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Chen J, Deng L, Wang X, Zhong C, Xia X, Liu H. Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters. mSystems 2024; 9:e0017624. [PMID: 39105582 PMCID: PMC11406894 DOI: 10.1128/msystems.00176-24] [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: 02/05/2024] [Accepted: 07/07/2024] [Indexed: 08/07/2024] Open
Abstract
Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters. IMPORTANCE Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.
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Affiliation(s)
- Jiawei Chen
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lixia Deng
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiao Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Cheng Zhong
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
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2
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Rose SA, Robicheau BM, Tolman J, Fonseca-Batista D, Rowland E, Desai D, Ratten JM, Kantor EJH, Comeau AM, Langille MG, Jerlström-Hultqvist J, Devred E, Sarthou G, Bertrand EM, LaRoche J. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni. SCIENCE ADVANCES 2024; 10:eadn1476. [PMID: 39083619 PMCID: PMC11290528 DOI: 10.1126/sciadv.adn1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.
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Affiliation(s)
- Sonja A. Rose
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Debany Fonseca-Batista
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ella Joy H. Kantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M. Comeau
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G.I. Langille
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Emmanuel Devred
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Halifax, Nova Scotia, Canada
| | | | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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3
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Chowdhury S, Berthelot H, Baudet C, González-Santana D, Reeder CF, L'Helguen S, Maguer JF, Löscher CR, Singh A, Blain S, Cassar N, Bonnet S, Planquette H, Benavides M. Fronts divide diazotroph communities in the Southern Indian Ocean. FEMS Microbiol Ecol 2024; 100:fiae095. [PMID: 38992179 PMCID: PMC11245648 DOI: 10.1093/femsec/fiae095] [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: 01/11/2024] [Revised: 06/20/2024] [Accepted: 07/10/2024] [Indexed: 07/13/2024] Open
Abstract
Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well-explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here, we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multifrontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving high N2 fixation rates (up to 13.96 nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.
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Affiliation(s)
- Subhadeep Chowdhury
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Hugo Berthelot
- IFREMER, DYNECO, Pelagos Laboratory, Plouzané, France
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Corentin Baudet
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - David González-Santana
- Univ Brest, CNRS, IRD, IFREMER, LEMAR, F-29280 Plouzané, France
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Christian Furbo Reeder
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Stéphane L'Helguen
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Jean-François Maguer
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Carolin R Löscher
- Nordcee, Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Arvind Singh
- Geosciences Division, Physical Research Laboratory, Ahmedabad 380009, India
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Nicolas Cassar
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
- Division of Earth and Climate Sciences, Nicholas School of the Environment, Duke University, Durham, NC 27708, United States
| | - Sophie Bonnet
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Hélène Planquette
- Laboratoire des Sciences de l'Environnement Marin, IUEM, Université de Brest-UMR 6539 CNRS/UBO/IRD, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Mar Benavides
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
- Turing Center for Living Systems, Aix-Marseille University, Marseille, France
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4
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Zhao Z, Zhao Y, Marotta F, Xamxidin M, Li H, Xu J, Hu B, Wu M. The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau. Front Microbiol 2024; 15:1424368. [PMID: 39132143 PMCID: PMC11312105 DOI: 10.3389/fmicb.2024.1424368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/18/2024] [Indexed: 08/13/2024] Open
Abstract
The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.
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Affiliation(s)
- Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yuxiang Zhao
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Federico Marotta
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Huan Li
- Lab of Plateau Ecology and Nature Conservation, The Altun Mountain National Nature Reserve, Xinjiang, China
| | - Junquan Xu
- Lab of Plateau Ecology and Nature Conservation, The Altun Mountain National Nature Reserve, Xinjiang, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
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5
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Gao M, Andrews J, Armin G, Chakraborty S, Zehr JP, Inomura K. Rapid mode switching facilitates the growth of Trichodesmium: A model analysis. iScience 2024; 27:109906. [PMID: 38947530 PMCID: PMC11214483 DOI: 10.1016/j.isci.2024.109906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/02/2024] Open
Abstract
Trichodesmium is one of the dominant dinitrogen (N2) fixers in the ocean, influencing global carbon and nitrogen cycles through biochemical reactions. Although its photosynthetic activity fluctuates rapidly, the physiological or ecological advantage of this fluctuation is unclear. We develop a metabolic model of Trichodesmium that can perform daytime N2 fixation. We examined (1) the effect of the duration of switches between photosynthetic and non-photosynthetic cellular states and (2) the effect of the presence and absence of N2 fixation in photosynthetic states. Results show that a rapid switch between photosynthetic and non-photosynthetic states increases Trichodesmium growth rates by improving metabolic efficiencies due to an improved balance of C and N metabolism. This provides a strategy for previous paradoxical observations that all Trichodesmium cells can contain nitrogenase. This study reveals the importance of fluctuating photosynthetic activity and provides a mechanism for daytime N2 fixation that allows Trichodesmium to fix N2 aerobically in the global ocean.
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Affiliation(s)
- Meng Gao
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Jamal Andrews
- Biological and Environmental Sciences Graduate Program, University of Rhode Island, Kingston, RI, USA
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Subhendu Chakraborty
- Systems Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
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6
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Zehr JP, Capone DG. Unsolved mysteries in marine nitrogen fixation. Trends Microbiol 2024; 32:532-545. [PMID: 37658011 DOI: 10.1016/j.tim.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.
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Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Douglas G Capone
- Marine and Environmental Biology Section of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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7
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Kang W, Mu L, Hu X. Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9236-9249. [PMID: 38748855 DOI: 10.1021/acs.est.4c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Product Safety, Key Laboratory for Environmental Factors Controlling Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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8
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Zhang H, Tan Y, Zhou Y, Liu J, Xia X. Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168702. [PMID: 37992836 DOI: 10.1016/j.scitotenv.2023.168702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Youping Zhou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
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9
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Raut Y, Barr CR, Paris ER, Kapili BJ, Dekas AE, Capone DG. Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments. Front Microbiol 2024; 14:1312843. [PMID: 38249476 PMCID: PMC10796445 DOI: 10.3389/fmicb.2023.1312843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Macroalgae, commonly known as seaweed, are foundational species in coastal ecosystems and contribute significantly to coastal primary production globally. However, the impact of macroalgal decomposition on benthic biological nitrogen fixation (BNF) after deposition to the seafloor remains largely unexplored. In this study, we measure BNF rates at three different sites at the Big Fisherman's Cove on Santa Catalina Island, CA, USA, which is representative of globally distributed rocky bottom macroalgal habitats. Unamended BNF rates varied among sites (0.001-0.05 nmol N g-1 h -1) and were generally within the lower end of previously reported ranges. We hypothesized that the differences in BNF between sites were linked to the availability of organic matter. Indeed, additions of glucose, a labile carbon source, resulted in 2-3 orders of magnitude stimulation of BNF rates in bottle incubations of sediment from all sites. To assess the impact of complex, autochthonous organic matter, we simulated macroalgal deposition and remineralization with additions of brown (i.e., Macrocystis pyrifera and Dictyopteris), green (i.e., Codium fragile), and red (i.e., Asparagopsis taxiformis) macroalgae. While brown and green macroalgal amendments resulted in 53- to 520-fold stimulation of BNF rates-comparable to the labile carbon addition-red alga was found to significantly inhibit BNF rates. Finally, we employed nifH sequencing to characterize the diazotrophic community associated with macroalgal decomposition. We observed a distinct community shift in potential diazotrophs from primarily Gammaproteobacteria in the early stages of remineralization to a community dominated by Deltaproteobacteria (e.g., sulfate reducers), Bacteroidia, and Spirochaeta toward the latter phase of decomposition of brown, green, and red macroalgae. Notably, the nifH-containing community associated with red macroalgal detritus was distinct from that of brown and green macroalgae. Our study suggests coastal benthic diazotrophs are limited by organic carbon and demonstrates a significant and phylum-specific effect of macroalgal loading on benthic microbial communities.
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Affiliation(s)
- Yubin Raut
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Emily R. Paris
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Bennett J. Kapili
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Anne E. Dekas
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Douglas G. Capone
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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10
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Sun X, Xiao Y, Yong C, Sun H, Li S, Huang H, Jiang H. Interactions between the nitrogen-fixing cyanobacterium Trichodesmium and siderophore-producing cyanobacterium Synechococcus under iron limitation. ISME COMMUNICATIONS 2024; 4:ycae072. [PMID: 38873030 PMCID: PMC11171426 DOI: 10.1093/ismeco/ycae072] [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: 12/06/2023] [Revised: 04/07/2024] [Indexed: 06/15/2024]
Abstract
As diazotrophic cyanobacteria of tremendous biomass, Trichodesmium continuously provide a nitrogen source for carbon-fixing cyanobacteria and drive the generation of primary productivity in marine environments. However, ocean iron deficiencies limit growth and metabolism of Trichodesmium. Recent studies have shown the co-occurrence of Trichodesmium and siderophore-producing Synechococcus in iron-deficient oceans, but whether siderophores secreted by Synechococcus can be used by Trichodesmium to adapt to iron deficiency is not clear. We constructed a mutant Synechococcus strain unable to produce siderophores to explore this issue. Synechococcus filtrates with or without siderophores were added into a Trichodesmium microbial consortium consisting of Trichodesmium erythraeum IMS 101 as the dominant microbe with chronic iron deficiency. By analyzing the physiological phenotype, metagenome, and metatranscriptome, we investigated the interactions between the nitrogen-fixing cyanobacterium Tricodesmium and siderophore-producing cyanobacterium Synechococcus under conditions of iron deficiency. The results indicated that siderophores secreted by Synechococcus are likely to chelate with free iron in the culture medium of the Trichodesmium consortium, reducing the concentration of bioavailable iron and posing greater challenges to the absorption of iron by Trichodesmium. These findings revealed the characteristics of iron-competitive utilization between diazotrophic cyanobacteria and siderophore-producing cyanobacteria, as well as potential interactions, and provide a scientific basis for understanding the regulatory effects of nutrient limitation on marine primary productivity.
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Affiliation(s)
- Xumei Sun
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
| | - Yan Xiao
- School of Life Sciences, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei, 430079, People’s Republic of China
| | - Chengwen Yong
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Hansheng Sun
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Shuangqing Li
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
- School of Life Sciences, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei, 430079, People’s Republic of China
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11
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Fernández-Juárez V, Hallstrøm S, Pacherres CO, Wang J, Coll-Garcia G, Kühl M, Riemann L. Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium. Appl Environ Microbiol 2023; 89:e0102723. [PMID: 37882569 PMCID: PMC10686084 DOI: 10.1128/aem.01027-23] [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: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The contribution of non-cyanobacterial diazotrophs (NCDs) to total N2 fixation in the marine water column is unknown, but their importance is likely constrained by the limited availability of dissolved organic matter and low O2 conditions. Light could support N2 fixation and growth by NCDs, yet no examples from bacterioplankton exist. In this study, we show that the phototrophic NCD, Rhodopseudomonas sp. BAL398, which is a member of the diazotrophic community in the surface waters of the Baltic Sea, can utilize light. Our study highlights the significance of biofilm formation for utilizing light and fixing N2 under oxic conditions and the role of cell plasticity in regulating these processes. Our findings have implications for the general understanding of the ecology and importance of NCDs in marine waters.
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Affiliation(s)
- Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Cesar O. Pacherres
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jiaqi Wang
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillem Coll-Garcia
- Microbiology, Biology Department, University of the Balearic Islands, Palma de Mallorca, Spain
- Environmental Microbiology Group, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Spain
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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12
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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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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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Santos DS, Pontes PVM, Leite AMDO, Ferreira AL, de Souza M, Araujo TDSS, dos Santos HF, de Oliveira GC, Bitencourt JA, Cavalcanti AB, Martins RL, Esteves FDA. Bioprospecting for Isoetes cangae Endophytes with Potential to Promote Plant Growth. Int J Microbiol 2023; 2023:5992113. [PMID: 37644978 PMCID: PMC10462435 DOI: 10.1155/2023/5992113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/29/2023] [Accepted: 07/22/2023] [Indexed: 08/31/2023] Open
Abstract
Isoetes cangae is a native plant found only in a permanent pond in Serra dos Carajás in the Amazon region. Plant-associated microbial communities are recognized to be responsible for biological processes essential for the health, growth, and even adaptation of plants to environmental stresses. In this sense, the aims of this work were to isolate, identify, and evaluate the properties of endophytic bacteria isolated from I. cangae. The bioprospecting of potentially growth-promoting endophytes required the following steps to be taken: isolation of endophytic colonies, molecular identification by 16S rDNA sequence analysis, and evaluation of the bacterial potential for nitrogen fixation, production of indole acetic acid and siderophores, as well as phosphate solubilization and mineralization. Bacillus sp., Rhizobium sp., Priestia sp., Acinetobacter sp., Rossellomorea sp., Herbaspirillum sp., Heyndrickxia sp., and Metabacillus sp., among other bacterial species, were identified. The isolates showed to be highly promising, evidencing the physiological importance for the plant and having the potential to promote plant growth.
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Affiliation(s)
- Danielle Silveira Santos
- Federal University of Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé 27965-045, Brazil
| | | | | | - Aline Lemos Ferreira
- Federal University of Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé 27965-045, Brazil
| | - Mariana de Souza
- Federal University of Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé 27965-045, Brazil
| | | | | | | | | | | | - Rodrigo Lemes Martins
- Federal University of Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé 27965-045, Brazil
| | - Francisco De Assis Esteves
- Federal University of Rio de Janeiro, Instituto de Biodiversidade e Sustentabilidade, Macaé 27965-045, Brazil
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15
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El-Seedi HR, El-Mallah MF, Yosri N, Alajlani M, Zhao C, Mehmood MA, Du M, Ullah H, Daglia M, Guo Z, Khalifa SAM, Shou Q. Review of Marine Cyanobacteria and the Aspects Related to Their Roles: Chemical, Biological Properties, Nitrogen Fixation and Climate Change. Mar Drugs 2023; 21:439. [PMID: 37623720 PMCID: PMC10456358 DOI: 10.3390/md21080439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Marine cyanobacteria are an ancient group of photosynthetic microbes dating back to 3.5 million years ago. They are prolific producers of bioactive secondary metabolites. Over millions of years, natural selection has optimized their metabolites to possess activities impacting various biological targets. This paper discusses the historical and existential records of cyanobacteria, and their role in understanding the evolution of marine cyanobacteria through the ages. Recent advancements have focused on isolating and screening bioactive compounds and their respective medicinal properties, and we also discuss chemical property space and clinical trials, where compounds with potential pharmacological effects, such as cytotoxicity, anticancer, and antiparasitic properties, are highlighted. The data have shown that about 43% of the compounds investigated have cytotoxic effects, and around 8% have anti-trypanosome activity. We discussed the role of different marine cyanobacteria groups in fixing nitrogen percentages on Earth and their outcomes in fish productivity by entering food webs and enhancing productivity in different agricultural and ecological fields. The role of marine cyanobacteria in the carbon cycle and their outcomes in improving the efficiency of photosynthetic CO2 fixation in the chloroplasts of crop plants, thus enhancing the crop plant's yield, was highlighted. Ultimately, climate changes have a significant impact on marine cyanobacteria where the temperature rises, and CO2 improves the cyanobacterial nitrogen fixation.
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Affiliation(s)
- Hesham R. El-Seedi
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu University, Jiangsu Education Department, Nanjing 210024, China
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Mohamed F. El-Mallah
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Nermeen Yosri
- Chemistry Department of Medicinal and Aromatic Plants, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef 62514, Egypt;
- China Light Industry Key Laboratory of Food Intelligent Detection & Processing, School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
| | - Muaaz Alajlani
- Faculty of Pharmacy, Al-Sham Private University, Damascus 0100, Syria;
| | - Chao Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Muhammad A. Mehmood
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China;
| | - Hammad Ullah
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Maria Daglia
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Zhiming Guo
- China Light Industry Key Laboratory of Food Intelligent Detection & Processing, School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
| | - Shaden A. M. Khalifa
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Psychiatry and Psychology Department, Capio Saint Göran’s Hospital, Sankt Göransplan 1, 112 19 Stockholm, Sweden
| | - Qiyang Shou
- Second Clinical Medical College, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou 310053, China
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16
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Luo W, Luo YW. Diurnally dynamic iron allocation promotes N 2 fixation in marine dominant diazotroph Trichodesmium. Comput Struct Biotechnol J 2023; 21:3503-3512. [PMID: 37484493 PMCID: PMC10362294 DOI: 10.1016/j.csbj.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/15/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023] Open
Abstract
Trichodesmium is the dominant photoautotrophic dinitrogen (N2) fixer (diazotroph) in the ocean. Iron is an important factor limiting growth of marine diazotrophs including Trichodesmium mainly because of high iron content of its N2-fixing enzyme, nitrogenase. However, it still lacks a quantitative understanding of how dynamic iron allocation among physiological processes acts to regulate growth and N2 fixation in Trichodesmium. Here, we constructed a model of Trichodesmium trichome in which intracellular iron could be dynamically re-allocated in photosystems and nitrogenase during the daytime. The results demonstrate that the dynamic iron allocation enhances modeled N2 fixation and growth rates of Trichodesmium, especially in iron-limited conditions, albeit having a marginal impact under high iron concentrations. Although the reuse of iron during a day is an apparent cause that dynamic iron allocation can benefit Trichodesmium under iron limitation, our model reveals two important mechanisms. First, the release of iron from photosystems downregulates the intracellular oxygen (O2) production and reduces the demand of respiratory protection, a process that Trichodesmium wastefully respires carbohydrates to create a lower O2 window for N2 fixation. Hence, more carbohydrates can be used in growth. Second, lower allocation of iron to nitrogenase during early daytime, a period when photosynthesis is active and intracellular O2 is high, reduces the amount of iron that is trapped in the inactivated nitrogenase induced by O2. This mechanism further increases the iron use efficiency in Trichodesmium. Overall, our study provides mechanistic and quantitative insight into the diurnal iron allocation that can alleviate iron limitation to Trichodesmium.
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17
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Bonnet S, Guieu C, Taillandier V, Boulart C, Bouruet-Aubertot P, Gazeau F, Scalabrin C, Bressac M, Knapp AN, Cuypers Y, González-Santana D, Forrer HJ, Grisoni JM, Grosso O, Habasque J, Jardin-Camps M, Leblond N, Le Moigne FAC, Lebourges-Dhaussy A, Lory C, Nunige S, Pulido-Villena E, Rizzo AL, Sarthou G, Tilliette C. Natural iron fertilization by shallow hydrothermal sources fuels diazotroph blooms in the ocean. Science 2023; 380:812-817. [PMID: 37228198 DOI: 10.1126/science.abq4654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Iron is an essential nutrient that regulates productivity in ~30% of the ocean. Compared with deep (>2000 meter) hydrothermal activity at mid-ocean ridges that provide iron to the ocean's interior, shallow (<500 meter) hydrothermal fluids are likely to influence the surface's ecosystem. However, their effect is unknown. In this work, we show that fluids emitted along the Tonga volcanic arc (South Pacific) have a substantial impact on iron concentrations in the photic layer through vertical diffusion. This enrichment stimulates biological activity, resulting in an extensive patch of chlorophyll (360,000 square kilometers). Diazotroph activity is two to eight times higher and carbon export fluxes are two to three times higher in iron-enriched waters than in adjacent unfertilized waters. Such findings reveal a previously undescribed mechanism of natural iron fertilization in the ocean that fuels regional hotspot sinks for atmospheric CO2.
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Affiliation(s)
- Sophie Bonnet
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO Marseille, France
| | - Cécile Guieu
- Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer de Villefranche, CNRS, Sorbonne Université, 06230 Villefranche-sur-Mer, France
| | - Vincent Taillandier
- Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer de Villefranche, CNRS, Sorbonne Université, 06230 Villefranche-sur-Mer, France
| | - Cédric Boulart
- Adaptation et Diversité en Milieu Marin, UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Pascale Bouruet-Aubertot
- Laboratoire d'Océanographie et du Climat: Expérimentation et Approches Numériques (LOCEAN-IPSL), Sorbonne University, CNRS-IRD-MNHN, 75005 Paris, France
| | - Frédéric Gazeau
- Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer de Villefranche, CNRS, Sorbonne Université, 06230 Villefranche-sur-Mer, France
| | - Carla Scalabrin
- Ifremer, Univ Brest, CNRS, UMR 6538 Geo-Ocean, F-29280 Plouzané, France
| | - Matthieu Bressac
- Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer de Villefranche, CNRS, Sorbonne Université, 06230 Villefranche-sur-Mer, France
| | - Angela N Knapp
- Department of Earth, Ocean, and Atmospheric Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Yannis Cuypers
- Laboratoire d'Océanographie et du Climat: Expérimentation et Approches Numériques (LOCEAN-IPSL), Sorbonne University, CNRS-IRD-MNHN, 75005 Paris, France
| | - David González-Santana
- CNRS, Univ Brest, IRD, Ifremer, UMR 6539, LEMAR, Plouzané, France
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas, Spain
| | - Heather J Forrer
- Department of Earth, Ocean, and Atmospheric Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jean-Michel Grisoni
- Institut de la Mer de Villefranche, IMEV, Sorbonne Université, Villefranche-sur-Mer, France
| | - Olivier Grosso
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO Marseille, France
| | - Jérémie Habasque
- CNRS, Univ Brest, IRD, Ifremer, UMR 6539, LEMAR, Plouzané, France
| | | | - Nathalie Leblond
- Institut de la Mer de Villefranche, IMEV, Sorbonne Université, Villefranche-sur-Mer, France
| | - Frédéric A C Le Moigne
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO Marseille, France
- CNRS, Univ Brest, IRD, Ifremer, UMR 6539, LEMAR, Plouzané, France
| | | | - Caroline Lory
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO Marseille, France
| | - Sandra Nunige
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO Marseille, France
| | | | - Andrea L Rizzo
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Milano, Via Alfonso Corti 12, 20133 Milano, Italy
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 4, 20126 Milan, Italy
| | | | - Chloé Tilliette
- Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer de Villefranche, CNRS, Sorbonne Université, 06230 Villefranche-sur-Mer, France
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18
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Patwardhan S, Phan J, Smedile F, Vetriani C. The Genome of Varunaivibrio sulfuroxidans Strain TC8 T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea. Microorganisms 2023; 11:1366. [PMID: 37374867 DOI: 10.3390/microorganisms11061366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jonathan Phan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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19
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Takuhei S, Nishimura Y, Yoshizawa S, Takami H, Hamasaki K, Fujiwara A, Nishino S, Harada N. Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean. THE ISME JOURNAL 2023:10.1038/s41396-023-01424-x. [PMID: 37217593 DOI: 10.1038/s41396-023-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023]
Abstract
Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.
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Affiliation(s)
- Shiozaki Takuhei
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yosuke Nishimura
- Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Center for Mathematical Science and Advanced Technology, JAMSTEC, Yokohama, 236-0001, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8564, Kashiwa, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 113-8657, Bunkyo-ku, Japan
| | - Amane Fujiwara
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Shigeto Nishino
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Naomi Harada
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
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20
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Jiang Z, Zhu Y, Sun Z, Zhai H, Zhou F, Yan X, Chen Q, Chen J, Zeng J. Size-fractionated N 2 fixation off the Changjiang Estuary during summer. Front Microbiol 2023; 14:1189410. [PMID: 37228373 PMCID: PMC10203160 DOI: 10.3389/fmicb.2023.1189410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Recent evidence has shown active N2 fixation in coastal eutrophic waters, yet the rate and controlling factors remain poorly understood, particularly in large estuaries. The Changjiang Estuary (CE) and adjacent shelf are characterized by fresh, nitrogen-replete Changjiang Diluted Water (CDW) and saline, nitrogen-depletion intruded Kuroshio water (Taiwan Warm Current and nearshore Kuroshio Branch Current), where N2 fixation may be contributed by different groups (i.e., Trichodesmium and heterotrophic diazotrophs). Here, for the first time, we provide direct measurement of size-fractionated N2 fixation rates (NFRs) off the CE during summer 2014 using the 15N2 bubble tracer method. The results demonstrated considerable spatial variations (southern > northern; offshore > inshore) in surface and depth-integrated NFRs, averaging 0.83 nmol N L-1 d-1 and 24.3 μmol N m-2 d-1, respectively. The highest bulk NFR (99.9 μmol N m-2 d-1; mostly contributed by >10 μm fraction) occurred in the southeastern East China Sea, where suffered from strong intrusion of the Kuroshio water characterized by low N/P ratio (<10) and abundant Trichodesmium (up to 10.23 × 106 trichomes m-2). However, low NFR (mostly contributed by <10 μm fraction) was detected in the CE controlled by the CDW, where NOx concentration (up to 80 μmol L-1) and N/P ratio (>100) were high and Trichodesmium abundance was low. The >10 μm fraction accounted for 60% of depth-integrated bulk NFR over the CE and adjacent shelf. We speculated that the present NFR of >10 μm fraction was mostly supported by Trichodesmium. Spearman rank correlation indicated that the NFR was significantly positively correlated with Trichodesmium abundance, salinity, temperature and Secchi depth, but was negatively with turbidity, N/P ratio, NOx, and chlorophyll a concentration. Our study suggests that distribution and size structure of N2 fixation off the CE are largely regulated by water mass (intruded Kuroshio water and CDW) movement and associated diazotrophs (particularly Trichodesmium) and nutrient conditions.
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Affiliation(s)
- Zhibing Jiang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
- Key Laboratory of Nearshore Engineering Environment and Ecological Security of Zhejiang Province, Hangzhou, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Yuanli Zhu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Zhenhao Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongchang Zhai
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Feng Zhou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Xiaojun Yan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Quanzhen Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jiangning Zeng
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
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21
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Kang W, Sun S, Hu X. Microplastics trigger the Matthew effect on nitrogen assimilation in marine diatoms at an environmentally relevant concentration. WATER RESEARCH 2023; 233:119762. [PMID: 36841163 DOI: 10.1016/j.watres.2023.119762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Microplastics (MPs, diameter <5 mm) are widely distributed on Earth, especially in the oceans. Diatoms account for ∼40% of marine primary productivity and affect the global biogeochemical cycles of macroelements. However, the effects of MPs on marine nitrogen cycling remain poorly understood, particularly comparisons between nitrogen-replete and nitrogen-limited conditions. We found that MPs trigger the Matthew effect on nitrogen assimilation in diatoms, where MPs inhibited nitrogen assimilation under nitrogen-limited conditions while enhancing nitrogen metabolism under nitrogen-replete conditions in Phaeodactylum tricornutum. Nitrate reductase (NR) and nitrite reductase (NIR) are upregulated, but nitrate transporter (NRT) and glutamine synthetase (GS) are downregulated by MPs under nitrogen-limited conditions. In contrast, NR, NIR, and GS are all upregulated by MPs under nitrogen-replete conditions. MPs accelerate nitrogen anabolic processes with an increase in the accumulation of carbohydrates by 80.7 ± 7.9% and enhance the activities of key nitrogen-metabolizing enzymes (8.20-44.90%) under nitrogen-replete conditions. In contrast, the abundance of carbohydrates decreases by 22.0-34.4%, and NRT activity is inhibited by 79.0-86.5% in nitrogen-limited algae exposed to MPs. Metabolomic and transcriptomic analyses were performed to further explore the molecular mechanisms of reprogrammed nitrogen assimilation, including carbon metabolism, nitrogen transport and ammonia assimilation. The aforementioned spatial redistribution (e.g., the Matthew effect between nitrogen-replete and -limited conditions) of nitrogen assimilation highlights the potential risks of MP contamination in the ocean.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shan Sun
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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22
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Kang J, Gill B, Reid R, Zhang F, Xiao S. Nitrate limitation in early Neoproterozoic oceans delayed the ecological rise of eukaryotes. SCIENCE ADVANCES 2023; 9:eade9647. [PMID: 36947611 PMCID: PMC10032604 DOI: 10.1126/sciadv.ade9647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
The early Neoproterozoic Era witnessed the initial ecological rise of eukaryotes at ca. 800 Ma. To assess whether nitrate availability played an important role in this evolutionary event, we measured nitrogen isotope compositions (δ15N) of marine carbonates from the early Tonian (ca. 1000 Ma to ca. 800 Ma) Huaibei Group in North China. The data reported here fill a critical gap in the δ15N record and indicate nitrate limitation in early Neoproterozoic oceans. A compilation of Proterozoic sedimentary δ15N data reveals a stepwise increase in δ15N values at ~800 Ma. Box model simulations indicate that this stepwise increase likely represents a ~50% increase in marine nitrate availability. Limited nitrate availability in early Neoproterozoic oceans may have delayed the ecological rise of eukaryotes until ~800 Ma when increased nitrate supply, together with other environmental and ecological factors, may have contributed to the transition from prokaryote-dominant to eukaryote-dominant marine ecosystems.
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Affiliation(s)
- Junyao Kang
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Benjamin Gill
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Rachel Reid
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Feifei Zhang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing 210023, China
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- Global Change Center, Virginia Tech, Blacksburg, VA, USA
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23
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Webb EA, Held NA, Zhao Y, Graham ED, Conover AE, Semones J, Lee MD, Feng Y, Fu FX, Saito MA, Hutchins DA. Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades. ISME COMMUNICATIONS 2023; 3:15. [PMID: 36823453 PMCID: PMC9950141 DOI: 10.1038/s43705-023-00214-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/13/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.
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Affiliation(s)
- Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Environmental Systems Science, ETH, Zurich, Switzerland
| | - Yiming Zhao
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Elaina D Graham
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Asa E Conover
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jake Semones
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | - Yuanyuan Feng
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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24
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Li H, Gao K. Deoxygenation enhances photosynthetic performance and increases N 2 fixation in the marine cyanobacterium Trichodesmium under elevated pCO 2. Front Microbiol 2023; 14:1102909. [PMID: 36876059 PMCID: PMC9975739 DOI: 10.3389/fmicb.2023.1102909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/27/2023] [Indexed: 02/17/2023] Open
Abstract
Effects of changed levels of dissolved O2 and CO2 on marine primary producers are of general concern with respect to ecological effects of ongoing ocean deoxygenation and acidification as well as upwelled seawaters. We investigated the response of the diazotroph Trichodesmium erythraeum IMS 101 after it had acclimated to lowered pO2 (~60 μM O2) and/or elevated pCO2 levels (HC, ~32 μM CO2) for about 20 generations. Our results showed that reduced O2 levels decreased dark respiration significantly, and increased the net photosynthetic rate by 66 and 89% under the ambient (AC, ~13 μM CO2) and the HC, respectively. The reduced pO2 enhanced the N2 fixation rate by ~139% under AC and only by 44% under HC, respectively. The N2 fixation quotient, the ratio of N2 fixed per O2 evolved, increased by 143% when pO2 decreased by 75% under the elevated pCO2. Meanwhile, particulate organic carbon and nitrogen quota increased simultaneously under reduced O2 levels, regardless of the pCO2 treatments. Nevertheless, changed levels of O2 and CO2 did not bring about significant changes in the specific growth rate of the diazotroph. Such inconsistency was attributed to the daytime positive and nighttime negative effects of both lowered pO2 and elevated pCO2 on the energy supply for growth. Our results suggest that Trichodesmium decrease its dark respiration by 5% and increase its N2-fixation by 49% and N2-fixation quotient by 30% under future ocean deoxygenation and acidification with 16% decline of pO2 and 138% rise of pCO2 by the end of this century.
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Affiliation(s)
- He Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
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25
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A Review on a Hidden Gem: Phycoerythrin from Blue-Green Algae. Mar Drugs 2022; 21:md21010028. [PMID: 36662201 PMCID: PMC9863059 DOI: 10.3390/md21010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Phycoerythrin (PE) is a pink/red-colored pigment found in rhodophytes, cryptophytes, and blue-green algae (cyanobacteria). The interest in PE is emerging from its role in delivering health benefits. Unfortunately, the current cyanobacterial-PE (C-PE) knowledge is still in the infant stage. It is essential to acquire a more comprehensive understanding of C-PE. This study aimed to review the C-PE structure, up and downstream processes of C-PE, application of C-PE, and strategies to enhance its stability and market value. In addition, this study also presented a strengths, weaknesses, opportunities, and threats (SWOT) analysis on C-PE. Cyanobacteria appeared to be the more promising PE producers compared to rhodophytes, cryptophytes, and macroalgae. Green/blue light is preferred to accumulate higher PE content in cyanobacteria. Currently, the prominent C-PE extraction method is repeated freezing-thawing. A combination of precipitation and chromatography approaches is proposed to obtain greater purity of C-PE. C-PE has been widely exploited in various fields, such as nutraceuticals, pharmaceuticals, therapeutics, cosmetics, biotechnology, food, and feed, owing to its bioactivities and fluorescent properties. This review provides insight into the state-of-art nature of C-PE and advances a step further in commercializing this prospective pigment.
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26
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Han Y, Zhou Y. Investigating biophysical control of marine phytoplankton dynamics via Bayesian mechanistic modeling. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
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Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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28
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Wrightson L, Yang N, Mahaffey C, Hutchins DA, Tagliabue A. Integrating the impact of global change on the niche and physiology of marine nitrogen-fixing cyanobacteria. GLOBAL CHANGE BIOLOGY 2022; 28:7078-7093. [PMID: 36054414 PMCID: PMC9826025 DOI: 10.1111/gcb.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Marine nitrogen fixation is a major source of new nitrogen to the ocean, which interacts with climate driven changes to physical nutrient supply to regulate the response of ocean primary production in the oligotrophic tropical ocean. Warming and changes in nutrient supply may alter the ecological niche of nitrogen-fixing organisms, or 'diazotrophs', however, impacts of warming on diazotroph physiology may also be important. Lab-based studies reveal that warming increases the nitrogen fixation-specific elemental use efficiency (EUE) of two prevalent marine diazotrophs, Crocosphaera and Trichodesmium, thus reducing their requirements for the limiting nutrients iron and phosphorus. Here, we coupled a new diazotroph model based upon observed diazotroph energetics of growth and resource limitation to a state-of-the-art global model of phytoplankton physiology and ocean biogeochemistry. Our model is able to address the integrated response of nitrogen fixation by Trichodesmium and Crocosphaera to warming under the IPCC high emission RCP8.5 scenario for the first time. Our results project a global decline in nitrogen fixation over the coming century. However, the regional response of nitrogen fixation to climate change is modulated by the diazotroph-specific thermal performance curves and EUE, particularly in the Pacific Ocean, which shapes global trends. Spatially, the response of both diazotrophs is similar with expansion towards higher latitudes and reduced rates of nitrogen fixation in the lower latitudes. Overall, 95%-97% of the nitrogen fixation climate signal can be attributed to the combined effect of temperature on the niche and physiology of marine diazotrophs, with decreases being associated with a reduced niche and increases resulting due to a combination of expanding niche and temperature driven changes to EUE. Climate change impacts on both the niche and physiology of marine diazotrophs interact to shape patterns of marine nitrogen fixation, which will have important implications for ocean productivity in the future.
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Affiliation(s)
- Lewis Wrightson
- Department of Earth, Ocean and Ecological SciencesUniversity of LiverpoolLiverpoolUK
| | - Nina Yang
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Claire Mahaffey
- Department of Earth, Ocean and Ecological SciencesUniversity of LiverpoolLiverpoolUK
| | - David A. Hutchins
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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29
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Wang X, Xing Y, Lv M, Zhang T, Ya H, Jiang B. Recent advances on the effects of microplastics on elements cycling in the environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157884. [PMID: 35944635 DOI: 10.1016/j.scitotenv.2022.157884] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (<5 mm) are an emerging pollutant which have received increasing concern in recent years. Microplastics pose a serious hazard and potential risk to the environment due to their migration, transformation, adsorption and degradation properties. The effects of different types of microplastics on the elemental cycles (carbon, nitrogen and phosphorus cycles) in ecosystems were comprehensively summarized. The impacts of microplastics on the element cycle occur mainly in the soil environment and to less extent in other environments. Microplastics affect carbon sources, carbon dioxide (CO2) emissions, and carbon conversion processes, mainly by affecting plant and animal activities, changing gene abundance, enzyme activity, and microbial community composition. Microplastics can affect nitrogen sources, nitrogen fixation, ammonification, nitrification and denitrification processes by changing gene abundance, enzyme activity and microbial community composition. Microplastics can also influence phosphorus content and phosphorus conversion processes by stimulating enzyme activity and changing the composition of microbial communities. Future research needs to analyze the coupling of multiple microplastics and influencing factors on elemental cycling processes. This work provides a better view of the impacts of microplastics on element cycles and the interaction between microplastics and organisms.
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Affiliation(s)
- Xin Wang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Mingjie Lv
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Tian Zhang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Haobo Ya
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China; Zhejiang Development & Planning Institute, Hangzhou 310030, PR China
| | - Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, PR China.
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Masuda T, Inomura K, Gao M, Armin G, Kotabová E, Bernát G, Lawrenz-Kendrick E, Lukeš M, Bečková M, Steinbach G, Komenda J, Prášil O. The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece. Comput Struct Biotechnol J 2022; 21:58-65. [PMID: 36514336 PMCID: PMC9732122 DOI: 10.1016/j.csbj.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Crocosphaera and Cyanothece are both unicellular, nitrogen-fixing cyanobacteria that prefer different environments. Whereas Crocosphaera mainly lives in nutrient-deplete, open oceans, Cyanothece is more common in coastal, nutrient-rich regions. Despite their physiological similarities, the factors separating their niches remain elusive. Here we performed physiological experiments on clone cultures and expand upon a simple ecological model to show that their different niches can be sufficiently explained by the observed differences in their photosynthetic capacities and rates of carbon (C) consumption. Our experiments revealed that Cyanothece has overall higher photosynthesis and respiration rates than Crocosphaera. A simple growth model of these microorganisms suggests that C storage and consumption are previously under-appreciated factors when evaluating the occupation of niches by different marine nitrogen fixers.
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Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Corresponding authors.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Meng Gao
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Eva Kotabová
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Gábor Bernát
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
| | - Evelyn Lawrenz-Kendrick
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Martin Lukeš
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Martina Bečková
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Gábor Steinbach
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Cellular Imaging Laboratory, Biological Research Center, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Josef Komenda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Corresponding authors.
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Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium. Nat Commun 2022; 13:6730. [PMID: 36344528 PMCID: PMC9640675 DOI: 10.1038/s41467-022-34586-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Growth of the prominent nitrogen-fixing cyanobacterium Trichodesmium is often limited by phosphorus availability in the ocean. How nitrogen fixation by phosphorus-limited Trichodesmium may respond to ocean acidification remains poorly understood. Here, we use phosphate-limited chemostat experiments to show that acidification enhanced phosphorus demands and decreased phosphorus-specific nitrogen fixation rates in Trichodesmium. The increased phosphorus requirements were attributed primarily to elevated cellular polyphosphate contents, likely for maintaining cytosolic pH homeostasis in response to acidification. Alongside the accumulation of polyphosphate, decreased NADP(H):NAD(H) ratios and impaired chlorophyll synthesis and energy production were observed under acidified conditions. Consequently, the negative effects of acidification were amplified compared to those demonstrated previously under phosphorus sufficiency. Estimating the potential implications of this finding, using outputs from the Community Earth System Model, predicts that acidification and dissolved inorganic and organic phosphorus stress could synergistically cause an appreciable decrease in global Trichodesmium nitrogen fixation by 2100.
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Abstract
Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.
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Chen M, Teng W, Zhao L, Han B, Song L, Shu W. Phylogenomics uncovers evolutionary trajectory of nitrogen fixation in Cyanobacteria. Mol Biol Evol 2022; 39:6659242. [PMID: 35946347 PMCID: PMC9435057 DOI: 10.1093/molbev/msac171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth’s biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.
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Affiliation(s)
- Mengyun Chen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Wenkai Teng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Liang Zhao
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Boping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, PR China
| | - Lirong Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Hubei 430072, PR China
| | - Wensheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
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34
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Alcamán-Arias ME, Cifuentes-Anticevic J, Castillo-Inaipil W, Farías L, Sanhueza C, Fernández-Gómez B, Verdugo J, Abarzua L, Ridley C, Tamayo-Leiva J, Díez B. Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula. Microorganisms 2022; 10:microorganisms10061140. [PMID: 35744658 PMCID: PMC9227844 DOI: 10.3390/microorganisms10061140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.
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Affiliation(s)
- María E. Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Jerónimo Cifuentes-Anticevic
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Wilson Castillo-Inaipil
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
| | - Cynthia Sanhueza
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Beatriz Fernández-Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas, Spain
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Leslie Abarzua
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
| | - Christina Ridley
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Javier Tamayo-Leiva
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
- Correspondence:
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Aerosol Nutrients and Their Biological Influence on the Northwest Pacific Ocean (NWPO) and Its Marginal Seas. BIOLOGY 2022; 11:biology11060842. [PMID: 35741363 PMCID: PMC9219953 DOI: 10.3390/biology11060842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary With intensifying human activities in the past decades, East Asia has recorded increasingly severe air pollution and become the second largest aerosol source on earth. The large quantity of aerosol emissions is not only a major health threat to humans, but can also be transported for a long distance and deposited in downwind seas and oceans. The aerosol contains major ions, heavy metals, and organic matters that are important external nutrients in upper oceans and potentially influence marine microbes and biogeochemical cycles. Therefore, the role of atmospheric deposition to oceans has received growing attention in recent years. In this paper, the current state of knowledge on the atmospheric nutrients and the biological effect of East Asian aerosol deposition on the northwest Pacific Ocean are reviewed, which could help us better understand the comprehensive influence of East Asian aerosols on marine ecosystems, and give insights into future research directions, especially under the future scenarios of changing human activities and climate. Abstract Atmospheric deposition is recognized as a significant source of nutrients in the surface ocean. The East Asia region is among the largest sources of aerosol emissions in the world, due to its large industrial, agricultural, and energy production. Thus, East Asian aerosols contain a large proportion of anthropogenic particles that are characterized by small size, complex composition, and high nutrient dissolution, resulting in important influences on marine microbes and biogeochemical cycles in the downwind areas of the northwest Pacific Ocean (NWPO). By using remote sensing, modeling, and incubation experimental methods, enhanced primary production due to the East Asian aerosol input has been observed in the NWPO, with subsequent promotion and inhibition impacts on different phytoplankton taxa. Changes of bacterial activity and diversity also occur in response to aerosol input. The impact of East Asian aerosol loadings is closely related to the amount and composition of the aerosol deposition as well as the hydrological condition of the receiving seawater. Here, we review the current state of knowledge on the atmospheric nutrients and the effects of the East Asian aerosols on microbes in the NWPO region. Future research perspectives are also proposed.
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36
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Bannon C, Rapp I, Bertrand EM. Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context. Front Microbiol 2022; 13:846890. [PMID: 35711751 PMCID: PMC9196195 DOI: 10.3389/fmicb.2022.846890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.
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Affiliation(s)
- Catherine Bannon
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - Insa Rapp
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Erin M. Bertrand
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
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37
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Effect of Culture pH on Properties of Exopolymeric Substances from Synechococcus PCC7942: Implications for Carbonate Precipitation. GEOSCIENCES 2022. [DOI: 10.3390/geosciences12050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The role of culture conditions on the production of exopolymeric substances (EPS) by Synechococcus strain PCC7942 was investigated. Carbonate mineral precipitation in these EPS was assessed in forced precipitation experiments. Cultures were grown in HEPES-buffered medium and non-buffered medium. The pH of buffered medium remained constant at 7.5, but in non-buffered medium it increased to 9.5 within a day and leveled off at 10.5. The cell yield at harvest was twice as high in non-buffered medium than in buffered medium. High molecular weight (>10 kDa) and low molecular weight (3–10 kDa) fractions of EPS were obtained from both cultures. The cell-specific EPS production in buffered medium was twice as high as in non-buffered medium. EPS from non-buffered cultures contained more negatively charged macromolecules and more proteins than EPS from buffered cultures. The higher protein content at elevated pH may be due to the induction of carbon-concentrating mechanisms, necessary to perform photosynthetic carbon fixation in these conditions. Forced precipitation showed smaller calcite carbonate crystals in EPS from non-buffered medium and larger minerals in polymers from buffered medium. Vaterite formed only at low EPS concentrations. Experimental results are used to conceptually model the impact of pH on the potential of cyanobacterial blooms to produce minerals. We hypothesize that in freshwater systems, small crystal production may benefit the picoplankton by minimizing the mineral ballast, and thus prolonging the residence time in the photic zone, which might result in slow sinking rates.
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38
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Lory C, Van Wambeke F, Fourquez M, Barani A, Guieu C, Tilliette C, Marie D, Nunige S, Berman-Frank I, Bonnet S. Assessing the contribution of diazotrophs to microbial Fe uptake using a group specific approach in the Western Tropical South Pacific Ocean. ISME COMMUNICATIONS 2022; 2:41. [PMID: 37938297 PMCID: PMC9723570 DOI: 10.1038/s43705-022-00122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/26/2022] [Accepted: 04/07/2022] [Indexed: 04/27/2023]
Abstract
Diazotrophs are often limited by iron (Fe) availability in the oligotrophic ocean. The Western Tropical South Pacific (WTSP) ocean has been suggested as an intense N2 fixation area due to Fe fertilizations through shallow hydrothermal activity. Yet, the Fe demand of diazotrophs in their natural habitat, where they cohabit with other microbial organisms also requiring Fe, remains unknown. Here we develop and apply a method consisting of coupling 55Fe uptake experiments with cell-sorting by flow cytometry, and provide group-specific rates of in situ Fe uptake by the microbial community in the WTSP, in addition to bulk and size fractionation rates. We reveal that the diazotrophs Crocosphaera watsonii and Trichodesmium contribute substantially to the bulk in situ Fe uptake (~33% on average over the studied area), despite being numerically less abundant compared to the rest of the planktonic community. Trichodesmium had the highest cell-specific Fe uptake rates, followed by C. watsonii, picoeukaryotes, Prochlorococcus, Synechococcus and finally heterotrophic bacteria. Calculated Fe:C quotas were higher (by 2 to 52-fold) for both studied diazotrophs compared to those of the non-diazotrophic plankton, reflecting their high intrinsic Fe demand. This translates into a diazotroph biogeographical distribution that appears to be influenced by ambient dissolved Fe concentrations in the WTSP. Despite having low cell-specific uptake rates, Prochlorococcus and heterotrophic bacteria were largely the main contributors to the bulk Fe uptake (~23% and ~12%, respectively). Overall, this group-specific approach increases our ability to examine the ecophysiological role of functional groups, including those of less abundant and/or less active microbes.
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Affiliation(s)
- C Lory
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
| | - F Van Wambeke
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - M Fourquez
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - A Barani
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - C Guieu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France
| | - C Tilliette
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France
| | - D Marie
- Sorbonne Université, CNRS, Station Biologique de Roscoff, Roscoff, France
| | - S Nunige
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - I Berman-Frank
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - S Bonnet
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
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39
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Riemann L, Rahav E, Passow U, Grossart HP, de Beer D, Klawonn I, Eichner M, Benavides M, Bar-Zeev E. Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens. Front Microbiol 2022; 13:875050. [PMID: 35464923 PMCID: PMC9019601 DOI: 10.3389/fmicb.2022.875050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.
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Affiliation(s)
- Lasse Riemann
- Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Uta Passow
- Ocean Science Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Isabell Klawonn
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Meri Eichner
- Institute of Microbiology CAS, Centre ALGATECH, Třeboň, Czechia
| | - Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.,Turing Center for Living Systems, Aix-Marseille University, Marseille, France
| | - Edo Bar-Zeev
- The Jacob Blaustein Institutes for Desert Research, Zuckerberg Institute for Water Research (ZIWR), Ben-Gurion University of the Negev, Be'er Sheva, Israel
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40
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Rabouille S, Tournier L, Duhamel S, Claquin P, Crispi O, Talec A, Landolfi A, Oschlies A. Organic Phosphorus Scavenging Supports Efficient Growth of Diazotrophic Cyanobacteria Under Phosphate Depletion. Front Microbiol 2022; 13:848647. [PMID: 35401448 PMCID: PMC8990761 DOI: 10.3389/fmicb.2022.848647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022] Open
Abstract
Considering the reported significant diazotrophic activities in open-ocean regions where primary production is strongly limited by phosphate, we explored the ability of diazotrophs to use other sources of phosphorus to alleviate the phosphate depletion. We tested the actual efficiency of the open-ocean, N2-fixer Crocosphaera watsonii to grow on organic phosphorus as the sole P source, and observed how the P source affects the cellular C, N, and P composition. We obtained equivalent growth efficiencies on AMP and DL-α-glycerophosphate as compared with identical cultures grown on phosphate, and survival of the population on phytic acid. Our results show that Crocosphaera cannot use all phosphomonoesters with the same efficiency, but it can grow without phosphate, provided that usable DOP and sufficient light energy are available. Also, results point out that organic phosphorus uptake is not proportional to alkaline phosphatase activity, demonstrating that the latter is not a suitable proxy to estimate DOP-based growth yields of organisms, whether in culture experiments or in the natural environment. The growth parameters obtained, as a function of the P source, will be critical to improve and calibrate mathematical models of diazotrophic growth and the distribution of nitrogen fixation in the global ocean.
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Affiliation(s)
- Sophie Rabouille
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France.,Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls-sur-Mer, France
| | - Lauralie Tournier
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
| | - Pascal Claquin
- UMR BOREA (CNRS 8067), MNHN, IRD (207), Normandie Université, Université de Caen Normandie, CREC, Luc-sur-Mer, France
| | - Olivier Crispi
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls-sur-Mer, France
| | - Amélie Talec
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France
| | - Angela Landolfi
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,CNR ISMAR, Rome, Italy
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41
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Qu PP, Fu FX, Wang XW, Kling JD, Elghazzawy M, Huh M, Zhou QQ, Wang C, Mak EWK, Lee MD, Yang N, Hutchins DA. Two co-dominant nitrogen-fixing cyanobacteria demonstrate distinct acclimation and adaptation responses to cope with ocean warming. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:203-217. [PMID: 35023627 DOI: 10.1111/1758-2229.13041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 05/28/2023]
Abstract
The globally dominant N2 -fixing cyanobacteria Trichodesmium and Crocosphaera provide vital nitrogen supplies to subtropical and tropical oceans, but little is known about how they will be affected by long-term ocean warming. We tested their thermal responses using experimental evolution methods during 2 years of selection at optimal (28°C), supra-optimal (32°C) and suboptimal (22°C) temperatures. After several hundred generations under thermal selection, changes in growth parameters, as well as N and C fixation rates, suggested that Trichodesmium did not adapt to the three selection temperature regimes during the 2-year evolution experiment, but could instead rapidly and reversibly acclimate to temperature shifts from 20°C to 34°C. In contrast, over the same timeframe apparent thermal adaptation was observed in Crocosphaera, as evidenced by irreversible phenotypic changes as well as whole-genome sequencing and variant analysis. Especially under stressful warming conditions (34°C), 32°C-selected Crocosphaera cells had an advantage in survival and nitrogen fixation over cell lines selected at 22°C and 28°C. The distinct strategies of phenotypic plasticity versus irreversible adaptation in these two sympatric diazotrophs are both viable ways to maintain fitness despite long-term temperature changes, and so could help to stabilize key ocean nitrogen cycle functions under future warming scenarios.
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Affiliation(s)
- Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xin-Wei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Joshua D Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mariam Elghazzawy
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Megan Huh
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Qian-Qian Zhou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, 361005, China
| | - Chunguang Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, 361005, China
| | - Esther Wing Kwan Mak
- Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, CA, 95064, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, 94035, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA
| | - Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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42
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Zavarzina DG, Prokofeva MI, Pikhtereva VA, Klyukina AA, Maslov AA, Merkel AY, Gavrilov SN. Deferrivibrio essentukiensis sp. nov., gen. nov., a Representative of Deferrivibrionaceae fam. nov., Isolated from the Subsurface Aquifer of Caucasian Mineral Drinking Waters. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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43
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Tian L, Jiang H, Song N, He S, Ali F. Comparing the effects of algae and macrophyte residues' degradation on biological nitrogen fixation in freshwater lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151129. [PMID: 34688766 DOI: 10.1016/j.scitotenv.2021.151129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
The degradation and mineralization of organic residues are important factors that drive biochemical processes in lake ecosystems. However, the effect of organic matter's degradation on biological nitrogen fixation (BNF) in freshwater lake sediments remains poorly understood. This study investigated the response of sediment nitrogen fixation to the degradations of algae and macrophyte residues through continuous flow mesocosms combined with nifH sequencing analysis and isotope tracing. The results suggested that the active nitrogen fixation of sediments only occurred in the first two weeks of the rapid degradation of organic residues. Degradation of algae and macrophytes residues quickly increased the nifH abundance and the nitrogenase activity (NA) in sediments; however, the maximum NA triggered by algae's degradation (658.2 ± 16.8 ng g-1 day-1) was six times higher than that induced by the degradation of macrophytes residues. There was no significant difference in NA of sediments with the degradation of Potamogeton and Phragmites. Redundancy analysis (RDA) showed that the variation of diazotrophic community in sediment was significantly (p < 0.01) correlated with the concentrations of SO42- and NH4+ in overlying water and the Fe(II) content and Eh in sediment. Overall, the BNF of sediments can quickly respond to the degradation of organic residues, and the degradation of algae has a stronger promoting effect on the nitrogen fixation in sediments than that of macrophyte residues.
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Affiliation(s)
- Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shangwei He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Farasat Ali
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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44
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Gavrilov SN, Potapov EG, Prokof’eva MI, Klyukina AA, Merkel AY, Maslov AA, Zavarzina DG. Diversity of Novel Uncultured Prokaryotes in Microbial Communities of the Yessentukskoye Underground Mineral Water Deposit. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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45
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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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46
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Fernández-Juárez V, Jaén-Luchoro D, Brito-Echeverría J, Agawin NSR, Bennasar-Figueras A, Echeveste P. Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration. MICROBIAL ECOLOGY 2022; 83:296-313. [PMID: 33954842 DOI: 10.1007/s00248-021-01766-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.
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Affiliation(s)
- Víctor Fernández-Juárez
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain.
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Jocelyn Brito-Echeverría
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Nona S R Agawin
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain
| | | | - Pedro Echeveste
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
- Instituto Milenio de Oceanografía, Concepción, Chile
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47
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Abstract
A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.
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Affiliation(s)
- David A Hutchins
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
| | - Sergio A Sañudo-Wilhelmy
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA;
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089, USA;
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48
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Mise K, Masuda Y, Senoo K, Itoh H. Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. mSphere 2021; 6:e0078521. [PMID: 34787447 PMCID: PMC8597730 DOI: 10.1128/msphere.00785-21] [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: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Nitrogen fixation, a distinct process incorporating the inactive atmospheric nitrogen into the active biological processes, has been a major topic in biological and geochemical studies. Currently, insights into diversity and distribution of nitrogen-fixing microbes are dependent upon homology-based analyses of nitrogenase genes, especially the nifH gene, which are broadly conserved in nitrogen-fixing microbes. Here, we report the pitfall of using nifH as a marker of microbial nitrogen fixation. We exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes) and cooccurrence and gene order patterns of nitrogenase genes (including nifH) therein. Up to 20% of nifH-harboring genomes lacked nifD and nifK, which encode essential subunits of nitrogenase, within 10 coding sequences upstream or downstream of nifH or on the same genome. According to a phenotypic database of prokaryotes, no species and strains harboring only nifH possess nitrogen-fixing activities, which shows that these nifH genes are "pseudo"-nifH genes. Pseudo-nifH sequences mainly belong to anaerobic microbes, including members of the class Clostridia and methanogens. We also detected many pseudo-nifH reads from metagenomic sequences of anaerobic environments such as animal guts, wastewater, paddy soils, and sediments. In some samples, pseudo-nifH overwhelmed the number of "true" nifH reads by 50% or 10 times. Because of the high sequence similarity between pseudo- and true-nifH, pronounced amounts of nifH-like reads were not confidently classified. Overall, our results encourage reconsideration of the conventional use of nifH for detecting nitrogen-fixing microbes, while suggesting that nifD or nifK would be a more reliable marker. IMPORTANCE Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases. Here, we report that public databases include a significant amount of incorrectly annotated nifH sequences (pseudo-nifH). We exhaustively investigated the genomic structures of nifH-harboring genomes and found hundreds of pseudo-nifH sequences in RefSeq and KEGG. Over half of these pseudo-nifH sequences belonged to members of the class Clostridia, which is supposed to be a prominent nitrogen-fixing clade. We also found that the abundance of nitrogen fixers in metagenomes could be overestimated by 1.5 to >10 times due to pseudo-nifH recorded in public databases. Our results encourage reconsideration of the prevalent use of nifH as a marker of nitrogen-fixing microbes.
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Affiliation(s)
- Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
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49
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Walworth NG, Saito MA, Lee MD, McIlvin MR, Moran DM, Kellogg RM, Fu FX, Hutchins DA, Webb EA. Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. J Proteome Res 2021; 21:77-89. [PMID: 34855411 DOI: 10.1021/acs.jproteome.1c00517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO2, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
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Affiliation(s)
- Nathan G Walworth
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington 98104, United States.,Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Riss M Kellogg
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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50
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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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