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Hu H, Wei XY, Liu L, Wang YB, Bu LK, Jia HJ, Pei DS. Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems. Appl Microbiol Biotechnol 2024; 108:130. [PMID: 38229334 DOI: 10.1007/s00253-023-12993-4] [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: 03/06/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yuan-Bo Wang
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ling-Kang Bu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Huang-Jie Jia
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [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: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Cao J, Yang X, Guo M, Wu Y, Wang C. Reclamation of abandoned cropland switches fungal community assembly from deterministic to stochastic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175494. [PMID: 39153623 DOI: 10.1016/j.scitotenv.2024.175494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/28/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024]
Abstract
Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of abandoned agricultural land reclamation on the soil microbe is still poorly understood, especially for the microbial community assembly mechanisms. Here, we investigated the influence of reclamation on the relative importance of stochastic and deterministic processes in shaping microbial community assembly. After reclaiming abandoned cropland for corn and soybean cultivation, the fungal community assembly was shifted to stochastic processes, while bacterial communities remained predominantly influenced by stochastic processes. Our study revealed that reclamation did not significantly affect bacterial diversity, community niche breadth, and community similarity. In contrast, fungal communities exhibited lower alpha diversity, narrower niche breadths, greater niche overlap and higher community similarity in corn and soybean cultivation treatment in response to reclamation. Moreover, soil pH and soil available phosphorus were the most important environmental factors influencing fungal richness, niche breadths, community assembly processes, and community similarity. Together, the reclamation of abandoned cropland promoted the transformation of the fungal community assembly from deterministic process to a stochastic process, leading to decreased fungal diversity and broader ecological niche width, ultimately resulting in greater similarity among fungal communities. This finding provides insight into the varied responses of microbial diversity and ecological process to abandoned cropland reclamation, offering valuable guidance for the conservation and sustainable management of abandoned cropland in future land-use practices.
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Affiliation(s)
- Jia Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Xi Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Mengyao Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Yafen Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Chong Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China.
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Guo R, Ma X, Zhu C, Liu C, Shou L, Zhang J, Li H, Li Z, Dai X, Priyadarshani WNC, Jayathilake RMRM, Lwin SM, Thu CA, Li G, Wang P, Zhou F. Diversity patterns and ecological assembly mechanisms of bacterial communities in the northeastern Indian Ocean epipelagic waters during the northeast monsoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175755. [PMID: 39182780 DOI: 10.1016/j.scitotenv.2024.175755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/18/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Disentangling microbial community diversity patterns and assembly mechanisms is critical for understanding ecological processes and evaluating biogeochemical cycling in ecosystems. However, the diversity patterns and assembly mechanism of the microbial communities in the epipelagic waters in the northeastern Indian Ocean (NEIO) on the spatial scale are still unclear. In this study, we investigated the spatial dynamics, geographic distribution pattern, and assembly process of the bacterial community using 532 samples collected from the epipelagic waters in the NEIO during the northeast monsoon. The results indicate that the bacterial richness and Bray-Curtis dissimilarity exhibited the strongest correlations with depth compared to the latitudinal and longitudinal scales. The dissolved oxygen was identified as the most important environmental factor affecting the bacterial richness and Bray-Curtis dissimilarity compared to temperature and salinity. The distance-decay relationship (DDR) of the bacterial community strengthened with increasing water depth. Turnover was the predominant β-diversity component influencing the spatial changes in the whole bacterial community. The dispersal limitation of the stochastic process and homogeneous selection of the deterministic process governed the bacterial ecological assembly process of the whole bacterial community. Abundant and rare subcommunities differed in terms of the niche breath, composition changes. The abundant subcommunities exhibited a much wider niche breath than the rare subcommunities. Regarding the abundant subcommunity species changes, the contributions of the turnover and nestedness varied with the water depth and oceanic region. In contrast, turnover was the major β-diversity component regarding the changes in the rare species. These data improve our understanding of the ecological processes of bacterial community assemblages in the NEIO.
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Affiliation(s)
- Ruoyu Guo
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China; Observation and Research Station of Yangtze River Delta Marine Ecosystems, Ministry of Natural Resources, 99 South Haida Road, Zhoushan 316053, PR China.
| | - Xiao Ma
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China; Observation and Research Station of Yangtze River Delta Marine Ecosystems, Ministry of Natural Resources, 99 South Haida Road, Zhoushan 316053, PR China
| | - Chenjie Zhu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Chenggang Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Jingjing Zhang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Zhongqiao Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - Xinfeng Dai
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China
| | - W N C Priyadarshani
- National institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency, Sri Lanka
| | - R M R M Jayathilake
- National institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency, Sri Lanka
| | | | - Chit Aung Thu
- Research and Development Section, Department of Fisheries, Ministry of Agriculture, Livestock and Irrigation, Myanmar
| | - Guanlin Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Pengbin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China; Observation and Research Station of Yangtze River Delta Marine Ecosystems, Ministry of Natural Resources, 99 South Haida Road, Zhoushan 316053, PR China.
| | - Feng Zhou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, PR China; Observation and Research Station of Yangtze River Delta Marine Ecosystems, Ministry of Natural Resources, 99 South Haida Road, Zhoushan 316053, PR China.
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Zhang Y, Resch MC, Schütz M, Liao Z, Frey B, Risch AC. Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175031. [PMID: 39069191 DOI: 10.1016/j.scitotenv.2024.175031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/03/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely 'Harvest only', 'Topsoil removal' and 'Topsoil removal + Propagules (plant seed addition)', affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that 'Topsoil removal' and 'Topsoil removal + Propagules', but not 'Harvest only', reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.
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Affiliation(s)
- Yongyong Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.
| | - Monika Carol Resch
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Martin Schütz
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ziyan Liao
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Anita Christina Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Jiao G, Huang Y, Tang H, Chen Y, Zhou D, Yu D, Ma Z, Ni S. Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175305. [PMID: 39117200 DOI: 10.1016/j.scitotenv.2024.175305] [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: 05/18/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.
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Affiliation(s)
- Ganghui Jiao
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; Yunnan Earthquake Agency, Yunnan 650000, China; Observation Station for Field Scientific Research of Crustal Tectonic Activity in Northwest Yunnan, Dali 671000, China
| | - Yi Huang
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China.
| | - Hua Tang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Ying Chen
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
| | - Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Daming Yu
- Pangang Group Company Limited, Sichuan 617050, China
| | - Zhongjian Ma
- Pangang Group Company Limited, Sichuan 617050, China
| | - Shijun Ni
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
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Sun P, Fan K, Jiang Y, Chu H, Chen Y, Wu Y. Accumulated temperature dictates the regional structural variation of prokaryotic periphyton at soil-water interface in paddy fields. WATER RESEARCH 2024; 265:122259. [PMID: 39154398 DOI: 10.1016/j.watres.2024.122259] [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: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
As a pervasive microbial aggregate found at the water-soil interface in paddy fields, periphyton plays crucial roles in modulating nutrient biogeochemical cycling. Consequently, it effectively mitigates non-point source pollution due to its diverse composition. Despite its significance, the mechanisms governing periphyton diversity across different rice planting regions remain poorly understood. To bridge this gap, we investigated periphyton grown in 200 paddy fields spanning 25° of latitude. Initially, we analyzed local diversity and latitudinal variations in prokaryotic communities within paddy field periphyton, identifying 7 abundant taxa, 42 moderate taxa, and 39 rare taxa as the fundamental prokaryotic framework. Subsequently, to elucidate the mechanisms governing periphyton diversity across large scales, we constructed interaction models illustrating triangular relationships among local richness, assembly, and regional variation of prokaryotic subcommunities. Our findings suggest that accumulated temperature-driven environmental filtering partially influences the assembly process of prokaryotes, thereby impacting local species richness and ultimately governing regional structural variations in periphyton. Furthermore, we determined that a latitude of 39° represents the critical threshold maximizing local species richness of periphyton in paddy fields. This study advances our understanding of the factors shaping periphyton geo-imprints and provides valuable insights into predicting their responses to environmental changes, potentially influencing rice production outcomes.
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Affiliation(s)
- Pengfei Sun
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Kunkun Fan
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yuji Jiang
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Haiyan Chu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yin Chen
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK.
| | - Yonghong Wu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China.
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Liu X, Pan B, Wang L, Zhang Y, Zhao X, Han X, Liu X, Hu J. Water temperature and salt ions respectively drive the community assembly of bacterial generalists and specialists in diverse plateau lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175271. [PMID: 39102958 DOI: 10.1016/j.scitotenv.2024.175271] [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: 05/25/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Plateau lakes (e.g., freshwater and saltwater lakes) are formed through intricate processes and harbor diverse microorganisms that mediate aquatic ecosystem functions. The adaptive mechanisms of lake microbiota to environmental changes and the ecological impacts of such changes on microbial community assembly are still poorly understood in plateau regions. This study investigated the structure and assembly of planktonic bacterial communities in 24 lakes across the Qinghai-Tibetan and Inner Mongolia Plateaus, with particular focus on habitat generalists, opportunists, and specialists. High-throughput sequencing of the 16S ribosomal RNA genes revealed that bacterial generalists had a lower species number (2196) but higher alpha diversity than the specialist and opportunist counterparts. Taxonomic dissimilarity and phylogenetic diversity analyses unraveled less pronounced difference in the community composition of bacterial generalists compared to the specialist and opportunist counterparts. Geographical scale (14.4 %) and water quality (12.6 %) emerged as major ecological variables structuring bacterial communities. Selection by water temperature and related variables, including mean annual temperature, elevation, longitude, and latitude, mainly shaped the assembly of bacterial generalists. Ecological drift coupled with selection by salt ions and related variables, including total phosphorus, chlorophyll a, and salinity, predominantly drove the assembly of bacterial specialists and opportunists. This study uncovers distinct bacterial responses to interacting ecological variables in diverse plateau lakes and the ecological processes structuring bacterial communities across various lake habitats under anthropogenic disturbance or climate change.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China.
| | - Lixin Wang
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region), Hohhot 010021, China
| | - Yichi Zhang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xu Han
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Jingxiang Hu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
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Liu S, Chen Q, Liu L, Dong C, Qiu X, Tang K. Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174845. [PMID: 39053558 DOI: 10.1016/j.scitotenv.2024.174845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
Abstract
Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.
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Affiliation(s)
- Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Xuanyun Qiu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, China.
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10
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Liu S, Zhang Z, Hao J, Zhao C, Han F, Xiong Q, Wang X, Du C, Xu H. Plastic debris mediates bacterial community coalescence by breaking dispersal limitation in the sediments of a large river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124603. [PMID: 39047888 DOI: 10.1016/j.envpol.2024.124603] [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: 05/23/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Plastic debris has recently been proposed as a novel habitat for bacterial colonization, which can raise perturbations in bacterial ecology after burial in riverine sediments. However, community coalescence, as a prevalent process involving the interrelationships of multiple communities and their surrounding environments, has been rarely discussed to reveal the impact of the plastisphere on sedimentary bacterial community. This study analyzed the bacterial community in plastic debris and sediment along the Nujiang River, elucidating the role of the plastisphere in mediating community coalescence in sediments. Our results demonstrated that the plastisphere and sedimentary bacterial communities exhibited distinct biogeography along the river (r = 0.694, p < 0.01). Based on overlapped taxa and SourceTracker, the extent of coalescence between adjacent communities was in following orders: plastic-plastic (0.589) > plastic-sediment (0.561) > sediment-sediment (0.496), indicating the plastisphere promoted bacterial community coalescence along the river. Flow velocity and geographic distance were the major factors driving the plastisphere changes, suggesting that the plastisphere were vulnerable to dispersal. The null model and the neutral model provided additional support for the higher immigration ability of the plastisphere to overcome dispersal limitation, highlighting the potential importance of the plastisphere in community coalescence. Network analysis indicated the critical role of keystone species (Proteobacteria, Bacteroidetes, and Gemmatimonadetes) in mediating the coalescence between sedimentary bacterial community and the plastisphere. In summary, the plastisphere could mediate the coalescence of bacterial communities by overcoming dispersal limitation, which provides new perspectives on the plastisphere altering bacterial ecology in riverine sediments.
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Affiliation(s)
- Sheng Liu
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China.
| | - Zixuan Zhang
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Jie Hao
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266000, China
| | - Chuanfu Zhao
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Fei Han
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Qingrong Xiong
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Chenggong Du
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, Jiangsu, 223300, China
| | - Hongzhe Xu
- Dept of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
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11
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Liu YJ, Gong S, Wang YB, Yang ZL, Hu WH, Feng B. Biogeography and community assembly of soil fungi from alpine meadows in southwestern China show the importance of climatic selection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174477. [PMID: 38964412 DOI: 10.1016/j.scitotenv.2024.174477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Soil fungi are pivotal in alpine and arctic ecosystems that are vulnerable to climate changes. Previous studies have shown broad connections between soil fungi in the arctic and alpine regions, but most of these studies are mainly from Europe and North America, with more sporadic studies from East Asia. Currently, little is known about the biogeographic relationships between soil fungi in alpine meadows of southwestern China (AMSC) and other regions of the world. In addition, the regional-scale spatial patterns of fungal communities in the AMSC, as well as their driving factors and ecological processes, are also poorly understood. In this study, we collected roots and surrounding soils of two dominant ectomycorrhizal plants, Bistorta vivipara and B. macrophylla from the AMSC, and performed bioinformatic and statistical analyses based on high-throughput sequencing of ITS2 amplicons. We found that: (1) fungi from the AMSC were closely related with those from boreal forests and tundra, and saprotrophic fungi had higher dispersal potential than ectomycorrhizal fungi; (2) community compositions exhibited clear divergences among geographic regions and between root and soil samples; (3) climate was the predominant factor driving regional-scale spatial patterns but had less explanatory power for saprotrophic and total fungi from roots than those from soils; (4) homogeneous selection and drift were the key ecological processes governing community assembly, but in communities of saprotrophic and total fungi from soil samples, drift contributed less and its role was partially replaced by dispersal limitation. This study highlights the importance of climatic selection and stochastic processes on fungal community assembly in alpine regions, and emphasizes the significance of simultaneously investigating fungi with different trophic modes and from both roots and soils.
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Affiliation(s)
- Yong Jie Liu
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China; School of Life Sciences, Yunnan University, China
| | - Sai Gong
- School of Horticulture, Anhui Agricultural University, China
| | - Yuan Bing Wang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China
| | - Zhu L Yang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China
| | - Wei Hong Hu
- School of Life Sciences, Yunnan University, China.
| | - Bang Feng
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, China.
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12
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Wang Z, Zhao Z, Wang H, Wu Q, Ke Q, Zhu L, Wu L, Chen L. Harvest residue recycling rather than slash-burning results in the enhancement of soil fertility and bacterial community stability in Eucalyptus plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173850. [PMID: 38901592 DOI: 10.1016/j.scitotenv.2024.173850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Deforestation and slash combustion have substantial adverse impacts on the atmosphere, soil and microbe. Despite this awareness, numerous individuals persist in opting for high-intensity Eucalyptus planting through slash-burning in pursuit of immediate profits while disregarding the environmental significance and destroying the soil. Slash-unburnt agriculture can effectively safeguard the ecological environment, and compared with slash-burning, there remains a limited understanding of its regulatory mechanisms on soil fertility and microbial community. Also, large uncertainty persists regarding the utilization of harvest residues. Thoroughly investigating these questions from various perspectives encompassing physical soil characteristics, nutrient availability, bacterial community structures, and stability is crucial. To explore the ecological advantages of slash-unburnt techniques on microorganisms and their associated ecosystems, we used two slash-unburnt (Unburnt) planting techniques: Spread (naturally and evenly covering the forest floor after logging) and Stack (residues are piled along contour lines) as well as the traditional slash Burnt method (Burnt) in a Eucalyptus plantation. A comparative analysis was conducted between the two methods. We observed that over a span of 4 years, despite the initial lower application of fertilizer in the Unburnt treatments compared with the Burnt treatment during the first 2 years, the Unburnt treatment gradually caught up or even surpassed and attained similar nutrient levels as the Burnt treatment. Alphaproteobacteria was the main phyla that indicated the difference in soil bacterial communities between Burnt and Unburnt treatments. The microbial networks also highlighted the significance of the Unburnt method, as it contributed to the preservation of crucial network nodes and the stability of soil bacterial communities. Therefore, rational utilization of harvest residue may effectively avoid the vast damage caused by slash-burning to Eucalyptus trees and the soil environment but may also increase the potential for restoring soil fertility, improving fertilizer utilization efficiency, and maintaining microbial community stability over time.
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Affiliation(s)
- Zhengye Wang
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ziqi Zhao
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; State-owned Gaofeng Forest Farm, Nanning, Guangxi 530002, China
| | - Huili Wang
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, Guangxi 530002, China
| | - Qinzhan Wu
- State-owned Daguishan Forest Farm, Hezhou, Guangxi 542800, China
| | - Qin Ke
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, Guangxi 530002, China
| | - Lingyue Zhu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lichao Wu
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of National Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Lijun Chen
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
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13
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Zhang L, Zhang G, Shi Z, He M, Ma D, Liu J. Effects of polypropylene micro(nano)plastics on soil bacterial and fungal community assembly in saline-alkaline wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173890. [PMID: 38885717 DOI: 10.1016/j.scitotenv.2024.173890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Microplastic pollution is a major environmental threat, especially to terrestrial ecosystems. To better understand the effects of microplastics on soil microbiota, the influence of micro- to nano-scale polypropylene plastics was investigated on microbial community diversity, functionality, co-occurrence, assembly, and their interaction with soil-plant using high-throughput sequencing approaches and multivariate analyses. The results showed that polypropylene micro/nano-plastics mainly reduced bacterial diversity, not fungal, and that plastic size had a stronger effect than concentration on the assembly of microbial communities. Nano-plastics decreased the complexity and connectivity of both bacterial and fungal networks compared to micro-plastics. Moreover, bacteria were more sensitive and deterministic to polypropylene micro/nano-plastic stress than fungi, as shown by their different growth rates, guanine-cytosine content, and cell structure. Interestingly, the dominant ecological process for bacteria shifted from stochastic drift to deterministic selection with polypropylene micro/nano-plastic exposure. Furthermore, nano-plastics directly or indirectly disrupted the interactions within intra-microbes and between soil-bacteria-plant by altering soil nutrients and stoichiometry (C:N:P) or plant diversity. Collectively, the results indicate that polypropylene nano-plastics pose more ecological risks to soil microbes and their plant-soil interactions. This study sheds light on the potential ecological consequences of polypropylene micro/nano-plastic pollution in terrestrial ecosystems.
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Affiliation(s)
- Lan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Guorui Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ziyue Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Mengxuan He
- School of Geographic and Environmental Science, Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin 300387, China..
| | - Dan Ma
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Jie Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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14
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Qian L, Yan B, Zhou J, Fan Y, Tao M, Zhu W, Wang C, Tu Q, Tian Y, He Q, Wu K, Niu M, Yan Q, Nikoloski Z, Liu G, Yu X, He Z. Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173961. [PMID: 38876338 DOI: 10.1016/j.scitotenv.2024.173961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O32- to SO32-, showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.
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Affiliation(s)
- Lu Qian
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bozhi Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Yijun Fan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Mei Tao
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China; College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wengen Zhu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN 37996, USA
| | - Kun Wu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Mingyang Niu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany; Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Guangli Liu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China.
| | - Xiaoli Yu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China.
| | - Zhili He
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510006, China.
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15
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Liu Q, Duan X, Zhang Y, Duan L, Zhang X, Liu F, Li D, Zhang H. Rainfall seasonality shapes microbial assembly and niche characteristics in Yunnan Plateau lakes, China. ENVIRONMENTAL RESEARCH 2024; 257:119410. [PMID: 38871273 DOI: 10.1016/j.envres.2024.119410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microorganisms are crucial components of freshwater ecosystems. Understanding the microbial community assembly processes and niche characteristics in freshwater ecosystems, which are poorly understood, is crucial for evaluating microbial ecological roles. The Yunnan Plateau lakes in China represent a freshwater ecosystem that is experiencing eutrophication due to anthropogenic activities. Here, variation in the assembly and niche characteristics of both prokaryotic and microeukaryotic communities was explored in Yunnan Plateau lakes across two seasons (dry season and rainy season) to determine the impacts of rainfall and environmental conditions on the microbial community and niche. The results showed that the environmental heterogeneity of the lakes decreased in the rainy season compared to the dry season. The microbial (bacterial and microeukaryotic) α-diversity significantly decreased during the rainy season. Deterministic processes were found to dominate microbial community assembly in both seasons. β-Diversity decomposition analysis revealed that microbial community compositional dissimilarities were dominated by species replacement processes. The co-occurrence networks indicated reduced species complexity for microbes and a destabilized network for prokaryotes prior to rainfall, while the opposite was found for microeukaryotes following rainfall. Microbial niche breadth decreased significantly in the rainy season. In addition, lower prokaryotic niche overlap, but greater microeukaryotic niche overlap, was observed after rainfall. Rainfall and environmental conditions significantly affected the microbial community assembly and niche characteristics. It can be concluded that rainfall and external pollutant input during the seasonal transition alter the lake environment, thereby regulating the microbial community and niche in these lakes. Our findings offer new insight into microbiota assembly and niche patterns in plateau lakes, further deepening the understanding of freshwater ecosystem functioning.
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Affiliation(s)
- Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Xinlu Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Donglin Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650500, China; Southwest United Graduate School, Kunming, 650500, Yunnan, China.
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16
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Yuan F, Zou X, Liao Q, Wang T, Zhang H, Xue Y, Chen H, Ding Y, Lu M, Song Y, Fu G. Insight into the bacterial community composition of the plastisphere in diverse environments of a coastal salt marsh. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124465. [PMID: 38942280 DOI: 10.1016/j.envpol.2024.124465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024]
Abstract
The microbial community colonized on microplastics (MPs), known as the 'plastisphere', has attracted extensive concern owing to its environmental implications. Coastal salt marshes, which are crucial ecological assets, are considered sinks for MPs. Despite their strong spatial heterogeneity, there is limited information on plastisphere across diverse environments in coastal salt marshes. Herein, a 1-year field experiment was conducted at three sites in the Yancheng salt marsh in China. This included two sites in the intertidal zone, bare flat (BF) and Spartina alterniflora vegetation area (SA), and one site in the supratidal zone, Phragmites australis vegetation area (PA). Petroleum-based MPs (polyethylene and expanded polystyrene) and bio-based MPs (polylactic acid and polybutylene succinate) were employed. The results revealed significant differences in bacterial community composition between the plastisphere and sediment at all three sites examined, and the species enriched in the plastisphere exhibited location-specific characteristics. Overall, the largest difference was observed at the SA site, whereas the smallest difference was observed at the BF site. Furthermore, the MP polymer types influenced the composition of the bacterial communities in the plastisphere, also exhibiting location-specific characteristics, with the most pronounced impact observed at the PA site and the least at the BF site. The polybutylene succinate plastisphere bacterial communities at the SA and PA sites were quite different from the plastispheres from the other three MP polymer types. Co-occurrence network analyses suggested that the bacterial community network in the BF plastisphere exhibited the highest complexity, whereas the network in the SA plastisphere showed relatively sparse interactions. Null model analyses underscored the predominant role of deterministic processes in shaping the assembly of plastisphere bacterial communities across all three sites, with a more pronounced influence observed in the intertidal zone than in the supratidal zone. This study enriches our understanding of the plastisphere in coastal salt marshes.
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Affiliation(s)
- Feng Yuan
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Xinqing Zou
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China; Collaborative Innovation Center of South China Sea Studies, Nanjing University, Nanjing, 210023, China
| | - Qihang Liao
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China; Collaborative Innovation Center of South China Sea Studies, Nanjing University, Nanjing, 210023, China
| | - Teng Wang
- College of Oceanography, Hohai University, Nanjing, 210098, China.
| | - Hexi Zhang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Yue Xue
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Hongyu Chen
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China; Collaborative Innovation Center of South China Sea Studies, Nanjing University, Nanjing, 210023, China
| | - Yongcheng Ding
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Ming Lu
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Yuyang Song
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China
| | - Guanghe Fu
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, China; Ministry of Education Key Laboratory for Coast and Island Development, Nanjing University, Nanjing, 210023, China; Collaborative Innovation Center of South China Sea Studies, Nanjing University, Nanjing, 210023, China
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Li B, Liu C, Bai J, Huang Y, Su R, Wei Y, Ma B. Strategy to mitigate substrate inhibition in wastewater treatment systems. Nat Commun 2024; 15:7920. [PMID: 39256375 PMCID: PMC11387818 DOI: 10.1038/s41467-024-52364-9] [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: 09/19/2023] [Accepted: 09/03/2024] [Indexed: 09/12/2024] Open
Abstract
Global urbanization requires more stable and sustainable wastewater treatment to reduce the burden on the water environment. To address the problem of substrate inhibition of microorganisms during wastewater treatment, which leads to unstable wastewater discharge, this study proposes an approach to enhance the tolerance of bacterial community by artificially setting up a non-lethal high substrate environment. And the feasibility of this approach was explored by taking the inhibition of anammox process by nitrite as an example. It was shown that the non-lethal high substrate environment could enhance the nitrite tolerance of anammox bacterial community, as the specific anammox activity increasing up to 24.71 times at high nitrite concentrations. Moreover, the system composed of anammox bacterial community with high nitrite tolerance also showed greater resistance (two-fold) in response to nitrite shock. The antifragility of the system was enhanced without affecting the operation of the main reactor, and the non-lethal high nitrite environment changed the dominant anammox genera to Candidatus Jettenia. This approach to enhance tolerance of bacterial community in a non-lethal high substrate environment not only allows the anammox system to operate stably, but also promises to be a potential strategy for achieving stable biological wastewater treatment processes to comply with standards.
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Affiliation(s)
- Beiying Li
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China
| | - Conghe Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China
| | - Jingjing Bai
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China
| | - Yikun Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China
| | - Run Su
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China
| | - Yan Wei
- State Key Laboratory of Marine Resources Utilization in the South China Sea, Hainan University, Haikou, 570228, China
| | - Bin Ma
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Environmental Science and Engineering, Hainan University, Haikou, 570228, China.
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18
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Yang X, Feng K, Wang S, Yuan MM, Peng X, He Q, Wang D, Shen W, Zhao B, Du X, Wang Y, Wang L, Cao D, Liu W, Wang J, Deng Y. Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation. MICROBIOME 2024; 12:166. [PMID: 39244624 PMCID: PMC11380791 DOI: 10.1186/s40168-024-01890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment. RESULTS During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions. CONCLUSIONS All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.
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Affiliation(s)
- Xingsheng Yang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94704, USA
| | - Xi Peng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Danrui Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Bo Zhao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingcheng Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Linlin Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Dong Cao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenzong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Jianjun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Jiang J, Fang G, Wu C, Wang P, Zhang Y, Zhang C, Wu F, Shan Z, Liu Q, Liu X. The Addition of Glutamine Enhances the Quality of Huangjiu by Modifying the Assembly and Metabolic Activities of Microorganisms during the Fermentation Process. Foods 2024; 13:2833. [PMID: 39272598 DOI: 10.3390/foods13172833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/29/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
In this study, the effects of adding glutamate (Glu), glutamine (Gln), aspartate (Asp), and asparagine (Asn) on the flavor formation of Huangjiu were investigated, and the effect of Gln concentration on the quality, microbial community structure, and flavor development of Huangjiu was further explored. Varied Gln concentrations influenced yeast growth, sugar utilization, microbial communities, and quality attributes. Additional Gln promoted yeast cell counts and sugar depletion. It increased the complexity of bacterial co-occurrence networks and reduced the impact of stochastic processes on assembly. Correlation analysis linked microorganisms to flavor compounds. Isolation experiments verified the role of Saccharomyces cerevisiae, Aspergillus chevalieri, Bacillus altitudinis, and Lactobacillus coryniformis in flavor production under Gln conditions. This research elucidated the microbiological mechanisms by which amino acid supplementation, especially Gln, enhances Huangjiu quality by modulating microbial metabolic functions and community dynamics during fermentation. This research is significant for guiding the production of Huangjiu and enhancing its quality.
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Affiliation(s)
- Jiajia Jiang
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Guanyu Fang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Changling Wu
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Peng Wang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Yongzhu Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Cheng Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Fenghua Wu
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Zhichu Shan
- Zhejiang Pagoda Brand Shaoxing Rice Wine Co., Ltd., Shaoxing 312000, China
| | - Qingru Liu
- Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, China
| | - Xingquan Liu
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
- National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
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20
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Ndayishimiye JC, Nyirabuhoro P, Gao X, Chen H, Wang W, Mazei Y, Yang J. Community responses of testate amoebae (Arcellinida and Euglyphida) to ecological disturbance explained by contrasting assembly mechanisms in two subtropical reservoirs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176058. [PMID: 39241884 DOI: 10.1016/j.scitotenv.2024.176058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/17/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Mechanisms underlying the effects of ecological disturbance on aquatic ecosystems remain uncertain in subtropical regions. Here, we used a proxy-based approach to explore the community dynamics of testate amoebae (Arcellinida and Euglyphida) in two subtropical deep reservoirs (Tingxi and Shidou) in Xiamen, southeastern China, over a three-year period. Specifically, we employed drought and typhoon events recorded by weather station as proxies for ecological disturbance and chlorophyll-a estimated through fluorometry as a proxy for testate amoeba food. We addressed three questions: (1) Does typhoon-induced ecological disturbance affect the distribution patterns of testate amoebae in subtropical reservoirs? (2) Do typhoon- and drought-induced ecological disturbances affect the testate amoeba community across different water layers of subtropical reservoirs similarly? (3) Do stochastic or deterministic processes shaping the testate amoeba community over time exhibit similar patterns in different water layers of subtropical reservoirs? The typhoon-induced ecological disturbance resulted in pronounced shifts in the distribution patterns of testate amoebae, characterized by lower shell influx in surface waters (11-12 ind. mL-1 d-1) and higher shell influx in middle and bottom waters (12-22 ind. mL-1 d-1). The impact of typhoon-and drought-induced ecological disturbance was more pronounced in surface waters, and its pure explanation accounted for 29.5-35.5 % community variation in a variation partitioning analysis. The effect of stochastic processes revealed by the neutral model increased with water depths, accounting for 63.3-76.5 % of the community variation in the surface, 77.4-82.6 % in the middle, and 82.8-88.1 % in the bottom water. The effect of deterministic processes shown by the null model decreased with water depth and remained relatively low across all water layers. These results suggest contrasting patterns of assembly mechanisms underlying the testate amoeba community responses to ecological disturbance, with the balance perhaps shaped by water depth and the average water residence time in a reservoir.
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Affiliation(s)
- Jean Claude Ndayishimiye
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Pascaline Nyirabuhoro
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaofei Gao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenping Wang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Huaibei Normal University, Huaibei 235000, China
| | - Yuri Mazei
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave. 33, Moscow 117071, Russia
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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21
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Huber P, De Angelis D, Sarmento H, Metz S, Giner CR, Vargas CD, Maiorano L, Massana R, Logares R. Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage. MICROBIOME 2024; 12:162. [PMID: 39232839 PMCID: PMC11373171 DOI: 10.1186/s40168-024-01874-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/16/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND The backbone of the eukaryotic tree of life contains taxa only found in molecular surveys, of which we still have a limited understanding. Such is the case of Picozoa, an enigmatic lineage of heterotrophic picoeukaryotes within the supergroup Archaeplastida, which has emerged as a significant component of marine microbial planktonic communities. To enhance our understanding of the diversity, distribution, and ecology of Picozoa, we conduct a comprehensive assessment at different levels, from assemblages to taxa, employing phylogenetic analysis, species distribution modeling, and ecological niche characterization. RESULTS Picozoa was among the ten most abundant eukaryotic groups, found almost exclusively in marine environments. The phylum was represented by 179 Picozoa's OTU (pOTUs) placed in five phylogenetic clades. Picozoa community structure had a clear latitudinal pattern, with polar assemblages tending to cluster separately from non-polar ones. Based on the abundance and occupancy pattern, the pOTUs were classified into four categories: Low-abundant, Widespread, Polar, and Non-polar. We calculated the ecological niche of each of these categories. Notably, pOTUs sharing similar ecological niches were not closely related species, indicating a phylogenetic overdispersion in Picozoa communities. This could be attributed to competitive exclusion and the strong influence of the seasonal amplitude of variations in environmental factors, such as temperature, shaping physiological and ecological traits. CONCLUSIONS Overall, this work advances our understanding of uncharted protists' evolutionary dynamics and ecological strategies. Our results highlight the importance of understanding the species-level ecology of marine heteroflagellates like Picozoa. The observed phylogenetic overdispersion challenges the concept of phylogenetic niche conservatism in protist communities, suggesting that closely related species do not necessarily share similar ecological niches. Video Abstract.
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Affiliation(s)
- Paula Huber
- Departamento de Hidrobiología, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Daniele De Angelis
- Dipartimento Di Biologia E Biotecnologie "Charles Darwin", Università Di Roma La Sapienza, Rome, Italy
| | - Hugo Sarmento
- Departamento de Hidrobiología, Universidade Federal de São Carlos, São Carlos, Brazil.
| | | | - Caterina R Giner
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Colomban De Vargas
- Sorbonne Universités, CNRS, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Luigi Maiorano
- Dipartimento Di Biologia E Biotecnologie "Charles Darwin", Università Di Roma La Sapienza, Rome, Italy
| | - Ramon Massana
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain.
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22
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Sun S, Qiao Z, Sun K, Huo D. Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution. Microbiol Spectr 2024; 12:e0105124. [PMID: 39058029 PMCID: PMC11370247 DOI: 10.1128/spectrum.01051-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH3), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH3 levels, suggesting their potential resilience or adaptive responses to NH3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions. IMPORTANCE The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.
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Affiliation(s)
- Shengjie Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Zhiyi Qiao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Kexin Sun
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Da Huo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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23
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Sun X, Su L, Zhen J, Wang Z, Panhwar KA, Ni SQ. The contribution of swine wastewater on environmental pathogens and antibiotic resistance genes: Antibiotic residues and beyond. CHEMOSPHERE 2024; 364:143263. [PMID: 39236924 DOI: 10.1016/j.chemosphere.2024.143263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 09/02/2024] [Indexed: 09/07/2024]
Abstract
Swine wastewater application can introduce antibiotics, antibiotic resistance genes (ARGs) into environments. Herein, the full-scale transmission of antibiotics, ARGs and their potential carriers from an intensive swine feedlot to its surroundings were explored. Results showed that lincomycin and doxycycline hydrochloride were dominant antibiotics in this ecosystem. Lincomycin concentration were strongly associated with soil bacterial communities. According to the risk quotient (RQ), lincomycin was identified as posing higher ecological risk in aquatic environments. ARGs and mobile genetic elements (MGEs) abundance in wastewater were reduced after anaerobic treatment. Notably, ARGs composition of environmental samples were clustered into two groups based on if they were directly affected by the wastewater. However, there were no remarkable difference of ARGs abundance among environmental samples. The total abundance of ARGs was positively related to that of MGEs. Pathogens Escherichia coli and Enterococcus revealed strong connection with qnrS, tet and sul. Overall, this study highlights the importance of responsible antibiotics use in livestock production and appropriate treatment technology before agricultural application and discharge.
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Affiliation(s)
- Xiaojie Sun
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Lei Su
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Jianyuan Zhen
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhibin Wang
- School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Kashif Ali Panhwar
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Shou-Qing Ni
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China.
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24
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Fang C, Liu KD, Tian FJ, Li JY, Li SJ, Zhang RM, Sun J, Fang LX, Ren H, Wang MG, Liao XP. Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124784. [PMID: 39182818 DOI: 10.1016/j.envpol.2024.124784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/06/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.
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Affiliation(s)
- Chang Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; College of Marine Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Kai-di Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Feng-Jie Tian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jin-Ying Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Si-Jie Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, PR China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, PR China
| | - Hao Ren
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Min-Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Phage Research Center, Liaocheng University, Liaocheng, 252000, PR China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China.
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Li X, Cheng X, Xu J, Wu J, Chan LL, Cai Z, Zhou J. Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms. Microbiol Res 2024; 286:127785. [PMID: 38851011 DOI: 10.1016/j.micres.2024.127785] [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: 01/27/2024] [Revised: 05/01/2024] [Accepted: 05/25/2024] [Indexed: 06/10/2024]
Abstract
Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.
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Affiliation(s)
- Xinyang Li
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Xueyu Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Junjie Xu
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong Province 518055, PR China.
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Huo L, Ma A, Liu H, Wang X, Song C. Diversity and ecological assembly process of aerobic anoxygenic phototrophic bacteria in a low irradiation area, Three Gorges Reservoir. J Environ Sci (China) 2024; 143:116-125. [PMID: 38644009 DOI: 10.1016/j.jes.2023.08.015] [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: 02/25/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 04/23/2024]
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) are significant bacterial groups in aquatic ecosystems, known for their rapid growth and photoheterotrophic characteristics. However, the distribution and ecological assembly process of AAPB in low irradiation freshwater basins remain unclear, warranting further investigation. In this study, we present the diversity, abundance, spatial variations, ecological process, and community interaction of AAPB in sediment of Three Gorges Reservoir (TGR) under low irradiation. Our findings demonstrate the dominant genera of AAPB community that exist in the TGR area also are appeared in different waters, with some regional preference. Moreover, the concentration of pufM gene, an indicator for AAPB, maintains a consistently high numerical level ranging from (2.21 ± 0.44) × 104 to (9.98 ± 0.30) × 107 gene copies/g. Although solar irradiation is suggested as the major factor affecting AAPB, it remains unclear whether and how AAPB differ between regions due to varying solar irradiation levels. Our results show spatial differences between total bacteria and AAPB communities, with significant differences observed only in AAPB. Geographical and environmental factor contributed less than 10% to the spatial difference of community, with sediment type and environmental factors being the key factors influencing microbial community structure. The stochastic process plays a dominant role in the aggregation and replacement of AAPB communities, among which the most contribution is dispersal limitation. For AAPB network, Yoonia and Gemmobacter are the hubs for modules. Those results valuable insights into the AAPB communities in TGR with low irradiation.
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Affiliation(s)
- Lixin Huo
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, College of Resources and Environment, Chongqing 400714, China; Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anran Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, College of Resources and Environment, Chongqing 400714, China; Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China
| | - Hong Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, College of Resources and Environment, Chongqing 400714, China; Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xingzu Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, College of Resources and Environment, Chongqing 400714, China; Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Cheng Song
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China
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Walsh C, Vanderburgh C, Grant L, Katz E, Kliebenstein DJ, Fierer N. Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea). THE NEW PHYTOLOGIST 2024; 243:1951-1965. [PMID: 38553428 DOI: 10.1111/nph.19708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 08/02/2024]
Abstract
Here, we characterized the independent role of soil microbiomes (bacterial and fungal communities) in determining the flavor chemistry of harvested mustard seed (Brassica juncea). Given the known impacts of soil microbial communities on various plant characteristics, we hypothesized that differences in rhizosphere microbiomes would result in differences in seed flavor chemistry (glucosinolate content). In a glasshouse study, we introduced distinct soil microbial communities to mustard plants growing in an otherwise consistent environment. At the end of the plant life cycle, we characterized the rhizosphere and root microbiomes and harvested produced mustard seeds for chemical characterization. Specifically, we measured the concentrations of glucosinolates, secondary metabolites known to create spicy and bitter flavors. We examined associations between rhizosphere microbial taxa or genes and seed flavor chemistry. We identified links between the rhizosphere microbial community composition and the concentration of the main glucosinolate, allyl, in seeds. We further identified specific rhizosphere taxa predictive of seed allyl concentration and identified bacterial functional genes, namely genes for sulfur metabolism, which could partly explain the observed associations. Together, this work offers insight into the potential influence of the belowground microbiome on the flavor of harvested crops.
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Affiliation(s)
- Corinne Walsh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Caihong Vanderburgh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Lady Grant
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | | | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
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Thompson C, Silva R, Gibran FZ, Bacha L, de Freitas MAM, Thompson M, Landuci F, Tschoeke D, Zhang XH, Wang X, Zhao W, Gatts PV, de Almeida MG, de Rezende CE, Thompson F. The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes. MICROBIAL ECOLOGY 2024; 87:110. [PMID: 39215820 PMCID: PMC11365853 DOI: 10.1007/s00248-024-02423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ13C and δ15N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.
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Affiliation(s)
- Cristiane Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| | - Raphael Silva
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Fernando Z Gibran
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), São Bernardo Do Campo, São Paulo, Brazil
| | - Leonardo Bacha
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Mayanne A M de Freitas
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Mateus Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Felipe Landuci
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Diogo Tschoeke
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil
- Biomedical Engineer Program, COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Xiao-Hua Zhang
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Wenbin Zhao
- Microbial Oceanography Lab, Ocean University of China, Qingdao, China
| | - Pedro Vianna Gatts
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Marcelo Gomes de Almeida
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Carlos Eduardo de Rezende
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos Dos Goytacazes, Brazil
| | - Fabiano Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Sala 102, Bloco A, CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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Vestergaard SZ, Dottorini G, Peces M, Murguz A, Dueholm MKD, Nierychlo M, Nielsen PH. Microbial core communities in activated sludge plants are strongly affected by immigration and geography. ENVIRONMENTAL MICROBIOME 2024; 19:63. [PMID: 39210447 PMCID: PMC11361056 DOI: 10.1186/s40793-024-00604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The microbiota in wastewater treatment plants (WWTPs) and incoming wastewater is critical for the treatment process, the preservation of natural ecosystems and human health, and for the recovery of resources and achievement of sustainability goals. Both core species and conditionally rare and abundant taxa (CRAT) are considered process-critical but little is known about identity as well as true functional and ecological importance. Here, we present a comprehensive investigation of the microbiota of 84 municipal activated sludge (AS) plants with nutrient removal treating ~ 70% of all wastewater within a confined geographical area, Denmark (43,000 km2). With the use of an ecosystem-specific database (MiDAS 5.2), species-level classification allowed us to investigate the core and CRAT species, whether they were active, and important factors determining their presence. RESULTS We established a comprehensive catalog of species with names or placeholder names showing each plant contained approx. 2,500 different species. Core and CRAT represented in total 258 species, constituting around 50% of all reads in every plant. However, not all core and CRAT could be regarded as process-critical as growth rate calculations revealed that 43% did not grow in the AS plants and were present only because of continuous immigration from the influent. Analyses of regional microbiota differences and distance decay patterns revealed a stronger effect for species than genera, demonstrating that geography had a clear effect on the AS microbiota, even across a limited geographical area such as Denmark (43,000 km2). CONCLUSIONS The study is the first comprehensive investigation of WWTPs in a confined geographical area providing new insights in our understanding of activated sludge microbiology by introducing a concept of combining immigration and growth calculation with identifying core and CRAT to reveal the true ecosystem-critical organisms. Additionally, the clear biogeographical pattern on this scale highlights the need for more region-level studies to find regional process-critical taxa (core and CRAT), especially at species and amplicon sequence variant (ASV) level.
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Affiliation(s)
- Sofie Zacho Vestergaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Giulia Dottorini
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Miriam Peces
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Admir Murguz
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Morten Kam Dahl Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
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Yuan H, Zhang R, Chen J, Wu J, Han Q, Li Q, Lu Q. Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175860. [PMID: 39214351 DOI: 10.1016/j.scitotenv.2024.175860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray-Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.
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Affiliation(s)
- Haijun Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runyu Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Jingan Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Jing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao Han
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuxing Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; College of Earth Science, Chengdu University of Technology, Chengdu 610059, China
| | - Qiping Lu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Zhu YX, Yang TY, Deng JH, Yin Y, Song ZR, Du YZ. Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet. mSphere 2024; 9:e0038624. [PMID: 39105581 DOI: 10.1128/msphere.00386-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects. IMPORTANCE Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.
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Affiliation(s)
- Yu-Xi Zhu
- Department of Entomology, College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Tian-Yue Yang
- Department of Entomology, College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Jing-Huan Deng
- Department of Entomology, College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yue Yin
- Institute for the Control of the Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhang-Rong Song
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
| | - Yu-Zhou Du
- Department of Entomology, College of Plant Protection, Yangzhou University, Yangzhou, China
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Lu W, Zheng Y, Wang Y, Song J, Weng Y, Ma W, Arslan M, Gamal El-Din M, Wang D, Wang Q, Chen C. Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils. ENVIRONMENTAL RESEARCH 2024; 262:119857. [PMID: 39197484 DOI: 10.1016/j.envres.2024.119857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/01/2024]
Abstract
This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.
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Affiliation(s)
- Wenyi Lu
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Yi Zheng
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Yi Wang
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Jiayu Song
- CNPC Research Institute of Safety and Environmental Technology, Beijing, 102200, China
| | - Yibin Weng
- CNPC Research Institute of Safety and Environmental Technology, Beijing, 102200, China
| | - Wenfeng Ma
- Shandong Institute of Petroleum and Chemical Technology, Dongying, 257061, China
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Dingyuan Wang
- School of Petroleum Engineering, China University of Petroleum, Qingdao, 266580, China
| | - Qinghong Wang
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China.
| | - Chunmao Chen
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
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Zhou H, Yu K, Deng C, Wu B, Gao Y. Deterministic processes influence bacterial more than fungal community assembly during the development of biological soil crusts in the desert ecosystem. Front Microbiol 2024; 15:1404602. [PMID: 39247695 PMCID: PMC11377341 DOI: 10.3389/fmicb.2024.1404602] [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: 03/21/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024] Open
Abstract
Biological soil crusts (biocrusts) constitute a crucial biological component of the soil surface in arid and semi-arid ecosystems. Understanding the variations in soil microbial community assembly across biocrust successional stages is essential for a deeper comprehension of microbial biodiversity and desert ecosystem functioning. However, knowledge about the mechanisms of microbial community assembly and the factors influencing its development remains limited. In this study, we utilized amplicons sequencing to assess the compositions of bacterial and fungal communities in bare sand and three types of biocrusts (light cyanobacterial biocrusts, dark cyanobacterial biocrusts, and moss crusts). Subsequently, we analyzed the ecological processes shaping microbial community composition and structure, along with the influencing factors. Our results revealed a significant increase in bacterial diversity and no significant changes in fungal diversity during biocrust development. The relative abundances of the copiotrophic bacteria (e.g., Actinobacteria, Acidobacteria, and Bacteroidetes) showed significant increases, while oligotrophic bacteria (e.g., Proteobacteria and Firmicutes) decreased over time. Moreover, the relative abundances of Ascomycota, which exhibit strong resistance to adverse environmental conditions, significantly decreased, whereas Basidiomycota, known for their ability to degrade lignin, significantly increased throughout biocrust development. Additionally, stochastic processes (dispersal limitation and drift) predominantly drove the assemblies of both bacterial and fungal communities. However, the relative importance of deterministic processes (homogeneous selection) in bacterial assembly increased during biocrust development. Structural equation modeling indicated that bacterial community assembly was primarily related to soil water content, whereas fungal community assembly was primarily related to total organic carbon. These findings provide a scientific foundation for investigating the formation and development of biocrusts, and further insights into the conservation and sustainable management of biocrust resources under future climate change scenarios.
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Affiliation(s)
- Hong Zhou
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Qinghai Guinan Desert Ecosystem Positioning Observation and Research Station, National Forestry and Grassland Administration, Beijing, China
- Key Laboratory of Desert Ecosystem and Global Change, State Administration of Forestry and Grassland, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chunfang Deng
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Bo Wu
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Desert Ecosystem and Global Change, State Administration of Forestry and Grassland, Beijing, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Ying Gao
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Desert Ecosystem and Global Change, State Administration of Forestry and Grassland, Beijing, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
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Rao G, Song WL, Yan SZ, Chen SL. Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers. Appl Environ Microbiol 2024:e0135924. [PMID: 39171904 DOI: 10.1128/aem.01359-24] [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: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, China
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Xin G, Xiaohong S, Yujiao S, Wenbao L, Yanjun W, Zhimou C, Arvolab L. Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China. Front Microbiol 2024; 15:1448919. [PMID: 39234542 PMCID: PMC11371557 DOI: 10.3389/fmicb.2024.1448919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms in lakes, especially in desert lakes with different salinities. To address this issue, we collected three samples from freshwater lakes, six from brackish lakes, and five from salt lakes in the Badanjilin Desert. The 16S rRNA gene sequencing was applied to investigate the bacterial interactions with rising salinity, community coexistence patterns, and assembly mechanisms. Our findings suggested that the increased lake salinity significantly reduces the bacterial community diversity and enhanced the community differentiation. Significant variations were observed in the contribution of biomarkers from Cyanobacteria, Chloroflexi, and Halobacterota to the composition of the lake bacterial communities. The bacterial communities in the salt lakes exhibited a higher susceptibility to salinity limitations than those in the freshwater and brackish lakes. In addition, the null modeling analyses confirmed the quantitative biases in the stochastic assembly processes of bacterial communities across freshwater, brackish, and saline lakes. With the increasing lake salinity, the significance of undominated and diffusion limitation decreased slightly, and the influence of homogenizing dispersal on community assembly increased. However, the stochasticity remained the dominant process across all lakes in the Badanjilin Desert. The analysis of co-occurring networks revealed that the rising salinity reduced the complexity of bacterial network structures and altered the interspecific interactions, resulting in the increased interspecies collaboration with increasing salinity levels. Under the influence of salinity stress, the key taxon Cyanobacteria in freshwater lakes (Schizothrix_LEGE_07164) was replaced by Proteobacteria (Thalassobaculum and Polycyclovorans) in brackish lakes, and Thermotogota (SC103) in salt lakes. The results indicated the symbiotic patterns of bacterial communities across varying salinity gradients in lakes and offer insights into potential mechanisms of community aggregation, thereby enhancing our understanding of bacterial distribution in response to salinity changes.
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Affiliation(s)
- Guo Xin
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Shi Xiaohong
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
- State Gauge and Research Station of Wetland Ecosystem, Wuliangsuhai Lake, Bayan Nur, China
| | - Shi Yujiao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Li Wenbao
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Wang Yanjun
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Cui Zhimou
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, China
| | - Lauri Arvolab
- Lammi Biological Station, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, Helsinki, Finland
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Wu Z, Xiong X, Liu G, Zhu H. The enhanced neutral process with decreasing cell size: a study on phytoplankton metacommunities from the glacier-fed river of Qinghai-Xizang Plateau. Appl Environ Microbiol 2024:e0045724. [PMID: 39150266 DOI: 10.1128/aem.00457-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/24/2024] [Indexed: 08/17/2024] Open
Abstract
The cell size of phytoplankton is an important defining functional trait that can serve as a driver and sentinel of phytoplankton community structure and function. However, the study of the assembly patterns and drivers of phytoplankton metacommunities with different cell sizes has not been widely carried out. In this study, we systematically investigated the biodiversity patterns, drivers, and assembly processes of the three phytoplankton cell sizes (micro: 20-200 μm; nano: 2-20 μm; pico: 0.2-2 μm) in the Za'gya Zangbo River from the source to the estuary using 18S rDNA amplicon sequencing. The results demonstrated that the alpha diversity and co-occurrence network complexity for all three sizes of phytoplankton increased to a peak downstream of the glacier sources and then decreased to the estuary. The nanophytoplankton subcommunity consistently had the highest alpha diversity and co-occurrence network complexity. On the other hand, total beta diversity followed a unimodal trend of decreasing and then increasing from source to estuary, and was dominated by species replacement components. In addition, deterministic processes driven mainly by physiochemical indices (PCIs) and biogenic elements (BGEs) dominated the assembly of micro- and nanophytoplankton subcommunities, whereas stochastic processes driven by geographical factors (GGFs) dominated the assembly of picophytoplankton subcommunities. The results explained the contradictions in previous studies of phytoplankton community assembly processes in highland aquatic ecosystems, elucidating the different contributions of deterministic and stochastic processes, and the complexity of compositional mechanisms in shaping the assembly of micro-, nano-, and picophytoplankton in this highland glacial river. IMPORTANCE The cell size of phytoplankton is a key life-history trait and key determinant, and phytoplankton of different cell sizes are differentially affected by ecological processes. However, the study of the assembly patterns and drivers of phytoplankton metacommunities with different cell sizes has not been widely carried out. We provide an in-depth analysis of phytoplankton community diversity across three cell sizes in the glacier-fed river, describing how the pattern of phytoplankton communities differs across cell sizes in response to geochemical gradients. The results show that the smaller phytoplankton (picophytoplankton) are relatively more influenced by dispersal-based stochastic processes, whereas larger ones (microphytoplankton and nanophytoplankton) are more structured by selection-based deterministic processes.
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Affiliation(s)
- Zhihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiong Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Huan Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Wu G, Shi W, Zheng L, Wang X, Tan Z, Xie E, Zhang D. Impacts of organophosphate pesticide types and concentrations on aquatic bacterial communities and carbon cycling. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134824. [PMID: 38876013 DOI: 10.1016/j.jhazmat.2024.134824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/01/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Organophosphorus pesticides (OPPs) are important chemical stressors in aquatic ecosystems, and they attract increasing more attentions recently. However, the impacts of different OPPs on carbon cycling remain unclear, particularly for those functional-yet-uncultivable microbes. This study investigated the change in lake aquatic microbial communities in the presence of dichlorvos, monocrotophos, omethoate and parathion. All OPPs significantly inhibited biomass (p < 0.05) and the expression of carbon cycle-related cbbLG gene (p < 0.01), and altered aquatic microbial community structure, interaction, and assembly. Variance partitioning analysis showed a stronger impact of pesticide type on microbial biomass and community structure, where pesticide concentration played more significant roles in carbon cycling. From analysis of cbbLG gene and PICRUSt2, Luteolibacter and Verrucomicrobiaceae assimilated inorganic carbon through Wood-Ljungdahl pathway, whereas it was Calvin-Benson-Bassham cycle for Cyanobium PCC-6307. This work provides a deeper insight into the behavior and mechanisms of microbial community change in aquatic system in response to OPPs, and explicitly unravels the impacts of OPPs on their carbon-cycling functions.
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Affiliation(s)
- Guanxiong Wu
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, PR China
| | - Wei Shi
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, PR China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Zhanming Tan
- College of Horticulture and Forestry, Tarim University, Alar, China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, PR China.
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China.
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Yao L, Wu J, Liu S, Xing H, Wang P, Gao W, Wu Z, Zhou Q. Distinct drivers of bacterial community assembly processes in riverine islands in the middle and lower reaches of the Yangtze River. Microbiol Spectr 2024; 12:e0081824. [PMID: 38869307 PMCID: PMC11302259 DOI: 10.1128/spectrum.00818-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/02/2024] [Indexed: 06/14/2024] Open
Abstract
Riverine islands are widespread alluvium wetlands developed in large rivers, and bacterial communities are crucial to their ecological function, yet their assembly processes are rarely addressed. The ecosystem services provided by the middle and the lower Yangtze are primarily threatened by pollution discharge from agricultural land use, and resource overutilization (e.g., embankments), respectively. Here, we assessed bacterial community assembly processes and their drivers within riverine islands in the middle Yangtze River (MR islands) and those in the lower reach (LR islands). A significant distance-decay relationship was observed, although the turnover rate was lower than that of the terrestrial ecosystem with less connectivity. Deterministic and stochastic processes jointly shaped community patterns, and the influence of stochastic increased from 26% in MR islands to 59% for those in LR islands. Meanwhile, the bacterial community in MR islands was controlled more by inorganic nitrogen availability, whereas those in LR islands were governed by pH and EC, although those factors explained a limited fraction of variation in the bacterial community. Potential indicator taxa (affiliated with Nocardioides and Lysobacter) characterized the waterway transport pollution. Overall, our study demonstrated that bacterial community dissimilarity and the importance of dispersal limitation increased concurrently along the flow direction, while distinct local factors further determined bacterial community compositions by selecting habitat-specificity taxa and particularly metabolism function. These findings enhanced our understanding of the mechanisms driving changes in bacterial communities of riverine islands subject to increased anthropogenic impacts.IMPORTANCERivers are among the most threatened ecosystems globally and face multiple stressors related to human activity. However, linkages between microbial diversity patterns and assembly processes in rivers remain unclear, especially in riverine islands developed in large rivers. Our findings reveal that distinct factors result in divergent bacterial community compositions and functional profiles in the riverine islands in the middle Yangtze and those in the lower Yangtze, with substantial differentiation in deterministic and stochastic processes that jointly contribute to bacterial community assemblages. Additionally, keystone species may play important metabolic roles in coping with human-related disturbances. This study provides an improved understanding of relationships between microbial diversity patterns and ecosystem functions under environmental changes in large river ecosystems.
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Affiliation(s)
- Lu Yao
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Junmei Wu
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shouzhuang Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hao Xing
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Pei Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenjuan Gao
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhenbin Wu
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Qiaohong Zhou
- Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Lin S, Li L, Zhou Z, Yuan H, Saad OS, Tang J, Cai W, Yu K, Lin S. Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef. Microbiol Spectr 2024; 12:e0051424. [PMID: 38874391 PMCID: PMC11302235 DOI: 10.1128/spectrum.00514-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
While in hospite Symbiodiniaceae dinoflagellates are essential for coral health, ambient free-living counterparts are crucial for coral recruitment and resilience. Comparing free-living and in hospite Symbiodiniaceae communities can potentially provide insights into endosymbiont acquisition and recurrent recruitment in bleaching recovery. In this study, we studied coral-endosymbiotic and ambient free-living Symbiodiniaceae communities in the South China Sea. We collected samples from 183 coral and ambient plankton samples and conducted metabarcoding to investigate the diversity distribution, driving factors, and assembly mechanisms of the two groups of Symbiodiniaceae. Results revealed Cladocopium C1 and Durusdinium D1 as dominant genotypes. We detected a higher genotypic diversity in free-living than in hospite symbiodiniacean communities, but with shared dominant genotypes. This indicates a genetically diverse pool of Symbiodiniaceae available for recruitment by corals. Strikingly, we found that the cooler area had more Symbiodiniaceae thermosensitive genotypes, whereas the warmer area had more Symbiodiniaceae thermotolerant genotypes. Furthermore, in hospite and free-living Symbiodiniaceae communities were similarly affected by environmental factors, but shaped by different assembly mechanisms. The in hospite communities were controlled mainly by deterministic processes, whereas the ambient communities by stochastic processes. This study sheds light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms influencing Symbiodiniaceae inside and outside corals.IMPORTANCESymbiodiniaceae dinoflagellates play a pivotal role as key primary producers within coral reef ecosystems. Coral-endosymbiotic Symbiodiniaceae communities have been extensively studied, but relatively little work has been reported on the free-living Symbiodiniaceae community. Conducting a comparative analysis between sympatric coral-endosymbiotic and free-living Symbiodiniaceae communities can potentially enhance the understanding of how endosymbiont communities change in response to changing environments and the mechanisms driving these changes. Our findings shed light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms shaping free-living and in hospite Symbiodiniaceae communities, with implications in evaluating the adaptive and resilient capacity of corals in response to future climate change.
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Affiliation(s)
- Sitong Lin
- 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
| | - Zhi Zhou
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Osama S. Saad
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jia Tang
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Wenqi Cai
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Kefu Yu
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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Schwob G, Almendras K, Veas-Mattheos K, Pezoa M, Orlando J. Host specialization and spatial divergence of bacteria associated with Peltigera lichens promote landscape gamma diversity. ENVIRONMENTAL MICROBIOME 2024; 19:57. [PMID: 39103916 DOI: 10.1186/s40793-024-00598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/21/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments -thalli, substrates, and neighboring soils- were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale. RESULTS The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks. CONCLUSIONS The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria.
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Affiliation(s)
- Guillaume Schwob
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Katerin Almendras
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Karla Veas-Mattheos
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Matías Pezoa
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Julieta Orlando
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
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Ma K, Li Y, Song W, Zhou J, Liu X, Wang M, Gong X, Wang L, Tu Q. Disentangling drivers of mudflat intertidal DOM chemodiversity using ecological models. Nat Commun 2024; 15:6620. [PMID: 39103321 DOI: 10.1038/s41467-024-50841-9] [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: 10/19/2023] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
Microorganisms consume and transform dissolved organic matter (DOM) into various forms. However, it remains unclear whether the ecological patterns and drivers of DOM chemodiversity are analogous to those of microbial communities. Here, a large-scale investigation is conducted along the Chinese coasts to resolve the intrinsic linkages among the complex intertidal DOM pools, microbial communities and environmental heterogeneity. The abundance of DOM molecular formulae best fits log-normal distribution and follows Taylor's Law. Distance-decay relationships are observed for labile molecular formulae, while latitudinal diversity gradients are noted for recalcitrant molecular formulae. Latitudinal patterns are also observed for DOM molecular features. Negative cohesion, bacterial diversity, and molecular traits are the main drivers of DOM chemodiversity. Stochasticity analyses demonstrate that determinism dominantly shapes the DOM compositional variations. This study unveils the intrinsic mechanisms underlying the intertidal DOM chemodiversity and microbial communities from ecological perspectives, deepening our understanding of microbially driven chemical ecology.
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Affiliation(s)
- Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaofan Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China.
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Zhu P, Hu X, Zou Q, Yang X, Jiang B, Zuo J, Bai X, Song J, Wu N, Hou Y. Shifts in fungal community diversity and potential function under natural forest succession and planted forest restoration in the Kunyu Mountains, East China. Ecol Evol 2024; 14:e70055. [PMID: 39157670 PMCID: PMC11327613 DOI: 10.1002/ece3.70055] [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: 12/11/2023] [Revised: 06/12/2024] [Accepted: 07/10/2024] [Indexed: 08/20/2024] Open
Abstract
Soil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine-broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural secondary deciduous broadleaved mixed forests and planted forests of Robinia pseudoacacia on Kunyu Mountain for analysis. We used ITS rRNA gene sequencing to characterize fungal communities and used the FUNGuild database to predict fungal functional groups. The results showed that forest succession affected fungal β-diversity, but not the α-diversity. There was a significant increase in Basidiomycota and a decrease in Ascomycota in the later successional stage, accompanied by an increase in the functional groups of ectomycorrhizal fungi (ECM). Conversely, planted forests exhibited decreased fungal α-diversity and altered community compositions, characterized by fewer Basidiomycota and more Ascomycota and Mucoromycota. Planted forests led to a decrease in the relative abundances of ECM and an increase in animal pathogens. The TK content was the major factor explaining the distinction in fungal communities among the three successional stages, whereas pH, AP, and NH4 + were the major factors explaining community variations between natural and planted forests. Changes in vegetation types significantly affected the diversity and functional groups of soil fungal communities during forest succession and reforestation, providing key insights for forest ecosystem management in temperate forests.
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Affiliation(s)
- Ping Zhu
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Xinyu Hu
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Qiang Zou
- Yantai Science and Technology BureauYantai Science and Technology Innovation Promotion CenterYantaiP.R. China
| | - Xiaoyan Yang
- Department of ParkYantai Kunyu Mountain Forest StationYantaiP.R. China
| | - Bohan Jiang
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Jincheng Zuo
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Xinfu Bai
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Jianqiang Song
- School of Life SciencesLudong UniversityYantaiP.R. China
| | - Nan Wu
- School of Resources and Environmental EngineeringLudong UniversityYantaiP.R. China
| | - Yuping Hou
- School of Life SciencesLudong UniversityYantaiP.R. China
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Chen CZ, Yin MH, Niu LJ, Wang JX, Liu L, Sun YJ, Ju WM, Li P, Li ZH. Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching. MARINE POLLUTION BULLETIN 2024; 205:116658. [PMID: 38964192 DOI: 10.1016/j.marpolbul.2024.116658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.
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Affiliation(s)
| | - Ming-Hao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Lin-Jing Niu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| | - Yong-Jun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wen-Ming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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Sun J, Zhou H, Cheng H, Chen Z, Wang Y. Distinct strategies of the habitat generalists and specialists in the Arctic sediments: Assembly processes, co-occurrence patterns, and environmental implications. MARINE POLLUTION BULLETIN 2024; 205:116603. [PMID: 38885575 DOI: 10.1016/j.marpolbul.2024.116603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 12/25/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
Microorganisms could be classified as habitat generalists and specialists according to their niche breadth, uncovering their survival strategy is a crucial topic in ecology. Here, differences in environmental adaptation, community assemblies, co-occurrence patterns, and ecological functions between generalists and specialists were explored in the Arctic marine sediments. Compared to specialists, generalists showed lower alpha diversity but stronger environmental adaption, and dispersal limitation contributed more to the community assembly of specialists (74 %) than generalists (46 %). Furthermore, the neutral theory model demonstrated that generalists (m = 0.20) had a higher immigration rate than specialists (m = 0.02), but specialists exhibited more complex co-occurrence patterns than generalists. Our results also found that generalists may play more important roles in C, N, S metabolism but are weaker in carbon fixation and xenobiotic biodegradation and metabolism. This study would broaden our understanding of bacterial generalists' and specialists' survival strategies, and further reveal their ecological functions in marine sediments.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China.
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Zheng P, Mao A, Meng S, Yu F, Zhang S, Lun J, Li J, Hu Z. Assembly mechanism of microbial community under different seasons in Shantou sea area. MARINE POLLUTION BULLETIN 2024; 205:116550. [PMID: 38878412 DOI: 10.1016/j.marpolbul.2024.116550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.
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Affiliation(s)
- Peng Zheng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Aihua Mao
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Shan Zhang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Jingsheng Lun
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Jin Li
- College of Life Sciences, China West Normal University, Nanchong 637002, PR China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China.
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46
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Hu M, Zhu Y, Hu X, Zhu B, Lyu S, A Y, Wang G. Assembly mechanism and stability of zooplankton communities affected by China's south-to-north water diversion project. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121497. [PMID: 38897077 DOI: 10.1016/j.jenvman.2024.121497] [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: 01/24/2024] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
Water diversion can effectively alleviate water resource shortages and improve water environmental conditions, while also causing unknown ecological consequences, in particular, the assembly mechanism of zooplankton communities in the affected areas will become more complex after long-term water transfer. Taking Nansi Lake, the second largest impounded lake along the eastern route of China's South to North Water Diversion Project (SNWDP), as an example, the composition and diversity of zooplankton communities in the lake area and estuaries during the water diversion period (WDP) and non-water diversion period (NWDP) were studied. The potential assembly process of zooplankton communities was further explored, and the stability of communities in different regions during different periods was compared. The related results indicated that the changes in water quality conditions induced by water diversion had a relatively weak impact on the zooplankton communities. In the assembly mechanism of zooplankton communities, stochastic process played a more important role during both WDP or NWDP, and the proportion of deterministic process was relatively higher during NWDP, which may be related to the greater role of total nitrogen (TN) in the assembly of the zooplankton communities. The network analysis and cohesion calculation results showed that the stability of the zooplankton communities in the lake area sites was higher than that in the estuary sites, and the stability during NWDP was higher than that during WDP. In sum, the stability of zooplankton communities displayed a degree of change affected by water diversion activities, but the community assembly was not significantly influenced by the water quality fluctuations after about relatively long-term water diversion. This study provides an in-depth understanding of the ecological effects of water diversion on the biological communities in the affected lake, which is beneficial to the management and regulation of long-term water diversion projects.
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Affiliation(s)
- Man Hu
- Key Laboratory of Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China.
| | - Yi Zhu
- Key Laboratory of Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China.
| | - Xiaoyi Hu
- Key Laboratory of Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China; China South-to-North Water Diversion Corporation Eco-environmental Protection Co., Ltd., Beijing, 100036, PR China
| | - Biru Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, PR China.
| | - Shengmei Lyu
- Key Laboratory of Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China.
| | - Yinglan A
- Innovation Research Center of Satellite Application, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, PR China.
| | - Guoqiang Wang
- Innovation Research Center of Satellite Application, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, PR China.
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study. BMC Vet Res 2024; 20:340. [PMID: 39090695 PMCID: PMC11293161 DOI: 10.1186/s12917-024-04125-5] [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: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding the relationship between resident microbiota and disease in cultured fish represents an important and emerging area of study. Marine gill disorders in particular are considered an important challenge to Atlantic salmon (Salmo salar) aquaculture, however relatively little is known regarding the role resident gill microbiota might play in providing protection from or potentiating different gill diseases. Here, 16S rRNA sequencing was used to examine the gill microbiome alongside fish health screening in farmed Atlantic salmon. Results were used to explore the relationship between microbial communities and gill disease. RESULTS Microbial community restructuring was observed throughout the sampling period and linked to varied drivers of change, including environmental conditions and severity of gill pathology. Taxa with significantly greater relative abundance on healthier gills included isolates within genus Shewanella, and taxa within family Procabacteriaceae. In contrast, altered abundance of Candidatus Branchiomonas and Rubritalea spp. were associated with damaged gills. Interestingly, more general changes in community richness and diversity were not associated with altered gill health, and thus not apparently deleterious to fish. Gross and histological gill scoring demonstrated seasonal shifts in gill pathology, with increased severity of gill damage in autumn. Specific infectious causes that contributed to observed pathology within the population included the gill disorder amoebic gill disease (AGD), however due to the uncontrolled nature of this study and likely mixed contribution of various causes of gill disease to observed pathology results do not strongly support an association between the microbial community and specific infectious or non-infectious drivers of gill pathology. CONCLUSIONS Results suggest that the microbial community of farmed Atlantic salmon gills undergo continual restructuring in the marine environment, with mixed influences upon this change including environmental, host, and pathogenic factors. A significant association of specific taxa with different gill health states suggests these taxa might make meaningful indicators of gill health. Further research with more frequent sampling and deliberate manipulation of gills would provide important advancement of knowledge in this area. Overall, although much is still to be learnt regarding what constitutes a healthy or maladapted gill microbial community, the results of this study provide clear advancement of the field, providing new insight into the microbial community structure of gills during an annual production cycle of marine-stage farmed Atlantic salmon.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Sitka Sound Science Center, Alaska, Sitka, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- Scottish Association for Marine Science, Oban, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, University of Aberdeen, Aberdeen, UK
| | | | - David E K Ferrier
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
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Wei J, Chen W, Wen D. Rare biosphere drives deterministic community assembly, co-occurrence network stability, and system performance in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2024; 190:108887. [PMID: 39024826 DOI: 10.1016/j.envint.2024.108887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Bacterial community is strongly associated with activated sludge performance, but there still remains a knowledge gap regarding the rare bacterial community assembly and their influence on the system performance in industrial wastewater treatment plants (IWWTPs). Here, we investigated bacterial communities in 11 full-scale IWWTPs with similar process designs, aiming to uncover ecological processes and functional traits regulating abundant and rare communities. Our findings indicated that abundant bacterial community assembly was governed by stochastic processes; thereby, abundant taxa are generally present in wastewater treatment compartments across different industrial types. On the contrary, rare bacterial taxa were primarily driven by deterministic processes (homogeneous selection 61.9%-79.7%), thus they only exited in specific IWWTPs compartments and wastewater types. The co-occurrence networks analysis showed that the majority of keystone taxa were rare bacterial taxa, with rare taxa contributing more to network stability. Furthermore, rare bacteria rather than abundant bacteria in the oxic compartment contributed more to the degradation of xenobiotics compounds, and they were main potential drivers of pollutant removal. This study demonstrated the irreplaceable roles of rare bacterial taxa in maintaining system performance of IWWTPs, and called for environmental engineers and microbial ecologists to increase their attention on rare biosphere.
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Affiliation(s)
- Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Zou J, Xiao Y, Wu P, Wang T, Lin L, Liu Y, Liu Y, Li C. Distribution, community structure and assembly patterns of phytoplankton in the northern South China Sea. Front Microbiol 2024; 15:1450706. [PMID: 39144206 PMCID: PMC11322478 DOI: 10.3389/fmicb.2024.1450706] [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: 06/18/2024] [Accepted: 07/23/2024] [Indexed: 08/16/2024] Open
Abstract
A cruise was conducted in the summer of 2023 from the Pearl River Estuary (PRE) to the adjacent waters of the Xisha Islands in the northern South China Sea (NSCS) to investigate the distribution, community structure, and assembly patterns of eukaryotic and prokaryotic phytoplankton using high-throughput sequencing (HTS) and microscopic observation. Dinophyta were the most abundant phylum in the eukaryotic phytoplankton community based on HTS, accounting for 92.17% of the total amplicon sequence variants (ASVs). Syndiniales was the most abundant order among eukaryotic phytoplankton, whereas Prochlorococcus was the most abundant genus within cyanobacteria. The alpha diversity showed the lowest values in the PRE area and decreased gradually with depth, while cyanobacteria exhibited higher alpha diversity indices in the PRE and at depths ranging from 75 m to 750 m. The morphological results were different from the data based on HTS. Diatoms (37 species) dominated the phytoplankton community, with an average abundance of 3.01 × 104 cells L-1, but only six species of dinoflagellate were observed. Spearman correlation analysis and redundancy analysis (RDA) showed that the distribution and community structure of phytoplankton were largely influenced by geographical location and environmental parameters in the NSCS. The neutral community model (NCM) and null model indicated that deterministic processes played a significant role in the assembly of eukaryotic phytoplankton, with heterogeneous selection and homogeneous selection accounting for 47.27 and 29.95%, respectively. However, stochastic processes (over 60%) dominated the assembly of cyanobacteria and undominated processes accounted for 63.44%. In summary, the formation of eukaryotic phytoplankton was mainly influenced by environmental factors and geographic location, but the assembly of cyanobacteria was shaped by both stochastic processes, which accounted for over 60%, and environmental selection in the NSCS.
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Affiliation(s)
- Jian Zou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
| | - Yayuan Xiao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
| | - Peng Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
| | - Teng Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
- Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Lin Lin
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
| | - Yu Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
- Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Yong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
| | - Chunhou Li
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou, China
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50
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Miao W, Wang S, Lin T, Yan Y, Bao Z, Zhang D, Jiang Z, Zhang H. Interaction patterns and assembly mechanisms of dinoflagellates and diatoms in a coastal bay suffering from long-term eutrophication. mSphere 2024; 9:e0036624. [PMID: 38940511 PMCID: PMC11288026 DOI: 10.1128/msphere.00366-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Dinoflagellates and diatoms are highly prevalent and ecologically important phytoplankton in coastal waters, greatly contributing to primary productivity in marine ecosystems. Although their composition and diversity have been extensively elucidated in the open ocean, their interaction patterns and community assembly in long-term eutrophic coastal waters remain poorly understood. This investigation aimed to elucidate the seasonal successional patterns of dinoflagellates and diatoms by 18S rRNA gene amplicon sequencing in a semi-enclosed bay. The results revealed that dinoflagellate and diatom communities have pronounced seasonal succession patterns, which are primarily associated with temperature. Furthermore, the most prevalent species throughout the year were Heterocapsa rotundata and Skeletonema costatum. Moreover, the assembly of dinoflagellate and diatom communities was mainly dominated by stochastic processes, with drift being the major factor. The co-occurrence of dinoflagellates and diatoms showed seasonal patterns, with the highest interactions observed in autumn. In addition, interactions of Syndiniales with dinoflagellates and diatoms highlighted the roles of parasites in eutrophic conditions. Flavobacteriaceae and Rhodobacteraceae are the bacterial taxa that most frequently interacted with dinoflagellates and diatoms, with interactions between dinoflagellates and bacteria being more complex than those between diatoms and bacteria. Overall, this study provides results that deepen our understanding of the phytoplankton dynamics in coastal eutrophic waters.IMPORTANCEDinoflagellates and diatoms are major phytoplankton groups in coastal waters. The composition and diversity of dinoflagellates and diatoms in the open ocean have been well documented; however, it remains uncertain to what extent their adaptation to long-term eutrophic conditions influences their response to environmental disturbances. Here, we investigated the interactions and assembly processes of dinoflagellates and diatoms in a eutrophic bay throughout the whole year. Our findings revealed that interactions between dinoflagellates and diatoms are primarily shaped by seasonal transitions, while prolonged eutrophic conditions tend to amplify stochastic processes in community assembly. These findings provide novel perspectives on the influence of long-term eutrophication on phytoplankton dynamics within eutrophic waters.
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Affiliation(s)
- Wenfei Miao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shuqi Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Tenghui Lin
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen Bao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Zhibing Jiang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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