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Cerdán-García E, Álvarez-Salgado XA, Arístegui J, Martínez-Marrero A, Benavides M. Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed. Commun Biol 2024; 7:929. [PMID: 39095605 PMCID: PMC11297262 DOI: 10.1038/s42003-024-06576-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.
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Affiliation(s)
- E Cerdán-García
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, France.
- Turing Centre for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | | | - J Arístegui
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - A Martínez-Marrero
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - M Benavides
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, France.
- Turing Centre for Living Systems, Aix-Marseille University, 13009, Marseille, France.
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2
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Rose SA, Robicheau BM, Tolman J, Fonseca-Batista D, Rowland E, Desai D, Ratten JM, Kantor EJH, Comeau AM, Langille MG, Jerlström-Hultqvist J, Devred E, Sarthou G, Bertrand EM, LaRoche J. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni. SCIENCE ADVANCES 2024; 10:eadn1476. [PMID: 39083619 PMCID: PMC11290528 DOI: 10.1126/sciadv.adn1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.
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Affiliation(s)
- Sonja A. Rose
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Debany Fonseca-Batista
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ella Joy H. Kantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M. Comeau
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G.I. Langille
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Emmanuel Devred
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Halifax, Nova Scotia, Canada
| | | | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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3
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Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
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Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
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4
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Robicheau BM, Tolman J, Rose S, Desai D, LaRoche J. Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities. FEMS Microbiol Ecol 2023; 99:fiad122. [PMID: 37951299 PMCID: PMC10656255 DOI: 10.1093/femsec/fiad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/30/2023] [Accepted: 11/09/2023] [Indexed: 11/13/2023] Open
Abstract
We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Sonja Rose
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
- Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
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5
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Zhang X, Cui L, Liu S, Li J, Wu Y, Ren Y, Huang X. Seasonal dynamics of bacterial community and co-occurrence with eukaryotic phytoplankton in the Pearl River Estuary. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106193. [PMID: 37832281 DOI: 10.1016/j.marenvres.2023.106193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
In this study, we investigated the taxonomic composition of the bacteria and phytoplankton communities in the Pearl River Estuary (PRE) through Illumina sequencing of the V3-V4 region of the 16 S rRNA gene. Furthermore, their relationships as well as recorded environmental variables were explored by co-occurrence networks. Bacterial community composition was different in two size fractions, as well as along the salinity gradient across two seasons. Free-living (FL) communities were dominated by pico-sized Cyanobacteria (Synechococcus CC9902) while Exiguobacterium, Halomonas and Pseudomonas were predominantly associated with particle-associated (PA) lifestyle, and Cyanobium PCC-6307 exhibited seasonal shifts in lifestyles in different seasons. In wet season, bacterial community composition was characterized by abundance of Cyanobacteria, Actinobacteria, and Bacteroidetes, which were tightly linked with high riverine inflow. While in dry season, Proteobacteria increased in prevalence, especially for Psychrobacter, NOR5/OM60 clade and Pseudomonas, which were thrived in lower water temperature and higher salinity. Moreover, we discovered that differences between PA and FL composition were more significant in the wet season than in the dry season, which may be due to better nutritional conditions of particles (indicated by POC%) in the wet season and then attract more diverse PA populations. Based on the analysis of plastidial 16 S rRNA genes, abundant small-sized mixotrophic phytoplankton (Dinophyceae, Euglenida and Haptophyta) were identified in the PRE. The complexity of co-occurrence network increased from FL to PA fractions in both seasons, which suggested that suspended particles can provide ecological niches for particle-associated colonizers contributing to the maintenance of a more stable community structure. In addition, the majority of phytoplankton species exhibited positive co-occurrences with both other phytoplankton species and bacterial counterparts, indicating the mutual cooperation between phytoplankton assemblages and specific bacterial populations e likely benefited from phytoplankton-derived organic compounds. This study enhances our understanding of the seasonal and spatial dynamics of bacterial communities and their potential relationship with phytoplankton assembly in estuarine waters.
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Yuzheng Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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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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7
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Jabir T, Jain A, Vipindas PV, Krishnan KP. Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard). MICROBIAL ECOLOGY 2023; 86:2733-2746. [PMID: 37532947 DOI: 10.1007/s00248-023-02276-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.
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Affiliation(s)
- Thajudeen Jabir
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India.
| | - Anand Jain
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama, Goa, 403 804, India
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8
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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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9
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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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10
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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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11
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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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12
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Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa. Microorganisms 2022; 10:microorganisms10020216. [PMID: 35208671 PMCID: PMC8880511 DOI: 10.3390/microorganisms10020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/04/2021] [Accepted: 12/23/2021] [Indexed: 12/10/2022] Open
Abstract
Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.
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13
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Wang G, Xia X, Liu S, Wang J, Zhang S. Low diffusive nitrogen loss of urban inland waters with high nitrogen loading. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148023. [PMID: 34323840 DOI: 10.1016/j.scitotenv.2021.148023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Little is known about the exchange of gaseous nitrogen (N2) with the atmosphere from urban inland waters, which are characterized by low carbon-to‑nitrogen ratios and low nitrogen-to‑phosphorus ratios. Here, we studied diffusive nitrogen loss based on the measurement of dissolved N2 concentrations and related gene abundance of N2 production and fixation in rivers and lakes in the megacity of Beijing, China, between 2018 and 2020. The excess dissolved N2 (△N2) ranged from -51.2 to 56.8 μmol L-1 (average - 0.03 ± 13.8 μmol L-1), and approximately 43% of the river samples and 72% of the lake samples being undersaturated with N2, suggesting that the lakes mainly acted as a role of N2 sink. The N2 removal fraction (△N2/DIN, average 3.5 ± 4.3%) at the sites of rivers with positive △N2 was lower than that in other rivers around the world. The average N2 flux (0.8 ± 23.9 mmol m-2 d-1) in the urban rivers was also lower than that in other rivers. The low carbon-to‑nitrogen ratios in Beijing inland waters are not beneficial for N2 production during denitrification, and low nitrogen-to‑phosphorus ratios potentially favor N2 fixation with a high abundance of the nitrogenase nifH gene in the sediment, resulting in low net N2 production. The traditional paradigm is that rivers constantly lose vast N to the atmosphere via denitrification and anammox, but this study indicates that urban inland rivers emit negligible N even under high nitrogen loading.
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Affiliation(s)
- Gongqin Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Shaoda Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junfeng Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Sibo Zhang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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14
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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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15
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In silico determination of nitrogen metabolism in microbes from extreme conditions using metagenomics. Arch Microbiol 2021; 203:2521-2540. [PMID: 33677634 DOI: 10.1007/s00203-021-02227-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/21/2020] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The acid ponds of the Danakil Depression in northern Ethiopia are polyextreme environments that exceed the normal physicochemical limits of pH, salinity, ion content, and temperature. We tested for the occurrence of DNA-based life in this environment using Metagenomic Shotgun DNA sequencing approaches. The obtained sequences were examined by the bioinformatic tools MetaSpades, DIAMOND and MEGAN 6-CE, and we were able to bin more than 90% of the metagenomics contigs of Dallol and Black Water to the Bacteria domain, and to the Proteobacteria phylum. Predictions of gene function based on SEED disclosed the presence of different nutrient cycles in the acid ponds. For this study, we focused on partial or completely sequenced genes involved in nitrogen metabolism. The KEGG nitrogen metabolism pathway mapping results for both acid ponds showed that all the predicted genes are involved directly or indirectly in the assimilation of ammonia and no dissimilation or nitrification process was identified. Furthermore, the deduced nitrogen fixation in the two acid ponds based on SEED classification indicated the presence of different sets of nitrogen fixing (nif) genes for biosynthesis and maturation of nitrogenase. Based on the in silico analysis, the predicted proteins involved in nitrogen fixation, especially the cysteine desulfurase and [4Fe-4S] ferredoxin, from both acid ponds are unique with less than 80% sequence similarity to the next closest protein sequence. Considering the extremity of the environmental conditions of the two acid ponds in the Danakil depression, this metagenomics dataset can add to the study of unique gene functions in nitrogen metabolism that enable thriving biocommunities in hypersaline and highly acidic conditions.
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16
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Cabello AM, Turk‐Kubo KA, Hayashi K, Jacobs L, Kudela RM, Zehr JP. Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California. JOURNAL OF PHYCOLOGY 2020; 56:1521-1533. [PMID: 32609873 PMCID: PMC7754506 DOI: 10.1111/jpy.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/10/2020] [Indexed: 05/20/2023]
Abstract
In the last decade, the known biogeography of nitrogen fixation in the ocean has been expanded to colder and nitrogen-rich coastal environments. The symbiotic nitrogen-fixing cyanobacteria group A (UCYN-A) has been revealed as one of the most abundant and widespread nitrogen-fixers, and includes several sublineages that live associated with genetically distinct but closely related prymnesiophyte hosts. The UCYN-A1 sublineage is associated with an open ocean picoplanktonic prymnesiophyte, whereas UCYN-A2 is associated with the coastal nanoplanktonic coccolithophore Braarudosphaera bigelowii, suggesting that different sublineages may be adapted to different environments. Here, we study the diversity of nifH genes present at the Santa Cruz Municipal Wharf in the Monterey Bay (MB), California, and report for the first time the presence of multiple UCYN-A sublineages, unexpectedly dominated by the UCYN-A2 sublineage. Sequence and quantitative PCR data over an 8-year time-series (2011-2018) showed a shift toward increasing UCYN-A2 abundances after 2013, and a marked seasonality for this sublineage which was present during summer-fall months, coinciding with the upwelling-relaxation period in the MB. Increased abundances corresponded to positive temperature anomalies in MB, and we discuss the possibility of a benthic life stage of the associated coccolithophore host to explain the seasonal pattern. The dominance of UCYN-A2 in coastal waters of the MB underscores the need to further explore the habitat preference of the different sublineages in order to provide additional support for the hypothesis that UCYN-A1 and UCYN-A2 sublineages are different ecotypes.
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Affiliation(s)
- Ana M. Cabello
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
- Centro Oceanográfico de MálagaInstituto Español de OceanografíaFuengirolaMálaga29001Spain
| | - Kendra A. Turk‐Kubo
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Kendra Hayashi
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Lucien Jacobs
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Raphael M. Kudela
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
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17
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Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A. ISME JOURNAL 2020; 15:124-128. [PMID: 32918066 DOI: 10.1038/s41396-020-00765-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Non-cyanobacterial diazotrophs (NCDs) have recently emerged as potentially important contributors to marine nitrogen fixation. One of the most widely distributed NCDs is Gamma-A, yet information about its autecology is still scarce and solely relies on the PCR-based detection of its nitrogenase (nifH) gene in seawater, since previous metagenomic surveys targeting free-living planktonic size fractions (<3 μm) have not detected it. Here, we explore the diversity, biogeography, size-distribution, and nitrogenase gene expression of Gamma-A across four larger planktonic size-fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) using metagenomes and metatranscriptomes from the Tara Oceans. We detected a single variant of a complete Gamma-A nifH gene along with other nitrogenase-related genes (nifKDT) within a metatranscriptomic-based contig of the Marine Atlas of Tara Ocean Unigenes. Gamma-A was detected in tropical and subtropical oceanic regions across all the size-fractions. However, the highest gene and transcript abundances were found in the 0.8-5 and 5-20 μm size-fractions at the surface, whereas abundances at the deep chlorophyll maximum were lower and similar across all size-fractions. The ubiquitous presence of active Gamma-A in large planktonic size-fractions suggests a filamentous or particle-attached lifestyle and places its potential to fix nitrogen in larger planktonic compartments.
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18
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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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19
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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20
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Abstract
Nitrogen fixation, the reduction of atmospheric dinitrogen gas (N2) to ammonia, is critical for biological productivity but is difficult to study in the vast expanse of the global ocean. Decades of field studies and the infusion of molecular biological, genomic, isotopic, and geochemical modeling approaches have led to new paradigms and questions. The discovery of previously unknown N2-fixing (diazotrophic) microorganisms and unusual physiological adaptations, combined with diagnostic distributions of nutrients and their isotopes as well as measured and modeled biogeographic patterns, have revolutionized our understanding of marine N2 fixation and its role in the global nitrogen cycle. Anthropogenic upper-ocean warming, increased dissolved carbon dioxide, and acidification will affect the distribution and relative importance of specific subgroups of N2 fixers in the sea; these changes have implications for foodwebs and biogeochemical cycles.
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Affiliation(s)
- Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95003, USA
| | - Douglas G. Capone
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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21
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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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22
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Dang H, Klotz MG, Lovell CR, Sievert SM. Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients. Front Microbiol 2019; 10:115. [PMID: 30800101 PMCID: PMC6375845 DOI: 10.3389/fmicb.2019.00115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- 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 University, Xiamen, China.,School of Molecular Biosciences, Washington State University, Richland, WA, United States
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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