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Cerdán-García E, Álvarez-Salgado XA, Arístegui J, Martínez-Marrero A, Benavides M. Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed. Commun Biol 2024; 7:929. [PMID: 39095605 PMCID: PMC11297262 DOI: 10.1038/s42003-024-06576-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.
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Affiliation(s)
- E Cerdán-García
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, France.
- Turing Centre for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | | | - J Arístegui
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - A Martínez-Marrero
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - M Benavides
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, France.
- Turing Centre for Living Systems, Aix-Marseille University, 13009, Marseille, France.
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2
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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3
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Wu C, Narale DD, Cui Z, Wang X, Liu H, Xu W, Zhang G, Sun J. Diversity, structure, and distribution of bacterioplankton and diazotroph communities in the Bay of Bengal during the winter monsoon. Front Microbiol 2022; 13:987462. [PMID: 36532434 PMCID: PMC9748438 DOI: 10.3389/fmicb.2022.987462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/03/2022] [Indexed: 10/31/2023] Open
Abstract
The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding "new" nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.
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Affiliation(s)
- Chao Wu
- 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
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dhiraj Dhondiram Narale
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Zhengguo Cui
- 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
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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Ding C, Wu C, Li L, Pujari L, Zhang G, Sun J. Comparison of Diazotrophic Composition and Distribution in the South China Sea and the Western Pacific Ocean. BIOLOGY 2021; 10:555. [PMID: 34202962 PMCID: PMC8235572 DOI: 10.3390/biology10060555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/31/2022]
Abstract
The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found that Proteobacteria dominated the diazotrophic community in the river-impacted SCS and cyanobacteria and Proteobacteria were more abundant in the ocean-dominated SCS and WPO. The qPCR analysis showed that cyanobacterial Trichodesmium was abundant in the Pearl River plume and in the SCS basin influenced by the Kuroshio intrusion, and it also thrived in the subequatorial region of the WPO. Unicellular cyanobacteria UCYN-A were mainly detected in the river-impacted area, UCYN-B was abundant in the WPO, UCYN-C had a relatively high abundance in the ocean-dominated area, and a preponderance of γ-Proteobacteria γ-24774A11 was observed in the ocean-dominated SCS and pelagic WPO. Diazotrophic communities had significant distance-decay relationships, reflecting clear biogeographic patterns in the study area. The variations of diazotrophic community structure were well explained by dissolved inorganic nitrogen, dissolved inorganic phosphate by an eigenvector spatial variable PCNM1. These results provide further information to help determine the ecological mechanism of elusive diazotrophic communities in different ocean ecosystems.
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Affiliation(s)
- Changling Ding
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
| | - Liuyang Li
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
| | - Laxman Pujari
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; (C.D.); (C.W.); (L.L.); (L.P.); (G.Z.)
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
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Abstract
Phytoplankton are known as important harbingers of climate change in aquatic ecosystems. Here, the influence of the oceanographic settings on the phytoplankton community structure in the western South China Sea (SCS) was investigated during two seasons, i.e., the winter (December 2006) and summer (August–September, 2007). The phytoplankton community was mainly composed of diatoms (192 taxa), dinoflagellates (109 taxa), and cyanobacteria (4 taxa). The chain-forming diatoms and cyanobacteria Trichodesmium were the dominants throughout the study period. The phytoplankton community structure displayed distinct variation between two seasons, shifting from a diatom-dominated regime in winter to a cyanobacteria-dominated system in summer. The increased abundance of overall phytoplankton and cyanobacteria in the water column during the summer signifies the impact of nutrient advection due to upwelling and enriched eddy activity. That the symbiotic cyanobacteria–diatom (Rhizosolenia–Richelia) association was abundant during the winter signifies the influence of cool temperature. On the contrary, Trichodesmium dominance during the summer implies its tolerance to increased temperature. Overall, the two seasonal variations within the local phytoplankton community in the western SCS could simulate their community shift over the forthcoming climatic conditions.
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Dai J, Ye Q, Wu Y, Zhang M, Zhang J. Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone. Front Microbiol 2020; 11:571199. [PMID: 33013804 PMCID: PMC7516215 DOI: 10.3389/fmicb.2020.571199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.
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Affiliation(s)
- Jinlong Dai
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Miao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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Wu C, Kan J, Liu H, Pujari L, Guo C, Wang X, Sun J. Heterotrophic Bacteria Dominate the Diazotrophic Community in the Eastern Indian Ocean (EIO) during Pre-Southwest Monsoon. MICROBIAL ECOLOGY 2019; 78:804-819. [PMID: 31037377 DOI: 10.1007/s00248-019-01355-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The diazotrophic communities play an important role in sustaining primary productivity through adding new nitrogen to oligotrophic marine ecosystems. Yet, their composition in the oligotrophic Indian Ocean is poorly understood. Here, we report the first observation of phylogenetic diversity and distribution of diazotrophs in the Eastern Indian Ocean (EIO) surface water (to 200 m) during the pre-southwest monsoon period. Through high throughput sequencing of nifH genes, we identified diverse groups of diazotrophs in the EIO including both non-cyanobacterial and cyanobacterial phylotypes. Proteobacteria (mainly Alpha-, Beta-, and Gamma-proteobacteria) were the most diverse and abundant groups within all the diazotrophs, which accounted for more than 86.9% of the total sequences. Cyanobacteria were also retrieved, and they were dominated by the filamentous non-heterocystous cyanobacteria Trichodesmium spp. Other cyanobacteria such as unicellular diazotrophic cyanobacteria were detected sporadically. Interestingly, our qPCR analysis demonstrated that the depth-integrated gene abundances of the diazotrophic communities exhibited spatial heterogeneity with Trichodesmium spp. appeared to be more abundant in the Bay of Bengal (p < 0.05), while Sagittula castanea (Alphaproteobacteria) was found to be more dominating in the equatorial region and offshores (p < 0.05). Non-metric multidimensional scaling analysis (NMDS) further confirmed distinct vertical and horizontal spatial variations in the EIO. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and phosphate were the major environmental factors driving the distribution of the diazotroph communities. Overall, our study provides the first insight into the diversity and distribution of the diazotrophic communities in EIO. The findings from this study highlight distinct contributions of both non-cyanobacteria and cyanobacteria to N2 fixation. Moreover, our study reveals information that is critical for understanding spatial heterogeneity and distribution of diazotrophs, and their vital roles in nitrogen and carbon cycling.
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Affiliation(s)
- Chao Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, 19311, USA
| | - Haijiao Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Laxman Pujari
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China
- Research Centre for Indian Ocean Ecosystem, Tianjin University of science and Technology, Tianjin, 300457, China
| | - Congcong Guo
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China
- Research Centre for Indian Ocean Ecosystem, Tianjin University of science and Technology, Tianjin, 300457, China
| | - Xingzhou Wang
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China
- Research Centre for Indian Ocean Ecosystem, Tianjin University of science and Technology, Tianjin, 300457, China
| | - Jun Sun
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China.
- Research Centre for Indian Ocean Ecosystem, Tianjin University of science and Technology, Tianjin, 300457, China.
- College of Marine & Environmental Sciences, Tianjin University of Science and Technology, No.29 13th Avenue, TEDA, Tianjin, 300457, People's Republic of China.
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Yang QS, Dong JD, Ahmad M, Ling J, Zhou WG, Tan YH, Zhang YZ, Shen DD, Zhang YY. Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs. BMC Microbiol 2019; 19:188. [PMID: 31416417 PMCID: PMC6694519 DOI: 10.1186/s12866-019-1565-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea. RESULTS The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high. CONCLUSIONS The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.
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Affiliation(s)
- Qing-Song Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wei-Guo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye-Hui Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yuan-Zhou Zhang
- State Oceanic Administration Sansha Marine Environmental Monitoring Center Station, Haikou, 570311, China
| | - Dan-Dan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, 18119, Warnemünde, Germany.
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
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Zhang Y, Li J, Cheng X, Luo Y, Mai Z, Zhang S. Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea. Ecol Evol 2018; 8:4932-4948. [PMID: 29876071 PMCID: PMC5980402 DOI: 10.1002/ece3.4064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 01/01/2023] Open
Abstract
The South China Sea (SCS) is the largest marginal sea in the western tropical Pacific Ocean and is characterized by complex physicochemical environments. To date, the biogeographic patterns of the microbial communities have rarely been reported at a basin scale in the SCS. In this study, the bacterial assemblages inhabiting the epipelagic zone across 110°E to 119°E along 14°N latitude were uncovered. The vertical stratification of both bacterial taxa and their potential functions were revealed. These results suggest that the water depth-specific environment is a driver of the vertical bacterioplankton distribution. Moreover, the bacterial communities were different between the eastern stations and the western stations, where the environmental conditions were distinct. However, the mesoscale eddy did not show an obvious effect on the bacterial community due to the large distance between the sampling site and the center of the eddy. In addition to the water depth and longitudinal location of the samples, the heterogeneity of the phosphate and salinity concentrations also significantly contributed to the variance in the epipelagic bacterial community in the SCS. To the best of our knowledge, this study is the first to report that the variability in epipelagic bacterioplankton is driven by the physicochemical environment at the basin scale in the SCS. Our results emphasize that the ecological significance of bacterioplankton can be better understood by considering the relationship between the biogeographic distribution of bacteria and the oceanic dynamics processes.
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Affiliation(s)
- Yi Zhang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xuhua Cheng
- State Key Laboratory of Tropical OceanographySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Yinfeng Luo
- Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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Nitrogen Fixation by Trichodesmium and unicellular diazotrophs in the northern South China Sea and the Kuroshio in summer. Sci Rep 2018; 8:2415. [PMID: 29402976 PMCID: PMC5799295 DOI: 10.1038/s41598-018-20743-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/18/2018] [Indexed: 11/08/2022] Open
Abstract
Distribution of diazotrophs and their nitrogen fixation activity were investigated in the northern South China Sea (nSCS) and the Kuroshio from July 16th to September 1st, 2009. N2 fixation activities in whole seawater and <10 μm fraction at the surface were measured by acetylene reduction assay. Higher activities were observed at the East China Sea (ECS) Kuroshio and the nSCS shelf. The nSCS basin showed a low N2 fixation activity. The <10 μm fractions (unicellular diazotrophs) contributed major portion to the whole-water activity in the survey time, indicating that nanoplanktonic cyanobacterias were the major diazotrophs in the survey area. Daily N2 fixation rates of Trichodesmium ranged from 0.11 to 9.83 pmolNtrichome-1 d-1 with an average of 4.03 pmolNtrichome-1 d-1. The Luzon Strait and the ECS Kuroshio had higher N2 fixation rates of Trichodesmium than the nSCS shelf and basin. Calculated activities of Trichodesmium at most stations were moderately low compared with that of the whole-water. The contribution of N2 fixation by the whole-water to primary production ranged from 1.7% to 18.5%. The estimated amount of new nitrogen introduced by Trichodesmium contributed up to 0.14% of the total primary production and 0.41% of the new production in the Luzon Strait.
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Martínez-Pérez C, Mohr W, Schwedt A, Dürschlag J, Callbeck CM, Schunck H, Dekaezemacker J, Buckner CRT, Lavik G, Fuchs BM, Kuypers MMM. Metabolic versatility of a novel N 2 -fixing Alphaproteobacterium isolated from a marine oxygen minimum zone. Environ Microbiol 2018; 20:755-768. [PMID: 29194930 DOI: 10.1111/1462-2920.14008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 11/27/2022]
Abstract
The N2 -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula (Rhodobacteraceae, Alphaproteobacteria) and its capability to fix N2 was confirmed in laboratory experiments. Genome sequencing revealed that it is a strict heterotroph with a high versatility in substrate utilization and energy acquisition mechanisms. Pathways for sulfide oxidation and nitrite reduction to nitrous oxide are encoded in the genome and might explain the presence throughout the Peruvian OMZ. The genome further indicates that this novel organism could be in direct interaction with other microbes or particles. NanoSIMS analyses were used to compare the metabolic potential of S. castanea with single-cell activity in situ; however, N2 fixation by this diazotroph could not be detected at the isolation site. While the biogeochemical impact of S. castanea is yet to be resolved, its abundance and widespread distribution suggests that its potential to contribute to the marine N input could be significant at a larger geographical scale.
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Affiliation(s)
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anne Schwedt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Julia Dürschlag
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Harald Schunck
- Institute for General Microbiology, University of Kiel, Kiel, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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12
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Li J, Jiang X, Li G, Jing Z, Zhou L, Ke Z, Tan Y. Distribution of picoplankton in the northeastern South China Sea with special reference to the effects of the Kuroshio intrusion and the associated mesoscale eddies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 589:1-10. [PMID: 28273592 DOI: 10.1016/j.scitotenv.2017.02.208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/23/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
We investigated picoplankton distribution patterns and environmental variables along an east-to-west transect in the northeastern South China Sea (SCS) during late winter 2016, giving us the opportunity to examine the impacts of the Kuroshio intrusion and the associated eddies. The results indicated that the subsurface (50-75m) phytoplankton biomass chlorophyll (Chl a) maximum (SCM) disappeared and was replaced by higher Chl a in the middle part of the transect due to the impacts of the Kuroshio intrusion and mesoscale eddies. Both flow cytometry and pyrosequencing data revealed that picoplankton abundance and community structure were significantly influenced by perturbations in complex physical processes. Picoeukaryotes represented most of the total phytoplankton biomass, and their maximum abundance (>104cellsmL-1) occurred within cyclonic eddy-affected regions (Stations 11 and 12), whereas the abundance of Prochlorococcus was the lowest in these regions. Prochlorococcus showed a higher abundance in the Kuroshio-affected area, while Synechococcus was mostly distributed at the upper well-lit depths, with its maximum abundance observed in surface waters (0-30m) adjacent to the cyclonic eddy center. Heterotrophic bacteria (HBA) displayed high abundance along the transect, consistent with the total phytoplankton biomass. Phylogenetic analysis revealed 26 bacterial phyla, with major components belonging to Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, as well as SAR406. Notably, relatively more Rhodobacterales, Flavobacteriales, Alteromonadales, and Vibrionales that were distributed in surface waters of the cyclonic eddy center were specifically associated with the phytoplankton (mainly picoeukaryotes) bloom. Our study highlights the impacts of the Kuroshio intrusion in regulating the microbial ecology of the northeastern SCS and the potential coupling between phytoplankton and bacteria.
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Affiliation(s)
- Jiajun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Xin Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Zhiyou Jing
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Linbin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Zhixin Ke
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China.
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13
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Bombar D, Paerl RW, Riemann L. Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection. Trends Microbiol 2016; 24:916-927. [PMID: 27476748 DOI: 10.1016/j.tim.2016.07.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/20/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
Abstract
The nitrogen input through biological N2 fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N2-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N2 at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N2 fixation on local and global scales.
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Affiliation(s)
- Deniz Bombar
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ryan W Paerl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
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14
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Wu W, Wang L, Liao Y, Huang B. Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea. Microbiologyopen 2015; 4:826-40. [PMID: 26268071 PMCID: PMC4618614 DOI: 10.1002/mbo3.282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/09/2015] [Accepted: 07/14/2015] [Indexed: 11/24/2022] Open
Abstract
To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS.
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Affiliation(s)
- Wenxue Wu
- Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Lei Wang
- Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yu Liao
- Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Bangqin Huang
- Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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15
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Langlois R, Großkopf T, Mills M, Takeda S, LaRoche J. Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype. PLoS One 2015; 10:e0128912. [PMID: 26103055 PMCID: PMC4477881 DOI: 10.1371/journal.pone.0128912] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/01/2015] [Indexed: 01/15/2023] Open
Abstract
Marine dinitrogen (N2) fixation studies have focused nearly exclusively on cyanobacterial diazotrophs; however γ-proteobacteria are an abundant component of the marine community and have been largely overlooked until recently. Here we present a phylogenetic analysis of all nifH γ-proteobacterial sequences available in public databases and qPCR data of a γ-proteobacterial phylotype, Gamma A (UMB), obtained during several research cruises. Our analysis revealed a complex diversity of diazotrophic γ-proteobacteria. One phylotype in particular, Gamma A, was described in several traditional and quantitative PCR studies. Though several γ-proteobacterial nifH sequences have been described as laboratory contaminants, Gamma A is part of a large cluster of sequences isolated from marine environments and distantly related to the clade of contaminants. Using a TaqMan probe and primer set, Gamma A nifH DNA abundance and expression were analyzed in nearly 1000 samples collected during 15 cruises to the Atlantic and Pacific Oceans. The data showed that Gamma A is an active, cosmopolitan diazotroph found throughout oxygenated, oligotrophic waters reaching maximum abundances of 8 x 104 nifH DNA copies l-1 and 5 x 105 nifH transcript copies l-1. Gamma A nifH transcript abundances were on average 3 fold higher than nifH DNA abundances. The widespread distribution and activity of Gamma A indicate that it has potential to be a globally important N2 fixing organism.
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Affiliation(s)
- Rebecca Langlois
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
- * E-mail:
| | | | - Matthew Mills
- Environmental Earth System Science, Stanford University, Stanford, California, United States of America
| | | | - Julie LaRoche
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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16
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Farnelid H, Harder J, Bentzon-Tilia M, Riemann L. Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters. Environ Microbiol 2013; 16:3072-82. [PMID: 24330580 DOI: 10.1111/1462-2920.12335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 11/07/2013] [Indexed: 11/30/2022]
Abstract
The wide distribution of diverse nitrogenase (nifH) genes affiliated with those of heterotrophic bacteria in marine and estuarine waters indicates ubiquity and an ecologically relevant role for heterotrophic N2 -fixers (diazotrophs) in aquatic nitrogen (N) cycling. However, the lack of cultivated representatives currently precludes an evaluation of their N2 -fixing capacity. In this study, microoxic or anoxic N-free media were inoculated with estuarine Baltic Sea surface water to select for N2 -fixers. After visible growth and isolation of single colonies on oxic plates or in anoxic agar tubes, nifH gene amplicons were obtained from 64 strains and nitrogenase activity, applying the acetylene reduction assay, was confirmed for 40 strains. Two strains, one Gammaproteobacterium affiliated with Pseudomonas and one Alphaproteobacterium affiliated with Rhodopseudomonas were shown to represent established members of the indigenous diazotrophic community in the Baltic Sea, with abundances of up to 7.9 × 10(4) and 4.7 × 10(4) nifH copies l(-1) respectively. This study reports media for successful isolation of heterotrophic diazotrophs. The applied methodology and the obtained strains will facilitate future identification of factors controlling heterotrophic diazotrophic activity in aquatic environments, which is a prerequisite for understanding and evaluating their ecology and contribution to N cycling at local and regional scales.
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Affiliation(s)
- Hanna Farnelid
- Department of Natural Sciences, Linnaeus University, Kalmar, Sweden
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17
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Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nat Commun 2013; 4:1767. [PMID: 23612308 PMCID: PMC3667715 DOI: 10.1038/ncomms2748] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/15/2013] [Indexed: 11/26/2022] Open
Abstract
Diatoms with symbiotic N2-fixing cyanobacteria are often abundant in the oligotrophic
open ocean gyres. The most abundant cyanobacterial symbionts form heterocysts (specialized
cells for N2 fixation) and provide nitrogen (N) to their hosts, but their
morphology, cellular locations and abundances differ depending on the host. Here we show
that the location of the symbiont and its dependency on the host are linked to the evolution
of the symbiont genome. The genome of Richelia (found inside the siliceous frustule
of Hemiaulus) is reduced and lacks ammonium transporters, nitrate/nitrite reductases
and glutamine:2-oxoglutarate aminotransferase. In contrast, the genome of the closely
related Calothrix (found outside the frustule of Chaetoceros) is more similar
to those of free-living heterocyst-forming cyanobacteria. The genome of Richelia is
an example of metabolic streamlining that has implications for the evolution of
N2-fixing symbiosis and
potentially for manipulating plant–cyanobacterial interactions. Cyanobacterial symbionts of marine diatoms can localize intracellularly or
externally to their host partners. Here Hilton et al. describe the genomes of two
diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont
affects expression of nitrogen assimilation genes.
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18
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Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles? Appl Environ Microbiol 2013; 79:2137-47. [PMID: 23335759 DOI: 10.1128/aem.03204-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.
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Environment-dependent distribution of the sediment nifH-harboring microbiota in the Northern South China Sea. Appl Environ Microbiol 2012; 79:121-32. [PMID: 23064334 DOI: 10.1128/aem.01889-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N(2) fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH(4)(+) concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N(2) fixation and NH(4)(+) production. Several other environmental factors, including sediment pore water PO(4)(3-) concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.
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