylor GT, Vdacny P, Taylor C, Suarez P, Epstein S. Accessing marine protists from the anoxic Cariaco Basin. ISME J 2011; 5:1237-41. [PMID: 21390076 DOI: 10.1038/ismej.2011.10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- V Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Fernández-Delgado M, García-Amado MA, Contreras M, Edgcomb V, Vitelli J, Gueneau P, Suárez P. Vibrio cholerae non-O1, non-O139 associated with seawater and plankton from coastal marine areas of the Caribbean Sea. Int J Environ Health Res 2009; 19:279-289. [PMID: 19358004 DOI: 10.1080/09603120802460368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The aim of this study was to characterize the virulence properties and the antimicrobial resistance of Vibrio cholerae isolates from a coastal area of the Caribbean Sea. Three V. cholerae isolates were obtained from seawater and plankton using the HP selective medium for Helicobacter pylori. These V. cholerae isolates belonged to the non-O1, non-O139 serogroups and they did not have cholera toxin genes. They were resistant to penicillins and some cephalosporins and were sensitive to netilmicin, tetracyclines, sulfamethoxazole-trimethoprim and quinolones. This is the first study that provides biochemical and molecular evidence of non-O1, non-O139 V. cholerae isolates, non-toxigenic, carrying antibiotic resistance in seawater and plankton from a coastal area of the Caribbean Sea.
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Teske A, Hinrichs KU, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 2002; 68:1994-2007. [PMID: 11916723 PMCID: PMC123873 DOI: 10.1128/aem.68.4.1994-2007.2002] [Citation(s) in RCA: 395] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The delta-(13)C values of these lipids (delta-(13)C = -89 to -58 per thousand) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.
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Affiliation(s)
- Andreas Teske
- Biology Department, Woods Hole Oceanographic Institution, Massachusetts 02543, USA.
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Walker G, Simpson AG, Edgcomb V, Sogin ML, Patterson DJ. Ultrastructural identities of Mastigamoeba punctachora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista). Eur J Protistol 2001. [DOI: 10.1078/0932-4739-00780] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Edgcomb V, Viscogliosi E, Simpson AG, Delgado-Viscogliosi P, Roger AJ, Sogin ML. New Insights into the Phylogeny of Trichomonads Inferred from Small Subunit rRNA Sequences. Protist 1998. [DOI: 10.1016/s1434-4610(98)70042-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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