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Li H, Chen J, Yu L, Fan G, Li T, Li L, Yuan H, Wang J, Wang C, Li D, Lin S. In situ community transcriptomics illuminates CO 2-fixation potentials and supporting roles of phagotrophy and proton pump in plankton in a subtropical marginal sea. Microbiol Spectr 2024; 12:e0217723. [PMID: 38319114 PMCID: PMC10913738 DOI: 10.1128/spectrum.02177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here, we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites in the South China Sea to investigate carbon fixation potential in different lineages. RuBisCO expression, the proxy of Calvin carbon fixation (CCF) potential, was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, and Haptophyta, which was differentially affected by environmental factors among lineages. CCF potential exhibited positive or negative correlations with phagotrophy gene expression, suggesting phagotrophy possibly enhances or complements CCF. Our data also reveal significant non-Calvin carbon fixation (NCF) potential, as indicated by the active expression of genes in all five currently recognized NCF pathways, mainly contributed by Flavobacteriales, Alteromonadales, and Oceanospirillales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales, and Rhodobacterales, NCF potential was positively correlated with proton-pump rhodopsin (PPR) expression, suggesting that NCF might be energetically supported by PPR. The novel insights into the lineage-differential potential of carbon fixation, widespread mixotrophy, and PPR as an energy source for NCF lay a methodological and informational foundation for further research to understand carbon fixation and the trophic landscape in the ocean.IMPORTANCEMarine plankton plays an important role in global carbon cycling and climate regulation. Phytoplankton and cyanobacteria fix CO2 to produce organic compounds using solar energy and mainly by the Calvin cycle, whereas autotrophic bacteria and archaea may fix CO2 by non-Calvin cycle carbon fixation pathways. How active individual lineages are in carbon fixation and mixotrophy, and what energy source bacteria may employ in non-Calvin carbon fixation, in a natural plankton assemblage are poorly understood and underexplored. Using metatranscriptomics, we studied carbon fixation in marine plankton with lineage resolution in tropical marginal shelf and slope areas. Based on the sequencing results, we characterized the carbon fixation potential of different lineages and assessed Calvin- and non-Calvin- carbon fixation activities and energy sources. Data revealed a high number of unigenes (4.4 million), lineage-dependent differential potentials of Calvin carbon fixation and responses to environmental conditions, major contributors of non-Calvin carbon fixation, and their potential energy source.
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Affiliation(s)
- Hongfei Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Jianwei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Guangyi Fan
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, Guangdong, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Denghui Li
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- Qingdao Innovation Center of Seaweed Biotechnology, Qingdao, Shandong, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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Sun P, Liao Y, Wang Y, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Xu D. Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer. Microorganisms 2022; 10:microorganisms10020248. [PMID: 35208705 PMCID: PMC8877492 DOI: 10.3390/microorganisms10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.
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Affiliation(s)
- Ping Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Yuyu Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Correspondence:
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Chan YF, Chiang PW, Tandon K, Rogozin D, Degermendzhi A, Zykov V, Tang SL. Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia. MICROBIAL ECOLOGY 2021; 81:357-369. [PMID: 32915303 DOI: 10.1007/s00248-020-01592-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.
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Affiliation(s)
- Ya-Fan Chan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Denis Rogozin
- Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
- Siberia Federal University, Krasnoyarsk, 660041, Russia
| | - Andrey Degermendzhi
- Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Vladimir Zykov
- Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan.
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Unusual marine cyanobacteria/haptophyte symbiosis relies on N 2 fixation even in N-rich environments. ISME JOURNAL 2020; 14:2395-2406. [PMID: 32523086 PMCID: PMC7490277 DOI: 10.1038/s41396-020-0691-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
The microbial fixation of N2 is the largest source of biologically available nitrogen (N) to the oceans. However, it is the most energetically expensive N-acquisition process and is believed inhibited when less energetically expensive forms, like dissolved inorganic N (DIN), are available. Curiously, the cosmopolitan N2-fixing UCYN-A/haptophyte symbiosis grows in DIN-replete waters, but the sensitivity of their N2 fixation to DIN is unknown. We used stable isotope incubations, catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH), and nanoscale secondary ion mass spectrometry (nanoSIMS), to investigate the N source used by the haptophyte host and sensitivity of UCYN-A N2 fixation in DIN-replete waters. We demonstrate that under our experimental conditions, the haptophyte hosts of two UCYN-A sublineages do not assimilate nitrate (NO3−) and meet little of their N demands via ammonium (NH4+) uptake. Instead the UCYN-A/haptophyte symbiosis relies on UCYN-A N2 fixation to supply large portions of the haptophyte’s N requirements, even under DIN-replete conditions. Furthermore, UCYN-A N2 fixation rates, and haptophyte host carbon fixation rates, were at times stimulated by NO3− additions in N-limited waters suggesting a link between the activities of the bulk phytoplankton assemblage and the UCYN-A/haptophyte symbiosis. The results suggest N2 fixation may be an evolutionarily viable strategy for diazotroph–eukaryote symbioses, even in N-rich coastal or high latitude waters.
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