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Huang Z, Shu L, He Z, Yan Q. Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits. ENVIRONMENTAL RESEARCH 2024; 257:119272. [PMID: 38823613 DOI: 10.1016/j.envres.2024.119272] [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: 03/16/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.
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Affiliation(s)
- Zhenyu Huang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for 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), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for 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), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Chang C, Hu E, Shi Y, Pan B, Li M. Linking microbial community coalescence to ecological diversity, community assembly and species coexistence in a typical subhumid river catchment in northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173367. [PMID: 38796011 DOI: 10.1016/j.scitotenv.2024.173367] [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: 01/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Community coalescence denotes the amalgamation of biotic and abiotic factors across multiple intact ecological communities. Despite the growing attention given to the phenomenon of coalescence, there remains limited investigation into community coalescence in single and multiple source habitats and its impact on microbial community assemblages in sinks. This study focused on a major river catchment in northern China. We investigated microbial community coalescence across different habitats (i.e., water, sediment, biofilm, and riparian soil) and seasons (i.e., summer and winter). Using 16S rRNA gene amplicon sequence variants, we examined the relationship between community coalescence and microbial diversity, assembly processes, and species coexistence. The results showed that the intensity of microbial community coalescence was higher in the same habitat pairs compared to disparate habitat pairs in both summer and winter. During the occurrence of microbial community coalescence, the assembly processes regulated the intensity of coalescence. When the microbial community exhibited strong heterogeneous selection (heterogeneous environmental conditions leading to more dissimilar community structures), the intensity of community coalescence was low. With the assembly process shifted towards stochasticity, coalescence intensity increased gradually. However, when homogeneous selection (homogeneous environmental conditions leading to more similar community structures) predominantly shaped microbial communities, coalescence intensity exceeded the threshold of 0.25-0.30. Moreover, the enhanced intensity of community coalescence could increase the complexity of microbial networks, thereby enhancing species coexistence. Furthermore, the assembly processes mediated the relationship between community coalescence and species coexistence, underscoring the pivotal role of intermediate intensity of community coalescence in maintaining efficient species coexistence. In conclusion, this study highlights the crucial role of community coalescence originating from single and multiple source habitats in shaping microbial communities in sinks, thus emphasizing its central importance in watershed ecosystems.
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Affiliation(s)
- Chao Chang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - En Hu
- Shaanxi Provincial Academy of Environmental Science, Xi'an 710061, Shaanxi, China
| | - Yifei Shi
- Shaanxi Environmental Investigation and Assessment Center, Xi'an 710054, Shaanxi, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
| | - Ming Li
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China.
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3
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Bandla A, Akhtar H, Lupascu M, Sukri RS, Swarup S. Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly. NPJ Biofilms Microbiomes 2024; 10:8. [PMID: 38253600 PMCID: PMC10803758 DOI: 10.1038/s41522-024-00478-9] [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: 04/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.
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Affiliation(s)
- Aditya Bandla
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hasan Akhtar
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
- School of Liberal Arts and Sciences, RV University, Bengaluru, Karnataka, India
| | - Massimo Lupascu
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Rahayu Sukmaria Sukri
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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4
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Liu X, Salles JF. Drivers and consequences of microbial community coalescence. THE ISME JOURNAL 2024; 18:wrae179. [PMID: 39288091 PMCID: PMC11447283 DOI: 10.1093/ismejo/wrae179] [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: 05/28/2024] [Revised: 07/14/2024] [Accepted: 09/16/2024] [Indexed: 09/19/2024]
Abstract
Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.
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Affiliation(s)
- Xipeng Liu
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Ecologie Microbienne Lyon, Centre National de la Recherche Scientifique (CNRS) UMR5557, Bâtiment Grégoire Mendel, 69100 Villeurbanne, France
| | - Joana Falcão Salles
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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5
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Simon E, Guseva K, Darcy S, Alteio L, Pjevac P, Schmidt H, Jenab K, Ranits C, Kaiser C. Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. THE ISME JOURNAL 2024; 18:wrae156. [PMID: 39105276 PMCID: PMC11325450 DOI: 10.1093/ismejo/wrae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/29/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.
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Affiliation(s)
- Eva Simon
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Sean Darcy
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, 3430 Tulln, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Kian Jenab
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christian Ranits
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
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Sieber G, Drees F, Shah M, Stach TL, Hohrenk-Danzouma L, Bock C, Vosough M, Schumann M, Sures B, Probst AJ, Schmidt TC, Beisser D, Boenigk J. Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:167457. [PMID: 37777125 DOI: 10.1016/j.scitotenv.2023.167457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods. The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.
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Affiliation(s)
- Guido Sieber
- Biodiversity, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany.
| | - Felix Drees
- Instrumental Analytical Chemistry, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Manan Shah
- Biodiversity, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Tom L Stach
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Lotta Hohrenk-Danzouma
- Instrumental Analytical Chemistry, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany
| | - Maryam Vosough
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Mark Schumann
- Aquatic Ecology, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany
| | - Bernd Sures
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Aquatic Ecology, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Alexander J Probst
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Torsten C Schmidt
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Universitätsstraße. 5, Germany
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Bosch J, Némethová E, Tláskal V, Brabcová V, Baldrian P. Bacterial, but not fungal, communities show spatial heterogeneity in European beech (Fagus sylvatica L.) deadwood. FEMS Microbiol Ecol 2023; 99:fiad023. [PMID: 36906283 PMCID: PMC10065134 DOI: 10.1093/femsec/fiad023] [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: 12/12/2022] [Revised: 02/09/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023] Open
Abstract
Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communities sampled with either traditional, composite samples, or small, 1 cm3 cylinders from a discrete location within decomposing European beech (Fagus sylvatica L.) tree trunks. We found that bacterial richness and evenness is lower in small samples when compared to composite samples. There was no significant difference in fungal alpha diversity between different sampling scales, suggesting that visually defined fungal domains are not restricted to a single species. Additionally, we found that composite sampling may obscure variation in community composition and this affects the understanding of microbial associations that are detected. For future experiments in environmental microbiology, we recommend that scale is explicitly considered as a factor and properly selected to correspond with the questions asked. Studies of microbial functions or associations may require samples to be collected at a finer scale than is currently practised.
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Affiliation(s)
- Jason Bosch
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Ema Némethová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
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