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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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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] [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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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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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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