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Stiefelmaier J, Keller J, Neupert W, Ulber R. Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment. Microbiologyopen 2024; 13:e1412. [PMID: 38711353 DOI: 10.1002/mbo3.1412] [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: 12/01/2023] [Revised: 04/12/2024] [Accepted: 04/20/2024] [Indexed: 05/08/2024] Open
Abstract
Cable bacteria, characterized by their multicellular filamentous growth, are prevalent in both freshwater and marine sediments. They possess the unique ability to transport electrons over distances of centimeters. Coupled with their capacity to fix CO2 and their record-breaking conductivity for biological materials, these bacteria present promising prospects for bioprocess engineering, including potential electrochemical applications. However, the cultivation of cable bacteria has been limited to their natural sediment, constraining their utility in production processes. To address this, our study designs synthetic sediment, drawing on ion exchange chromatography data from natural sediments and existing literature on the requirements of cable bacteria. We examined the effects of varying bentonite concentrations on water retention and the impacts of different sands. For the first time, we cultivated cable bacteria on synthetic sediment, specifically the freshwater strain Electronema aureum GS. This cultivation was conducted over 10 weeks in a specially developed sediment bioreactor, resulting in an increased density of cable bacteria in the sediment and growth up to a depth of 5 cm. The creation of this synthetic sediment paves the way for the reproducible cultivation of cable bacteria. It also opens up possibilities for future process scale-up using readily available components. This advancement holds significant implications for the broader field of bioprocess engineering.
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Affiliation(s)
- Judith Stiefelmaier
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Joshua Keller
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Wiebke Neupert
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Roland Ulber
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
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2
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Liu B, Zheng Y, Wang X, Qi L, Zhou J, An Z, Wu L, Chen F, Lin Z, Yin G, Dong H, Li X, Liang X, Han P, Liu M, Hou L. Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169833. [PMID: 38190922 DOI: 10.1016/j.scitotenv.2023.169833] [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: 08/23/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m-2 d-1, respectively), compared to low-salinity zone (0.07-0.19 mmol C m-2 d-1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Xinyu Wang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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3
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Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [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: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
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Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
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Yu X, Tu Q, Liu J, Peng Y, Wang C, Xiao F, Lian Y, Yang X, Hu R, Yu H, Qian L, Wu D, He Z, Shu L, He Q, Tian Y, Wang F, Wang S, Wu B, Huang Z, He J, Yan Q, He Z. Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes. MLIFE 2023; 2:253-266. [PMID: 38817818 PMCID: PMC10989796 DOI: 10.1002/mlf2.12077] [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: 01/22/2023] [Revised: 05/21/2023] [Accepted: 06/29/2023] [Indexed: 06/01/2024]
Abstract
Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH4), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (Kandelia obovata, KO), the introduced mangrove (Sonneratia apetala, SA) rhizosphere microbiome had significantly (p < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH4 cycling (e.g., mcrABCDG and pmoABC), N2 fixation (nifHDK), and inorganic S cycling (dsrAB, dsrC, dsrMKJOP, soxB, sqr, and fccAB). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH4, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.
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Affiliation(s)
- Xiaoli Yu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Qichao Tu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Jihua Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Yisheng Peng
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Cheng Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Fanshu Xiao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yingli Lian
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Xueqin Yang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Ruiwen Hu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Huang Yu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Lu Qian
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Daoming Wu
- College of Forestry & Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Ziying He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
| | - Longfei Shu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Qiang He
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life SciencesXiamen UniversityXiamenChina
| | - Faming Wang
- Xiaoliang Research Station for Tropical Coastal Ecosystems and Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Shanquan Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Bo Wu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhijian Huang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qingyun Yan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhili He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
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Huang J, Yang J, Han M, Wang B, Sun X, Jiang H. Microbial carbon fixation and its influencing factors in saline lake water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162922. [PMID: 36933719 DOI: 10.1016/j.scitotenv.2023.162922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (14C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L-1 h-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L-1 h-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China.
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Vineis JH, Bulseco AN, Bowen JL. Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment. FEMS Microbiol Lett 2023; 370:fnad082. [PMID: 37541957 DOI: 10.1093/femsle/fnad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.
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Affiliation(s)
- Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
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Liu B, Hou L, Zheng Y, Zhang Z, Tang X, Mao T, Du J, Bi Q, Dong H, Yin G, Han P, Liang X, Liu M. Dark carbon fixation in intertidal sediments: Controlling factors and driving microorganisms. WATER RESEARCH 2022; 216:118381. [PMID: 35381430 DOI: 10.1016/j.watres.2022.118381] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y-1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using 14C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m-2 day-1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM-harboring bacteria, rather than cbbL-harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM-harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus, and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Tieqiang Mao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Qianqian Bi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies. Extremophiles 2021; 26:3. [PMID: 34878610 DOI: 10.1007/s00792-021-01252-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022]
Abstract
Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.
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