1
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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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Coale TH, Loconte V, Turk-Kubo KA, Vanslembrouck B, Mak WKE, Cheung S, Ekman A, Chen JH, Hagino K, Takano Y, Nishimura T, Adachi M, Le Gros M, Larabell C, Zehr JP. Nitrogen-fixing organelle in a marine alga. Science 2024; 384:217-222. [PMID: 38603509 DOI: 10.1126/science.adk1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."
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Affiliation(s)
- Tyler H Coale
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Valentina Loconte
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Bieke Vanslembrouck
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Shunyan Cheung
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Axel Ekman
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
| | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kyoko Hagino
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Yoshihito Takano
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Tomohiro Nishimura
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Hiroshima, Japan
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Mark Le Gros
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
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3
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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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4
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Robicheau BM, Tolman J, Desai D, LaRoche J. Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series. SCIENCE ADVANCES 2023; 9:eadh9768. [PMID: 37774025 PMCID: PMC10541017 DOI: 10.1126/sciadv.adh9768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/28/2023] [Indexed: 10/01/2023]
Abstract
UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A's rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A's microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.
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Affiliation(s)
- Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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Fletcher-Hoppe C, Yeh YC, Raut Y, Weissman JL, Fuhrman JA. Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California. ISME COMMUNICATIONS 2023; 3:63. [PMID: 37355737 PMCID: PMC10290647 DOI: 10.1038/s43705-023-00268-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.
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Affiliation(s)
- Colette Fletcher-Hoppe
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Yi-Chun Yeh
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford University, Stanford, CA, USA
| | - Yubin Raut
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - J L Weissman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA.
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6
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Bonnet S, Benavides M, Le Moigne FAC, Camps M, Torremocha A, Grosso O, Dimier C, Spungin D, Berman-Frank I, Garczarek L, Cornejo-Castillo FM. Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean. THE ISME JOURNAL 2023; 17:47-58. [PMID: 36163270 PMCID: PMC9750961 DOI: 10.1038/s41396-022-01319-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.
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Affiliation(s)
- Sophie Bonnet
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Mar Benavides
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.5399.60000 0001 2176 4817Turing Center for Living Systems, Aix-Marseille University, 13009 Marseille, France
| | - Frédéric A. C. Le Moigne
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.463763.30000 0004 0638 0577LEMAR, Laboratoire des sciences de l’environnement marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280 Plouzané, Technopôle Brest-Iroise France
| | - Mercedes Camps
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Antoine Torremocha
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Olivier Grosso
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Céline Dimier
- grid.499565.20000 0004 0366 8890Laboratoire d’Océanographie de Villefranche (LOV), Sorbonne Université, CNRS, 06230 Villefranche sur mer, France
| | - Dina Spungin
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Ilana Berman-Frank
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Laurence Garczarek
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Francisco M. Cornejo-Castillo
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France ,grid.418218.60000 0004 1793 765XInstitut de Ciènces del Mar (ICM-CSIC), E08003 Barcelona, Spain
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7
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Endo H, Umezawa Y, Takeda S, Suzuki K. Haptophyte communities along the Kuroshio current reveal their geographical sources and ecological traits. Mol Ecol 2023; 32:110-123. [PMID: 36221794 DOI: 10.1111/mec.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/29/2022]
Abstract
Haptophytes are one of the most ecologically successful phytoplankton groups in the modern ocean and tend to maintain balanced and stable communities across various environments. However, little is known about the mechanisms that enable community stability and ecological success. To reveal the community characteristics and interactions among haptophytes, we conducted comprehensive observations from the upstream to downstream regions of the Kuroshio Current. Haptophyte abundance and taxonomy were assessed using quantitative polymerase chain reaction and metabarcoding of 18S rRNA sequences, respectively. The haptophyte community structure changed abruptly at sites on the shelf-slope of the East China Sea, indicating the strong influence of shelf waters with high phytoplankton biomass on downstream communities. Correlation network analysis combined with the phylogeny suggested that haptophytes can coexist with their close relatives, possibly owing to their nutritional flexibility, thereby escaping from resource competition. Consistently, some noncalcifying haptophyte genera with high mixotrophic capacities such as Chrysochromulina constituted a major component of the co-occurrence network, whereas coccolithophores such as Emiliania/Gephyrocapsa were rarely observed. Our study findings suggest that noncalcifying haptophytes play crucial roles in community diversity and stability, and in sustaining the food web structure in the Kuroshio ecosystems.
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Affiliation(s)
- Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shigenobu Takeda
- Faculty of Environmental Earth Science, Hokkaido University, Hokkaido, Sapporo, Japan
| | - Koji Suzuki
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
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8
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Salas K, Cabello AM, Turk-Kubo KA, Zehr JP, Cornejo-Castillo FM. Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1. Front Microbiol 2023; 14:1130695. [PMID: 37138636 PMCID: PMC10150950 DOI: 10.3389/fmicb.2023.1130695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/21/2023] [Indexed: 05/05/2023] Open
Abstract
The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis.
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Affiliation(s)
- Krystal Salas
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Ana M. Cabello
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Málaga, Spain
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- *Correspondence: Jonathan P. Zehr,
| | - Francisco M. Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
- Francisco M. Cornejo-Castillo,
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9
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Muñoz-Marín MDC, Magasin JD, Zehr JP. Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes. PLoS One 2023; 18:e0272674. [PMID: 37130101 PMCID: PMC10153697 DOI: 10.1371/journal.pone.0272674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 02/18/2023] [Indexed: 05/03/2023] Open
Abstract
Decades of research on marine N2 fixation focused on Trichodesmium, which are generally free-living cyanobacteria, but in recent years the endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) has received increasing attention. However, few studies have shed light on the influence of the host versus the habitat on UCYN-A N2 fixation and overall metabolism. Here we compared transcriptomes from natural populations of UCYN-A from oligotrophic open-ocean versus nutrient-rich coastal waters, using a microarray that targets the full genomes of UCYN-A1 and UCYN-A2 and known genes for UCYN-A3. We found that UCYN-A2, usually regarded as adapted to coastal environments, was transcriptionally very active in the open ocean and appeared to be less impacted by habitat change than UCYN-A1. Moreover, for genes with 24 h periodic expression we observed strong but inverse correlations among UCYN-A1, A2, and A3 to oxygen and chlorophyll, which suggests distinct host-symbiont relationships. Across habitats and sublineages, genes for N2 fixation and energy production had high transcript levels, and, intriguingly, were among the minority of genes that kept the same schedule of diel expression. This might indicate different regulatory mechanisms for genes that are critical to the symbiosis for the exchange of nitrogen for carbon from the host. Our results underscore the importance of N2 fixation in UCYN-A symbioses across habitats, with consequences for community interactions and global biogeochemical cycles.
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Affiliation(s)
- María Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Jonathan D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
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10
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Overlooked and widespread pennate diatom-diazotroph symbioses in the sea. Nat Commun 2022; 13:799. [PMID: 35145076 PMCID: PMC8831587 DOI: 10.1038/s41467-022-28065-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 01/06/2022] [Indexed: 01/21/2023] Open
Abstract
Persistent nitrogen depletion in sunlit open ocean waters provides a favorable ecological niche for nitrogen-fixing (diazotrophic) cyanobacteria, some of which associate symbiotically with eukaryotic algae. All known marine examples of these symbioses have involved either centric diatom or haptophyte hosts. We report here the discovery and characterization of two distinct marine pennate diatom-diazotroph symbioses, which until now had only been observed in freshwater environments. Rhopalodiaceae diatoms Epithemia pelagica sp. nov. and Epithemia catenata sp. nov. were isolated repeatedly from the subtropical North Pacific Ocean, and analysis of sequence libraries reveals a global distribution. These symbioses likely escaped attention because the endosymbionts lack fluorescent photopigments, have nifH gene sequences similar to those of free-living unicellular cyanobacteria, and are lost in nitrogen-replete medium. Marine Rhopalodiaceae-diazotroph symbioses are a previously overlooked but widespread source of bioavailable nitrogen in marine habitats and provide new, easily cultured model organisms for the study of organelle evolution.
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11
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Wen Z, Browning TJ, Cai Y, Dai R, Zhang R, Du C, Jiang R, Lin W, Liu X, Cao Z, Hong H, Dai M, Shi D. Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific. SCIENCE ADVANCES 2022; 8:eabl7564. [PMID: 35119922 PMCID: PMC8816331 DOI: 10.1126/sciadv.abl7564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nitrogen fixation is critical for the biological productivity of the ocean, but clear mechanistic controls on this process remain elusive. Here, we investigate the abundance, activity, and drivers of nitrogen-fixing diazotrophs across the tropical western North Pacific. We find a basin-scale coherence of diazotroph abundances and N2 fixation rates with the supply ratio of iron:nitrogen to the upper ocean. Across a threshold of increasing supply ratios, the abundance of nifH genes and N2 fixation rates increased, phosphate concentrations decreased, and bioassay experiments demonstrated evidence for N2 fixation switching from iron to phosphate limitation. In the northern South China Sea, supply ratios were hypothesized to fall around this critical threshold and bioassay experiments suggested colimitation by both iron and phosphate. Our results provide evidence for iron:nitrogen supply ratios being the most important factor in regulating the distribution of N2 fixation across the tropical ocean.
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Affiliation(s)
- Zuozhu Wen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Thomas J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Yihua Cai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Rongbo Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Chuanjun Du
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruotong Jiang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenfang Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xin Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Zhimian Cao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Haizheng Hong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
- Corresponding author.
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12
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Suzuki S, Kawachi M, Tsukakoshi C, Nakamura A, Hagino K, Inouye I, Ishida KI. Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont. FRONTIERS IN PLANT SCIENCE 2021; 12:749895. [PMID: 34925404 PMCID: PMC8679911 DOI: 10.3389/fpls.2021.749895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.
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Affiliation(s)
- Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Chinatsu Tsukakoshi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Atsushi Nakamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Kyoko Hagino
- Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
| | - Isao Inouye
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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13
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Li L, Wu C, Huang D, Ding C, Wei Y, Sun J. Integrating Stochastic and Deterministic Process in the Biogeography of N 2-Fixing Cyanobacterium Candidatus Atelocyanobacterium Thalassa. Front Microbiol 2021; 12:654646. [PMID: 34745020 PMCID: PMC8566894 DOI: 10.3389/fmicb.2021.654646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
UCYN-A is one of the most widespread and important marine diazotrophs. Its unusual distribution in both cold/warm and coastal/oceanic waters challenges current understanding about what drives the biogeography of diazotrophs. This study assessed the community assembly processes of the nitrogen-fixing cyanobacterium UCYN-A, developing a framework of assembly processes underpinning the microbial biogeography and diversity. High-throughput sequencing and a qPCR approach targeting the nifH gene were used to investigate three tropical seas: the Bay of Bengal, the Western Pacific Ocean, and the South China Sea. Based on the neutral community model and two types of null models calculating the β-nearest taxon index and the normalized stochasticity ratio, we found that stochastic assembly processes could explain 66-92% of the community assembly; thus, they exert overwhelming influence on UCYN-A biogeography and diversity. Among the deterministic processes, temperature and coastal/oceanic position appeared to be the principal environmental factors driving UCYN-A diversity. In addition, a close linkage between assembly processes and UCYN-A abundance/diversity/drivers can provide clues for the unusual global distribution of UCYN-A.
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Affiliation(s)
- Liuyang Li
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Danyue Huang
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Changling Ding
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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14
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Turk-Kubo KA, Mills MM, Arrigo KR, van Dijken G, Henke BA, Stewart B, Wilson ST, Zehr JP. UCYN-A/haptophyte symbioses dominate N 2 fixation in the Southern California Current System. ISME COMMUNICATIONS 2021; 1:42. [PMID: 36740625 PMCID: PMC9723760 DOI: 10.1038/s43705-021-00039-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
The availability of fixed nitrogen (N) is an important factor limiting biological productivity in the oceans. In coastal waters, high dissolved inorganic N concentrations were historically thought to inhibit dinitrogen (N2) fixation, however, recent N2 fixation measurements and the presence of the N2-fixing UCYN-A/haptophyte symbiosis in nearshore waters challenge this paradigm. We characterized the contribution of UCYN-A symbioses to nearshore N2 fixation in the Southern California Current System (SCCS) by measuring bulk community and single-cell N2 fixation rates, as well as diazotroph community composition and abundance. UCYN-A1 and UCYN-A2 symbioses dominated diazotroph communities throughout the region during upwelling and oceanic seasons. Bulk N2 fixation was detected in most surface samples, with rates up to 23.0 ± 3.8 nmol N l-1 d-1, and was often detected at the deep chlorophyll maximum in the presence of nitrate (>1 µM). UCYN-A2 symbiosis N2 fixation rates were higher (151.1 ± 112.7 fmol N cell-1 d-1) than the UCYN-A1 symbiosis (6.6 ± 8.8 fmol N cell-1 d-1). N2 fixation by the UCYN-A1 symbiosis accounted for a majority of the measured bulk rates at two offshore stations, while the UCYN-A2 symbiosis was an important contributor in three nearshore stations. This report of active UCYN-A symbioses and broad mesoscale distribution patterns establishes UCYN-A symbioses as the dominant diazotrophs in the SCCS, where heterocyst-forming and unicellular cyanobacteria are less prevalent, and provides evidence that the two dominant UCYN-A sublineages are separate ecotypes.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA.
| | - Matthew M Mills
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Kevin R Arrigo
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Gert van Dijken
- Earth System Science, Stanford University, Stanford, CA, USA
| | - Britt A Henke
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Brittany Stewart
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Samuel T Wilson
- Center for Microbial Oceanography: Research and Education, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
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15
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Gradoville MR, Cabello AM, Wilson ST, Turk-Kubo KA, Karl DM, Zehr JP. Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A. Environ Microbiol 2021; 23:4518-4531. [PMID: 34227720 PMCID: PMC9291983 DOI: 10.1111/1462-2920.15645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022]
Abstract
The symbiotic cyanobacterium UCYN‐A is one of the most globally abundant marine dinitrogen (N2)‐fixers, but cultures have not been available and its biology and ecology are poorly understood. We used cultivation‐independent approaches to investigate how UCYN‐A single‐cell N2 fixation rates (NFRs) and nifH gene expression vary as a function of depth and photoperiod. Twelve‐hour day/night incubations showed that UCYN‐A only fixed N2 during the day. Experiments conducted using in situ arrays showed a light‐dependence of NFRs by the UCYN‐A symbiosis, with the highest rates in surface waters (5–45 m) and lower rates at depth (≥ 75 m). Analysis of NFRs versus in situ light intensity yielded a light saturation parameter (Ik) for UCYN‐A of 44 μmol quanta m−2 s−1. This is low compared with other marine diazotrophs, suggesting an ecological advantage for the UCYN‐A symbiosis under low‐light conditions. In contrast to cell‐specific NFRs, nifH gene‐specific expression levels did not vary with depth, indicating that light regulates N2 fixation by UCYN‐A through processes other than transcription, likely including host–symbiont interactions. These results offer new insights into the physiology of the UCYN‐A symbiosis in the subtropical North Pacific Ocean and provide clues to the environmental drivers of its global distributions.
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Affiliation(s)
- Mary R Gradoville
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ana M Cabello
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.,Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain
| | - Samuel T Wilson
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David M Karl
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
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16
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Cheung S, Zehr JP, Xia X, Tsurumoto C, Endo H, Nakaoka SI, Mak W, Suzuki K, Liu H. Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean. Environ Microbiol 2021; 23:4246-4259. [PMID: 34046993 DOI: 10.1111/1462-2920.15604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/15/2021] [Accepted: 05/16/2021] [Indexed: 11/30/2022]
Abstract
Despite the increasing reports of non-cyanobacterial diazotrophs (NCDs) in pelagic waters, only one NCD (GammaA) has been relatively well described, whose genome and physiology are still unclear. Here we present a comprehensive analysis of the biogeography and ecophysiology of a widely distributed NCD, Gamma4. Gamma4 was the most abundant Gammaproteobacterial NCD along transects across the subtropical North Pacific. Using quantitative PCR, Gamma4 was detectable throughout the surface waters of North Pacific (7°N-55°N, 138°E-80°W), whereas GammaA was detected at <2/3 of the stations. Gamma4 was abundant during autumn-winter and positively correlated with chlorophyll a, while GammaA thrived during spring-summer and was positively correlated with temperature. Environmental clones affiliated with Gamma4 were widely detected in pelagic waters, oxygen minimum zones and even dinoflagellate microbiomes. By analysing the metabolic potential of a genome of Gamma4 reconstructed from the Tara Oceans dataset, we suggest that Gamma4 is a versatile heterotrophic NCD equipped with multiple strategies in scavenging phosphate (and iron) and for respiratory protection of nitrogenase. The transcription of nitrogenase genes is putatively regulated by Fnr-NifL-NifA and GlnD-GlnK systems that respond to intracellular oxygen and glutamate concentration. These results provide important implications for the potential life strategies of pelagic NCDs.
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Affiliation(s)
- Shunyan Cheung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chihiro Tsurumoto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Shin-Ichiro Nakaoka
- Center for Global Environmental Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Wingkwan Mak
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Koji Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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17
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Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling. PLoS Comput Biol 2021; 17:e1008983. [PMID: 33961619 PMCID: PMC8143392 DOI: 10.1371/journal.pcbi.1008983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/24/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A (Candidatus Atelocyanobacterium thalassa). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems. Reduction of dinitrogen gas to biologically useful forms via nitrogen fixation is a key component of the biogeochemical cycle. In the marine environment, the cyanobacteria UCYN-A (Candidatus Atelocyanobacterium thalassa) has been found to be a primary contributor to biological nitrogen fixation at a global scale. UCYN-A exhibits a highly streamlined genome which lacks genes coding for essential cyanobacterial processes such as the energy-generating TCA cycle, oxygen-producing photosystem II, the carbon-fixing RuBisCo and de novo production pathways for numerous amino acids and nucleotides. Thus, it exists in a symbiosis with unicellular planktonic algae where it exchanges fixed nitrogen for fixed carbon with its host. However, both UCYN-A and its symbiotic partner remain uncultured under laboratory conditions. This necessitates implementing a computational approach to glean insights into UCYN-A’s unique physiology and metabolic processes governing the symbiotic association. To this end, we develop a constraints-based framework that infers all possible trophic scenarios consistent with the observed data. Possible mechanisms employed by UCYN-A to accommodate diazotrophy with daytime carbon fixation by the host (i.e., two mutually incompatible processes) are also elucidated. We envision that the developed framework using UCYN-A and its algal host will be used as a roadmap and motivate the study of similarly unique microbial systems in the future.
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18
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Landa M, Turk-Kubo KA, Cornejo-Castillo FM, Henke BA, Zehr JP. Critical Role of Light in the Growth and Activity of the Marine N 2-Fixing UCYN-A Symbiosis. Front Microbiol 2021; 12:666739. [PMID: 34025621 PMCID: PMC8139342 DOI: 10.3389/fmicb.2021.666739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
The unicellular N2-fixing cyanobacteria UCYN-A live in symbiosis with haptophytes in the Braarudosphaera bigelowii lineage. Maintaining N2-fixing symbioses between two unicellular partners requires tight coordination of multiple biological processes including cell growth and division and, in the case of the UCYN-A symbiosis, N2 fixation of the symbiont and photosynthesis of the host. In this system, it is thought that the host photosynthesis supports the high energetic cost of N2 fixation, and both processes occur during the light period. However, information on this coordination is very limited and difficult to obtain because the UCYN-A symbiosis has yet to be available in culture. Natural populations containing the UCYN-A2 symbiosis were manipulated to explore the effects of alterations of regular light and dark periods and inhibition of host photosynthesis on N2 fixation (single cell N2 fixation rates), nifH gene transcription, and UCYN-A2 cell division (fluorescent in situ hybridization and nifH gene abundances). The results showed that the light period is critical for maintenance of regular patterns of gene expression, N2 fixation and symbiont replication and cell division. This study suggests a crucial role for the host as a producer of fixed carbon, rather than light itself, in the regulation and implementation of these cellular processes in UCYN-A.
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Affiliation(s)
- Marine Landa
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Britt A Henke
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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19
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Mutalipassi M, Riccio G, Mazzella V, Galasso C, Somma E, Chiarore A, de Pascale D, Zupo V. Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives. Mar Drugs 2021; 19:227. [PMID: 33923826 PMCID: PMC8074062 DOI: 10.3390/md19040227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Mirko Mutalipassi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Mazzella
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Christian Galasso
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Emanuele Somma
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri, 34127 Trieste, Italy;
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Antonia Chiarore
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy;
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Zupo
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
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20
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Jabir T, Vipindas PV, Jesmi Y, Divya PS, Adarsh BM, Nafeesathul Miziriya HS, Mohamed Hatha AA. Influence of environmental factors on benthic nitrogen fixation and role of sulfur reducing diazotrophs in a eutrophic tropical estuary. MARINE POLLUTION BULLETIN 2021; 165:112126. [PMID: 33667934 DOI: 10.1016/j.marpolbul.2021.112126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 05/20/2023]
Abstract
Benthic nitrogen fixation in the tropical estuaries plays a major role in marine nitrogen cycle, its contribution to nitrogen budget and players behind process is not well understood. The present study was estimated the benthic nitrogen fixation rate in a tropical estuary (Cochin) and also evaluated the contribution of various diazotrophic bacterial communities. Nitrogen fixation was detected throughout year (0.1-1.11 nmol N g-1 h-1); higher activity was observed in post-monsoon. The nifH gene abundance was varied from 0.8 × 104 to 0.6 × 108 copies g-1dry sediment; highest was detected in post-monsoon. The Cluster I and Cluster III were the dominant diazotrophs. Sulfur reducing bacterial phylotypes (Deltaproteobacteria) contributed up to 2-72% of total nitrogen fixation. These bacteria may provide new nitrogen to these systems, counteracting nitrogen loss via denitrification and anammox. Overall, the study explained the importance of benthic nitrogen fixation and role of diazotrophs in a monsoon influenced tropical estuarine environments.
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Affiliation(s)
- T Jabir
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India; National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco-da-Gama, Goa 403 804, India.
| | - P V Vipindas
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India; National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco-da-Gama, Goa 403 804, India
| | - Y Jesmi
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India
| | - P S Divya
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India
| | - B M Adarsh
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India
| | - H S Nafeesathul Miziriya
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682016, India; CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi 682 016, India.
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21
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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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22
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Jabir T, Vipindas PV, Krishnan KP, Mohamed Hatha AA. Abundance and diversity of diazotrophs in the surface sediments of Kongsfjorden, an Arctic fjord. World J Microbiol Biotechnol 2021; 37:41. [PMID: 33544264 DOI: 10.1007/s11274-020-02993-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Diazotrophy in the Arctic environment is poorly understood compared to tropical and subtropical regions. Hence in this study, we report the abundance and diversity of diazotrophs in Arctic fjord sediments and elucidate the role of environmental factors on the distribution of diazotrophs. The study was conducted during the boreal summer in the Kongsfjorden, an Arctic fjord situated in the western coast of Spitsbergen. The abundance of nifH gene was measured through quantitative real-time PCR and the diversity of diazotrophs was assessed by nifH targeted clone library and next generation sequence analysis. Results revealed that the abundance of nifH gene in the surface sediments ranged from 2.3 × 106 to 3.7 × 107 copies g- 1. The δ-proteobacterial diazotrophs (71% of total sequence) were the dominant class observed in this study. Major genera retrieved from the sequence analysis were Desulfovibrionaceae (25% of total sequence), Desulfuromonadaceae (18% of total sequence) and Desulfobacteriaceae (10% of total sequence); these are important diazotrophic iron and sulfur-reducing bacterial clade in the Kongsfjorden sediments. The abundance of nifH gene showed a significant positive correlation TOC/TN ratio (r2 = 0.96, p ≤ 0.05) and total organic carbon (p ≤ 0.05) content in the fjord sediments. The higher TOC/TN ratio (4.24-14.5) indicated low nitrogen content organic matter in the fjord sediments through glacier runoff, which enhances the abundance and diversity of nitrogen fixing microorganisms.
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Affiliation(s)
- T Jabir
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India
| | - P V Vipindas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India. .,CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India.
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India.,CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India
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23
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von Friesen LW, Riemann L. Nitrogen Fixation in a Changing Arctic Ocean: An Overlooked Source of Nitrogen? Front Microbiol 2021; 11:596426. [PMID: 33391213 PMCID: PMC7775723 DOI: 10.3389/fmicb.2020.596426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans – challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean – with the aim of guiding and encouraging future research on nitrogen fixation in this region.
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Affiliation(s)
- Lisa W von Friesen
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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24
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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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25
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Unusual marine cyanobacteria/haptophyte symbiosis relies on N 2 fixation even in N-rich environments. ISME JOURNAL 2020; 14:2395-2406. [PMID: 32523086 PMCID: PMC7490277 DOI: 10.1038/s41396-020-0691-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
The microbial fixation of N2 is the largest source of biologically available nitrogen (N) to the oceans. However, it is the most energetically expensive N-acquisition process and is believed inhibited when less energetically expensive forms, like dissolved inorganic N (DIN), are available. Curiously, the cosmopolitan N2-fixing UCYN-A/haptophyte symbiosis grows in DIN-replete waters, but the sensitivity of their N2 fixation to DIN is unknown. We used stable isotope incubations, catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH), and nanoscale secondary ion mass spectrometry (nanoSIMS), to investigate the N source used by the haptophyte host and sensitivity of UCYN-A N2 fixation in DIN-replete waters. We demonstrate that under our experimental conditions, the haptophyte hosts of two UCYN-A sublineages do not assimilate nitrate (NO3−) and meet little of their N demands via ammonium (NH4+) uptake. Instead the UCYN-A/haptophyte symbiosis relies on UCYN-A N2 fixation to supply large portions of the haptophyte’s N requirements, even under DIN-replete conditions. Furthermore, UCYN-A N2 fixation rates, and haptophyte host carbon fixation rates, were at times stimulated by NO3− additions in N-limited waters suggesting a link between the activities of the bulk phytoplankton assemblage and the UCYN-A/haptophyte symbiosis. The results suggest N2 fixation may be an evolutionarily viable strategy for diazotroph–eukaryote symbioses, even in N-rich coastal or high latitude waters.
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26
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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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27
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Foster RA, Zehr JP. Diversity, Genomics, and Distribution of Phytoplankton-Cyanobacterium Single-Cell Symbiotic Associations. Annu Rev Microbiol 2020; 73:435-456. [PMID: 31500535 DOI: 10.1146/annurev-micro-090817-062650] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cyanobacteria are common in symbiotic relationships with diverse multicellular organisms (animals, plants, fungi) in terrestrial environments and with single-celled heterotrophic, mixotrophic, and autotrophic protists in aquatic environments. In the sunlit zones of aquatic environments, diverse cyanobacterial symbioses exist with autotrophic taxa in phytoplankton, including dinoflagellates, diatoms, and haptophytes (prymnesiophytes). Phototrophic unicellular cyanobacteria related to Synechococcus and Prochlorococcus are associated with a number of groups. N2-fixing cyanobacteria are symbiotic with diatoms and haptophytes. Extensive genome reduction is involved in the N2-fixing endosymbionts, most dramatically in the unicellular cyanobacteria associated with haptophytes, which have lost most of the photosynthetic apparatus, the ability to fix C, and the tricarboxylic acid cycle. The mechanisms involved in N2-fixing symbioses may involve more interactions beyond simple exchange of fixed C for N. N2-fixing cyanobacterial symbioses are widespread in the oceans, even more widely distributed than the best-known free-living N2-fixing cyanobacteria, suggesting they may be equally or more important in the global ocean biogeochemical cycle of N.Despite their ubiquitous nature and significance in biogeochemical cycles, cyanobacterium-phytoplankton symbioses remain understudied and poorly understood.
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Affiliation(s)
- Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden;
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, California 95064, USA;
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28
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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics. Genome Res 2020; 30:647-659. [PMID: 32205368 PMCID: PMC7197479 DOI: 10.1101/gr.253070.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
Abstract
Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.
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29
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Mareš J, Johansen JR, Hauer T, Zima J, Ventura S, Cuzman O, Tiribilli B, Kaštovský J. Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria. JOURNAL OF PHYCOLOGY 2019; 55:578-610. [PMID: 30830691 DOI: 10.1111/jpy.12853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
The systematics of single-celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval-shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free-living cyanobacteria from the Crocosphaera lineage to nitrogen-fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and "Cyanothece") important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N2 -fixing capability in the chroococcalean lineage.
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Affiliation(s)
- Jan Mareš
- Institute of Hydrobiology, Biology Centre, The Czech Academy of Sciences, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Jeffrey R Johansen
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- John Carroll University, Department of Biology, University Heights, Ohio, 44118, USA
| | - Tomáš Hauer
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jan Zima
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice
| | - Stefano Ventura
- Firenze Unit, Institute of Ecosystem Study, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Oana Cuzman
- Institute for the Conservation and Valorization of Cultural Heritage, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Bruno Tiribilli
- Firenze Unit, Institute for Complex Systems, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Jan Kaštovský
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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30
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Moreira-Coello V, Mouriño-Carballido B, Marañón E, Fernández-Carrera A, Bode A, Sintes E, Zehr JP, Turk-Kubo K, Varela MM. Temporal variability of diazotroph community composition in the upwelling region off NW Iberia. Sci Rep 2019; 9:3737. [PMID: 30842510 PMCID: PMC6403370 DOI: 10.1038/s41598-019-39586-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Knowledge of the ecology of N2-fixing (diazotrophic) plankton is mainly limited to oligotrophic (sub)tropical oceans. However, diazotrophs are widely distributed and active throughout the global ocean. Likewise, relatively little is known about the temporal dynamics of diazotrophs in productive areas. Between February 2014 and December 2015, we carried out 9 one-day samplings in the temperate northwestern Iberian upwelling system to investigate the temporal and vertical variability of the diazotrophic community and its relationship with hydrodynamic forcing. In downwelling conditions, characterized by deeper mixed layers and a homogeneous water column, non-cyanobacterial diazotrophs belonging mainly to nifH clusters 1G (Gammaproteobacteria) and 3 (putative anaerobes) dominated the diazotrophic community. In upwelling and relaxation conditions, affected by enhanced vertical stratification and hydrographic variability, the community was more heterogeneous vertically but less diverse, with prevalence of UCYN-A (unicellular cyanobacteria, subcluster 1B) and non-cyanobacterial diazotrophs from clusters 1G and 3. Oligotyping analysis of UCYN-A phylotype showed that UCYN-A2 sublineage was the most abundant (74%), followed by UCYN-A1 (23%) and UCYN-A4 (2%). UCYN-A1 oligotypes exhibited relatively low frequencies during the three hydrographic conditions, whereas UCYN-A2 showed higher abundances during upwelling and relaxation. Our findings show the presence of a diverse and temporally variable diazotrophic community driven by hydrodynamic forcing in an upwelling system.
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Affiliation(s)
| | | | - Emilio Marañón
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, Spain
| | | | - Antonio Bode
- Instituto Español de Oceanografía, A Coruña, Spain
| | - Eva Sintes
- Instituto Español de Oceanografía, Baleares, Spain
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California, USA
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, California, USA
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31
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The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium " Candidatus Atelocyanobacterium thalassa" (UCYN-A). mBio 2019; 10:mBio.02495-18. [PMID: 30602582 PMCID: PMC6315102 DOI: 10.1128/mbio.02495-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as found in other unicellular marine cyanobacteria. Symbiosis between a marine alga and a N2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N2-fixing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but, surprisingly, UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.
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32
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Abstract
Biological dinitrogen (N2) fixation (BNF) is an important source of nitrogen in marine systems. Until recently, it was believed to be primarily limited to subtropical open oceans. Marine BNF is mainly attributed to cyanobacteria. However, recently an unusual N2-fixing unicellular cyanobacteria (UCYN-A)/haptophyte symbiosis was reported with a broader temperature range than other N2-fixing cyanobacteria. We report that the UCYN-A symbiosis is present and fixing N2 in the Western Arctic and Bering Seas, further north than any previously reported N2-fixing marine cyanobacteria. Nanoscale secondary ion mass spectrometry enabled us to directly show that the symbiosis was fixing N2. These results show that N2-fixing cyanobacteria are not constrained to subtropical waters and challenge commonly held ideas about global marine N2 fixation. Biological dinitrogen (N2) fixation is an important source of nitrogen (N) in low-latitude open oceans. The unusual N2-fixing unicellular cyanobacteria (UCYN-A)/haptophyte symbiosis has been found in an increasing number of unexpected environments, including northern waters of the Danish Straight and Bering and Chukchi Seas. We used nanoscale secondary ion mass spectrometry (nanoSIMS) to measure 15N2 uptake into UCYN-A/haptophyte symbiosis and found that UCYN-A strains identical to low-latitude strains are fixing N2 in the Bering and Chukchi Seas, at rates comparable to subtropical waters. These results show definitively that cyanobacterial N2 fixation is not constrained to subtropical waters, challenging paradigms and models of global N2 fixation. The Arctic is particularly sensitive to climate change, and N2 fixation may increase in Arctic waters under future climate scenarios.
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Cornejo-Castillo FM, Muñoz-Marín MDC, Turk-Kubo KA, Royo-Llonch M, Farnelid H, Acinas SG, Zehr JP. UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa. Environ Microbiol 2018; 21:111-124. [PMID: 30255541 DOI: 10.1111/1462-2920.14429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 09/06/2018] [Accepted: 09/22/2018] [Indexed: 12/01/2022]
Abstract
The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Maria Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Hanna Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
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Anderson EE, Wilson C, Knap AH, Villareal TA. Summer diatom blooms in the eastern North Pacific gyre investigated with a long-endurance autonomous surface vehicle. PeerJ 2018; 6:e5387. [PMID: 30128189 PMCID: PMC6098680 DOI: 10.7717/peerj.5387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
Satellite chlorophyll a (chl a) observations have repeatedly noted summertime phytoplankton blooms in the North Pacific subtropical gyre (NPSG), a region of open ocean that is far removed from any land-derived or Ekman upwelling nutrient sources. These blooms are dominated by N2-fixing diatom-cyanobacteria associations of the diatom genera Rhizosolenia Brightwell and Hemiaulus Ehrenberg. Their nitrogen fixing endosymbiont, Richelia intracellularis J.A. Schmidt, is hypothesized to be critical to the development of blooms in this nitrogen limited region. However, due to the remote location and unpredictable duration of the summer blooms, prolonged in situ observations are rare outside of the Station ALOHA time-series off of Hawai'i. In summer, 2015, a proof-of-concept mission using the autonomous vehicle, Honey Badger (Wave Glider SV2; Liquid Robotics, a Boeing company, Sunnyvale, CA, USA), collected near-surface (<20 m) observations in the NPSG using hydrographic, meteorological, optical, and imaging sensors designed to focus on phytoplankton abundance, distribution, and physiology of this bloom-forming region. Hemiaulus and Rhizosolenia cell abundance was determined using digital holography for the entire June-November mission. Honey Badger was not able to reach the 30°N subtropical front region where most of the satellite chl a blooms have been observed, but near-real time navigational control allowed it to transect two blooms near 25°N. The two taxa did not co-occur in large numbers, rather the blooms were dominated by either Hemiaulus or Rhizosolenia. The August 2-4, 2015 bloom was comprised of 96% Hemiaulus and the second bloom, August 15-17, 2015, was dominated by Rhizosolenia (75%). The holograms also imaged undisturbed, fragile Hemiaulus aggregates throughout the sampled area at ∼10 L-1. Aggregated Hemiaulus represented the entire observed population at times and had a widespread distribution independent of the summer export pulse, a dominant annual event suggested to be mediated by aggregate fluxes. Aggregate occurrence was not consistent with a density dependent formation mechanism and may represent a natural growth form in undisturbed conditions. The photosynthetic potential index (Fv:Fm) increased from ∼0.4 to ∼0.6 during both blooms indicating a robust, active phytoplankton community in the blooms. The diel pattern of Fv:Fm (nocturnal maximum; diurnal minimum) was consistent with macronutrient limitation throughout the mission with no evidence of Fe-limitation despite the presence of nitrogen fixing diatom-diazotroph assemblages. During the 5-month mission, Honey Badger covered ∼5,690 km (3,070 nautical miles), acquired 9,336 holograms, and reliably transmitted data onshore in near real-time. Software issues developed with the active fluorescence sensor that terminated measurements in early September. Although images were still useful at the end of the mission, fouling of the LISST-Holo optics was considerable, and appeared to be the most significant issue facing deployments of this duration.
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Affiliation(s)
- Emily E. Anderson
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
| | - Cara Wilson
- National Marine Fisheries, National Oceanic and Atmospheric Administration, Monterey, CA, USA
| | - Anthony H. Knap
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, USA
| | - Tracy A. Villareal
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
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Turk-Kubo KA, Connell P, Caron D, Hogan ME, Farnelid HM, Zehr JP. In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre. Front Microbiol 2018; 9:1616. [PMID: 30090092 PMCID: PMC6068237 DOI: 10.3389/fmicb.2018.01616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Major advances in understanding the diversity, distribution, and activity of marine N2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-A1 were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N2 in the presence of nitrate. Net growth rates for UCYN-A1, UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 ± 0.5 d-1), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-A1 and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-A1. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models.
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Affiliation(s)
- Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Paige Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - David Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Mary E. Hogan
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Hanna M. Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
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Endo H, Ogata H, Suzuki K. Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean. Sci Rep 2018; 8:10916. [PMID: 30026492 PMCID: PMC6053411 DOI: 10.1038/s41598-018-29039-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
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Affiliation(s)
- Hisashi Endo
- Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,CREST, Japan Science and Technology, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan. .,CREST, Japan Science and Technology, North 10 West 5, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.
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Henke BA, Turk-Kubo KA, Bonnet S, Zehr JP. Distributions and Abundances of Sublineages of the N 2-Fixing Cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) in the New Caledonian Coral Lagoon. Front Microbiol 2018; 9:554. [PMID: 29674998 PMCID: PMC5895702 DOI: 10.3389/fmicb.2018.00554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/12/2018] [Indexed: 11/21/2022] Open
Abstract
Nitrogen (N2) fixation is a major source of nitrogen that supports primary production in the vast oligotrophic areas of the world’s oceans. The Western Tropical South Pacific has recently been identified as a hotspot for N2 fixation. In the Noumea lagoon (New Caledonia), high abundances of the unicellular N2-fixing cyanobacteria group A (UCYN-A), coupled with daytime N2 fixation rates associated with the <10 μm size fraction, suggest UCYN-A may be an important diazotroph (N2-fixer) in this region. However, little is known about the seasonal variability and diversity of UCYN-A there. To assess this, surface waters from a 12 km transect from the mouth of the Dumbea River to the Dumbea Pass were sampled monthly between July 2012 and March 2014. UCYN-A abundances for two of the defined sublineages, UCYN-A1 and UCYN-A2, were quantified using qPCR targeting the nifH gene, and the nifH-based diversity of UCYN-A was characterized by identifying oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. UCYN-A abundances were dominated by the UCYN-A1 sublineage, peaked in September and October and could be predicted by a suite of nine environmental parameters. At the sublineage level, UCYN-A1 abundances could be predicted based on lower temperatures (<23°C), nitrate concentrations, precipitation, wind speed, while UCYN-A2 abundances could be predicted based on silica, and chlorophyll a concentrations, wind direction, precipitation, and wind speed. Using UCYN-A nifH oligotyping, similar environmental variables explained the relative abundances of sublineages and their associated oligotypes, with the notable exception of the UCYN-A2 oligotype (oligo43) which had relative abundance patterns distinct from the dominant UCYN-A2 oligotype (oligo3). The results support an emerging pattern that UCYN-A is comprised of a diverse group of strains, with sublineages that may have different ecological niches. By identifying environmental factors that influence the composition and abundance of UCYN-A sublineages, this study helps to explain global UCYN-A abundance patterns, and is important for understanding the significance of N2 fixation at local and global scales.
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Affiliation(s)
- Britt A Henke
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sophie Bonnet
- IRD, MIO, UM 110 - IRD Centre of Noumea, Aix-Marseille University, University of South Toulon Var, CNRS/INSU, Noumea, France
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
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Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. ISME JOURNAL 2018; 12:1360-1374. [PMID: 29426951 DOI: 10.1038/s41396-018-0050-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 01/09/2023]
Abstract
Symbioses between eukaryotic algae and nitrogen-fixing cyanobacteria have been recognized in recent years as a key source of new nitrogen in the oceans. We investigated the composition of the small photosynthetic eukaryote communities associated with nitrogen-fixing cyanobacteria in the Brazilian South Atlantic Bight using a combination of flow cytometry sorting and high throughput sequencing of two genes: the V4 region of 18S rRNA and nifH. Two distinct eukaryotic communities were often encountered, one dominated by the Mamiellophyceae Bathycoccus and Ostreococcus, and one dominated by a prymnesiophyte known to live in symbiosis with the UCYN-A1 nitrogen-fixing cyanobacterium. Among nifH sequences, those from UCYN-A1 were most abundant but three other UCYN-A clades (A2, A3, A4) were also found. Network analysis confirmed the relation between A1 and A2 clades and their hypothesized hosts and pointed out to the potential association between novel clade A4 with Braarudosphaera bigelowii, previously hypothesized to host A2.
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Cheung S, Suzuki K, Saito H, Umezawa Y, Xia X, Liu H. Highly heterogeneous diazotroph communities in the Kuroshio Current and the Tokara Strait, Japan. PLoS One 2017; 12:e0186875. [PMID: 29059241 PMCID: PMC5653367 DOI: 10.1371/journal.pone.0186875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 11/18/2022] Open
Abstract
In this study, we used 454-pyrosequencing to report the highly diverse diazotroph communities in the Kuroshio and its adjacent waters along a transect across the Tokara Strait, Japan. Terrestrial input from the islands resulted in a highly heterogeneous diazotroph community within a relatively small geographic region, which was presumably caused by the remarkably different responses of UCYN-A2, UCYN-C and Trichodesmium to the steep environmental gradient. On the other hand, most major cyanobacterial OTUs found in this study were also detected in an unpublished dataset from the upstream Kuroshio, which suggests transportation of diazotrophs by the Kuroshio in large geographic scale. A significant amount of UCYN-C was found in the Kuroshio and offshore stations, suggesting the importance of this potentially overlooked group in the western North Pacific Ocean (WNPO). Moreover, a novel sublineage of UCYN-B was defined, which was predominant in an oligotrophic water sample; and it was also found to be widely distributed in oceanic waters. In addition, the apparent increase in relative abundance of UCYN-A2 from offshore to near-shore water provides evidence for the earlier and under-debating view that UCYN-A2 prefers coastal conditions. Our report provides new knowledge for understanding the phylogeny and ecology of unicellular cyanobacterial diazotrophs in WNPO.
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Affiliation(s)
- Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hiroaki Saito
- Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Yu Umezawa
- Faculty of Fisheries, Nagasaki University, Nagasaki, Japan
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
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40
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Conroy BJ, Steinberg DK, Song B, Kalmbach A, Carpenter EJ, Foster RA. Mesozooplankton Graze on Cyanobacteria in the Amazon River Plume and Western Tropical North Atlantic. Front Microbiol 2017; 8:1436. [PMID: 28824569 PMCID: PMC5540951 DOI: 10.3389/fmicb.2017.01436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
Diazotrophic cyanobacteria, those capable of fixing di-nitrogen (N2), are considered one of the major sources of new nitrogen (N) in the oligotrophic tropical ocean, but direct incorporation of diazotrophic N into food webs has not been fully examined. In the Amazon River-influenced western tropical North Atlantic (WTNA), diatom diazotroph associations (DDAs) and the filamentous colonial diazotrophs Trichodesmium have seasonally high abundances. We sampled epipelagic mesozooplankton in the Amazon River plume and WTNA in May-June 2010 to investigate direct grazing by mesozooplankton on two DDA populations: Richelia associated with Rhizosolenia diatoms (het-1) and Hemiaulus diatoms (het-2), and on Trichodesmium using highly specific qPCR assays targeting nitrogenase genes (nifH). Both DDAs and Trichodesmium occurred in zooplankton gut contents, with higher detection of het-2 predominantly in calanoid copepods (2.33-16.76 nifH copies organism-1). Abundance of Trichodesmium was low (2.21-4.03 nifH copies organism-1), but they were consistently detected at high salinity stations (>35) in calanoid copepods. This suggests direct grazing on DDAs, Trichodesmium filaments and colonies, or consumption as part of sinking aggregates, is common. In parallel with the qPCR approach, a next generation sequencing analysis of 16S rRNA genes identified that cyanobacterial assemblage associated with zooplankton guts was dominated by the non-diazotrophic unicellular phylotypes Synechococcus (56%) and Prochlorococcus (26%). However, in two separate calanoid copepod samples, two unicellular diazotrophs Candidatus Atelocyanobacterium thalassa (UCYN-A) and Crocosphaera watsonii (UCYN-B) were present, respectively, as a small component of cyanobacterial assemblages (<2%). This study represents the first evidence of consumption of DDAs, Trichodesmium, and unicellular cyanobacteria by calanoid copepods in an area of the WTNA known for high carbon export. These diazotroph populations are quantitatively important in the global N budget, widespread and hence, the next step is to accurately quantify grazing. Nonetheless, these results highlight a direct pathway of diazotrophic N into the food web and have important implications for biogeochemical cycles, particularly oligotrophic regions where N2 fixation is the main source of new nitrogen.
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Affiliation(s)
- Brandon J. Conroy
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Deborah K. Steinberg
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Bongkuen Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Andrew Kalmbach
- Department of Biology, Romberg Tiburon Center for Environmental Studies, San Francisco State University, TiburonCA, United States
| | - Edward J. Carpenter
- Department of Biology, Romberg Tiburon Center for Environmental Studies, San Francisco State University, TiburonCA, United States
| | - Rachel A. Foster
- Ocean Sciences, University of California, Santa Cruz, Santa CruzCA, United States
- Department of Ecology, Environment and Plant Sciences, Stockholm UniversityStockholm, Sweden
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Tian W, Zhang H, Zhang J, Zhao L, Miao M, Huang H. Biodiversity effects on resource use efficiency and community turnover of plankton in Lake Nansihu, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:11279-11288. [PMID: 28299569 DOI: 10.1007/s11356-017-8758-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
The relationship between biodiversity and ecosystem functioning is a central issue in ecology, especially in aquatic ecosystems due to the ecophysiological characteristics of plankton. Recently, ecologists have obtained conflicting conclusions while analyzing the influence of species diversity on plankton resource use efficiency (RUE) and community turnover. In this study, both phytoplankton and zooplankton communities were investigated seasonally from 2011 to 2013 in Lake Nansihu, a meso-eutrophic and recovering lake in China. The effects of phytoplankton diversity on RUE of phytoplankton (RUEPP), zooplankton (RUEZP), and community turnover were analyzed. Results showed that both phytoplankton species richness and evenness were positively correlated with RUEPP. RUEZP had a negative relationship with phytoplankton species richness, but a weak unimodal relationship with phytoplankton evenness. Cyanobacteria community had the opposite influence on RUEPP and RUEZP. Thus, cyanobacteria dominance will benefit RUEPP in eutrophic lakes, but the growth and reproduction of zooplankton are greatly limited. The strong negative relationship between total phosphorus and RUEZP confirmed these results. Phytoplankton community turnover tended to decrease with increasing phytoplankton evenness, which was consistent with most previous studies. The correlation coefficient between phytoplankton species richness and community turnover was negative, but not significant (p > 0.05). Therefore, phytoplankton community turnover was more sensitive to the variation of evenness than species richness. These results will be helpful in understanding the effects of species diversity on ecosystem functioning in aquatic ecosystems.
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Affiliation(s)
- Wang Tian
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, People's Republic of China
| | - Huayong Zhang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, People's Republic of China.
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, People's Republic of China
| | - Lei Zhao
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, People's Republic of China
| | - Mingsheng Miao
- College of Life Science, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Hai Huang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing, 102206, People's Republic of China
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43
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Turk-Kubo KA, Farnelid HM, Shilova IN, Henke B, Zehr JP. Distinct ecological niches of marine symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages. JOURNAL OF PHYCOLOGY 2017; 53:451-461. [PMID: 27992651 DOI: 10.1111/jpy.12505] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
A recently described symbiosis between the metabolically streamlined nitrogen-fixing cyanobacterium UCYN-A and a single-celled eukaryote prymnesiophyte alga is widely distributed throughout tropical and subtropical marine waters, and is thought to contribute significantly to nitrogen fixation in these regions. Several UCYN-A sublineages have been defined based on UCYN-A nitrogenase (nifH) sequences. Due to the low abundances of UCYN-A in the global oceans, currently existing molecular techniques are limited for detecting and quantifying these organisms. A targeted approach is needed to adequately characterize the diversity of this important marine cyanobacterium, and to advance understanding of its ecological importance. We present findings on the distribution of UCYN-A sublineages based on high throughput sequencing of UCYN-A nifH PCR amplicons from 78 samples distributed throughout many major oceanic provinces. These UCYN-A nifH fragments were used to define oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. The data set was dominated by a single oligotype associated with the UCYN-A1 sublineage, consistent with previous observations of relatively high abundances in tropical and subtropical regions. However, this analysis also revealed for the first time the widespread distribution of the UCYN-A3 sublineage in oligotrophic waters. Furthermore, distinct assemblages of UCYN-A oligotypes were found in oligotrophic and coastally influenced waters. This unique data set provides a framework for determining the environmental controls on UCYN-A distributions and the ecological importance of the different sublineages.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Hanna M Farnelid
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 34, Kalmar, Sweden
| | - Irina N Shilova
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Britt Henke
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
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44
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Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A. Nat Microbiol 2016; 2:16214. [PMID: 27996008 DOI: 10.1038/nmicrobiol.2016.214] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/23/2016] [Indexed: 11/08/2022]
Abstract
Nitrogen fixation - the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) - is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the 'spheroid bodies' of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N2-fixing organelles.
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Baumgartner D, Kopf M, Klähn S, Steglich C, Hess WR. Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome. BMC Microbiol 2016; 16:285. [PMID: 27894276 PMCID: PMC5126843 DOI: 10.1186/s12866-016-0896-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Background Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-proteins) are a systematically underestimated class of gene products in bacteria. Photosynthetic cyanobacteria provide a paradigm for small protein functions due to extensive work on the photosynthetic apparatus that led to the functional characterization of 19 small proteins of less than 50 amino acids. In analogy, previously unstudied small ORFs with similar degrees of conservation might encode small proteins of high relevance also in other functional contexts. Results Here we used comparative transcriptomic information available for two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechocystis sp. PCC 6714 for the prediction of small ORFs. We found 293 transcriptional units containing candidate small ORFs ≤80 codons in Synechocystis sp. PCC 6803, also including the known mRNAs encoding small proteins of the photosynthetic apparatus. From these transcriptional units, 146 are shared between the two strains, 42 are shared with the higher plant Arabidopsis thaliana and 25 with E. coli. To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6(nitrogen stress-induced RNA 6) and hliR1(high light-inducible RNA 1) , which originally were considered non-coding. Upon activation of expression via the Cu2+.responsive petE promoter or from the native promoters, all five proteins were detected in Western blot experiments. Conclusions The distribution and conservation of these five genes as well as their regulation of expression and the physico-chemical properties of the encoded proteins underline the likely great bandwidth of small protein functions in bacteria and makes them attractive candidates for functional studies.
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Affiliation(s)
- Desiree Baumgartner
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Matthias Kopf
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.,Present Address: Molecular Health GmbH, Kurfürsten-Anlage 21, 69115, Heidelberg, Germany
| | - Stephan Klähn
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.
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Martínez-Pérez C, Mohr W, Löscher CR, Dekaezemacker J, Littmann S, Yilmaz P, Lehnen N, Fuchs BM, Lavik G, Schmitz RA, LaRoche J, Kuypers MMM. The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. Nat Microbiol 2016; 1:16163. [DOI: 10.1038/nmicrobiol.2016.163] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 08/05/2016] [Indexed: 11/09/2022]
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Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nat Commun 2016; 7:11071. [PMID: 27002549 PMCID: PMC4804200 DOI: 10.1038/ncomms11071] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/17/2016] [Indexed: 01/08/2023] Open
Abstract
The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean. Both symbiotic systems are lineage specific and differ in the number of UCYN-A cells involved. Our analyses infer a streamlined genome expression towards nitrogen fixation in both UCYN-A lineages. Comparative genomics reveal a strong purifying selection in UCYN-A1 and UCYN-A2 with a diversification process ∼91 Myr ago, in the late Cretaceous, after the low-nutrient regime period occurred during the Jurassic. These findings suggest that UCYN-A diversified in a co-evolutionary process, wherein their prymnesiophyte partners acted as a barrier driving an allopatric speciation of extant UCYN-A lineages. Nitrogen fixation in oceans is facilitated by associations between marine phytoplankton and cyanobacteria such as UCYN-A. Here, Cornejo-Castillo et al. show that UCYN-A diversified in the late Cretaceous under strong purifying selection to become lineage-specific symbiont partners with different prymnesiophytes.
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Cabello AM, Cornejo-Castillo FM, Raho N, Blasco D, Vidal M, Audic S, de Vargas C, Latasa M, Acinas SG, Massana R. Global distribution and vertical patterns of a prymnesiophyte-cyanobacteria obligate symbiosis. THE ISME JOURNAL 2016; 10:693-706. [PMID: 26405830 PMCID: PMC4817677 DOI: 10.1038/ismej.2015.147] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/15/2015] [Accepted: 07/21/2015] [Indexed: 11/09/2022]
Abstract
A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte-UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte-UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml(-1)) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages.
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Affiliation(s)
- Ana M Cabello
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | | | - Nicolas Raho
- Department of molecular Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dolors Blasco
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Montserrat Vidal
- Departament of Ecology, University of Barcelona, Barcelona, Spain
| | - Stéphane Audic
- Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 6, Roscoff, France
- Laboratoire Adaptation et Diversité en Milieu Marin, CNRS, UMR 7144, Roscoff, France
| | - Colomban de Vargas
- Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 6, Roscoff, France
- Laboratoire Adaptation et Diversité en Milieu Marin, CNRS, UMR 7144, Roscoff, France
| | - Mikel Latasa
- Centro Oceanográfico de Gijón (IEO), Gijón, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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Choi DH, An SM, Chun S, Yang EC, Selph KE, Lee CM, Noh JH. Dynamic changes in the composition of photosynthetic picoeukaryotes in the northwestern Pacific Ocean revealed by high-throughput tag sequencing of plastid 16S rRNA genes. FEMS Microbiol Ecol 2015; 92:fiv170. [PMID: 26712350 DOI: 10.1093/femsec/fiv170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic picoeukaryotes (PPEs) are major oceanic primary producers. However, the diversity of such communities remains poorly understood, especially in the northwestern (NW) Pacific. We investigated the abundance and diversity of PPEs, and recorded environmental variables, along a transect from the coast to the open Pacific Ocean. High-throughput tag sequencing (using the MiSeq system) revealed the diversity of plastid 16S rRNA genes. The dominant PPEs changed at the class level along the transect. Prymnesiophyceae were the only dominant PPEs in the warm pool of the NW Pacific, but Mamiellophyceae dominated in coastal waters of the East China Sea. Phylogenetically, most Prymnesiophyceae sequences could not be resolved at lower taxonomic levels because no close relatives have been cultured. Within the Mamiellophyceae, the genera Micromonas and Ostreococcus dominated in marginal coastal areas affected by open water, whereas Bathycoccus dominated in the lower euphotic depths of oligotrophic open waters. Cryptophyceae and Phaeocystis (of the Prymnesiophyceae) dominated in areas affected principally by coastal water. We also defined the biogeographical distributions of Chrysophyceae, prasinophytes, Bacillariophyceaea and Pelagophyceae. These distributions were influenced by temperature, salinity and chlorophyll a and nutrient concentrations.
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Affiliation(s)
- Dong H Choi
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea Department of Marine Biology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sung M An
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea
| | - Sungjun Chun
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea Department of Marine Biology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Eun C Yang
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea Department of Marine Biology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Karen E Selph
- Deparment of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Charity M Lee
- Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea
| | - Jae H Noh
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, Republic of Korea Department of Marine Biology, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
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High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation. ISME JOURNAL 2015; 10:1499-513. [PMID: 26613341 DOI: 10.1038/ismej.2015.205] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/05/2015] [Accepted: 10/07/2015] [Indexed: 11/08/2022]
Abstract
Australia's tropical waters represent predicted 'hotspots' for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of diazotrophs within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size-fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (δ-proteobacteria and γ-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from <1 to 91 nmol l(-1) day(-1), and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than in spring. Relative abundances of UCYN-A1 and γ-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia's tropical waters are indeed hotspots for N2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.
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