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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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Fang H, Zhen Z, Yang F, Su H, Wei Y. Epiphytic bacterial community composition on four submerged macrophytes in different regions of Taihu Lake. FRONTIERS IN PLANT SCIENCE 2024; 15:1404718. [PMID: 39119501 PMCID: PMC11306141 DOI: 10.3389/fpls.2024.1404718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024]
Abstract
The epiphytic bacteria in aquatic ecosystems, inhabiting a unique ecological niche with significant ecological function, have long been the subject of attention. Habitat characteristics and plant species are believed to be important in controlling the assembly of epiphytic bacteria. However, the underlying principle governing the assembly of the epiphytic bacterial community on macrophytes is far from clear. In this study, we systematically compared the diversity and community composition of epiphytic bacteria both in different habitats and on different species of macrophytes where they were attached. Results suggested that neither the plant species nor the habitat had a significant effect on the diversity and community of epiphytic bacteria independently, indicating that the epiphytic bacterial community composition was correlated to both geographical distance and individual species of macrophytes. Furthermore, almost all of the abundant taxa were shared between different lake regions or macrophyte species, and the most abundant bacteria belonged to Proteobacteria and Firmicutes. Our results demonstrated that the competitive lottery model may explain the pattern of epiphytic bacterial colonization of submerged macrophyte surfaces. This research could provide a new perspective for exploring plant-microbe interaction in aquatic systems and new evidence for the lottery model as the mechanism best explaining the assembly of epiphytic bacteria.
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Affiliation(s)
- Hongda Fang
- College of Harbour and Coastal Engineering, Jimei University, Xiamen, China
| | - Zhuo Zhen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Fan Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Hailei Su
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yuan Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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Kayiranga A, Isabwe A, Yao H, Shangguan H, Coulibaly JLK, Breed M, Sun X. Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities. Ecol Evol 2024; 14:e11672. [PMID: 38988351 PMCID: PMC11236429 DOI: 10.1002/ece3.11672] [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: 03/06/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024] Open
Abstract
Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.
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Affiliation(s)
- Alexis Kayiranga
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Huayuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Justin Louis Kafana Coulibaly
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Martin Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
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Liu X, Zhang L, Wang Y, Hu S, Zhang J, Huang X, Li R, Hu Y, Yao H, Wang Z. Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems. iScience 2024; 27:110053. [PMID: 38947525 PMCID: PMC11214296 DOI: 10.1016/j.isci.2024.110053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/02/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.
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Affiliation(s)
- Xi Liu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingcai Wang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Sheng Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Jing Zhang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Xiaolong Huang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Ruiwen Li
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Yuxin Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, Hubei, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, Hubei, China
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Li S, Luo N, Li C, Mao S, Huang H. Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106451. [PMID: 38492505 DOI: 10.1016/j.marenvres.2024.106451] [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: 11/08/2023] [Revised: 01/04/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2-2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.
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Affiliation(s)
- Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Ningjian Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Chuang Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shuoqian Mao
- Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
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Wang Y, Kong J, Gu S, Huang B, Sun P. Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170231. [PMID: 38246384 DOI: 10.1016/j.scitotenv.2024.170231] [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: 11/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.
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Affiliation(s)
- Ying Wang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Ping Sun
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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7
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Bontemps Z, Moënne-Loccoz Y, Hugoni M. Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave. mSystems 2024; 9:e0123323. [PMID: 38289092 PMCID: PMC10878041 DOI: 10.1128/msystems.01233-23] [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: 11/27/2023] [Accepted: 12/28/2023] [Indexed: 02/21/2024] Open
Abstract
Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.
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Affiliation(s)
- Zélia Bontemps
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Yvan Moënne-Loccoz
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Mylène Hugoni
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
- UMR 5240 Microbiologie Adaptation et Pathogénie, INSA Lyon, CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
- Institut Universitaire de France (IUF), France
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Guo Z, Lu W, Minpeng S, Liyuan S, Zhenlin L, Wenjing C, Xiaoyong L, Bo Z, Jeong Ha K, Zhaoyang J. Seasonal dynamics response mechanism of benthic microbial community to artificial reef habitats. ENVIRONMENTAL RESEARCH 2024; 243:117867. [PMID: 38070848 DOI: 10.1016/j.envres.2023.117867] [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: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 02/06/2024]
Abstract
Artificial reefs (ARs) have been globally deployed to enhance and restore coastal resource and ecosystems. Microorganisms play an essential role in marine ecosystems, while the knowledge regarding the impact of ARs on microecology is still limited, particularly data concerning the response of benthic microbial community to AR habitats. In this study, the seasonal dynamics of benthic microbial community in AR and adjacent non-artificial reef (NAR) areas surrounding Xiaoshi Island were investigated with high-throughput sequencing technology. The results revealed that the diversity and structure of microbial community between AR and NAR both displayed pronounced seasonal dynamics. There was a greater influence of season factors on microbial communities than that of habitat type. The microbial communities in AR and NAR habitats were characterized by a limited number of abundant taxa (ranging from 5 to 12 ASVs) with high relative abundance (8.35-25.53%) and numerous rare taxa (from 5994 to 12412 ASVs) with low relative abundance (11.91%-24.91%). Proteobacteria, Bacteroidota and Desulfobacterota were the common predominant phyla, with the relative abundances ranging from 50.94% to 76.76%. A total of 52 biomarkers were discovered, with 15, 4, 6, and 27 biomarkers identified in spring, summer, autumn and winter, respectively. Co-occurrence network analysis indicated that AR displayed a more complex interaction pattern and higher susceptibility to external disturbances. Furthermore, the neutral model and βNTI analyses revealed that the assembly of microbial communities in both AR and NAR is significantly influenced by stochastic processes. This study could provide valuable insights into the impact of ARs construction on the benthic ecosystems and would greatly facilitate the development and implementation of the future AR projects.
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Affiliation(s)
- Zhansheng Guo
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Wang Lu
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Song Minpeng
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Sun Liyuan
- Shandong Fisheries Development and Resources Conservation Center, Yantai, 264003, China
| | - Liang Zhenlin
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Chen Wenjing
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Liu Xiaoyong
- Shandong Haizhibao Ocean Science and Technology Co., Ltd, Weihai, 264300, China
| | - Zhang Bo
- Shandong Haizhibao Ocean Science and Technology Co., Ltd, Weihai, 264300, China
| | - Kim Jeong Ha
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Jiang Zhaoyang
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China.
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Jiang R, Wang D, Jia S, Li Q, Liu S, Zhang XX. Dynamics of bacterioplankton communities in the estuary areas of the Taihu Lake: Distinct ecological mechanisms of abundant and rare communities. ENVIRONMENTAL RESEARCH 2024; 242:117782. [PMID: 38036201 DOI: 10.1016/j.envres.2023.117782] [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: 10/07/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
As the crucial confluences of rivers and lakes, the estuary areas with varied hydrodynamic exchanges intensively affect the bacterioplankton communities, whereas the ecological characteristics of the bacterioplankton in the areas have not been well understood. Here, the distribution patterns and assembly mechanisms of bacterioplankton communities in the estuary areas of the Taihu Lake were investigated using high-throughput sequencing and multivariate statistical analyses. Our results showed obvious seasonal variations in bacterioplankton diversity and community composition, which had significant correlations with water temperature. Neutral and null models together revealed that stochastic processes (especially dispersal limitation) were the major processes in shaping the communities across different seasons. By contrast, heterogeneous selection in deterministic processes exhibited increased impacts on community assembly during summer and autumn, which was significantly related to the comprehensive water quality index (WQI) rather than any single factor. In this study, rare communities displayed more pronounced seasonal dynamics compared to abundant communities, likely due to their sensitivity towards environmental factors. Accordingly, the heterogeneous selection of deterministic processes largely shaped the rare communities. These results enriched our understanding of the assembly mechanisms of bacterioplankton communities in estuary areas and emphasized the specific co-occurrence patterns of abundant and rare communities.
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Affiliation(s)
- Ruiming Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China.
| | - Shuyu Jia
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qisheng Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China; China Three Gorges Construction Engineering Corporation, Beijing, 100048, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of Environment, Nanjing University, Nanjing, 210023, China.
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10
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Niu S, Xie J, Wang G, Li Z, Zhang K, Li H, Xia Y, Tian J, Yu E, Xie W, Gong W. Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167913. [PMID: 37858824 DOI: 10.1016/j.scitotenv.2023.167913] [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: 08/22/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.
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Affiliation(s)
- Shuhui Niu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Kai Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Hongyan Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Yun Xia
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Jingjing Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Ermeng Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wenping Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, Guangdong 510380, China; Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, Hainan 572000, China.
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11
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Zhang Y, Qu Z, Zhang K, Li J, Lin X. Different Microeukaryotic Trophic Groups Show Different Latitudinal Spatial Scale Dependences in Assembly Processes across the Continental Shelves of China. Microorganisms 2024; 12:124. [PMID: 38257952 PMCID: PMC10821338 DOI: 10.3390/microorganisms12010124] [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: 11/29/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The relative role of stochasticity versus determinism is critically dependent on the spatial scale over which communities are studied. However, only a few studies have attempted to reveal how spatial scales influence the balance of different assembly processes. In this study, we investigated the latitudinal spatial scale dependences in assembly processes of microeukaryotic communities in surface water and sediment along the continental shelves of China. It was hypothesized that different microeukaryotic trophic groups (i.e., autotroph, heterotroph, mixotroph, and parasite) showed different latitudinal scale dependences in their assembly processes. Our results disclosed that the relative importance of different assembly processes depended on a latitudinal space scale for planktonic microeukaryotes. In surface water, as latitudinal difference increased, the relative contributions of homogenous selection and homogenizing dispersal decreased for the entire community, while those of heterogeneous selection and drift increased. The planktonic autotrophic and heterotrophic groups shifted from stochasticity-dominated processes to heterogeneous selection as latitudinal differences surpassed thresholds of 8° and 16°, respectively. For mixotrophic and parasitic groups, however, the assembly processes were always dominated by drift across different spatial scales. The balance of different assembly processes for the autotrophic group was mainly driven by temperature, whereas that of the heterotrophic group was driven by salinity and geographical distance. In sediment, neither the entire microeukaryotic community nor the four trophic groups showed remarkable spatial scale dependences in assembly processes; they were always overwhelmingly dominated by the drift. This work provides a deeper understanding of the distribution mechanisms of microeukaryotes along the continental shelves of China from the perspective of trophic groups.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (Y.Z.); (Z.Q.); (K.Z.); (J.L.)
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Zhishuai Qu
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (Y.Z.); (Z.Q.); (K.Z.); (J.L.)
| | - Kexin Zhang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (Y.Z.); (Z.Q.); (K.Z.); (J.L.)
| | - Jiqiu Li
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (Y.Z.); (Z.Q.); (K.Z.); (J.L.)
| | - Xiaofeng Lin
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (Y.Z.); (Z.Q.); (K.Z.); (J.L.)
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12
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Liu L, Wang H, Luo Z, Chen J. Biogeographic patterns of micro-eukaryotic generalists and specialists and their effects on regional α-diversity at inter-oceanic scale. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106261. [PMID: 37981448 DOI: 10.1016/j.marenvres.2023.106261] [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: 11/24/2022] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Inter-oceanic scale studies allow us to understand the global spread of micro-organisms in marine ecosystems. In this study, micro-eukaryotic communities in marine surface sediment were collected from tropical to Arctic sites. We found that micro-eukaryotic generalists had much higher intraspecific variation than specialists which allow them to distribute more widely through higher spatiotemporal asynchrony and complementary niche preferences among conspecific taxa. Moreover, comparing to the host-associated protozoa and small metazoa, the algae and free-living protozoa with higher intraspecific variation allow them to have wider distribution ranges. Species abundance also played an important role in driving the distribution ranges of generalists and specialists. The generalists had important effects on regional α-diversity even at an inter-oceanic scale which led to the micro-eukaryotic species richness in polar sites to be mainly influenced by the regional generalists but not the local specialists. In particular, more than 97% of algal species in polar sites were shared with the tropical and subtropical sites (including toxic dinoflagellate). Overall, our study suggests that the effects of global change and human activities on the vulnerable high latitude habitats may lead to biotic homogenization for the whole microbial community (not only the dispersal of some harmful algae) through the potential long-distance spread of generalists.
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Affiliation(s)
- Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
| | - Hongwei Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
| | - Zhaohe Luo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen 361005, China.
| | - Jianfeng Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
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13
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Liu L, Zhong KX, Chen Q, Wang Y, Zhang T, Jiao N, Zheng Q. Selective cell lysis pressure on rare and abundant prokaryotic taxa across a shelf-to-slope continuum in the Northern South China Sea. Appl Environ Microbiol 2023; 89:e0139323. [PMID: 38014961 PMCID: PMC10734510 DOI: 10.1128/aem.01393-23] [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: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
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Affiliation(s)
- Lu Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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14
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Li H, Hong Y, Gao M, An X, Yang X, Zhu Y, Chen J, Su J. Distinct responses of airborne abundant and rare microbial communities to atmospheric changes associated with Chinese New Year. IMETA 2023; 2:e140. [PMID: 38868217 PMCID: PMC10989829 DOI: 10.1002/imt2.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 06/14/2024]
Abstract
Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time-resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour-scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%-74.2% variations of abundant community but only 13.3%-21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the "holiday effect" of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - You‐Wei Hong
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Regional Atmospheric Environment, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Meng‐Ke Gao
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- College of Resource and Environmental ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xin‐Li An
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiao‐Ru Yang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong‐Guan Zhu
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
- State Key Lab of Urban and Regional Ecology, Research Center for Eco‐environmental SciencesChinese Academy of SciencesBeijingChina
| | - Jin‐Sheng Chen
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Regional Atmospheric Environment, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Jian‐Qiang Su
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
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Chen W, Zhou H, Wu Y, Wang J, Zhao Z, Li Y, Qiao L, Chen K, Liu G, Ritsema C, Geissen V, Sha X. Effects of deterministic assembly of communities caused by global warming on coexistence patterns and ecosystem functions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118912. [PMID: 37678020 DOI: 10.1016/j.jenvman.2023.118912] [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: 05/17/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023]
Abstract
Seasonal rhythms in biological and ecological dynamics are fundamental in regulating the structuring of microbial communities. Evaluating the seasonal rhythms of microorganisms in response to climate change could provide information on their variability and stability over longer timescales (>20-year). However, information on temporal variability in microorganism responses to medium- and long-term global warming is limited. In this study, we aimed to elucidate the temporal dynamics of microbial communities in response to global warming; to this end, we integrated data on the maintenance of species diversity, community composition, temporal turnover rates (v), and community assembly process in two typical ecosystems (meadows and shrub habitat) on the Qinghai-Tibet Plateau. Our results showed that 21 years of global warming would increase the importance of the deterministic process for microorganisms in both ecosystems across all seasons (R2 of grassland (GL) control: 0.524, R2 of GL warming: 0.467; R2 of shrubland (SL) control: 0.556, R2 of SL warming: 0.543), reducing species diversity and altering community composition. Due to environmental filtration pressure from 21 years of warming, the low turnover rate (v of warming: -3.13/-2.00, v of control: -2.44/-1.48) of soil microorganisms reduces the resistance and resilience of ecological communities, which could lead to higher community similarity and more clustered taxonomic assemblages occurring across years. Changes to temperature might increase selection pressure on specialist taxa, which directly causes dominant species (v of warming: -1.63, v of control: -2.49) primarily comprising these taxa to be more strongly impacted by changing temperature than conditionally (v of warming: -1.47, v of control: -1.75) or always rare taxa (v of warming: -0.57, v of control: -1.33). Evaluation of the seasonal rhythms of microorganisms in response to global warming revealed that the variability and stability of different microbial communities in different habitats had dissimilar biological and ecological performances when challenged with an external disturbance. The balance of competition and cooperation, because of environmental selection, also influenced ecosystem function in complex terrestrial ecosystems. Overall, our study enriches the limited information on the temporal variability in microorganism responses to 21 years of global warming, and provides a scientific basis for evaluating the impact of climate warming on the temporal stability of soil ecosystems.
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Affiliation(s)
- Wenjing Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China; Moutai Institute, Renhuai, 564500, PR China
| | - Huakun Zhou
- Qinghai Provincial Key Laboratory of Restoration Ecology in Cold Regions, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810000, PR China
| | - Yang Wu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Jie Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Ziwen Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Yuanze Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Leilei Qiao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, PR China; University of Chinese Academy of Sciences, Beijing, China
| | - Kelu Chen
- Qinghai Provincial Key Laboratory of Restoration Ecology in Cold Regions, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, PR China; Moutai Institute, Renhuai, 564500, PR China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, PR China
| | - Coen Ritsema
- Wageningen University & Research, Soil Physics and Land Management, POB 47, NL-6700, AA Wageningen, Netherlands
| | - Violette Geissen
- Wageningen University & Research, Soil Physics and Land Management, POB 47, NL-6700, AA Wageningen, Netherlands
| | - Xue Sha
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810000, PR China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, PR China.
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16
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Zhao X, Xie E. Reclaimed water influences bacterioplankton and bacteriobenthos communities differently in river networks. WATER RESEARCH 2023; 243:120389. [PMID: 37494747 DOI: 10.1016/j.watres.2023.120389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Reclaimed water reuse is a promising strategy for addressing water scarcity; however, its potential ecological impact remains largely unknown. In particular, the differential effects of reclaimed water on microbial communities in various habitats remain poorly understood. Here, we aimed to elucidate the distinct effects of reclaimed water on bacterioplankton and bacteriobenthos communities in reclaimed water-receiving river networks from multiple perspectives, including community structure, co-occurrence patterns, assembly mechanisms, and nitrogen cycle function. Significant differences in microbial composition were observed between the plankton and benthic habitats, and the average numbers of amplicon sequence variants (ASVs) that originated from the wastewater treatment plants (WWTP) sites were 310.0 and 613.3, respectively, indicating a stronger association between WWTP and benthic habitats. Random forest and network co-occurrence analyses identified the genus Clostridium_sensu_stricto as a biomarker and key module hub. The assembly of bacteriobenthos communities was driven primarily by deterministic processes (58.74% for River-S and 58.94% for WWTP-S), whereas for bacterioplankton communities, this proportion was reduced to 18.02% (River-W) and 19.09% (WWTP-W). The qPCR revealed a large difference in abundance between the N cycling related genes of bacteriobenthos (average 2.47 × 106 copies/ng) and bacterioplankton (average 3.11 × 103 copies/ng) communities, and different interaction patterns with functional genes. Variance partitioning analysis (VPA) indicated that nitrogen was the most important pollutant, affecting the structure and ecological functions of microbial communities. Moreover, pathway analysis suggested that the reuse of reclaimed water may have enhanced the N-cycling functions of microbial communities and the emission of nitrous oxide.
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Affiliation(s)
- Xiaohui Zhao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, PR China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, PR China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, 17 Qinghua Donglu, Beijing 100083, PR China; Engineering Research Center of Agricultural Water-Saving and Water Resources, Ministry of Education, China Agricultural University, Beijing 100083, PR China.
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17
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An L, Yan YC, Tian HL, Chi CQ, Nie Y, Wu XL. Roles of sulfate-reducing bacteria in sustaining the diversity and stability of marine bacterial community. Front Microbiol 2023; 14:1218828. [PMID: 37637129 PMCID: PMC10448053 DOI: 10.3389/fmicb.2023.1218828] [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: 05/08/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Microbes play central roles in ocean food webs and global biogeochemical processes. Yet, the information available regarding the highly diverse bacterial communities in these systems is not comprehensive. Here we investigated the diversity, assembly process, and species coexistence frequency of bacterial communities in seawater and sediment across ∼600 km of the eastern Chinese marginal seas using 16S rRNA gene amplicon sequencing. Our analyses showed that compared with seawater, bacterial communities in sediment possessed higher diversity and experienced tight phylogenetic distribution. Neutral model analysis showed that the relative contribution of stochastic processes to the assembly process of bacterial communities in sediment was lower than that in seawater. Functional prediction results showed that sulfate-reducing bacteria (SRB) were enriched in the core bacterial sub-communities. The bacterial diversities of both sediment and seawater were positively associated with the relative abundance of SRB. Co-occurrence analysis showed that bacteria in seawater exhibited a more complex interaction network and closer co-occurrence relationships than those in sediment. The SRB of seawater were centrally located in the network and played an essential role in sustaining the complex network. In addition, further analysis indicated that the SRB of seawater helped maintain the high stability of the bacterial network. Overall, this study provided further comprehensive information regarding the characteristics of bacterial communities in the ocean, and provides new insights into keystone taxa and their roles in sustaining microbial diversity and stability in ocean.
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Affiliation(s)
- Liyun An
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Ying-Chun Yan
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Hai-Long Tian
- College of Agriculture, Henan University, Kaifeng, China
| | - Chang-Qiao Chi
- College of Engineering, Peking University, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, China
- Institute of Ocean Research, Peking University, Beijing, China
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18
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Hu W, Zheng N, Zhang Y, Bartlam M, Wang Y. Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions. Front Microbiol 2023; 14:1219655. [PMID: 37601370 PMCID: PMC10433394 DOI: 10.3389/fmicb.2023.1219655] [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: 05/09/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Studies of high nucleic acid-content (HNA) and low nucleic acid-content (LNA) bacterial communities are updating our view of their distributions and taxonomic composition. However, there are still large gaps in our knowledge of the composition, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities. Here, using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities in the samples collected in summer and winter in Chinese coastal seas. The communities of HNA and LNA bacteria had clear spatiotemporal patterns and LNA bacteria was phylogenetically less diverse than HNA bacteria in both seasons. The distribution of HNA and LNA bacteria were significantly affected by the environmental factors and a significant seasonal-consistent distance-decay patterns were found in HNA and LNA bacteria. Furthermore, a quantitative assessment of ecological processes revealed that dispersal limitation, homogeneous selection exerted important roles in the community assembly of HNA and LNA bacteria. More importantly, we observed seasonality in the co-occurrence relationships: closer inter-taxa connections of HNA bacterial communities in winter than in summer and the opposite is true in the LNA bacterial communities. Some ecological functions, such as: phototrophy, photoautotrophy, oxygenic photoautotrophy, were different between HNA and LNA bacteria. These results provide a better understanding of spatiotemporal patterns, processes, and the ecological functions of HNA and LNA bacterial communities in Chinese coastal seawater.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Ningning Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yadi Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
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19
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Lin X, Zhang C, Xie W. Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea. Front Microbiol 2023; 14:1185436. [PMID: 37426005 PMCID: PMC10324572 DOI: 10.3389/fmicb.2023.1185436] [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: 03/13/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.
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Affiliation(s)
- Xizheng Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
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20
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Saraiva JP, Bartholomäus A, Toscan RB, Baldrian P, Nunes da Rocha U. Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes. Mol Ecol Resour 2023. [PMID: 36847735 DOI: 10.1111/1755-0998.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 01/23/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
| | | | - Rodolfo Brizola Toscan
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, Leipzig, Germany
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21
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Chen W, Sang S, Shao L, Li Y, Li T, Gan L, Liu L, Wang D, Zhou L. Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China. Microbiol Spectr 2023; 11:e0368322. [PMID: 36507672 PMCID: PMC9927264 DOI: 10.1128/spectrum.03683-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.
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Affiliation(s)
- Wenjian Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shilei Sang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, MEE, Guangzhou, China
| | - Liyi Shao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yusen Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Tongzhou Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Lihong Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Dapeng Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Lei Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
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22
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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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Zhang Z, Han P, Zheng Y, Jiao S, Dong H, Liang X, Gao D, Niu Y, Yin G, Liu M, Hou L. Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone. MICROBIAL ECOLOGY 2023; 85:383-399. [PMID: 35298685 DOI: 10.1007/s00248-022-01996-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.
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Affiliation(s)
- Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Shuo Jiao
- 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, 712100, Shaanxi, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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24
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Guo Y, Zhang A, Qin C, Yu G, Ma H. Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159675. [PMID: 36280051 DOI: 10.1016/j.scitotenv.2022.159675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.
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Affiliation(s)
- Yu Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China; Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
| | - Ankai Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chuanxin Qin
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China; Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China.
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongmei Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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25
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Hardoim CCP, Hardoim PR, Lôbo-Hajdu G, Custódio MR, Thomas T. The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact. FEMS Microbiol Lett 2023; 370:fnad064. [PMID: 37401172 DOI: 10.1093/femsle/fnad064] [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: 03/17/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by a different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara; however, assembly processes are largely determined by the sponge host.
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Affiliation(s)
- Cristiane C P Hardoim
- São Paulo State University, Praça Infante Dom Henrique s/nº, Parque Bitaru, São Vicente, São Paulo, CEP 11.330-900, Brazil
- Graduate Program in Evolution and Diversity of the Federal University of ABC, Av. dos Estados, 5001, Bairro Bangu, Santo André, São Paulo, CEP 09210-580, Brazil
| | - Pablo R Hardoim
- São Paulo State University, Praça Infante Dom Henrique s/nº, Parque Bitaru, São Vicente, São Paulo, CEP 11.330-900, Brazil
| | - Gisele Lôbo-Hajdu
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
| | - Márcio R Custódio
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
- Department of Physiology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14 , 101, São Paulo, CEP 05508-090, Brazil
| | - Torsten Thomas
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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26
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Ji F, Sun Y, Yang Q. Early warning of red tides using bacterial and eukaryotic communities in nearshore waters. ENVIRONMENTAL RESEARCH 2023; 216:114711. [PMID: 36334824 DOI: 10.1016/j.envres.2022.114711] [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: 09/15/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH4-N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH4-N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO3-N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO4-P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.
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Affiliation(s)
- Fengyun Ji
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China; Panjin Institute of Industrial Technology, Dalian University of Technology, Panjin 124221, Liaoning, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China.
| | - Qing Yang
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China.
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27
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Li T, Liu G, Yuan H, Chen J, Lin X, Li H, Yu L, Wang C, Li L, Zhuang Y, Senjie L. Eukaryotic plankton community assembly and influencing factors between continental shelf and slope sites in the northern South China Sea. ENVIRONMENTAL RESEARCH 2023; 216:114584. [PMID: 36270532 DOI: 10.1016/j.envres.2022.114584] [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: 06/27/2022] [Revised: 09/11/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Eukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in marine food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern SCS over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in the abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity appeared to be the most important deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22-3 μm) community (24%) than larger-sized (3-200 μm) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study sheds light on the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, 266555, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, 266555, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Lin Senjie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
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Gong X, Chen Z, Deng Y, Zhao D, Gao P, Zhang L, Tu Q, Qu L, Zheng L, Zhang Y, Song C, Liu J. Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158411. [PMID: 36055486 DOI: 10.1016/j.scitotenv.2022.158411] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China; Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373, USA.
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ping Gao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266237, China
| | - Liang Zhang
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lingyun Qu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266237, China
| | - Liwen Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yong Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Chao Song
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China.
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29
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Fine-Scale Structuring of Planktonic Vibrio spp. in the Chinese Marginal Seas. Appl Environ Microbiol 2022; 88:e0126222. [PMID: 36346224 PMCID: PMC9746320 DOI: 10.1128/aem.01262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Vibrio is ubiquitous in marine environments with high metabolism flexibility and genome plasticity. Studies have investigated the ecological distribution of Vibrio spp. in several narrow zones, but a broad scale pattern of distribution and community assembly is still lacking. Here, we elucidated the distribution of Vibrio spp. in seawater along the Chinese marginal seas with a high spatial range. Comparison of Vibrio abundance between 3- and 0.2-μm-pore-size membranes showed distinction in preferential lifestyle. Vibrio spp. in the Yellow Sea (YS) was low in abundance and adopted a particle-associated lifestyle, whereas that in the East China Sea (ECS) and South China Sea (SCS) was more abundant and was likely in a temporary free-living state as a strategy to cope with nutrient limitation. Vibrio community compositions were also separated by sampling area, with different dominant groups in YS (Vibrio chagasii and Vibrio harveyi), ECS and SCS (Vibrio japonicus and V. chagasii). The community niche breadth was significantly wider in ECS and SCS than that of YS. Among species, V. chagasii and V. harveyi had the largest niche breadths likely reflecting strong competitive positions. Stochastic processes played important roles in shaping the geographical pattern of the vibrionic community. Environmental selection (e.g., temperature, salinity, and dissolved oxygen) had a much greater impact on the community in surface than in bottom water. The large proportions of unexplained variations (78.9%) imply complex mechanisms in their community assembly. Our study provides insights into the spatial distribution patterns and underlying assembly mechanisms of Vibrio at a broad spatial scale. IMPORTANCE Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale. Our results showed that the abundances of the Vibrio population increased with decreasing latitude and their preferential lifestyle differed among adjacent coastal areas. The compositions of Vibrio spp. were also separated by geographical location, which was mainly attributable to stochastic processes. Overall, this work contributes to the understanding of the ecological distribution patterns and the community assembly mechanisms of marine vibrios at a high spatial range. The large proportion of unexplained variations indicates the existence of complex mechanisms in the assembly of vibrionic community which should be considered comprehensively in future.
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Xiao Z, Li H, Li XC, Li RH, Huo SL, Yu GL. Geographic pattern of phytoplankton community and their drivers in lakes of middle and lower reaches of Yangtze River floodplain, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83993-84005. [PMID: 35778664 DOI: 10.1007/s11356-022-21657-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the relative contributions of deterministic and stochastic processes was critical to compressive understanding of underlying mechanism governing geographic pattern and assembly of phytoplankton community, while it was seldom performed in connected lakes under human pressure. Here, we investigated phytoplankton community pattern in relation to environmental and spatial factors over 81 lakes located in the middle and lower reaches of Yangtze River (MLYR) floodplain, where many lakes suffered from eutrophication and cyanobacterial blooms. A majority of MLYR lakes had higher phytoplankton abundance surpassing 107 cells/L and were dominated by common bloom-forming cyanobacterial genera, including Pseudanabaena, Microcystis, Merismopedia, Dolichospermum, Limnothrix, and Raphidiopsis. Phytoplankton community exhibited a striking geographical pattern both for taxonomic and functional compositions, while functional groups were less sensitive, and dissimilarity in communities displayed no significant increases with increasing geographical distance. Further, species richness explained much higher percentage of community variations than species turnover, indicating a reduced effect of environmental filtering of phytoplankton species with tolerance to similar environments in connected MLYR lakes. Both deterministic and stochastic processes governed assembly and biogeographic of phytoplankton community. Variation partition analysis showed that spatial factors exhibited greater influence on phytoplankton community compared to environmental variables. The stronger influence of spatial factors was further demonstrated by Mantel test and neutral community model. These findings indicate that deterministic and stochastic processes exhibited similar biogeographic patterns for phytoplankton community in MLYR lakes, but stochastic process was overwhelmingly dominated. Moreover, a large proportion of unexplained variation implies that complex interactions exist to shape assembly mechanism of phytoplankton community in MLYR lakes.
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Affiliation(s)
- Zhe Xiao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Xiao-Chuang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Ren-Hui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang, China
| | - Shou-Liang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Gong-Liang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
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31
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Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust's microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
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Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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32
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Gill JG, Hill-Spanik KM, Whittaker KA, Jones ML, Plante C. Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 2022; 10:e12835. [PMID: 35251777 PMCID: PMC8893026 DOI: 10.7717/peerj.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
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Affiliation(s)
- John Geoffrey Gill
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | | | - Kerry A. Whittaker
- Sea Education Association, Woods Hole, MA, United States,Maine Maritime Academy, Castine, Maine, United States
| | - Martin L. Jones
- Department of Mathematics, College of Charleston, Charleston, SC, United States
| | - Craig Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
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Xu Q, Ling N, Quaiser A, Guo J, Ruan J, Guo S, Shen Q, Vandenkoornhuyse P. Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes. MICROBIAL ECOLOGY 2022; 83:137-150. [PMID: 33792742 DOI: 10.1007/s00248-021-01741-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France.
| | - Achim Quaiser
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianyun Ruan
- Key Laboratory of Tea Plant Biology and Resources Utilization (Ministry of Agriculture), Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang, 310008, Hangzhou, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
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Prodinger F, Endo H, Takano Y, Li Y, Tominaga K, Isozaki T, Blanc-Mathieu R, Gotoh Y, Hayashi T, Taniguchi E, Nagasaki K, Yoshida T, Ogata H. Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales, and prokaryotes in a coastal ecosystem. FEMS Microbiol Ecol 2021; 97:6486443. [PMID: 34962982 DOI: 10.1093/femsec/fiab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 12/25/2021] [Indexed: 11/13/2022] Open
Abstract
Coastal microbial communities are affected by seasonal environmental change, biotic interactions, and fluctuating nutrient availability. We investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses that infect eukaryotes (order Imitervirales; phylum Nucleocytoviricota), and prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and viral polB genes as markers in 43 seawater samples collected over 20 months. Eukaryotes, prokaryotes, and Imitervirales communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles. However, the community dynamics showed intriguing differences in several aspects, such as the recovery rate after a year. We also showed that the differences in community dynamics were at least partially explained by differences in recurrence/persistence levels of individual ASVs among eukaryotes, prokaryotes, and Imitervirales. Prokaryotic ASVs were the most persistent, followed by eukaryotic ASVs and Imitervirales ASVs, which were the least persistent. We argue that the differences in the specificity of interactions (virus-eukaryote vs. prokaryote-eukaryote) as well as the niche breadth of community members were at the origin of the distinct community dynamics among eukaryotes, their viruses, and prokaryotes.
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Affiliation(s)
- Florian Prodinger
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Yoshihito Takano
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Yanze Li
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Tatsuhiro Isozaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Romain Blanc-Mathieu
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan.,Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | | | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
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Chen L, Wang M, Li Y, Shang W, Tang J, Zhang Z, Liu F. Effects of Magnetic Minerals Exposure and Microbial Responses in Surface Sediment across the Bohai Sea. Microorganisms 2021; 10:microorganisms10010006. [PMID: 35056455 PMCID: PMC8778929 DOI: 10.3390/microorganisms10010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Extensive production and application of magnetic minerals introduces significant amounts of magnetic wastes into the environment. Exposure to magnetic minerals could affect microbial community composition and geographic distribution. Here, we report that magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across the Bohai Sea by high-throughput sequencing analysis of the 16S rRNA gene. The results showed that environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure to a magnetite center may shape the geographical distribution of five dissimilatory iron reducing bacteria. The microbial iron reduction ability and electroactive activity in sediment close to a magnetite center are stronger than those far away. Our study provides a novel understanding for the response of DIRB and electroactive bacteria to magnetic minerals exposure.
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Affiliation(s)
- Lei Chen
- School of Life Science, Qufu Normal University, Qufu 273165, China;
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Mingpeng Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China;
- Correspondence: (M.W.); (F.L.)
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Weitao Shang
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Jianhui Tang
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA;
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Correspondence: (M.W.); (F.L.)
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36
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Hussain S, Liu H, Liu S, Yin Y, Yuan Z, Zhao Y, Cao H. Distribution and Assembly Processes of Soil Fungal Communities along an Altitudinal Gradient in Tibetan Plateau. J Fungi (Basel) 2021; 7:jof7121082. [PMID: 34947064 PMCID: PMC8706254 DOI: 10.3390/jof7121082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
In soil ecosystems, fungi exhibit diverse biodiversity and play an essential role in soil biogeochemical cycling. Fungal diversity and assembly processes across soil strata along altitudinal gradients are still unclear. In this study, we investigated the structure and abundance of soil fungal communities among soil strata and elevational gradients on the Tibetan Plateau using Illumina MiSeq sequencing of internal transcribed spacer1 (ITS1). The contribution of neutral and niche ecological processes were quantified using a neutral community model and a null model-based methodology. Our results showed that fungal gene abundance increased along altitudinal gradients, while decreasing across soil strata. Along with altitudinal gradients, fungal α-diversity (richness) decreased from surface to deeper soil layers, while β-diversity showed weak correlations with elevations. The neutral community model showed an excellent fit for neutral processes and the lowest migration rate (R2 = 0.75). The null model showed that stochastic processes dominate in all samples (95.55%), dispersal limitations were dominated at the surface layer and decreased significantly with soil strata, while undominated processes (ecological drift) show a contrary trend. The log-normal model and the null model (βNTI) correlation analysis also neglect the role of niche-based processes. We conclude that stochastic dispersal limitations, together with ecological drifts, drive fungal communities.
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Affiliation(s)
- Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Zhongyuan Yuan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
- Correspondence:
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Liu W, McManus GB, Lin X, Huang H, Zhang W, Tan Y. Distribution Patterns of Ciliate Diversity in the South China Sea. Front Microbiol 2021; 12:689688. [PMID: 34539599 PMCID: PMC8446678 DOI: 10.3389/fmicb.2021.689688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022] Open
Abstract
Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. The ciliate communities in intertidal, neritic and oceanic water areas were compared in terms of taxonomy, motility and feeding habit composition, respectively. Significant community variation was revealed among the three areas, but the difference between the intertidal area and the other two areas was more significant than that between neritic and oceanic areas. The distributions of ciliates within each of the three areas were also analyzed. In the intertidal water, the community was not significantly different among sites but did differ among habitat types. In neritic and oceanic areas, the spatial variation of communities among different sites was clearly observed. Comparison of communities by taxonomic and ecological traits (motility and feeding habit) indicated that these traits similarly revealed the geographical pattern of ciliates on a large scale in the SCS, but to distinguish the community variation on a local scale, taxonomic traits has higher resolution than ecological traits. In addition, we assessed the relative influences of environmental and spatial factors on assembly of ciliate communities in the SCS and found that environmental selection is the major process structuring the taxonomic composition in intertidal water, while spatial processes played significant roles in influencing the taxonomic composition in neritic and oceanic water. Among ecological traits, environmental selection had the most important impact on distributions.
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Affiliation(s)
- Weiwei Liu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - George B. McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Xiaofeng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Honghui Huang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, P. R. China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wenjing Zhang
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Zhang S, Zhang L, Chen P, Rong H, Li S. Deciphering the microbial patterns of anammox process under hexavalent chromium stress: Abundant and rare subcommunity respond differently. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125850. [PMID: 34492801 DOI: 10.1016/j.jhazmat.2021.125850] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
This study aims to unravel the microbial responses to Cr(VI) stress in anaerobic ammonium oxidation (anammox) reactor. The result showed that anammox process could tolerate 2 mg/L Cr(VI) after acclimation, while 5 mg/L Cr(VI) stress resulted in significant inhibition on anammox bacterial activity. Ca. Jettenia was the predominant anammox genus, whose abundance showed a decreasing tendency with increasing Cr(VI) dosage. Cr(VI) addition resulted in significant and irreversible changes in microbial community structure, and increased the relative influence of stochastic processes on community assembly. Furthermore, rare subcommunity contributed greatly to biodiversity of whole community (90.35%), while abundant subcommunity were more similar to the whole community. Importantly, Cr(VI) exposure caused greater variations in rare subcommunity compared with abundant one, indicating that rare taxa were more sensitive to Cr(VI) stress. This was further confirmed by ABT model, which showed higher relative influence of Cr(VI) on rare subcommunity. In addition, results suggested that rare taxa play essential roles in whole community stability, because of their great contribution to species richness and community variations, and keystone roles in ecosystem network. Moreover, network analysis showed that conditionally rare taxa frequently and positively interacted with abundant taxa, which may contribute to the community resilience to Cr(VI) stress.
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Affiliation(s)
- Shaoqing Zhang
- School of Civil Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Liqiu Zhang
- School of Civil Engineering, Guangzhou University, Guangzhou 510006, PR China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, PR China
| | - Peng Chen
- School of Civil Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Hongwei Rong
- School of Civil Engineering, Guangzhou University, Guangzhou 510006, PR China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, PR China.
| | - Shugeng Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, PR China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, PR China.
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Li L, Pujari L, Wu C, Huang D, Wei Y, Guo C, Zhang G, Xu W, Liu H, Wang X, Wang M, Sun J. Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean. Front Microbiol 2021; 12:616956. [PMID: 34456881 PMCID: PMC8385211 DOI: 10.3389/fmicb.2021.616956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.
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Affiliation(s)
- Liuyang Li
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Laxman Pujari
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Danyue Huang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqiu Wei
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Congcong Guo
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2021; 23:4778-4796. [PMID: 34258839 DOI: 10.1111/1462-2920.15668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/12/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.
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Affiliation(s)
- Changyu Zhu
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.,Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weiwei Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, and Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Yusen Xu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Oceanography, College of Science, Port Said University, Port Said, 42511, Egypt
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhenzhen Yi
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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Lei J, Liu C, Zhang M, Yang J, Wu F, Ren M, Wu Q, Shi X. The daily effect is more important than the diurnal effect when shaping photosynthetic picoeukaryotes (PPEs) communities in Lake Taihu at a small temporal scale. FEMS Microbiol Ecol 2021; 97:6308367. [PMID: 34160594 DOI: 10.1093/femsec/fiab090] [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: 01/24/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
As major primary producers in aquatic systems, the diversity and community composition dynamics of photosynthetic picoeukaryotes (PPEs) have been investigated in recent years. Here, we explored the 3-day diurnal succession of the PPE community in a highly eutrophic lake in early spring using a combination of flow cytometric sorting and high-throughput sequencing. Our results showed that the PPEs were the dominant group of autotrophic picophytoplankton, although they had relatively low diversity and were dominated by the Stephanodiscaceae family in early spring in Lake Taihu. Furthermore, PPE abundance was significantly higher at night than during the day, probably due to their high specific rate of carbon uptake during the day and rapid proliferation at night. Several environmental variables had a significant influence on the PPE community composition, and the daily effect was more important than the diurnal effect when shaping the PPE community in Lake Taihu at a temporal scale of 3 days. Furthermore, based on the variation partitioning analysis (VPA), the relative importance of abiotic factors (deterministic processes) to short-term succession was low, explaining only 20.44% of the PPE community variation. We therefore conclude that stochastic processes determined PPE community assembly over a short temporal scale based on a neutral community model (NCM).
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Affiliation(s)
- Jin Lei
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China
| | - Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China
| | - Jinsheng Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Beijing East Road 73, Nanjing 210008, China
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Zou K, Wang R, Xu S, Li Z, Liu L, Li M, Zhou L. Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence. WATER RESEARCH 2021; 200:117294. [PMID: 34102388 DOI: 10.1016/j.watres.2021.117294] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Ruili Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shannan Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China
| | - Zhuoying Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China.
| | - Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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Hardoim CCP, Lôbo-Hajdu G, Custódio MR, Hardoim PR. Prokaryotic, Fungal, and Unicellular Eukaryotic Core Communities Across Three Sympatric Marine Sponges From the Southwestern Atlantic Coast Are Dominated Largely by Deterministic Assemblage Processes. Front Microbiol 2021; 12:674004. [PMID: 34168631 PMCID: PMC8217869 DOI: 10.3389/fmicb.2021.674004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to harbor a diverse and complex microbiota; however, a vast majority of surveys have been investigating the prokaryotic communities in the north hemisphere and Australia. In addition, the mechanisms of microbial community assembly are poorly understood in this pivotal player of the ecosystem. Thus, this survey addressed the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and investigated the contribution of neutral and niche processes of prokaryotic, fungal, and unicellular eukaryotic assemblage in three sympatric species Aplysina caissara, Aplysina fulva, and Tedania ignis along with environmental samples. The compositions of the holobiome associated with the sponges and detected in environmental samples were strikingly different. Remarkably, between 47 and 88% of the assigned operational taxonomic units (OTUs) were specifically associated with sponge species. Moreover, around 77, 69, and 53% of the unclassified OTUs from prokaryotic, fungal, and unicellular eukaryotic communities, respectively, showed less than 97% similarity with well-known databases, suggesting that sponges from the southwestern Atlantic coast are an important source of microbial novelty. These values are even higher, around 80 and 61% of the unclassified OTUs, when excluding low abundance samples from fungal and unicellular eukaryotic datasets, respectively. Host species were the major driver shaping the sponge-associated microbial community. Deterministic processes were primarily responsible for the assembly of microbial communities in all sponge species, while neutral processes of prokaryotic and fungal community assembly were also detected in the sympatric A. caissara and T. ignis replicates, respectively. Most of the species-rich sponge-associated lineages from this region are also found in the Northern seas and many of them might play essential roles in the symbioses, such as biosynthesis of secondary metabolites that exhibit antimicrobial and antiviral activities, as well as provide protection against host predation. Overall, in this study the microbiota was assembled by interactions with the host sponge in a deterministic-based manner; closely related sponge species shared a strong phylogenetic signal in their associated prokaryotic and fungal community traits and Brazilian sponges were a reservoir of novel microbial species.
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Affiliation(s)
| | - Gisele Lôbo-Hajdu
- Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Márcio R. Custódio
- Department of Physiology, Biosciences Institute and NP-Biomar, Center for Marine Biology, University of São Paulo, São Paulo, Brazil
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Li Y, Xu Z, Liu H. Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota. BMC Genomics 2021; 22:37. [PMID: 33413098 PMCID: PMC7791863 DOI: 10.1186/s12864-020-07333-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet. Results Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R2 = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R2 = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet. Conclusions Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07333-z.
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Affiliation(s)
- Yingdong Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, SAR, China
| | - Zhimeng Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, SAR, China.,SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, China.,Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, SAR, China. .,Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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Li M, Mi T, He H, Chen Y, Zhen Y, Yu Z. Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142252. [PMID: 33182220 DOI: 10.1016/j.scitotenv.2020.142252] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.
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Affiliation(s)
- Mingyue Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Hui He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Ye Chen
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
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Gu R, Sun P, Wang Y, Yu F, Jiao N, Xu D. Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China. Front Microbiol 2020; 11:592489. [PMID: 33424795 PMCID: PMC7785585 DOI: 10.3389/fmicb.2020.592489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/27/2020] [Indexed: 11/28/2022] Open
Abstract
Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.
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Affiliation(s)
- Rong Gu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Fengling Yu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient. mSystems 2020; 5:5/6/e01150-20. [PMID: 33361326 PMCID: PMC7762797 DOI: 10.1128/msystems.01150-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata. Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes. IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.
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Gad M, Hou L, Li J, Wu Y, Rashid A, Chen N, Hu A. Distinct mechanisms underlying the assembly of microeukaryotic generalists and specialists in an anthropogenically impacted river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141434. [PMID: 32814298 DOI: 10.1016/j.scitotenv.2020.141434] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Microeukaryotic communities are sensitive to environmental changes; and are considered essential for microbial food webs and biogeochemical cycles. Therefore, understanding the community responses of microeukaryotes to environmental changes is of great ecological significance. Very little is known about the assembly mechanisms underlying the microeukaryotic communities, especially for the key ecological groups (e.g., habitat generalists/specialists) in the riverine ecosystems. Here, we employed 18S rDNA amplicon sequencing to study the assembly processes governing the microeukaryotic communities and their habitat generalists and specialists across three hydrological seasons in a subtropical river in China. The results showed that deterministic and stochastic processes jointly shaped the microeukaryotic communities, where the relative importance of stochastic processes decreased in the following order: wet > normal > dry seasons. However, deterministic processes played more important role in shaping the microeukaryotic communities than those of prokaryotes. Meanwhile, stochastic and deterministic processes were responsible for structuring the microeukaryotic habitat generalists and specialists, respectively. Generally, the pure effects of physicochemical factors on the microeukaryotic communities and their key ecological groups were ~ 1.7 folds than those of the micropollutants. However, several micropollutants (e.g., acetaminophen, benzophenone-3, bisphenol A, sulfadiazine, triclocarban and triclosan) were found to have a strong effect on the habitat specialists. Altogether, we suggested that the ecological responses of the riverine microeukaryotes to micropollutants may vary among species due to the intrinsic differences in their environmental plasticity.
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Affiliation(s)
- Mahmoud Gad
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Liyuan Hou
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Jiangwei Li
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wu
- Department of Biology and Environmental Engineering, Hefei University, Hefei 230601, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Guo X, Wu L, Huang L. Spatiotemporal Patterns in Diversity and Assembly Process of Marine Protist Communities of the Changjiang (Yangtze River) Plume and Its Adjacent Waters. Front Microbiol 2020; 11:579290. [PMID: 33123109 PMCID: PMC7573215 DOI: 10.3389/fmicb.2020.579290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/16/2020] [Indexed: 12/02/2022] Open
Abstract
Marine protists are highly heterogeneous and play key roles in the structure and functioning of marine ecosystems. However, little is known on the underlying biogeographic processes and seasonal diversity patterns that shape their community assembly in a regional scale in marginal sea. In this study, we conducted high-throughput sequencing of 18S rRNA gene to survey the protist community compositions (PCCs) of the Changjiang (Yangtze River) plume, an intensely human-affected coastal area, to the adjacent continental shelf waters over three seasons. Furthermore, the different impacts of environmental and spatial factors on marine PCCs were examined. The results revealed significant dissimilarities of PCC’s diversity among seasons and habitats, with more obvious seasonal variations in the Changjiang plume. Procrustes analysis showed better consistency of the community-environment relationship in shelf area, further supported by stronger correlation coefficients computed in the Mantel tests. This might be explained by seasonal dynamics of Changjiang Diluted Waters (i.e., the mixing of the Changjiang runoff with inshore water of the East China Sea) that changed the environmental conditions of coastal area dramatically, resulting in lower importance of spatial factors (dispersal limitation) on PCCs compared with environmental filters, including physicochemical properties (e.g., water temperature, salinity, dissolved oxygen, and nutrients), as well as biotic factors (e.g., Chl a and food abundance). This was further explained by higher immigration rate and fitness to neutral model, which suggested a predominant role of neutral process in shaping the PCCs in coastal area. Different richness, diversity, and taxonomic compositions but comparable biogeographic patterns were observed among abundant and rare sub-communities. In general, the abundant sub-communities exhibited higher dispersal ability which tend to respond to environmental selection during dispersal, whereas the rare sub-communities appeared to be present only in few samples due to dispersal limitation. Co-occurrence network further indicated the importance of biotic interactions in community assembly and potential roles of rare taxa in maintaining the community structure. Overall, this study suggests the dynamic in the biogeographic patterns of PCCs of the Changjiang plume to the adjacent waters in the ECS responding with the changing environmental conditions and geographical factors.
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Affiliation(s)
- Xin Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Linnan Wu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Seasonality and Community Separation of Fungi in a Municipal Wastewater Treatment Plant. Appl Environ Microbiol 2020; 86:AEM.00991-20. [PMID: 32651202 DOI: 10.1128/aem.00991-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Fungi are known to play important roles in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). However, the seasonality and distributions of fungal populations in different-sized flocs have still remained largely unknown. In this study, seasonal population dynamics and community separation of fungi in a municipal WWTP across a 1-year period were investigated. We classified all taxa into six categories based on abundances to assess their roles and contributions to the whole community. The results showed that the rare taxa (<0.01%) contributed greatly to species richness (95.27%). Conversely, although low in species diversity, abundant taxa (≥1%) accounted for the majority (89.45%) of the total relative abundance, which suggested that a few core abundant fungi existed in the activated sludge ecosystem. The abundant, conditionally rare, and rare taxa contributed 30.14%, 31.11%, and 38.75%, respectively, to temporal shifts in community structure, and their abundances responded differently to environmental variables, suggesting that these three subcommunities exhibited a large difference in environmental sensitivity. Importantly, the results revealed seasonal dynamics of the whole fungal community and the subcommunities of all the microbial taxon categories, resulting in significant differences in community structures between warm and cold seasons. Furthermore, fungal diversity and the compositions of the whole community and subcommunities differed significantly among flocs of different sizes, which underlined the size-based fungal community separation in activated sludge of WWTPs. The findings of this work improved our understanding of fungal population dynamics and community separation in WWTPs.IMPORTANCE Fungi are important contributors to the various functions of activated sludge in wastewater treatment plants (WWTPs). Unlike previous studies, this work demonstrated the seasonality of the fungal community over a longer time span while it also systematically assessed the contributions of abundant, conditionally rare, and rare taxa to the whole community. Importantly, in the present study, we considered sludge flocs of a certain size range rather than the whole sludge flocs as a community. Our results revealed significant differences in fungal community structure among different-sized flocs, which supported the idea that size-based fungal community segregation is occurring in activated sludge ecosystems. The findings provide new insights into the dynamic changes or distribution of fungi in the bioaggregates of sludge flocs in WWTPs.
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