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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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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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3
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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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4
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Messer LF, Brown MV, Van Ruth PD, Doubell M, Seymour JR. Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs. PeerJ 2021; 9:e10809. [PMID: 33717676 PMCID: PMC7931716 DOI: 10.7717/peerj.10809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/30/2020] [Indexed: 11/20/2022] Open
Abstract
Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and 15N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10-64 nmol L-1 d-1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L-1 d-1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N2 fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N2 fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N2 fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.
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Affiliation(s)
- Lauren F Messer
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia.,Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Paul D Van Ruth
- Aquatic Sciences, South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Mark Doubell
- Aquatic Sciences, South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
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5
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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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6
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Yousuf J, Thajudeen J, Rahiman M, Krishnankutty S, P. Alikunj A, A. Abdulla MH. Nitrogen fixing potential of various heterotrophicBacillusstrains from a tropical estuary and adjacent coastal regions. J Basic Microbiol 2017; 57:922-932. [DOI: 10.1002/jobm.201700072] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/18/2017] [Accepted: 07/07/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Jesmi Yousuf
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences; Cochin University of Science and Technology; Cochin Kerala India
- School of Environmental Sciences; Mahatma Gandhi University; Kottayam Kerala India
| | - Jabir Thajudeen
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences; Cochin University of Science and Technology; Cochin Kerala India
| | - Mujeeb Rahiman
- Post Graduate and Research Department of Aquaculture and Fishery Microbiology; M.E.S Ponnani College; Ponnani Kerala India
| | - Soumya Krishnankutty
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences; Cochin University of Science and Technology; Cochin Kerala India
| | - Aneesa P. Alikunj
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences; Cochin University of Science and Technology; Cochin Kerala India
| | - Mohamed H. A. Abdulla
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences; Cochin University of Science and Technology; Cochin Kerala India
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7
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Effects of Gelling Agent and Extracellular Signaling Molecules on the Culturability of Marine Bacteria. Appl Environ Microbiol 2017; 83:AEM.00243-17. [PMID: 28213548 DOI: 10.1128/aem.00243-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/15/2017] [Indexed: 01/08/2023] Open
Abstract
Only 1% of marine bacteria are currently culturable using standard laboratory procedures, and this is a major obstacle for our understanding of the biology of marine microorganisms and for the discovery of novel microbial natural products. Therefore, the purpose of this study was to investigate if improved cultivation conditions, including the use of an alternative gelling agent and supplementation with signaling molecules, improve the culturability of bacteria from seawater. Replacing agar with gellan gum improved viable counts 3- to 40-fold, depending on medium composition and incubation conditions, with a maximum of 6.6% culturability relative to direct cell counts. Through V4 amplicon sequencing we found that culturable diversity was also affected by a change in gelling agent, facilitating the growth of orders not culturable on agar-based substrates. Community analyses showed that communities grown on gellan gum substrates were significantly different from communities grown on agar and that they covered a larger fraction of the seawater community. Other factors, such as incubation temperature and time, had less obvious effects on viable counts and culturable diversity. Supplementation with acylated homoserine lactones (AHLs) did not have a positive effect on total viable counts or a strong effect on culturable diversity. However, low concentrations of AHLs increased the relative abundance of sphingobacteria. Hence, with alternative growth substrates, it is possible to significantly increase the number and diversity of cultured marine bacteria.IMPORTANCE Serious challenges to human health, such as the occurrence and spread of antibiotic resistance and an aging human population in need of bioactive pharmaceuticals, have revitalized the search for natural microbial products. The marine environment, representing the largest ecosystem in the biosphere, harbors an immense and virtually untapped microbial diversity producing unique bioactive compounds. However, we are currently able to cultivate only a minute fraction of this diversity. The lack of cultivated microbes is hampering not only bioprospecting efforts but also our general understanding of marine microbes. In this study, we present a means to increase the number and diversity of cultured bacteria from seawater, showing that relatively simple changes to medium components may facilitate the isolation and growth of hitherto unknown bacterial orders.
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8
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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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9
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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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10
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Cheung S, Xia X, Guo C, Liu H. Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome. JOURNAL OF PLANKTON RESEARCH 2016; 38:380-391. [PMID: 27275037 PMCID: PMC4889993 DOI: 10.1093/plankt/fbw003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 01/11/2016] [Indexed: 05/10/2023]
Abstract
Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.
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11
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Screening of bacteria for self-healing of concrete cracks and optimization of the microbial calcium precipitation process. Appl Microbiol Biotechnol 2016; 100:6661-6670. [PMID: 26883348 DOI: 10.1007/s00253-016-7382-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
Abstract
A novel high-throughput strategy was developed to determine the calcium precipitation activity (CPA) of mineralization bacteria used for self-healing of concrete cracks. A bacterial strain designated as H4 with the highest CPA of 94.8 % was screened and identified as a Bacillus species based on 16S rDNA sequence and phylogenetic tree analysis. Furthermore, the effects of certain influential factors on the microbial calcium precipitation process of H4 were evaluated. The results showed that lactate and nitrate are the best carbon and nitrogen sources, with optimal concentrations of approximately 25 and 18 mM, respectively. The H4 strain is able to maintain a high CPA in the pH range of 9.5-11.0, and a suitable initial spore concentration is 4.0 × 10(7) spores/ml. Moreover, an ambient Ca(2+) concentration greater than 60 mM resulted in a serious adverse impact not only on the CPA but also on the growth of H4, suggesting that the maintenance of the Ca(2+) concentration at a low level is necessary for microbial self-healing of concrete cracks.
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12
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Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water. mBio 2015; 6:e00929. [PMID: 26152586 PMCID: PMC4495170 DOI: 10.1128/mbio.00929-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas stutzeri strain BAL361 and Raoultella ornithinolytica strain BAL286, which are gammaproteobacteria, and Rhodopseudomonas palustris strain BAL398, an alphaproteobacterium. Genome sequencing revealed that all were metabolically versatile and that the gene clusters encoding the N2 fixation complex varied in length and complexity between isolates. All three isolates could sustain growth by N2 fixation in the absence of reactive N, and this fixation was stimulated by low concentrations of oxygen in all three organisms (≈4 to 40 µmol O2 liter−1). P. stutzeri BAL361 did, however, fix N at up to 165 µmol O2 liter−1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4+) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations between nitrogenase reductase gene expression and ethylene (C2H4) production indicated tight posttranscriptional-level control. The N2 fixation rates obtained suggested that, given the right conditions, these heterotrophic diazotrophs could contribute significantly to in situ rates. The biological process of importing atmospheric N2 is of paramount importance in terrestrial and aquatic ecosystems. In the oceans, a diverse array of prokaryotes seemingly carry the genetic capacity to perform this process, but lack of knowledge about their autecology and the factors that constrain their N2 fixation hamper an understanding of their ecological importance in marine waters. The present study documents a high variability of genomic and ecophysiological properties related to N2 fixation in three heterotrophic isolates obtained from estuarine surface waters and shows that these organisms fix N2 under a surprisingly broad range of conditions and at significant rates. The observed intricate regulation of N2 fixation for the isolates indicates that indigenous populations of heterotrophic diazotrophs have discrete strategies to cope with environmental controls of N2 fixation. Hence, community-level generalizations about the regulation of N2 fixation in marine heterotrophic bacterioplankton may be problematic.
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13
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Significant N₂ fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries. ISME JOURNAL 2014; 9:273-85. [PMID: 25026373 DOI: 10.1038/ismej.2014.119] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 11/08/2022]
Abstract
Nitrogen (N) fixation is fueling planktonic production in a multitude of aquatic environments. In meso- and poly-haline estuaries, however, the contribution of N by pelagic N₂ fixation is believed to be insignificant due to the high input of N from land and the presumed absence of active N₂-fixing organisms. Here we report N₂ fixation rates, nifH gene composition and nifH gene transcript abundance for key diazotrophic groups over 1 year in two contrasting, temperate, estuarine systems: Roskilde Fjord (RF) and the Great Belt (GB) strait. Annual pelagic N₂ fixation rates averaged 17 and 61 mmol N m(-2) per year at the two sites, respectively. In RF, N₂ fixation was mainly accompanied by transcripts related to heterotrophic (for example, Pseudomonas sp.) and photoheterotrophic bacteria (for example, unicellular diazotrophic cyanobacteria group A). In the GB, the first of two N₂ fixation peaks coincided with a similar nifH-expressing community as in RF, whereas the second peak was synchronous with increased nifH expression by an array of diazotrophs, including heterotrophic organisms as well as the heterocystous cyanobacterium Anabaena. Thus, we show for the first time that significant planktonic N₂ fixation takes place in mesohaline, temperate estuaries and that the importance of heterotrophic, photoheterotrophic and photosynthetic diazotrophs is clearly variable in space and time.
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