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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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2
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Joublin-Delavat A, Touahri K, Crétin P, Morot A, Rodrigues S, Jesus B, Trigodet F, Delavat F. Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph. Environ Microbiol 2022; 24:6510-6523. [PMID: 36302093 PMCID: PMC10099842 DOI: 10.1111/1462-2920.16261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/21/2022] [Indexed: 01/12/2023]
Abstract
Nitrogen (N2 ) fixation, or diazotrophy, supports a large part of primary production in oceans. Culture-independent approaches highlighted the presence in abundance of marine non-cyanobacterial diazotrophs (NCD), but their ecophysiology remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. Physiological characterization of the first marine NCD mutant obtained so far was performed using a soft-gellan assay, demonstrating that a ΔnifH mutant is not able to grow in nitrogen-free media. Furthermore, we demonstrated that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.
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Affiliation(s)
| | - Katia Touahri
- Nantes Université, CNRS, US2B, UMR6286, Nantes, France.,Laboratoire Chimie et Biochimie de Molécules Bioactives, Université de Strasbourg/CNRS, UMR7177, Strasbourg, France
| | | | - Amandine Morot
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France.,Université de Bretagne-Sud, UR3884, LBCM, IUEM, Lorient, France
| | | | - Bruno Jesus
- Nantes Université, RSBE2 ISOMer, UR2160, Nantes, France
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
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3
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Harding KJ, Turk-Kubo KA, Mak EWK, Weber PK, Mayali X, Zehr JP. Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre. Nat Commun 2022; 13:6979. [PMID: 36379938 PMCID: PMC9666432 DOI: 10.1038/s41467-022-34585-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous 15N-dinitrogen and 13C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell-1 d-1) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation.
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Affiliation(s)
- Katie J Harding
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | | | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
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4
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Hallstrøm S, Raina JB, Ostrowski M, Parks DH, Tyson GW, Hugenholtz P, Stocker R, Seymour JR, Riemann L. Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N 2 fixation in the pelagic ocean. THE ISME JOURNAL 2022; 16:2525-2534. [PMID: 35915168 PMCID: PMC9561647 DOI: 10.1038/s41396-022-01299-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 06/05/2023]
Abstract
Heterotrophic bacterial diazotrophs (HBDs) are ubiquitous in the pelagic ocean, where they have been predicted to carry out the anaerobic process of nitrogen fixation within low-oxygen microenvironments associated with marine pelagic particles. However, the mechanisms enabling particle colonization by HBDs are unknown. We hypothesized that HBDs use chemotaxis to locate and colonize suitable microenvironments, and showed that a cultivated marine HBD is chemotactic toward amino acids and phytoplankton-derived DOM. Using an in situ chemotaxis assay, we also discovered that diverse HBDs at a coastal site are motile and chemotactic toward DOM from various phytoplankton taxa and, indeed, that the proportion of diazotrophs was up to seven times higher among the motile fraction of the bacterial community compared to the bulk seawater community. Finally, three of four HBD isolates and 16 of 17 HBD metagenome assembled genomes, recovered from major ocean basins and locations along the Australian coast, each encoded >85% of proteins affiliated with the bacterial chemotaxis pathway. These results document the widespread capacity for chemotaxis in diverse and globally relevant marine HBDs. We suggest that HBDs could use chemotaxis to seek out and colonize low-oxygen microenvironments suitable for nitrogen fixation, such as those formed on marine particles. Chemotaxis in HBDs could therefore affect marine nitrogen and carbon biogeochemistry by facilitating nitrogen fixation within otherwise oxic waters, while also altering particle degradation and the efficiency of the biological pump.
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Affiliation(s)
- Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
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5
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Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. THE ISME JOURNAL 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
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Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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6
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Alcamán-Arias ME, Cifuentes-Anticevic J, Castillo-Inaipil W, Farías L, Sanhueza C, Fernández-Gómez B, Verdugo J, Abarzua L, Ridley C, Tamayo-Leiva J, Díez B. Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula. Microorganisms 2022; 10:microorganisms10061140. [PMID: 35744658 PMCID: PMC9227844 DOI: 10.3390/microorganisms10061140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.
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Affiliation(s)
- María E. Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Jerónimo Cifuentes-Anticevic
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Wilson Castillo-Inaipil
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
| | - Cynthia Sanhueza
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Beatriz Fernández-Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas, Spain
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Leslie Abarzua
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
| | - Christina Ridley
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Javier Tamayo-Leiva
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
- Correspondence:
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7
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Riemann L, Rahav E, Passow U, Grossart HP, de Beer D, Klawonn I, Eichner M, Benavides M, Bar-Zeev E. Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens. Front Microbiol 2022; 13:875050. [PMID: 35464923 PMCID: PMC9019601 DOI: 10.3389/fmicb.2022.875050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.
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Affiliation(s)
- Lasse Riemann
- Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Uta Passow
- Ocean Science Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Isabell Klawonn
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Meri Eichner
- Institute of Microbiology CAS, Centre ALGATECH, Třeboň, Czechia
| | - Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.,Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Edo Bar-Zeev
- The Jacob Blaustein Institutes for Desert Research, Zuckerberg Institute for Water Research (ZIWR), Ben-Gurion University of the Negev, Be'er Sheva, Israel
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8
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Meunier V, Bonnet S, Camps M, Benavides M, Dubosc J, Rodolfo-Metalpa R, Houlbrèque F. Ingestion of Diazotrophs Makes Corals More Resistant to Heat Stress. Biomolecules 2022; 12:biom12040537. [PMID: 35454126 PMCID: PMC9027526 DOI: 10.3390/biom12040537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 01/27/2023] Open
Abstract
Over the past decade, coral bleaching events have continued to recur and intensify. During bleaching, corals expel millions of their symbionts, depriving the host from its main food source. One mechanism used by corals to resist bleaching consists in exploiting food sources other than autotrophy. Among the food sources available in the reefs, dinitrogen (N2)-fixing prokaryotes or planktonic diazotrophs (hereafter called ‘PD’) have the particularity to reduce atmospheric dinitrogen (N2) and release part of this nitrogen (diazotroph-derived nitrogen or DDN) in bioavailable form. Here, we submitted coral colonies of Stylophora pistillata, fed or not with planktonic diazotrophs, to a temperature stress of up to 31 ± 0.5 °C and measured their physiological responses (photosynthetic efficiency, symbiont density, and growth rates). Heat-unfed colonies died 8 days after the heat stress while heat-PD-fed corals remained alive after 10 days of heat stress. The supply of PD allowed corals to maintain minimal chlorophyll concentration and symbiont density, sustaining photosynthetic efficiency and stimulating coral growth of up to 48% compared to unfed ones. By providing an alternative source of bioavailable nitrogen and carbon, this specific planktonic diazotroph feeding may have a profound potential for coral bleaching recovery.
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Affiliation(s)
- Valentine Meunier
- ENTROPIE UMR 9220 (CNRS, IRD, UR, UNC, IFREMER) Institut de Recherche pour le Développement, Nouméa 98848, New Caledonia; (R.R.-M.); (F.H.)
- Correspondence:
| | - Sophie Bonnet
- Aix-Marseille University, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (S.B.); (M.C.); (M.B.)
| | - Mercedes Camps
- Aix-Marseille University, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (S.B.); (M.C.); (M.B.)
| | - Mar Benavides
- Aix-Marseille University, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (S.B.); (M.C.); (M.B.)
| | - Jeff Dubosc
- Laboratory of Marine Biology and Ecology, Aquarium des Lagons, Noumea 98807, New Caledonia;
| | - Riccardo Rodolfo-Metalpa
- ENTROPIE UMR 9220 (CNRS, IRD, UR, UNC, IFREMER) Institut de Recherche pour le Développement, Nouméa 98848, New Caledonia; (R.R.-M.); (F.H.)
| | - Fanny Houlbrèque
- ENTROPIE UMR 9220 (CNRS, IRD, UR, UNC, IFREMER) Institut de Recherche pour le Développement, Nouméa 98848, New Caledonia; (R.R.-M.); (F.H.)
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9
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Geisler E, Rahav E, Bar-Zeev E. Contribution of Heterotrophic Diazotrophs to N2 Fixation in a Eutrophic River: Free-Living vs. Aggregate-Associated. Front Microbiol 2022; 13:779820. [PMID: 35237246 PMCID: PMC8882987 DOI: 10.3389/fmicb.2022.779820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Recent studies have indicated that heterotrophic diazotrophs are highly diverse and fix N2 in aquatic environments with potentially adverse conditions for diazotrophy, such as oxic and rich in total nitrogen. In this study, we compared the activity and diversity of heterotrophic diazotrophs associated with aggregates (>12 μm) to free-living cells in the eutrophic Qishon River during the winter and summer seasons. Overall, measured heterotrophic N2 fixation rates in the Qishon River ranged between 2.6–3.5 nmol N L–1 d–1. Heterotrophic N2 fixation was mainly associated with aggregates in the summer samples (74 ± 24%), whereas during the winter the bulk diazotrophic activity was mostly ascribed to the free-living fraction (90 ± 6%). In addition, immunolabeled micrographs indicated the presence of aggregate-associated heterotrophic diazotrophs in both seasons, while phototrophic diazotrophs were also captured during the winter. The richness of free-living and aggregate-associated heterotrophic diazotrophs were overall similar, yet the evenness of the later was significantly smaller, suggesting that few of the species gained advantage from particle lifestyle. The differences in the activity, micro-localization and diversity of the diazotrophic community were mostly attributed to spatiotemporal changes in the ambient C:N ratios (total organic carbon, TOC: total nitrogen) and the TOC concentrations. Taken together, our results shed new light on the contribution of heterotrophic diazotroph associated with aggregates to total heterotrophic N2 fixation in oxic, highly eutrophic aquatic environments.
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Affiliation(s)
- Eyal Geisler
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
- *Correspondence: Eyal Rahav,
| | - Edo Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
- Edo Bar-Zeev,
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10
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Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME JOURNAL 2021; 16:927-936. [PMID: 34697433 DOI: 10.1038/s41396-021-01135-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022]
Abstract
Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.
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Affiliation(s)
- Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.
| | - Juan José Pierella Karlusich
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Iva Veseli
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Fuessel
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University Stockholm, Stockholm, 106 91, Sweden
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
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11
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Chakraborty S, Andersen KH, Visser AW, Inomura K, Follows MJ, Riemann L. Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles. Nat Commun 2021; 12:4085. [PMID: 34215729 PMCID: PMC8253789 DOI: 10.1038/s41467-021-23875-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.
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Affiliation(s)
- Subhendu Chakraborty
- grid.5254.60000 0001 0674 042XDepartment of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark ,grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark ,grid.461729.f0000 0001 0215 3324Present Address: Systems Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Ken H. Andersen
- grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - André W. Visser
- grid.5170.30000 0001 2181 8870Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Keisuke Inomura
- grid.20431.340000 0004 0416 2242Graduate School of Oceanography, University of Rhode Island, Narragansett, RI USA
| | - Michael J. Follows
- grid.116068.80000 0001 2341 2786Department of Earth, Atmospheric and Planetary Sciences, MIT, Cambridge, MA USA
| | - Lasse Riemann
- grid.5254.60000 0001 0674 042XDepartment of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
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12
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Geisler E, Bogler A, Bar-Zeev E, Rahav E. Heterotrophic Nitrogen Fixation at the Hyper-Eutrophic Qishon River and Estuary System. Front Microbiol 2020; 11:1370. [PMID: 32670236 PMCID: PMC7326945 DOI: 10.3389/fmicb.2020.01370] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/27/2020] [Indexed: 12/04/2022] Open
Abstract
Planktonic heterotrophic diazotrophs (N2-fixers) are widely distributed in marine and freshwater systems, yet limited information is available on their activity, especially in environments with adverse conditions for diazotrophy (e.g., N-rich and oxygenated). Here, we followed the localization and activity of heterotrophic diazotrophs in the hyper-eutrophic N-rich Qishon River—an environment previously considered to be unfavorable for diazotrophy. Our results indicate high heterotrophic N2 fixation rates (up to 6.9 nmol N L–1 d–1), which were approximately three fold higher at an upstream location (freshwater) compared to an estuary (brackish) site. Further, active heterotrophic diazotrophs were capture associated with free-floating aggregates by a newly developed immunolocalization approach. These findings provide new insights on the activity of heterotrophic diazotrophs on aggregates in environments previously considered with adverse conditions for diazotrophy. Moreover, these new insights may be applicable to other aquatic regimes worldwide with similar N-rich/oxygenated conditions that should potentially inhibit N2 fixation.
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Affiliation(s)
- Eyal Geisler
- The Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR), Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Anne Bogler
- The Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edo Bar-Zeev
- The Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
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13
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Meunier V, Bonnet S, Pernice M, Benavides M, Lorrain A, Grosso O, Lambert C, Houlbrèque F. Bleaching forces coral's heterotrophy on diazotrophs and Synechococcus. THE ISME JOURNAL 2019; 13:2882-2886. [PMID: 31249389 PMCID: PMC6794269 DOI: 10.1038/s41396-019-0456-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 05/20/2019] [Accepted: 06/02/2019] [Indexed: 11/08/2022]
Abstract
Coral reefs are threatened by global warming, which disrupts the symbiosis between corals and their photosynthetic symbionts (Symbiodiniaceae), leading to mass coral bleaching. Planktonic diazotrophs or dinitrogen (N2)-fixing prokaryotes are abundant in coral lagoon waters and could be an alternative nutrient source for corals. Here we incubated untreated and bleached coral colonies of Stylophora pistillata with a 15N2-pre-labelled natural plankton assemblage containing diazotrophs. 15N2 assimilation rates in Symbiodiniaceae cells and tissues of bleached corals were 5- and 30-fold higher, respectively, than those measured in untreated corals, demonstrating that corals incorporate more nitrogen derived from planktonic diazotrophs under bleaching conditions. Bleached corals also preferentially fed on Synechococcus, nitrogen-rich picophytoplanktonic cells, instead of Prochlorococcus and picoeukaryotes, which have a lower cellular nitrogen content. By providing an alternative source of bioavailable nitrogen, both the incorporation of nitrogen derived from planktonic diazotrophs and the ingestion of Synechococcus may have profound consequences for coral bleaching recovery, especially for the many coral reef ecosystems characterized by high abundance and activity of planktonic diazotrophs.
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Affiliation(s)
- Valentine Meunier
- Laboratoire d'Excellence CORAIL, ENTROPIE (UMR9220), IRD, 98848, Nouméa cedex, New Caledonia.
| | - Sophie Bonnet
- Aix Marseille University, Université́ de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Mar Benavides
- Aix Marseille University, Université́ de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Anne Lorrain
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Olivier Grosso
- Aix Marseille University, Université́ de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | | | - Fanny Houlbrèque
- Laboratoire d'Excellence CORAIL, ENTROPIE (UMR9220), IRD, 98848, Nouméa cedex, New Caledonia
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14
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Li D, Liu J, Zhang R, Chen M, Yang W, Li J, Fang Z, Wang B, Qiu Y, Zheng M. N 2 fixation impacted by carbon fixation via dissolved organic carbon in the changing Daya Bay, South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:592-602. [PMID: 31022548 DOI: 10.1016/j.scitotenv.2019.04.176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
We present the first concurrent measurements of N2 fixation rates (15N2 uptake), primary production (14C uptake), dissolved organic carbon (DOC) concentrations, and diazotrophic community composition derived from nitrogenase (nifH) abundance in the subtropical Daya Bay (DB) of the coastal northern South China Sea (NSCS) from 2015 to 2017. N2 fixation rates ranged from n.d. - 4.51 nmol N L-1 h-1. Such values were generally higher than those reported in the neighbouring NSCS open waters and several well-studied oligotrophic waters, thereby suggesting that N-replete conditions do not prevent N2 fixation in coastal waters. N2 fixation rates were positively and significantly correlated with the primary production and the concentration of DOC in DB in the spring and summer. Combined with other lines of evidence, we suggest that N2 fixation may be facilitated by non-diazotrophic phytoplankton via a probable regulation of the quantity and quality (bioavailability) of DOC in DB. Since DB represents a suitable site that has experienced dramatic human-induced changes in environmental conditions, our results likely provide insights in understanding how N2 fixation and relevant biogeochemical processes may respond to intensified global anthropogenic forcing in similar coastal settings.
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Affiliation(s)
- Danyang Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 164, West Xingang Road, Guangzhou 510301, China
| | - Run Zhang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Weifeng Yang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
| | - Junjie Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ziming Fang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Bo Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Minfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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15
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Direct Detection of Heterotrophic Diazotrophs Associated with Planktonic Aggregates. Sci Rep 2019; 9:9288. [PMID: 31243322 PMCID: PMC6594930 DOI: 10.1038/s41598-019-45505-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/24/2019] [Indexed: 12/03/2022] Open
Abstract
N2 fixation by planktonic heterotrophic diazotrophs is more wide spread than previously thought, including environments considered “unfavorable” for diazotrophy. These environments include a substantial fraction of the aquatic biosphere such as eutrophic estuaries with high ambient nitrogen concentrations and oxidized aphotic water. Different studies suggested that heterotrophic diazotrophs associated with aggregates may promote N2 fixation in such environments. However, this association was never validated directly and relies mainly on indirect relationships and different statistical approaches. Here, we identified, for the first time, a direct link between active heterotrophic diazotrophs and aggregates that comprise polysaccharides. Our new staining method combines fluorescent tagging of active diazotrophs by nitrogenase-immunolabeling, polysaccharides staining by Alcian blue or concanavalin-A, and total bacteria via nucleic-acid staining. Concomitant to N2 fixation rates and bacterial activity, this new method provided specific localization of heterotrophic diazotrophs on artificial and natural aggregates. We postulate that the insights gained by this new visualization approach will have a broad significance for future research on the aquatic nitrogen cycle, including environments in which diazotrophy has traditionally been overlooked.
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16
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Inomura K, Bragg J, Riemann L, Follows MJ. A quantitative model of nitrogen fixation in the presence of ammonium. PLoS One 2018; 13:e0208282. [PMID: 30496286 PMCID: PMC6264846 DOI: 10.1371/journal.pone.0208282] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022] Open
Abstract
Nitrogen fixation provides bioavailable nitrogen, supporting global ecosystems and influencing global cycles of other elements. It provides an additional source of nitrogen to organisms at a cost of lower growth efficiency, largely due to respiratory control of intra-cellular oxygen. Nitrogen-fixing bacteria can, however, utilize both dinitrogen gas and fixed nitrogen, decreasing energetic costs. Here we present an idealized metabolic model of the heterotrophic nitrogen fixer Azotobacter vinelandii which, constrained by laboratory data, provides quantitative predictions for conditions under which the organism uses either ammonium or nitrogen fixation, or both, as a function of the relative supply rates of carbohydrate, fixed nitrogen as well as the ambient oxygen concentration. The model reveals that the organism respires carbohydrate in excess of energetic requirements even when nitrogen fixation is inhibited and respiratory protection is not essential. The use of multiple nitrogen source expands the potential niche and range for nitrogen fixation. The model provides a quantitative framework which can be employed in ecosystem and biogeochemistry models.
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Affiliation(s)
- Keisuke Inomura
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
| | - Jason Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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17
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Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N 2-Fixation Associated With Particles in Coastal Estuarine Waters. Front Microbiol 2018; 9:2759. [PMID: 30505296 PMCID: PMC6250843 DOI: 10.3389/fmicb.2018.02759] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Putative heterotrophic bacteria carrying out N2-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O2-inhibited N2-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N2-fixation. First, water enriched with natural particles or sediment showed higher N2-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N2-fixation, and indicates that resuspension of sediment material can elevate pelagic N2-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by “pioneer” bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N2-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.
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Affiliation(s)
- Jeppe N Pedersen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Deniz Bombar
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ryan W Paerl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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18
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Hazan O, Silverman J, Sisma-Ventura G, Ozer T, Gertman I, Shoham-Frider E, Kress N, Rahav E. Mesopelagic Prokaryotes Alter Surface Phytoplankton Production during Simulated Deep Mixing Experiments in Eastern Mediterranean Sea Waters. FRONTIERS IN MARINE SCIENCE 2018. [PMID: 0 DOI: 10.3389/fmars.2018.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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19
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Martínez-Pérez C, Mohr W, Schwedt A, Dürschlag J, Callbeck CM, Schunck H, Dekaezemacker J, Buckner CRT, Lavik G, Fuchs BM, Kuypers MMM. Metabolic versatility of a novel N 2 -fixing Alphaproteobacterium isolated from a marine oxygen minimum zone. Environ Microbiol 2018; 20:755-768. [PMID: 29194930 DOI: 10.1111/1462-2920.14008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 11/27/2022]
Abstract
The N2 -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula (Rhodobacteraceae, Alphaproteobacteria) and its capability to fix N2 was confirmed in laboratory experiments. Genome sequencing revealed that it is a strict heterotroph with a high versatility in substrate utilization and energy acquisition mechanisms. Pathways for sulfide oxidation and nitrite reduction to nitrous oxide are encoded in the genome and might explain the presence throughout the Peruvian OMZ. The genome further indicates that this novel organism could be in direct interaction with other microbes or particles. NanoSIMS analyses were used to compare the metabolic potential of S. castanea with single-cell activity in situ; however, N2 fixation by this diazotroph could not be detected at the isolation site. While the biogeochemical impact of S. castanea is yet to be resolved, its abundance and widespread distribution suggests that its potential to contribute to the marine N input could be significant at a larger geographical scale.
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Affiliation(s)
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anne Schwedt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Julia Dürschlag
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Harald Schunck
- Institute for General Microbiology, University of Kiel, Kiel, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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20
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Broman E, Sachpazidou V, Pinhassi J, Dopson M. Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism. Front Microbiol 2017; 8:2453. [PMID: 29312168 PMCID: PMC5733055 DOI: 10.3389/fmicb.2017.02453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 01/24/2023] Open
Abstract
The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.
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Affiliation(s)
- Elias Broman
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Varvara Sachpazidou
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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21
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Moisander PH, Benavides M, Bonnet S, Berman-Frank I, White AE, Riemann L. Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments. Front Microbiol 2017; 8:1736. [PMID: 28943875 PMCID: PMC5596534 DOI: 10.3389/fmicb.2017.01736] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/25/2017] [Indexed: 11/22/2022] Open
Abstract
Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N2) fixation. Other potentially N2-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N2 fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N2 fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L−1 d−1). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that nifH transcription data for NCDs have been reported in only a few studies where N2 fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.
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Affiliation(s)
- Pia H Moisander
- Department of Biology, University of Massachusetts DartmouthNorth Dartmouth, MA, United States
| | - Mar Benavides
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
| | - Sophie Bonnet
- Centre National de la Recherche Scientifique, IRD, Aix-Marseille Université, Université de ToulonMarseille, France
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat Gan, Israel
| | - Angelicque E White
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State UniversityCorvallis, OR, United States
| | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
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22
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Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean. ISME JOURNAL 2017; 11:2356-2367. [PMID: 28742073 DOI: 10.1038/ismej.2017.97] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/31/2017] [Accepted: 05/12/2017] [Indexed: 11/08/2022]
Abstract
Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day-1) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day-1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N2-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.
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23
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Dissolved organic matter uptake by Trichodesmium in the Southwest Pacific. Sci Rep 2017; 7:41315. [PMID: 28117432 PMCID: PMC5259775 DOI: 10.1038/srep41315] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022] Open
Abstract
The globally distributed diazotroph Trichodesmium contributes importantly to nitrogen inputs in the oligotrophic oceans. Sites of dissolved organic matter (DOM) accumulation could promote the mixotrophic nutrition of Trichodesmium when inorganic nutrients are scarce. Nano-scale secondary ion mass spectrometry (nanoSIMS) analyses of individual trichomes sampled in the South Pacific Ocean, showed significant 13C-enrichments after incubation with either 13C-labeled carbohydrates or amino acids. These results suggest that DOM could be directly taken up by Trichodesmium or primarily consumed by heterotrophic epibiont bacteria that ultimately transfer reduced DOM compounds to their host trichomes. Although the addition of carbohydrates or amino acids did not significantly affect bulk N2 fixation rates, N2 fixation was enhanced by amino acids in individual colonies of Trichodesmium. We discuss the ecological advantages of DOM use by Trichodesmium as an alternative to autotrophic nutrition in oligotrophic open ocean waters.
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24
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Frank IE, Turk-Kubo KA, Zehr JP. Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:905-916. [PMID: 27557869 DOI: 10.1111/1758-2229.12455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.
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Affiliation(s)
- Ildiko E Frank
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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25
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Bombar D, Paerl RW, Riemann L. Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection. Trends Microbiol 2016; 24:916-927. [PMID: 27476748 DOI: 10.1016/j.tim.2016.07.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/20/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
Abstract
The nitrogen input through biological N2 fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N2-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N2 at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N2 fixation on local and global scales.
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Affiliation(s)
- Deniz Bombar
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ryan W Paerl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
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26
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Zhou H, Dang H, Klotz MG. Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas. Front Microbiol 2016; 7:1111. [PMID: 27489551 PMCID: PMC4951488 DOI: 10.3389/fmicb.2016.01111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments.
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Affiliation(s)
- Haixia Zhou
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China; Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China)Qingdao, China; Department of Food Quality and Safety, College of Life Science, Dezhou UniversityDezhou, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University Xiamen, China
| | - Martin G Klotz
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China; Department of Biology and School of Earth and Environmental Sciences, Queens College, City University of New YorkQueens, NY, USA
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27
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Rahav E, Giannetto MJ, Bar-Zeev E. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline. Sci Rep 2016; 6:27858. [PMID: 27306501 PMCID: PMC4910064 DOI: 10.1038/srep27858] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/26/2016] [Indexed: 11/15/2022] Open
Abstract
N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.
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Affiliation(s)
- E. Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, 8030, Israel
| | - M. J. Giannetto
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, USA
| | - E. Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Midreshet Ben-Gurion, Israel
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28
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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29
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Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific). PLoS One 2015; 10:e0143775. [PMID: 26659074 PMCID: PMC4684240 DOI: 10.1371/journal.pone.0143775] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/09/2015] [Indexed: 01/31/2023] Open
Abstract
Dinitrogen (N2) fixation was investigated together with organic matter composition in the mesopelagic zone of the Bismarck (Transect 1) and Solomon (Transect 2) Seas (Southwest Pacific). Transparent exopolymer particles (TEP) and the presence of compounds sharing molecular formulae with saturated fatty acids and sugars, as well as dissolved organic matter (DOM) compounds containing nitrogen (N) and phosphorus (P) were higher on Transect 1 than on Transect 2, while oxygen concentrations showed an opposite pattern. N2 fixation rates (up to ~1 nmol N L-1 d-1) were higher in Transect 1 than in Transect 2, and correlated positively with TEP, suggesting a dependence of diazotroph activity on organic matter. The scores of the multivariate ordination of DOM molecular formulae and their relative abundance correlated negatively with bacterial abundances and positively with N2 fixation rates, suggesting an active bacterial exploitation of DOM and its use to sustain diazotrophic activity. Sequences of the nifH gene clustered with Alpha-, Beta-, Gamma- and Deltaproteobacteria, and included representatives from Clusters I, III and IV. A third of the clone library included sequences close to the potentially anaerobic Cluster III, suggesting that N2 fixation was partially supported by presumably particle-attached diazotrophs. Quantitative polymerase chain reaction (qPCR) primer-probe sets were designed for three phylotypes and showed low abundances, with a phylotype within Cluster III at up to 103nifH gene copies L-1. These results provide new insights into the ecology of non-cyanobacterial diazotrophs and suggest that organic matter sustains their activity in the mesopelagic ocean.
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30
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Raveh O, David N, Rilov G, Rahav E. The Temporal Dynamics of Coastal Phytoplankton and Bacterioplankton in the Eastern Mediterranean Sea. PLoS One 2015; 10:e0140690. [PMID: 26474399 PMCID: PMC4608699 DOI: 10.1371/journal.pone.0140690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022] Open
Abstract
This study considers variability in phytoplankton and heterotrophic bacterial abundances and production rates, in one of the most oligotrophic marine regions in the world–the Levantine Basin. The temporal dynamics of these planktonic groups were studied in the coastal waters of the southeastern Mediterranean Sea approximately every two weeks for a total of two years. Heterotrophic bacteria were abundant mostly during late summer and midwinter, and were positively correlated with bacterial production and with N2 fixation. Based on size fractionating, picophytoplankton was abundant during the summer, whereas nano-microphytoplankton predominated during the winter and early spring, which were also evident in the size-fractionated primary production rates. Autotrophic abundance and production correlated negatively with temperature, but did not correlate with inorganic nutrients. Furthermore, a comparison of our results with results from the open Levantine Basin demonstrates that autotrophic and heterotrophic production, as well as N2 fixation rates, are considerably higher in the coastal habitat than in the open sea, while nutrient levels or cell abundance are not different. These findings have important ecological implications for food web dynamics and for biological carbon sequestration in this understudied region.
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Affiliation(s)
- Ofrat Raveh
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Niv David
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gil Rilov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
- * E-mail:
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31
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Bar-Zeev E, Rahav E. Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system. Front Microbiol 2015; 6:403. [PMID: 26042092 PMCID: PMC4436900 DOI: 10.3389/fmicb.2015.00403] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/17/2015] [Indexed: 12/03/2022] Open
Abstract
This study explores the role of transparent exopolymer particles (TEP) as an additional carbon source for heterotrophic microbial activity in the eutrophic Qishon estuary. From the coastal station and upstream the estuary; TEP concentrations, β-glucosidase activity, bacterial production and abundance have gradually increased. TEP were often found as bio-aggregates, scaffolding algae, detritus matter and bacteria that likely formed “hotspots” for enhance microbial activity. To further demonstrate the link between TEP and heterotrophic bacterial activity, confined incubations with ambient and polysaccharide-enriched estuary water were carried out. Following polysaccharide addition, elevated (~50%) β-glucosidase activity rates were observed, leading to TEP hydrolysis. This newly formed bioavailable carbon resulted in significantly higher growth rates, with up to a 5-fold increase in heterotrophic bacterial biomass, comprising mostly high nucleic acid content bacteria. Taking together the findings from this research, we conclude that even in highly eutrophic environments heterotrophic bacteria may still be carbon limited. Further, TEP as a polysaccharide matrix can act as a metabolic surrogate, adding fresh bioavailable carbon through tight associations with bacteria in eutrophic ecosystems such as the Qishon estuary.
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Affiliation(s)
- Edo Bar-Zeev
- Department of Chemical and Environmental Engineering, Yale University New Haven, CT, USA
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography Haifa, Israel
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32
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Techtmann SM, Fortney JL, Ayers KA, Joyner DC, Linley TD, Pfiffner SM, Hazen TC. The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth. PLoS One 2015; 10:e0120605. [PMID: 25807542 PMCID: PMC4373936 DOI: 10.1371/journal.pone.0120605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/24/2015] [Indexed: 11/26/2022] Open
Abstract
The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.
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Affiliation(s)
- Stephen M. Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Julian L. Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kati A. Ayers
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Dominique C. Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas D. Linley
- Ocean Lab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom
| | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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33
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Klawonn I, Bonaglia S, Brüchert V, Ploug H. Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates. ISME JOURNAL 2015; 9:1456-66. [PMID: 25575306 DOI: 10.1038/ismej.2014.232] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/31/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022]
Abstract
Colonies of N(2)-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates' anoxic centres. (15)N-isotope labelling experiments and nutrient analyses revealed that N(2) fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N(2) were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (⩾1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (<1 to ⩾0.1 mm) may only arise in low-oxygenated waters (⩽25 μM). We propose that the net effect of aggregates on nitrogen loss is negligible in NO(3)(-)-depleted, fully oxygenated (surface) waters. In NO(3)(-)-enriched (>1.5 μM), O(2)-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes.
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Affiliation(s)
- Isabell Klawonn
- Stockholm University, Department of Ecology, Environment and Plant Sciences, Stockholm, Sweden
| | - Stefano Bonaglia
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm, Sweden
| | - Volker Brüchert
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm, Sweden
| | - Helle Ploug
- 1] Stockholm University, Department of Ecology, Environment and Plant Sciences, Stockholm, Sweden [2] University of Gothenburg, Department of Biology and Environmental Sciences, Gothenburg, Sweden
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34
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Bonnet S, Dekaezemacker J, Turk-Kubo KA, Moutin T, Hamersley RM, Grosso O, Zehr JP, Capone DG. Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean. PLoS One 2013; 8:e81265. [PMID: 24349048 PMCID: PMC3861260 DOI: 10.1371/journal.pone.0081265] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/10/2013] [Indexed: 12/02/2022] Open
Abstract
We examined rates of N2 fixation from the surface to 2000 m depth in the Eastern Tropical South Pacific (ETSP) during El Niño (2010) and La Niña (2011). Replicated vertical profiles performed under oxygen-free conditions show that N2 fixation takes place both in euphotic and aphotic waters, with rates reaching 155 to 509 µmol N m−2 d−1 in 2010 and 24±14 to 118±87 µmol N m−2 d−1 in 2011. In the aphotic layers, volumetric N2 fixation rates were relatively low (<1.00 nmol N L−1 d−1), but when integrated over the whole aphotic layer, they accounted for 87–90% of total rates (euphotic+aphotic) for the two cruises. Phylogenetic studies performed in microcosms experiments confirm the presence of diazotrophs in the deep waters of the Oxygen Minimum Zone (OMZ), which were comprised of non-cyanobacterial diazotrophs affiliated with nifH clusters 1K (predominantly comprised of α-proteobacteria), 1G (predominantly comprised of γ-proteobacteria), and 3 (sulfate reducing genera of the δ-proteobacteria and Clostridium spp., Vibrio spp.). Organic and inorganic nutrient addition bioassays revealed that amino acids significantly stimulated N2 fixation in the core of the OMZ at all stations tested and as did simple carbohydrates at stations located nearest the coast of Peru/Chile. The episodic supply of these substrates from upper layers are hypothesized to explain the observed variability of N2 fixation in the ETSP.
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Affiliation(s)
- Sophie Bonnet
- Mediterranean Institute of Oceanography, Institut de Recherche pour le Développement, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille/Noumea, New Caledonia, France
- * E-mail:
| | - Julien Dekaezemacker
- Mediterranean Institute of Oceanography, Institut de Recherche pour le Développement, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille/Noumea, New Caledonia, France
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Thierry Moutin
- Mediterranean Institute of Oceanography, Institut de Recherche pour le Développement, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille/Noumea, New Caledonia, France
| | - Robert M. Hamersley
- Environmental Studies, Soka University of America, Aliso Viejo, California, United States of America
| | - Olivier Grosso
- Mediterranean Institute of Oceanography, Institut de Recherche pour le Développement, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille/Noumea, New Caledonia, France
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Douglas G. Capone
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
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