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Liu S, Chen Q, Liu L, Dong C, Qiu X, Tang K. Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174845. [PMID: 39053558 DOI: 10.1016/j.scitotenv.2024.174845] [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: 05/21/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
Abstract
Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.
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Affiliation(s)
- Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Xuanyun Qiu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China.
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2
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Pu W, Wang M, Song D, Zhao W, Sheng X, Huo T, Du X, Sui X. Bacterial Diversity in Sediments from Lianhuan Lake, Northeast China. Microorganisms 2024; 12:1914. [PMID: 39338588 PMCID: PMC11433699 DOI: 10.3390/microorganisms12091914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Lake microbiota play a crucial role in geochemical cycles, influencing both energy flow and material production. However, the distribution patterns of bacterial communities in lake sediments remain largely unclear. In this study, we used 16S rRNA high-throughput sequencing technology to investigate the bacterial structure and diversity in sediments across different locations (six independent lakes) within Lianhuan Lake and analyzed their relationship with environmental factors. Our findings revealed that both the alpha and beta diversity of sediment bacterial communities varied significantly among the six independent lakes. Furthermore, changes between lakes had a significant impact on the relative abundance of bacterial phyla, such as Pseudomonadota and Chloroflexota. The relative abundance of Pseudomonadota was highest in Habuta Lake and lowest in Xihulu Lake, while Chloroflexota abundance was lowest in Habuta Lake and highest in Tiehala Lake. At the genus level, the relative abundance of Luteitalea was highest in Xihulu Lake compared to the other five lakes, whereas the relative abundances of Clostridium, Thiobacillus, and Ilumatobacter were highest in Habuta Lake. Mantel tests and heatmaps revealed that the relative abundance of Pseudomonadota was significantly negatively correlated with pH, while the abundance of Chloroflexota was significantly positively correlated with total phosphorus and total nitrogen in water, and negatively correlated with electrical conductivity. In conclusion, this study significantly enhances our understanding of bacterial communities in the different lakes within the Lianhuan Lake watershed.
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Affiliation(s)
- Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
| | - Dan Song
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Wei Zhao
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
- College of Marine Science and Environment, Dalian Ocean University, No. 52, Heishijiao Street, Shahekou District, Dalian 116023, China
| | - Xuran Sheng
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Tangbin Huo
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Xue Du
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
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Rao G, Song WL, Yan SZ, Chen SL. Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers. Appl Environ Microbiol 2024; 90:e0135924. [PMID: 39171904 PMCID: PMC11409670 DOI: 10.1128/aem.01359-24] [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: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, China
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Yang Z, Wang Y, Lukwambe B, Nicholaus R, Yang W, Zhu J, Zheng Z. Using ozone nanobubbles, and microalgae to promote the removal of nutrients from aquaculture wastewater: Insights from the changes of microbiomes. ENVIRONMENTAL RESEARCH 2024; 257:119349. [PMID: 38844029 DOI: 10.1016/j.envres.2024.119349] [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: 03/10/2024] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
Integrated aquaculture wastewater treatment systems (IAWTSs) are widely used in treating aquaculture wastewater with the aeration-microalgae unit serving as an important component. In this study, we artificially constructed an IAWTS and applied two aeration-microalgae methods: ordinary aeration or ozone nanobubbles (ONBs) with microalgae (Nannochloropsis oculata). The impact of N.oculata and ONBs on the removal performance of nutrients and the underlying micro-ecological mechanisms were investigated using 16S rRNA gene amplicon sequencing. The results demonstrated that the combined use of ONBs and N.oculata exhibited superior purification effects with 78.25%, 76.59% and 86.71% removal of CODMn, TN and TP. N.oculata played a pivotal role as the primary element in wastewater purification, while ONBs influenced nutrient dynamics by affecting both N.oculata and bacterial communities. N.oculata actively shaped bacterial communities, with a specific focus on nitrogen and phosphorus cycling in the micro-environment remodeled by ONBs. Rare bacterial communities displayed heightened activity in response to the changes in N.oculata, ONBs, and nutrient levels. These findings provide a novel approach to improve the technological processes the IAWTS, contributing to the advancement of sustainable aquaculture practices by offering valuable insights into wastewater purification efficiency and micro-ecological mechanisms.
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Affiliation(s)
- Zhao Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yangcai Wang
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315048, China.
| | - Betina Lukwambe
- School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, Tanzania
| | - Regan Nicholaus
- Department of Natural Sciences, Mbeya University of Science and Technology, Tanzania
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Xin G, Xiaohong S, Yujiao S, Wenbao L, Yanjun W, Zhimou C, Arvolab L. Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China. Front Microbiol 2024; 15:1448919. [PMID: 39234542 PMCID: PMC11371557 DOI: 10.3389/fmicb.2024.1448919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms in lakes, especially in desert lakes with different salinities. To address this issue, we collected three samples from freshwater lakes, six from brackish lakes, and five from salt lakes in the Badanjilin Desert. The 16S rRNA gene sequencing was applied to investigate the bacterial interactions with rising salinity, community coexistence patterns, and assembly mechanisms. Our findings suggested that the increased lake salinity significantly reduces the bacterial community diversity and enhanced the community differentiation. Significant variations were observed in the contribution of biomarkers from Cyanobacteria, Chloroflexi, and Halobacterota to the composition of the lake bacterial communities. The bacterial communities in the salt lakes exhibited a higher susceptibility to salinity limitations than those in the freshwater and brackish lakes. In addition, the null modeling analyses confirmed the quantitative biases in the stochastic assembly processes of bacterial communities across freshwater, brackish, and saline lakes. With the increasing lake salinity, the significance of undominated and diffusion limitation decreased slightly, and the influence of homogenizing dispersal on community assembly increased. However, the stochasticity remained the dominant process across all lakes in the Badanjilin Desert. The analysis of co-occurring networks revealed that the rising salinity reduced the complexity of bacterial network structures and altered the interspecific interactions, resulting in the increased interspecies collaboration with increasing salinity levels. Under the influence of salinity stress, the key taxon Cyanobacteria in freshwater lakes (Schizothrix_LEGE_07164) was replaced by Proteobacteria (Thalassobaculum and Polycyclovorans) in brackish lakes, and Thermotogota (SC103) in salt lakes. The results indicated the symbiotic patterns of bacterial communities across varying salinity gradients in lakes and offer insights into potential mechanisms of community aggregation, thereby enhancing our understanding of bacterial distribution in response to salinity changes.
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Affiliation(s)
- Guo Xin
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Shi Xiaohong
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
- State Gauge and Research Station of Wetland Ecosystem, Wuliangsuhai Lake, Bayan Nur, China
| | - Shi Yujiao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Li Wenbao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Wang Yanjun
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Cui Zhimou
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Lauri Arvolab
- Lammi Biological Station, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, Helsinki, Finland
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Schwob G, Almendras K, Veas-Mattheos K, Pezoa M, Orlando J. Host specialization and spatial divergence of bacteria associated with Peltigera lichens promote landscape gamma diversity. ENVIRONMENTAL MICROBIOME 2024; 19:57. [PMID: 39103916 DOI: 10.1186/s40793-024-00598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/21/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments -thalli, substrates, and neighboring soils- were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale. RESULTS The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks. CONCLUSIONS The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria.
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Affiliation(s)
- Guillaume Schwob
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Katerin Almendras
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Karla Veas-Mattheos
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Matías Pezoa
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Julieta Orlando
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
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Qiu Z, He S, Lian CA, Qiao X, Zhang Q, Yao C, Mu R, Wang L, Cao XA, Yan Y, Yu K. Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments. NPJ Biofilms Microbiomes 2024; 10:62. [PMID: 39069527 DOI: 10.1038/s41522-024-00537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Shuhang He
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qing Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ciqin Yao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Li Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiao-Ai Cao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China.
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Yang Y, Chen C, Yao K, Grossart HP. Seasonal dynamics of free-living (FL) and particle-attached (PA) bacterial communities in a plateau reservoir. Front Microbiol 2024; 15:1428701. [PMID: 39101032 PMCID: PMC11295932 DOI: 10.3389/fmicb.2024.1428701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
In terms of lifestyle, bacterioplankton can be classified as free-living (FL) and particle-attached (PA) forms, and both play essential roles in biogeochemical cycling in aquatic ecosystems. Structure, distribution, and community assembly of FL and PA bacteria in plateau riverine waterbodies are largely unknown. Therefore, we explored the seasonal dynamics of FLand PA bacterial communities in the Wujiangdu reservoir, Yungui Plateau using 16S rRNA gene high-throughput sequencing. Results revealed there was a significant environmental heterogeneity in Wujiangdu reservoir seasonally. The dominant phylum was Actinomycetota for FL and Pseudomonadota for PA bacteria. Species richness and diversity was higher in autumn and winter compared to spring and summer. In general, PA diversity was greater than FL, but with some temporal variations. Species turnover was the major contributor to β-diversity of both FL and PA lifestyles, and significant differences were noticed between FL and PA bacterial community composition. Distinct co-occurrence network patterns implied that more connections exist between FL bacteria, while more complex PA networks were in parallel to their greater diversity and stronger interactions in biofilms on particles. Dispersal limitation was the major driving force for both FL and PA bacterial community assembly. Deterministic processes were of relatively low importance, with homogeneous selection for FL and heterogeneous selection for PA bacteria. Temperature was the most important environmental driver of seasonal bacterial dynamics, followed by nitrate for FL and Secchi depth for PA bacteria. This study allows for a better understanding of the temporal variability of different bacteria lifestyles in reservoirs in the vulnerable and rapidly changing plateau environment, facilitating further microbial research related to global warming and eutrophication.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chen Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Kai Yao
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Potsdam University, Potsdam, Germany
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Sun Y, Du P, Li H, Zhou K, Shou L, Chen J, Meng Li. Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column. ENVIRONMENTAL RESEARCH 2024; 252:119011. [PMID: 38670213 DOI: 10.1016/j.envres.2024.119011] [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: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO43-, and distance offshore (p < 0.05). Water depth, NH4+, and PO43- were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3- (or NO2-) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.
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Affiliation(s)
- Yihua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Konglin Zhou
- Institute of Oceanography, Minjiang University, No. 200 xiyuangong Road, 350108 Fuzhou, Fujian, PR China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Synthetic Biology Research Center, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China.
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Demircan T, Gül S, Taşçı EA. Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:291-302. [PMID: 38808529 DOI: 10.1089/omi.2024.0075] [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: 05/30/2024]
Abstract
The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.
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Affiliation(s)
- Turan Demircan
- School of Medicine, Department of Medical Biology, Muğla Sıtkı Koçman University, Muğla, Türkiye
| | - Sultan Gül
- Institute of Health Sciences, İstanbul Medipol University, İstanbul, Türkiye
- Graduate School of Science And Engineering, Yıldız Technical University, İstanbul, Türkiye
| | - Ebru Altuntaş Taşçı
- Institute of Natural Sciences, Muğla Sıtkı Koçman University, Muğla, Türkiye
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11
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Qu Y, Zhao Y, Yao X, Wang J, Liu Z, Hong Y, Zheng P, Wang L, Hu B. Salinity causes differences in stratigraphic methane sources and sinks. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 19:100334. [PMID: 38046178 PMCID: PMC10692758 DOI: 10.1016/j.ese.2023.100334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 12/05/2023]
Abstract
Methane metabolism, driven by methanogenic and methanotrophic microorganisms, plays a pivotal role in the carbon cycle. As seawater intrusion and soil salinization rise due to global environmental shifts, understanding how salinity affects methane emissions, especially in deep strata, becomes imperative. Yet, insights into stratigraphic methane release under varying salinity conditions remain sparse. Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata (15-40 m depth) through in situ and microcosm simulation studies. Coastal strata, exhibiting a salinity level five times greater than terrestrial strata, manifested a 12.05% decrease in total methane production, but a staggering 687.34% surge in methane oxidation, culminating in 146.31% diminished methane emissions. Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics, impacting the methanogenic archaeal, methanotrophic archaeal, and methanotrophic bacterial communities by 16.53%, 27.25%, and 22.94%, respectively. Furthermore, microbial interactions influenced strata system methane metabolism. Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition, facilitating methane production via Methanofastidiosales. This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.
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Affiliation(s)
- Ying Qu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yi Hong
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lizhong Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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12
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Mo L, Zanella A, Squartini A, Ranzani G, Bolzonella C, Concheri G, Pindo M, Visentin F, Xu G. Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity. Microbiol Res 2024; 282:127651. [PMID: 38430888 DOI: 10.1016/j.micres.2024.127651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.
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Affiliation(s)
- Lingzi Mo
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou, Guangdong 510006, China.
| | - Augusto Zanella
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Andrea Squartini
- Department Agronomy, Food, Natural Resources, Animals, Environment, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Giulia Ranzani
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Cristian Bolzonella
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Giuseppe Concheri
- Department Agronomy, Food, Natural Resources, Animals, Environment, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Massimo Pindo
- Fondazione Edmund Mach, San Michele all'Adige 38098, Italy.
| | - Francesca Visentin
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy.
| | - Guoliang Xu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou, Guangdong 510006, China.
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13
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Yang B, Feng W, Zhou W, He K, Yang Z. Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems. Microorganisms 2024; 12:728. [PMID: 38674672 PMCID: PMC11052384 DOI: 10.3390/microorganisms12040728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.
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Affiliation(s)
- Bing Yang
- Sichuan Academy of Giant Panda, Chengdu 610041, China; (W.F.); (W.Z.); (Z.Y.)
| | - Wanju Feng
- Sichuan Academy of Giant Panda, Chengdu 610041, China; (W.F.); (W.Z.); (Z.Y.)
| | - Wenjia Zhou
- Sichuan Academy of Giant Panda, Chengdu 610041, China; (W.F.); (W.Z.); (Z.Y.)
| | - Ke He
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637002, China;
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu 610041, China; (W.F.); (W.Z.); (Z.Y.)
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14
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Liu Y, Guo W, Wei C, Huang H, Nan F, Liu X, Liu Q, Lv J, Feng J, Xie S. Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis. ENVIRONMENTAL RESEARCH 2024; 246:118107. [PMID: 38181848 DOI: 10.1016/j.envres.2024.118107] [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: 11/12/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.
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Affiliation(s)
- Yang Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Weinan Guo
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Caihua Wei
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Hanjie Huang
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Fangru Nan
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xudong Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qi Liu
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Junping Lv
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jia Feng
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shulian Xie
- Shanxi Key Laboratory for Research and Development of Regional Plants, School of Life Science, Shanxi University, Taiyuan 030006, China.
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15
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Zhang W, Ye J, Liu X, Zhang Y, Zhang J, Shen L, Jin Y, Zhang J, Li H. Spatiotemporal dynamics of bacterioplankton communities in the estuaries of two differently contaminated coastal areas: Composition, driving factors and ecological process. MARINE POLLUTION BULLETIN 2024; 201:116263. [PMID: 38531208 DOI: 10.1016/j.marpolbul.2024.116263] [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: 12/06/2023] [Revised: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Seasonal variations of environmental parameters usually lead to considerable changes in microbial communities. Nevertheless, the specific response patterns of these communities in coastal areas subjected to different levels of contamination remain unclear. Our results revealed notable fluctuations in the bacterioplankton community both seasonally and spatially, with seasonal variations being particularly significant. The diversity and composition of bacterioplankton communities in the estuaries varied significantly across seasons and between seas. Some bacterial phyla that were highly abundant in the dry season (e.g., Patescibacteria and Epsilonbacteraeota) were almost absent in the wet season. Furthermore, the network analysis revealed that the bacterioplankton networks were more complex during the wet season than in the dry season. In the wet season, the estuarine bacterioplankton network in the Yellow Sea region was more complex and stable, while the opposite was true in the dry season. According to the neutral community model, stochastic processes played a more significant role in the formation of bacterioplankton communities during the wet season than during the dry season. Estuarine bacterioplankton communities in the Yellow Sea region were more affected by stochastic processes compared to those in the Bohai Sea. In summary, in the estuaries of two differently contaminated coastal areas, the seasonal increase in nutrient levels enhanced the deterministic processes and network complexity of the bacterioplankton communities.
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Affiliation(s)
- Weiyue Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinqing Ye
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
| | - Xiaohan Liu
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yunlei Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinyong Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Lingyu Shen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yuan Jin
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
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16
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Wang T, Liu R, Huang G, Tian X, Zhang Y, He M, Wang C. Assembly dynamics of eukaryotic plankton and bacterioplankton in the Yangtze River estuary: A hybrid community perspective. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106414. [PMID: 38394975 DOI: 10.1016/j.marenvres.2024.106414] [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: 10/30/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Estuaries, acting as transitional habitats receiving species introductions from both freshwater and marine sources, undergo significant impacts from global climate changes. Planktonic microorganisms contribute significantly to estuarine biodiversity and ecological stability. These microorganisms primarily fall into three groups: eukaryotic plankton, particle-associated bacteria, and free-living bacteria. Understanding the structural characteristics and interactions within these subcommunities is crucial for comprehending estuarine dynamics. We collected samples from three distinct locations (< 0.1 PSU, 6.6 PSU, and 19 PSU) within the Yangtze River estuary. Samples underwent analysis for physicochemical indicators, while microbial communities were subjected to 16S/18S rRNA amplicon sequencing. Additionally, simulated mixing experiments were conducted using samples of varying salinities. Estuary samples, combined with simulated experiments, were employed to collectively examine the structural characteristics and assembly processes of estuarine microbes. Our research highlights the considerable impact of phylogenetic classification on prokaryotic behavior in these communities. We observed a transition in assembly processes from primarily stochastic for particle-associated bacteria to a predominant influence of homogeneous selection as salinity increased. Particle-associated bacterial communities exhibited a greater influence of stochastic processes compared to free-living bacteria, showcasing higher stability in diversity. The variations in composition and structure of estuarine microbial subcommunities were influenced by diverse environmental factors. Particle-associated bacteria displayed elevated network characterization values and established closer interactions with eukaryotic plankton. Structural equation modeling (SEM) analysis revealed that free-living bacteria displayed a heightened sensitivity to environmental factors and exerted a more significant influence on assembly processes and network characteristics. Simulated mixing in these environments resulted in the loss of species with similar microbial taxonomic relationships. The functioning of bacterioplankton is influenced by salinity and the processes governing their assembly, particularly in relation to different living states. These findings significantly contribute to our understanding of the intricate interplay between prokaryotic and eukaryotic plankton microorganisms in highly dynamic environments, laying a robust foundation for further exploration into the ecological mechanisms governing microbial dynamics in estuaries.
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Affiliation(s)
- Tong Wang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruiqing Liu
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guolin Huang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Tian
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaru Zhang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meilin He
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Changhai Wang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China; Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Lianyungang, 222005, China
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17
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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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18
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Zhou L, Wu Y, Zhou Y, Zhang Y, Xu H, Jang KS, Dolfing J, Spencer RGM, Jeppesen E. Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes. WATER RESEARCH 2024; 249:120955. [PMID: 38071902 DOI: 10.1016/j.watres.2023.120955] [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: 06/21/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Yunlin Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Hai Xu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Kyoung-Soon Jang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Robert G M Spencer
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States
| | - Erik Jeppesen
- Department of Ecoscience and Center for Water Technology (WATEC), Aarhus University, C.F. Møllers Allé 3, DK-8000 Aarhus, Denmark; Sino-Danish Centre for Education and Research, Beijing 100190, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, Mersin 33731, Turkey; Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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19
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Barbour KM, Martiny JBH. Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system. THE ISME JOURNAL 2024; 18:wrae043. [PMID: 38506671 PMCID: PMC11008689 DOI: 10.1093/ismejo/wrae043] [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: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.
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Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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20
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Peng Z, Yang Y, Liu Y, Bu L, Qi J, Gao H, Chen S, Pan H, Chen B, Liang C, Li X, An Y, Wang S, Wei G, Jiao S. The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems. GLOBAL CHANGE BIOLOGY 2024; 30:e16996. [PMID: 37916454 DOI: 10.1111/gcb.16996] [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: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.
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Affiliation(s)
- Ziheng Peng
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yu Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lianyan Bu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiejun Qi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hang Gao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Haibo Pan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Beibei Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunling Liang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yining An
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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21
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Seppey CVW, Cabrol L, Thalasso F, Gandois L, Lavergne C, Martinez-Cruz K, Sepulveda-Jauregui A, Aguilar-Muñoz P, Astorga-España MS, Chamy R, Dellagnezze BM, Etchebehere C, Fochesatto GJ, Gerardo-Nieto O, Mansilla A, Murray A, Sweetlove M, Tananaev N, Teisserenc R, Tveit AT, Van de Putte A, Svenning MM, Barret M. Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes. Environ Microbiol 2023; 25:3364-3386. [PMID: 37897125 DOI: 10.1111/1462-2920.16526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.
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Affiliation(s)
- Christophe V W Seppey
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam-Golm, Germany
| | - Léa Cabrol
- Aix-Marseille University, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Frederic Thalasso
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
- Environmental Physics Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | | | - Polette Aguilar-Muñoz
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Bruna Martins Dellagnezze
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Gilberto J Fochesatto
- Department of Atmospheric Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Oscar Gerardo-Nieto
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Alison Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada, USA
| | - Maxime Sweetlove
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Nikita Tananaev
- Melnikov Permafrost Institute, Russian Academy of Sciences, Yakutsk, Russia
- Institute of Natural Sciences, North-Eastern Federal University, Yakutsk, Russia
| | - Roman Teisserenc
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anton Van de Putte
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
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22
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Chen C, Li P, Yin M, Wang J, Sun Y, Ju W, Liu L, Li ZH. Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes. MARINE POLLUTION BULLETIN 2023; 197:115739. [PMID: 37925991 DOI: 10.1016/j.marpolbul.2023.115739] [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: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.
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Affiliation(s)
- Chengzhuang Chen
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Minghao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jinxin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Yongjun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wenming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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23
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Lumpi T, Guo X, Lindström ES. Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence. Environ Microbiol 2023; 25:2289-2302. [PMID: 37381117 DOI: 10.1111/1462-2920.16450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.
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Affiliation(s)
- Theresa Lumpi
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Xin Guo
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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24
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Lu M, Luo X, Jiao JJ, Li H, Kuang X, Wang X, Feng Y, Zheng C. Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118714. [PMID: 37542806 DOI: 10.1016/j.jenvman.2023.118714] [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: 03/15/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.
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Affiliation(s)
- Meiqing Lu
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Luo
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiu Jimmy Jiao
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China.
| | - Hailong Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xingxing Kuang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuejing Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqing Feng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
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25
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Li T, Gao J. Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1168760. [PMID: 37941678 PMCID: PMC10628812 DOI: 10.3389/fpls.2023.1168760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.
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Affiliation(s)
| | - Jiangyun Gao
- Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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26
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Qi L, Li R, Wu Y, Ibeanusi V, Chen G. Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs. ENVIRONMENTAL RESEARCH 2023; 235:116584. [PMID: 37454793 DOI: 10.1016/j.envres.2023.116584] [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: 04/27/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.
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Affiliation(s)
- Lin Qi
- Department of Civil and Environmental Engineering at FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, 32310, USA.
| | - Runwei Li
- Department of Civil Engineering, College of Engineering, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yudi Wu
- College of Engineering and Applied Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Victor Ibeanusi
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, FL, 32307, USA
| | - Gang Chen
- Department of Civil and Environmental Engineering at FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, 32310, USA
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27
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Ghafouri M, Pourjafar F, Ghobadi Nejad Z, Yaghmaei S. Biological treatment of triclosan using a novel strain of Enterobacter cloacae and introducing naphthalene dioxygenase as an effective enzyme. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:131833. [PMID: 37473572 DOI: 10.1016/j.jhazmat.2023.131833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/22/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
In recent years, triclosan (TCS) has been widely used as an antibacterial agent in personal care products due to the spread of the Coronavirus. TSC is an emerging contaminant, and due to its stability and toxicity, it cannot be completely degraded through traditional wastewater treatment methods. In this study, a novel strain of Enterobacter cloacae was isolated and identified that can grow in high TCS concentrations. Also, we introduced naphthalene dioxygenase as an effective enzyme in TCS biodegradation, and its role during the removal process was investigated along with the laccase enzyme. The change of cell surface hydrophobicity during TCS removal revealed that a glycolipid biosurfactant called rhamnolipid was involved in TCS removal, leading to enhanced biodegradation of TCS. The independent variables, such as initial TCS concentration, pH, removal duration, and temperature, were optimized using the response surface method (RSM). As a result, the maximum TCS removal (97%) was detected at a pH value of 7 and a temperature of 32 °C after 9 days and 12 h of treatment. Gas chromatography-mass spectrometry (GC/MS) analysis showed five intermediate products and a newly proposed pathway for TCS degradation. Finally, the phytotoxicity experiment conducted on Cucumis sativus and Lens culinaris seeds demonstrated an increase in germination power and growth of stems and roots in comparison to untreated water. These results indicate that the final treated water was less toxic.
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Affiliation(s)
- Mahsa Ghafouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Fatemeh Pourjafar
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Zahra Ghobadi Nejad
- Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran
| | - Soheila Yaghmaei
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran; Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran.
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28
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Bier RL, Mosher JJ, Kaplan LA, Kan J. Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America. Environ Microbiol 2023; 25:1860-1874. [PMID: 37177981 DOI: 10.1111/1462-2920.16396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.
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Affiliation(s)
- Raven L Bier
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | - Jennifer J Mosher
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Marshall University, Department of Biological Sciences, Huntington, West Virginia, USA
| | - Louis A Kaplan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
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Qin H, Cai R, Wang Y, Deng X, Chen J, Xing J. Intensive management facilitates bacterial invasion on soil microbial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117963. [PMID: 37105104 DOI: 10.1016/j.jenvman.2023.117963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/12/2023]
Abstract
Intensive management has greatly altered natural forests, especially forests around the world are increasingly being converted into economic plantations. Soil microbiota are critical for community functions in all ecosystems, but the effects of microbial disturbance during economic plantation remain unclear. Here, we used Escherichia coli O157:H7, a model pathogenic species for bacterial invasion, to assess the invasion impacts on the soil microbial community under intensive management. The E. coli invasion was tracked for 135 days to explore the instant and legacy impacts on the resident community. Our results showed that bamboo economic plantations altered soil abiotic and biotic properties, especially increasing pH and community diversity. Higher pH in bamboo soils resulted in longer pathogen survivals than in natural hardwood soils, indicating that pathogen suppression during intensive management should arouse our attention. A longer invasion legacy effect on the resident community (P < 0.05) were found in bamboo soils underlines the need to quantify the soil resilience even when the invasion was unsuccessful. Deterministic processes drove community assembly in bamboo plantations, and this selection acted more strongly during by E. coli invasion than in hardwood soils. We also showed more associated co-occurrence patterns in bamboo plantations, suggesting more complex potential interactions within the microbial community. Apart from community structure, community functions are also strongly related to the resident species associated with invaders. These findings provide new perspectives to understand intensive management facilitates the bacterial invasion, and the impacts would leave potential risks on environmental and human health.
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Affiliation(s)
- Hua Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ruihang Cai
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 310021, China
| | - Yanan Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 310021, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiajia Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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Yokoyama D, Kikuchi J. Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water. ENVIRONMENTAL RESEARCH 2023; 231:116202. [PMID: 37211183 DOI: 10.1016/j.envres.2023.116202] [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: 02/20/2023] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.
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Affiliation(s)
- Daiki Yokoyama
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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31
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Jiao C, Zhao D, Zhou T, Wu QL, Zeng J. Habitat-specific regulation of bacterial community dynamics during phytoplankton bloom succession in a subtropical eutrophic lake. WATER RESEARCH 2023; 242:120252. [PMID: 37393808 DOI: 10.1016/j.watres.2023.120252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023]
Abstract
Phytoplankton blooms, an important indicator of severe eutrophication, are a globally significant consequence of anthropogenic activities and climate change on freshwater lakes. Shifts in microbial communities during phytoplankton blooms have been extensively investigated, yet we have a limited understanding of how distinct assembly processes underlying the temporal dynamics of freshwater bacterial communities within different habitats respond to the succession of phytoplankton blooms. To address this knowledge gap, we collected both water and sediment samples in a subtropical eutrophic lake over a complete period of phytoplankton blooms to assess the dynamics of bacterial communities and the temporal shifts in assembly processes. Our results showed that phytoplankton blooms strongly altered the diversity, composition, and coexistence patterns of both planktonic and sediment bacterial communities (PBC and SBC), but the successional patterns differed between PBC and SBC. PBC were less temporally stable under bloom-induce disturbances, with higher variations in temporal dynamics and greater sensitivity to environmental fluctuations. Furthermore, the temporal assembly patterns of bacterial communities in both habitats were mainly driven by homogeneous selection and ecological drift. In the PBC, the role of selection decreased over time, while ecological drift became increasingly important. Conversely, in the SBC, the relative impact of selection and ecological drift on community assemblages fluctuated less over time, with selection remaining the dominant process throughout the bloom.
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Affiliation(s)
- Congcong Jiao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Tianxu Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
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32
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Ontiveros VJ, Capitán JA, Casamayor EO, Alonso D. Colonization-persistence trade-offs in natural bacterial communities. Proc Biol Sci 2023; 290:20230709. [PMID: 37403500 PMCID: PMC10320335 DOI: 10.1098/rspb.2023.0709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Fitness equalizing mechanisms, such as trade-offs, are recognized as one of the main factors promoting species coexistence in community ecology. However, they have rarely been explored in microbial communities. Although microbial communities are highly diverse, the coexistence of their multiple taxa is largely attributed to niche differences and high dispersal rates, following the principle 'everything is everywhere, but the environment selects'. We use a dynamical stochastic model based on the theory of island biogeography to study highly diverse bacterial communities over time across three different systems (soils, alpine lakes and shallow saline lakes). Assuming fitness equalization mechanisms, here we newly analytically derive colonization-persistence trade-offs, and report a signal of such trade-offs in natural bacterial communities. Moreover, we show that different subsets of species in the community drive this trade-off. Rare taxa, which are occasional and more likely to follow independent colonization/extinction dynamics, drive this trade-off in the aquatic communities, while the core sub-community did it in the soils. We conclude that equalizing mechanisms may be more important than previously recognized in bacterial communities. Our work also emphasizes the fundamental value of dynamical models for understanding temporal patterns and processes in highly diverse communities.
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Affiliation(s)
- Vicente J. Ontiveros
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
| | - José A. Capitán
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
- Complex Systems Group. Department of Applied Mathematics, Universidad Politécnica de Madrid. Av. Juan de Herrera, 6. E-28040 Madrid, Spain
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
| | - David Alonso
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
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Sha C, Wu J, Shen C, Wu J, Yan Z, Wang M. The ecology of bacterial communities in groundwater of industrial areas: Diversity, composition, network, and assembly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121207. [PMID: 36738877 DOI: 10.1016/j.envpol.2023.121207] [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: 10/07/2022] [Revised: 12/27/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Groundwater provides freshwater resources necessary for mankind, but its quality is significantly impacted by anthropologic activities. The unique characteristics of groundwater provide a special niche for bacterial colonization. To maintain the sustainability of groundwater ecosystem, a good understanding of the influencing factors and assembly mechanisms for bacterial communities is necessary. Here, we investigated the bacterial communities of groundwater from two industrial zones in Shanghai, a highly industrialized city, during the wet and dry seasons using the high-throughput sequencing technology. Our study uncovered the significant effects of season, geographical location, and industrial type on the diversity and composition of groundwater bacterial communities, particularly, we found that season was the most dominant factor with much stronger influences (give the explanation 17.7%) in comparison with geographical location (8.8%) and industrial type (7.5%). Co-occurrence networks revealed that geographical location explained more variations of bacterial ecological network than season did. Both distance-decay of similarities and variation partitioning analyses indicated that the assembly of groundwater bacterial communities was more governed by environmental filtering compared to spatial-related dispersal. Finally, null model analysis suggested the role of stochastic processes, including dispersal and drift, in shaping the groundwater bacterial communities cannot be ignored. These findings would benefit to improve our understanding of the bacterial communities in groundwater ecosystem and provide a theoretical foundation for groundwater health management.
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Affiliation(s)
- Chenyan Sha
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Cheng Shen
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Jian Wu
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Zhongchun Yan
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Min Wang
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China.
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34
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Retter A, Haas JC, Birk S, Stumpp C, Hausmann B, Griebler C, Karwautz C. From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor. Microorganisms 2023; 11:microorganisms11030779. [PMID: 36985351 PMCID: PMC10055094 DOI: 10.3390/microorganisms11030779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
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Affiliation(s)
- Alice Retter
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | | | - Steffen Birk
- Institute of Earth Sciences, NAWI Graz Geocenter, University of Graz, 8010 Graz, Austria
| | - Christine Stumpp
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences (BOKU), 1180 Wien, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Wien, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Wien, Austria
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | - Clemens Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
- Correspondence:
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35
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Wu J, Song Q, Wu Y, Liu J, Wu Z, Zhou J, Wang Y, Wu W. Application of phosphorus amendments reduces metal uptake and increases yield of Oryza saliva L. (rice) in Cd/Cu-contaminated paddy field. CHEMOSPHERE 2023; 318:137875. [PMID: 36646182 DOI: 10.1016/j.chemosphere.2023.137875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/30/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
To alleviate worldwide food safety issues caused by metal contamination, an easily available material is urgently needed for extensive application. In this study, calcium magnesium phosphate fertiliser (Pcm) was applied to a Cd/Cu co-contaminated paddy field in comparison with limestone and organic fertiliser. The results showed that only Pcm is effective in simultaneously reducing Cd uptake by 56.7% and Cu uptake by 36.2% in Oryza saliva L. (rice). The rice yield, reduced mainly by Cu, also increased by 30.1% with respect to the enhancement of soil pH, cation exchange capacity and availability of phosphorus, as well as the reduction in availabilities of Cd and Cu. Additionally, Pcm dramatically shaped the bacterial community structure, with Proteobacteria and Firmicutes predominant in the soils. The beneficial genera Exiguobacterium, Citrobacter, and Acinetobacter, which are vital for phosphate dissolution and Cd/Cu immobilisation, were also enriched. The results demonstrated that the application of Pcm at 0.4% (w:w) was able to enhance both crop quantity and quality in Cd/Cu co-contaminated paddy fields by reducing Cu/Cd availability, promoting rice yield, and reshaping bacterial community structures.
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Affiliation(s)
- Jiahui Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Qingmei Song
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Yingxin Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China.
| | - Junjun Liu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Zhuohao Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Jingyan Zhou
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Yuntao Wang
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China
| | - Wencheng Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou, 510655, PR China.
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36
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Zhang J, Yu D, Wang Y, Shi L, Wang T, Simayijiang H, Yan J. Tracing recent outdoor geolocation by analyzing microbiota from shoe soles and shoeprints even after indoor walking. Forensic Sci Int Genet 2023; 65:102869. [PMID: 37054666 DOI: 10.1016/j.fsigen.2023.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
The microbial communities on shoe soles and shoeprints could carry microbial information about where someone walked. This is possible evidence to link a suspect in a crime case to a geographic location. A previous study had shown that the microbiota found on shoe soles depend on the microbiota of the soil on which people walk. However, there is a turnover of microbial communities on shoe soles during walking. The impact of microbial community turnover on tracing recent geolocation from shoe soles has not been adequately studied. In addition, it is still unclear whether the microbiota of shoeprints can be used to determine recent geolocation. In this preliminary study, we investigated whether the microbial characteristics of shoe soles and shoeprints can be used to trace geolocation and whether this information can be destroyed by walking on indoor floors. In this study, participants were asked to walk outdoors on exposed soil, then walk indoors on a hard wood floor. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial communities of shoe soles, shoeprints, indoor dust, and outdoor soil. Samples of shoe soles and shoeprints were collected at steps 5, 20, and 50 while walking indoors. The PCoA result showed that the samples were clustered by geographic origin. The shoeprint showed a more rapid turnover of microbial community than the shoe sole during indoor walking. The result of FEAST showed that the microbial communities of shoe sole and shoeprint were mainly (shoe sole, 86.21∼92.34 %; shoeprint, 61.66∼90.41 %) from the soil of the outdoor ground where the individual recently walked, and a small portion (shoe sole, 0.68∼3.33 %; shoeprint, 1.43∼27.14 %) from the indoor dust. Based on the matching of microbial communities between geolocation and shoe sole or shoeprint, we were able to infer the recent geolocation of the individual with relatively high accuracy using the random forest prediction model (shoe sole: 100.00 %, shoeprint: 93.33∼100.00 %). Overall, we are able to accurately infer the geolocation of an individual's most recent outdoor walk based on the microbiota of shoe sole and shoeprint, even though these microbiotas show a turnover when walking indoor floor. The pilot study was expected to provide a potential method for tracing recent geolocation of suspects.
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Wang L, Liu J, Zhang M, Wu T, Chai B. Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development. Microbiol Spectr 2023; 11:e0505122. [PMID: 36688664 PMCID: PMC9927475 DOI: 10.1128/spectrum.05051-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.
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Affiliation(s)
- Lixiao Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
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Yan ZG, Zhu XM, Zhang SW, Jiang H, Wang SP, Wei C, Wang J, Shao Y, Liu C, Wang H. Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters. Front Microbiol 2023; 14:1132925. [PMID: 36846757 PMCID: PMC9956185 DOI: 10.3389/fmicb.2023.1132925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
The diversity and community assembly mechanisms of eukaryotic plankton in coastal waters is so far not clear. In this study, we selected the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area, which is a highly developed region in China, as the research area. By use of high-throughput sequencing technologies, the diversity and community assembly mechanisms of eukaryotic marine plankton were studied in which a total of 7,295 OTUs were obtained, and 2,307 species were annotated by doing environmental DNA survey of 17 sites consist of surface and bottom layer. Ultimately, the analysis reveals that the species abundance of bottom layer is, by and large, higher than that in the surface layer. In the bottom, Arthropoda is the first largest group, accounting for more than 20% while Arthropoda and Bacillariophyta are dominant groups in surface waters accounting for more than 40%. It is significant of the variance in alpha-diversity between sampling sites, and the difference of alpha-diversity between bottom sites is greater than that of surface sites. The result suggests that the environmental factors that have significant influence on alpha-diversity are total alkalinity and offshore distance for surface sites, and water depth and turbidity for bottom sites. Likewise, the plankton communities obey the typical distance-decay pattern. Analysis about community assembly mechanisms reveals that, overall, dispersal limitation is the major pattern of community formation, which accounts for more than 83% of the community formation processes, suggesting that stochastic processes are the crucial assembly mechanism of the eukaryotic plankton community in the study area.
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Affiliation(s)
- Zhen-Guang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China,*Correspondence: Zhen-Guang Yan, ✉
| | - Xue-Ming Zhu
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shou-Wen Zhang
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hua Jiang
- Marine Climate Prediction and Assessment Center, National Marine Environmental Forecasting Center, Beijing, China
| | - Shu-Ping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Chao Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jie Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yun Shao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Chen Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hui Wang
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China,Marine Climate Prediction and Assessment Center, National Marine Environmental Forecasting Center, Beijing, China
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39
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Wan W, Grossart H, He D, Liu W, Wang S, Yang Y. Differentiation strategies for planktonic bacteria and eukaryotes in response to aggravated algal blooms in urban lakes. IMETA 2023; 2:e84. [PMID: 38868338 PMCID: PMC10989909 DOI: 10.1002/imt2.84] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/14/2024]
Abstract
Aggravated algal blooms potentially decreased environmental heterogeneity. Different strategies of planktonic bacteria and eukaryotes in response to aggravated algal blooms. Environmental constraints of plankton showed different patterns over time.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical GardenChinese Academy of SciencesWuhanPeople's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research StationChinese Academy of Sciences & Hubei ProvinceWuhanPeople's Republic of China
| | - Hans‐Peter Grossart
- Departent of Plankton and Microbial EcologyLeibniz‐Institute for Freshwater Ecology and Inland Fisheries (IGB)NeuglobsowGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Donglan He
- College of Life ScienceSouth‐Central Minzu UniversityWuhanPeople's Republic of China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical GardenChinese Academy of SciencesWuhanPeople's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research StationChinese Academy of Sciences & Hubei ProvinceWuhanPeople's Republic of China
| | - Shuai Wang
- College of Life ScienceSouth‐Central Minzu UniversityWuhanPeople's Republic of China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical GardenChinese Academy of SciencesWuhanPeople's Republic of China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research StationChinese Academy of Sciences & Hubei ProvinceWuhanPeople's Republic of China
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40
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Hanashiro FTT, De Meester L, Vanhamel M, Mukherjee S, Gianuca AT, Verbeek L, van den Berg E, Souffreau C. Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition. MICROBIAL ECOLOGY 2023; 85:400-410. [PMID: 35306576 DOI: 10.1007/s00248-022-01994-x] [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: 08/21/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.
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Affiliation(s)
- Fabio Toshiro T Hanashiro
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium.
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB), Müggelseedamm 310, 12587, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195, Berlin, Germany
| | - Matthias Vanhamel
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Laboratory of Reproductive Genomics, KU Leuven, ON I Herestraat 49, 3000, Leuven, Belgium
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, 59078-900, Brazil
| | - Laura Verbeek
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Edwin van den Berg
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
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41
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Hu J, Vandenkoornhuyse P, Khalfallah F, Causse‐Védrines R, Mony C. Ecological corridors homogenize plant root endospheric mycobiota. THE NEW PHYTOLOGIST 2023; 237:1347-1362. [PMID: 36349407 PMCID: PMC10107361 DOI: 10.1111/nph.18606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind, while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of 1 m over 2 years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We showed that plant root endospheric mycobiota were sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.
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Affiliation(s)
- Jie Hu
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
- Ecology and Biodiversity group, Institute of Environmental BiologyUniversity of UtrechtH.R. Kruyt building, Padualaan 83584 CHUtrechtthe Netherlands
- Present address:
Department of Microbial EcologyNetherlands Institute of EcologyDroevendaalsesteeg 106708 PBWageningenthe Netherlands
| | | | - Fadwa Khalfallah
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
- UMR IAM, INRAEUniversité de LorraineRue d'amance54280ChampenouxFrance
| | - Romain Causse‐Védrines
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
| | - Cendrine Mony
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
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42
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Doane MP, Ostrowski M, Brown M, Bramucci A, Bodrossy L, van de Kamp J, Bissett A, Steinberg P, Doblin MA, Seymour J. Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions. Environ Microbiol 2023. [PMID: 36700447 DOI: 10.1111/1462-2920.16341] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high- and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.
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Affiliation(s)
- Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Martin Ostrowski
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mark Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, New South Wales, Australia
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | | | | | - Peter Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Centre for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
| | - Martina A Doblin
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
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43
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Li Q, Qiu J, Liang Y, Lan G. Soil bacterial community changes along elevation gradients in karst graben basin of Yunnan-Kweichow Plateau. Front Microbiol 2022; 13:1054667. [PMID: 36620048 PMCID: PMC9813600 DOI: 10.3389/fmicb.2022.1054667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Elevation gradients could provide natural experiments to examine geomorphological influences on biota ecology and evolution, however little is known about microbial community structures with soil depths along altitudinal gradients in karst graben basin of Yunnan-Kweichow Plateau. Here, bulk soil in A layer (0 ~ 10 cm) and B layer (10 ~ 20 cm) from two transect Mounts were analyzed by using high-throughput sequencing coupled with physicochemical analysis. It was found that the top five phyla in A layer were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia, and the top five phyla in B layer were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi in a near-neutral environment. Edaphic parameters were different in two layers along altitudinal gradients. Besides that, soil microbial community compositions varied along altitudinal gradient, and soil organic carbon (SOC) and total nitrogen (TN) increased monotonically with increasing elevation. It was further observed that Shannon indexes with increasing altitudes in two transect Mounts decreased monotonically with significant difference (p = 0.001), however beta diversity followed U-trend with significant difference (p = 0.001). The low proportions of unique operational taxonomic units (OTUs) appeared at high altitude areas which impact the widely accepted elevation Rapoport's rules. The dominant Bradyrhizobium (alphaproteobacterial OTU 1) identified at high altitudes in two layers constitutes the important group of free-living diazotrophs and could bring fixed N into soils, which simultaneously enhances SOC and TN accumulation at high altitudes (p < 0.01). Due to different responses of bacterial community to environmental changes varying with soil depths, altitudinal gradients exerted negative effects on soil bacterial communities via soil physical properties and positive effects on soil bacterial diversities via soil chemical properties in A layer, however the results in B layer were opposite. Overall, our study is the first attempt to bring a deeper understanding of soil microbial structure patterns along altitudinal gradients at karst graben basin areas.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China,*Correspondence: Qiang Li, ✉
| | - Jiangmei Qiu
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Yueming Liang
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Gaoyong Lan
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, MNR, Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
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44
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Bier RL, Vass M, Székely AJ, Langenheder S. Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms. THE ISME JOURNAL 2022; 16:2635-2643. [PMID: 35982230 PMCID: PMC9666552 DOI: 10.1038/s41396-022-01286-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022]
Abstract
Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.
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Affiliation(s)
- Raven L. Bier
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden ,grid.213876.90000 0004 1936 738XPresent Address: Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802 USA
| | - Máté Vass
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden
| | - Anna J. Székely
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007 Uppsala, Sweden
| | - Silke Langenheder
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden
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45
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Groult B, Bredin P, Lazar CS. Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada). Environ Microbiol 2022; 24:5898-5910. [PMID: 36135934 DOI: 10.1111/1462-2920.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km2 in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.
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Affiliation(s)
- Benjamin Groult
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Pascal Bredin
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Cassandre Sara Lazar
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
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46
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Zhao Y, Lin H, Liu Y, Jiang Y, Zhang W. Abundant bacteria shaped by deterministic processes have a high abundance of potential antibiotic resistance genes in a plateau river sediment. Front Microbiol 2022; 13:977037. [DOI: 10.3389/fmicb.2022.977037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.
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47
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMID: 36314747 PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns. METHODS The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact. Water inlet samples were collected at six drinking water treatment plants over 3 years, totaling 230 samples. The bacterial communities of DNA sequenced samples (n = 175), obtained by 16S metabarcoding, were analyzed using a joint model for taxa abundance. RESULTS Two major groups of well-defined metacommunities of microorganisms were identified, in addition to a third, less distinct, and taxonomically more diverse group. These three metacommunities showed various associations to the measured environmental data. Predictions for the well-defined metacommunities revealed differing sets of favored metabolic pathways and life strategies. In one community, taxa with methanogenic metabolism were common, while a second community was dominated by taxa with carbohydrate and lipid-focused metabolism. CONCLUSION The identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources.
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Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Melle Säve‐Söderbergh
- Science DivisionSwedish Food AgencyUppsalaSweden
- Institute of Environmental Medicine, Karolinska InstitutetStockholmSweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public HealthSwedish University of Agricultural SciencesUppsalaSweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
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48
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Pan B, Liu X, Chen Q, Sun H, Zhao X, Huang Z. Hydrological connectivity promotes coalescence of bacterial communities in a floodplain. Front Microbiol 2022; 13:971437. [PMID: 36212880 PMCID: PMC9532515 DOI: 10.3389/fmicb.2022.971437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Floodplains play essential roles in the ecological functions of regional environments. The merging and coalescence of bacterial communities in aquatic environments results in periodic patterns driven by regular hydrological activities, which may, in turn, influence ecological activities. However, the degree of bacterial community coalescence in the lateral and vertical directions as well as the underlying hydrological mechanism of floodplain ecosystems is poorly understood. Therefore, we investigated the spatiotemporal patterns and coalescence processes of planktonic and sedimentary bacterial communities during normal and high-water periods in a floodplain ecosystem of the Yellow River source region. We classified bacterial operational taxonomic units (OTUs) based on 16S rRNA gene sequencing, and quantified community coalescence by calculating the proportions of overlapping OTUs, the contributions of upstream sources to downstream sinks, and positive/negative cohesion. The results revealed major differences in the composition and diversity of planktonic and sedimentary bacterial communities. Bacterial community diversity in the high-water period was higher than in the normal period. Laterally, hydrological connectivity promoted the immigration and coalescence of bacterial communities to oxbow lakes in both the mainstream and tributaries, with the coalescence degree of planktonic bacteria (2.9%) higher than that of sedimentary bacteria (1.7%). Vertically, the coalescence degree of mainstream planktonic and sedimentary bacterial communities was highest, reaching 2.9%. Co-occurrence network analysis revealed that hydrological connectivity increased the complexity of the bacterial network and enhanced the coalescence of keystone species to oxbow lakes. Furthermore, community coalescence improved the competitiveness and dispersal of bacterial communities. This study demonstrated that coalescence of bacterial communities is driven by hydrological connectivity in a floodplain ecosystem. Further studies should investigate the processes of bacterial community coalescence in floodplains in more detail, which could provide new approaches for environmental protection and ecological function preservation.
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Affiliation(s)
- Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- *Correspondence: Qiuwen Chen,
| | - He Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Zhenyu Huang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
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49
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Qin Z, Zhao Z, Xia L, Wang S. Pollution pressure and soil depth drive prokaryotic microbial assemblage and co-occurrence patterns in an organic polluted site. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129570. [PMID: 35999754 DOI: 10.1016/j.jhazmat.2022.129570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Organic polluted sites have become a global concern of soil contamination, yet little is known about microbial vertical distribution and community assembly in organic polluted sites. Here, high-throughput sequencing technology was employed to investigate prokaryotic microbial diversity and community assembly along soil profile in an abandoned chemical organic contaminated site. Results showed that there was no significant difference (P > 0.05) observed in microbial alpha diversity among different soil layers, whereas the structure of microbial communities presented significantly different (P < 0.05) in the superficial layer (0-0.5 m) compared with intermediate (1-1.5 m) and bottom (2.5-3 m) layers. Soil prokaryotic microbial community evolved to possess the potential of degrading organic pollutants under long-term organic pollution stress. A relatively homogeneous environment created by the organic polluted site mainly induced the ecological process of homogeneous selection driving community assembly, while dispersal limitation gained importance with the increase of soil depth. Organic contaminants were identified as the key driver of destabilizing co-occurrence networks, while the frequent cooperative behaviors among species could combat organic pollution stress and sustain prokaryotic community stability. Collectively, pollution pressure and soil depth jointly affected prokaryotic microbial assemblage and co-occurrence that underpinned the spatial scaling patterns of organic contaminated sites microbiota.
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Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China
| | - Shiyu Wang
- Beijing Municipal Ecological and Environmental Monitoring Center, Beijing 100048, China
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50
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Li B, Shen C, Wu HY, Zhang LM, Wang J, Liu S, Jing Z, Ge Y. Environmental selection dominates over dispersal limitation in shaping bacterial biogeographical patterns across different soil horizons of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156177. [PMID: 35613642 DOI: 10.1016/j.scitotenv.2022.156177] [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: 02/18/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial biogeographical patterns have been widely explored from horizontal to vertical scales. However, studies of microbial vertical distributions were still limited (e.g., how soil genetic horizons influence microbial distributions). To shed light on this question, we investigated soil bacterial communities across three soil horizons (topsoil: horizon A; midsoil: horizon B; subsoil: horizon C) of 60 soil profiles along a 3500 km transect in the Qinghai-Tibet Plateau. We found that bacterial diversity was highest in the topsoil and lowest in the subsoil, and community composition significantly differed across soil horizons. The network complexity decreased from topsoil to subsoil. There were significant geographical/environmental distance-decay relationships (DDR) in three soil horizons, with a lower slope from topsoil to subsoil due to the decreased environmental heterogeneity. Variation partitioning analysis (VPA) showed that bacterial community variations were explained more by environmental than spatial factors. Although environmental selection processes played a dominant role, null model analysis revealed that deterministic processes (mainly variable selection) decreased with deeper soil horizons, while stochastic processes (mainly dispersal limitation) increased from topsoil to subsoil. These results suggested that microbial biogeographical patterns and community assembly processes were soil horizon dependent. Our study provides new insights into the microbial vertical distributions in large-scale alpine regions and highlights the vital role of soil genetic horizons in affecting microbial community assembly, which has implications for understanding the pedogenetic process and microbial responses to extreme environment under climate change.
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Affiliation(s)
- Bojian Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Yong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongwang Jing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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