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Chen X, Sheng Y, Wang G, Zhou P, Liao F, Mao H, Zhang H, Qiao Z, Wei Y. Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season. WATER RESEARCH 2024; 251:121105. [PMID: 38184913 DOI: 10.1016/j.watres.2024.121105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.
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Affiliation(s)
- Xianglong Chen
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences, Beijing 100083, PR China.
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China.
| | - Pengpeng Zhou
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Fu Liao
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Hairu Mao
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Hongyu Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Zhiyuan Qiao
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Yuquan Wei
- College of Resources and Environmental Science, China Agricultural University, Beijing 100094, PR China
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Liu X, Li P, Wang H, Han LL, Yang K, Wang Y, Jiang Z, Cui L, Kao SJ. Nitrogen fixation and diazotroph diversity in groundwater systems. THE ISME JOURNAL 2023; 17:2023-2034. [PMID: 37715043 PMCID: PMC10579273 DOI: 10.1038/s41396-023-01513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.
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Affiliation(s)
- Xiaohan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China.
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China.
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Li-Li Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Zhou Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, PR China
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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Yang M, Liu N, Wang B, Li Y, Li J, Liu CQ. Archaeal contribution to carbon-functional composition and abundance in China's coastal wetlands: Not to be underestimated. Front Microbiol 2022; 13:1013408. [PMID: 36439847 PMCID: PMC9685420 DOI: 10.3389/fmicb.2022.1013408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/27/2022] [Indexed: 01/16/2024] Open
Abstract
Microbial diversity, together with carbon function, plays a key role in driving the wetland carbon cycle; however, the composition, driving factors of carbon-functional genes and the relationship with microbial community have not been well characterized in coastal wetlands. To understand these concerns, microbes, carbon-functional genes, and related environmental factors were investigated in twenty wetlands along China's coast. The results indicate that carbon-functional gene composition is dominated by archaeal rather than bacterial community and that Nanoarchaeaeota is the dominant archaeal phylum associated with carbon cycling in anoxic sediments. Compared with microbes, carbon-functional composition was more stable because they showed the highest Shannon diversity and archaeal functional redundancy. Deterministic processes dominated microbial community, and stochastic processes were more important for carbon-functional genes. Labile Fe governed archaeal and carbon-functional composition by coupling with nitrogen and carbon biogeochemical cycles, while bacterial community was affected by NH4-N and SOC/SON. This study highlights the predominant contributions of archaea to carbon-functional genes and to the stability of carbon-functional composition, thus providing new insights into the microbial dominance of the carbon cycle and the evaluation of carbon function in coastal wetlands.
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Affiliation(s)
- Meiling Yang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Na Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Baoli Wang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
| | - Yajun Li
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Jianfeng Li
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Cong-Qiang Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
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Ma J, Ma K, Liu J, Chen N. Rhizosphere Soil Microbial Community Under Ice in a High-Latitude Wetland: Different Community Assembly Processes Shape Patterns of Rare and Abundant Microbes. Front Microbiol 2022; 13:783371. [PMID: 35677902 PMCID: PMC9169045 DOI: 10.3389/fmicb.2022.783371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
The rhizosphere soil microbial community under ice exhibits higher diversity and community turnover in the ice-covered stage. The mechanisms by which community assembly processes shape those patterns are poorly understood in high-latitude wetlands. Based on the 16S rRNA gene and ITS sequencing data, we determined the diversity patterns for the rhizosphere microbial community of two plant species in a seasonally ice-covered wetland, during the ice-covered and ice-free stages. The ecological processes of the community assembly were inferred using the null model at the phylogenetic bins (taxonomic groups divided according to phylogenetic relationships) level. Different effects of ecological processes on rare and abundant microbial sub-communities (defined by the relative abundance of bins) and bins were further analyzed. We found that bacterial and fungal communities had higher alpha and gamma diversity under the ice. During the ice-free stage, the dissimilarity of fungal communities decreased sharply, and the spatial variation disappeared. For the bacterial community, homogeneous selection, dispersal limitation, and ecological processes (undominated processes) were the main processes, and they remained relatively stable across all stages. For the fungal community, during the ice-covered stage, dispersal limitation was the dominant process. In contrast, during the ice-free stage, ecological drift processes were more important in the Scirpus rhizosphere, and ecological drift and homogeneous selection processes were more important in the Phragmites rhizosphere. Regarding the different effects of community assembly processes on abundant and rare microbes, abundant microbes were controlled more by homogeneous selection. In contrast, rare microbes were controlled more by ecological drift, dispersal limitation, and heterogeneous selection, especially bacteria. This is potentially caused by the low growth rates or the intermediate niche breadths of rare microbes under the ice. Our findings suggest the high diversity of microbial communities under the ice, which deepens our understanding of various ecological processes of community assembly across stages and reveals the distinct effects of community assembly processes on abundant and rare microbes at the bin level.
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Affiliation(s)
- Jiaming Ma
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Kang Ma
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Jingling Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Nannan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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Hu Y, Wang Y, Han X, Shan Y, Li F, Shi L. Biofilm Biology and Engineering of Geobacter and Shewanella spp. for Energy Applications. Front Bioeng Biotechnol 2021; 9:786416. [PMID: 34926431 PMCID: PMC8683041 DOI: 10.3389/fbioe.2021.786416] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 01/04/2023] Open
Abstract
Geobacter and Shewanella spp. were discovered in late 1980s as dissimilatory metal-reducing microorganisms that can transfer electrons from cytoplasmic respiratory oxidation reactions to external metal-containing minerals. In addition to mineral-based electron acceptors, Geobacter and Shewanella spp. also can transfer electrons to electrodes. The microorganisms that have abilities to transfer electrons to electrodes are known as exoelectrogens. Because of their remarkable abilities of electron transfer, Geobacter and Shewanella spp. have been the two most well studied groups of exoelectrogens. They are widely used in bioelectrochemical systems (BESs) for various biotechnological applications, such as bioelectricity generation via microbial fuel cells. These applications mostly associate with Geobacter and Shewanella biofilms grown on the surfaces of electrodes. Geobacter and Shewanella biofilms are electrically conductive, which is conferred by matrix-associated electroactive components such as c-type cytochromes and electrically conductive nanowires. The thickness and electroactivity of Geobacter and Shewanella biofilms have a significant impact on electron transfer efficiency in BESs. In this review, we first briefly discuss the roles of planktonic and biofilm-forming Geobacter and Shewanella cells in BESs, and then review biofilm biology with the focus on biofilm development, biofilm matrix, heterogeneity in biofilm and signaling regulatory systems mediating formation of Geobacter and Shewanella biofilms. Finally, we discuss strategies of Geobacter and Shewanella biofilm engineering for improving electron transfer efficiency to obtain enhanced BES performance.
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Affiliation(s)
- Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yinghui Wang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xi Han
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yawei Shan
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan, China
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