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Von Eggers JM, Wisnoski NI, Calder JW, Capo E, Groff DV, Krist AC, Shuman B. Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environ Microbiol 2024; 26:e16607. [PMID: 38477387 DOI: 10.1111/1462-2920.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes-like dispersal limitation-contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.
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Affiliation(s)
- Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
| | - Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, Wyoming, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - John W Calder
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Dulcinea V Groff
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
| | - Amy C Krist
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Bryan Shuman
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
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2
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Yuan Y, Zhang G, Fang H, Guo H, Li Y, Li Z, Peng S, Wang F. Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:13075-13088. [PMID: 38240967 DOI: 10.1007/s11356-024-31941-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: 07/17/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems.
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Affiliation(s)
- Yiming Yuan
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Guangyi Zhang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China.
| | - Hongyuan Fang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Haifeng Guo
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Yongkang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Zezhuang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Siwei Peng
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Fuming Wang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
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3
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Sun X, Tan E, Wang B, Gan Z, Yang J, Han J, Zhang X, Kao SJ, King G, Dong H, Jiang H. Salinity change induces distinct climate feedbacks of nitrogen removal in saline lakes. WATER RESEARCH 2023; 245:120668. [PMID: 37776589 DOI: 10.1016/j.watres.2023.120668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/19/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Current estimations of nitrogen biogeochemical cycling and N2O emissions in global lakes as well as predictions of their future changes are overrepresented by freshwater datasets, while less consideration is given to widespread saline lakes with different salinity (representing salinization or desalinization). Here, we show that N2O production by denitrification is the main process of reactive nitrogen (Nr, the general abbreviations of NH4+-N, NO2--N and NO3--N) removal in hypersaline lake sediments (e.g. Lake Chaka). The integration of our field measurements and literature data shows that in response to natural salinity decrease, potential Nr removal increases while N2O production decreases. Furthermore, denitrification-induced N2 production exhibits higher salinity sensitivity than denitrification-induced N2O production, suggesting that the contribution of N2O to Nr removal decreases with decreasing salinity. This field-investigation-based salinity response model of Nr removal indicates that under global climate change, saline lakes in the process of salinization or desalination may have distinct Nr removal and climate feedback effects: salinized lakes tend to generate a positive climate feedback, while desalinated lakes show a negative feedback. Therefore, salinity change should be considered as an important factor in assessing future trend of N2O emissions from lakes under climate change.
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Affiliation(s)
- Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zixuan Gan
- College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616-5270, United States of America
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jibin Han
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Xiying Zhang
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Gary King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China; Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China.
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Pu H, Yuan Y, Qin L, Liu X. pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments. Microorganisms 2023; 11:microorganisms11030676. [PMID: 36985249 PMCID: PMC10056738 DOI: 10.3390/microorganisms11030676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
As microorganisms are very sensitive to changes in the lake environment, a comprehensive and systematic understanding of the structure and diversity of lake sediment microbial communities can provide feedback on sediment status and lake ecosystem protection. Xiao Xingkai Lake (XXL) and Xingkai Lake (XL) are two neighboring lakes hydrologically connected by a gate and dam, with extensive agricultural practices and other human activities existing in the surrounding area. In view of this, we selected XXL and XL as the study area and divided the area into three regions (XXLR, XXLD, and XLD) according to different hydrological conditions. We investigated the physicochemical properties of surface sediments in different regions and the structure and diversity of bacterial communities using high-throughput sequencing. The results showed that various nutrients (nitrogen, phosphorus) and carbon (DOC, LOC, TC) were significantly enriched in the XXLD region. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla in the sediments, accounting for more than 60% of the entire community in all regions. Non-metric multidimensional scaling analysis and analysis of similarities confirmed that β-diversity varied among different regions. In addition, the assembly of bacterial communities was dominated by a heterogeneous selection in different regions, indicating the important influence of sediment environmental factors on the community. Among these sediment properties, the partial least squares path analysis revealed that pH was the best predictor variable driving differences in bacterial communities in different regions, with higher pH reducing beta diversity among communities. Overall, our study focused on the structure and diversity of bacterial communities in lake sediments of the Xingkai Lake basin and revealed that high pH causes the β-diversity of bacterial communities in the sediment to decrease. This provides a reference for further studies on sediment microorganisms in the Xingkai Lake basin in the future.
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Affiliation(s)
- Haiguang Pu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxiang Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiaohui Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- Correspondence:
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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6
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She W, Yang J, Wu G, Jiang H. The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153446. [PMID: 35092771 DOI: 10.1016/j.scitotenv.2022.153446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/16/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH4 and CO2), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH4 and CO2, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH4 and CO2 fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH4 fluxes and spatial variations of CO2, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.
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Affiliation(s)
- Weiyu She
- 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
| | - Geng Wu
- 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; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
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7
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Yang J, Han M, Zhao Z, Han J, Zhang X, Xie Z, Jiang H. Microbial response to multiple-level addition of grass organic matter in lake sediments with different salinity. FEMS Microbiol Ecol 2022; 98:6568899. [DOI: 10.1093/femsec/fiac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Water surface expansion of saline lakes usually causes the inundation of surrounding grassland, leading to the increase of terrestrial grass organic matter (OM) input to the lakes and the decrease of lake salinity. However, the influence of terrestrial grass OM input increase and salinity decrease on organic carbon mineralization and microbial community composition remains unknown in saline lakes. Here, microbial mineralization of terrestrial grass (Achnatherum splendens) OM at different quantity levels in lake sediments with different salinity was investigated by performing microcosm experiments. The results showed that the CO2 production rates increased with the increase of grass OM supply in the studied sediments with different salinity, which may be driven by certain microbial groups (e.g., Bacteroidota, Firmicutes and Ascomycota). The increase of grass OM supply reduced the richness of prokaryotic community, which will decrease the size and complexity of the studied microbial networks, but increase the interaction between prokaryotic and fungal taxa. Taken together, our results suggest that the increase of terrestrial grass OM input caused by lake expansion would enhance the mineralization of organic carbon and affect the community composition and interactions of related microorganisms in lake sediments with different salinity.
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Affiliation(s)
- 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
| | - Zhuoli Zhao
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
| | - Jinbin Han
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Xiying Zhang
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, 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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8
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6521440. [DOI: 10.1093/femsec/fiac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
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He J, Jiao S, Tan X, Wei H, Ma X, Nie Y, Liu J, Lu X, Mo J, Shen W. Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest. Front Microbiol 2021; 12:689674. [PMID: 34512567 PMCID: PMC8424203 DOI: 10.3389/fmicb.2021.689674] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 01/28/2023] Open
Abstract
Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha–1 yr–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO3––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.
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Affiliation(s)
- Jinhong He
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiangping Tan
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Wei
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xiaomin Ma
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Juxiu Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiankai Lu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiangming Mo
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Weijun Shen
- College of Forestry, Guangxi University, Nanning, China
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10
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Jiang H, Huang J, Li L, Huang L, Manzoor M, Yang J, Wu G, Sun X, Wang B, Egamberdieva D, Panosyan H, Birkeland NK, Zhu Z, Li W. Onshore soil microbes and endophytes respond differently to geochemical and mineralogical changes in the Aral Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142675. [PMID: 33077208 DOI: 10.1016/j.scitotenv.2020.142675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
There is limited knowledge about how microbiome develops along the geochemical and mineralogical change in onshore soils derived from continuous desiccation of lakes. In this study, geochemistry and mineralogy were studied in the Aral Sea onshore soils exposed in different periods (from the 1970s to 2018), followed by microbial analyses on the studied soils and the aboveground organs of dominant plants. The soils exhibited an increasing gradient of total soluble salts (TSS: 0.4-0.5 g/L to 71.3 g/L) and evaporite minerals (e.g., gypsum, halite) from the farshore to the nearshore. In the studied soils, microbial diversity decreased with increasing TSS, and microbial community dissimilarities among samples was positively correlated with the contents of gypsum and calcite minerals. Among the measured environmental variables, minerals contributed most to the observed microbial variation. In contrast, the endophytic microbial communities in the aboveground organs of dominant plants were not related to any of the measured variables, indicating that they differed from their soil counterparts with respect to their responses to geochemical and mineralogical variations in soils. In summary, these results help us understand the response of onshore soil microbiome to the decline of lake water caused by continuous desiccation.
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Affiliation(s)
- Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mehvish Manzoor
- 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
| | - Geng Wu
- 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
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Dilfuza Egamberdieva
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany; Faculty of Biology, National University of Uzbekistan, Tashkent, Uzbekistan.
| | - Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
| | - Zihua Zhu
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wenjun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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11
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Yang J, Jiang H, Sun X, Huang J, Han M, Wang B. Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity. FEMS Microbiol Ecol 2020; 97:5989694. [PMID: 33206972 DOI: 10.1093/femsec/fiaa234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.
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Affiliation(s)
- Jian Yang
- 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.,Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jianrong Huang
- 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
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12
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Huang J, Yang J, Jiang H, Wu G, Liu W, Wang B, Xiao H, Han J. Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes. Front Microbiol 2020; 11:1772. [PMID: 32849396 PMCID: PMC7426462 DOI: 10.3389/fmicb.2020.01772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO2 reduction with H2, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Urumqi, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Haiyi Xiao
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, China
| | - Jibin Han
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining, China
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13
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Cary C, Cowan DA, McMinn A, Häggblom MM. Editorial: Thematic issue on polar and alpine microbiology. FEMS Microbiol Ecol 2020; 96:5875089. [PMID: 32697840 DOI: 10.1093/femsec/fiaa136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato - Te Whare Wānanga o Waikato, Hamilton 3240, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, College of Science and Engineering, University of Tasmania, Battery Point, Tasmania, Australia
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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