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Zhang D, Bao Y, Wang Y, Feng J, Li R, Du Y, Wang D, Chen F, Li S, Wen J, Chen Z. Coalescence characteristics of free-living and particle-attached bacteria in a cascade river-reservoir system: A case study of the Jinsha River. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 374:124088. [PMID: 39805160 DOI: 10.1016/j.jenvman.2025.124088] [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: 09/13/2024] [Revised: 12/11/2024] [Accepted: 01/07/2025] [Indexed: 01/16/2025]
Abstract
Microbial coalescence plays a crucial role in shaping aquatic ecosystems by facilitating the merging of neighboring microbial communities, thereby influencing ecosystem structure. Although this phenomenon is commonly observed in natural environments, comprehensive quantitative comparative studies on different lifestyle bacteria involved in this process are still lacking. The study focuses on 16S rRNA Amplicon Sequence Variants (ASVs) at the Jinsha River hydropower stations (Wudongde [WDD], Baihetan [BHT], Xiluodu [XLD], Xiangjiaba [XJB]), specifically examining free-living (FL) and particle-attached (PA) bacteria. Minimal differences in microbial composition were observed across water layers (surface, middle, and bottom). Analyses of overlapping ASVs, Bray-Curtis dissimilarity, and the SourceTracker algorithm revealed a significant difference in the coalescence ability of FL and PA bacteria, particularly in the surface water of XJB (FL: 31.1% ± 2.0%, PA: 27.6% ± 2.5%, p < 0.05). The coalescence of FL bacteria was primarily influenced by the mixing of adjacent water layers, while PA bacteria exhibited significant geographical variations across water layers (p < 0.05), displaying lower coalescence compared to FL bacteria. Using a cohesion metric, 12 keystone species in PA bacteria were identified and 7 in FL bacteria. Proteobacteria and Bacteroidetes were the most abundant phyla at the keystone species in PA and FL bacteria, respectively. The abundance of keystone ASVs decreased with distance in PA bacteria, whereas FL bacteria showed the opposite trend. At the genus level, Brevundimonas and Chryseobacterium were identified as keystone species in both lifestyles. Moreover, the impact of community coalescence on the stability tends to exhibit differences downstream in cascade stations. This study provides novel insights into the dynamic variations of microbial communities with diverse lifestyles in stratified aquatic environments and assesses the impact of dam construction on microbial coalescence and the alteration of keystone species.
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Affiliation(s)
- Dan Zhang
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China; State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China; Ecological Environment Engineering Research Center of the Yangtze River, China Three Gorges Corporation, Wuhan, 430014, China
| | - Yufei Bao
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China.
| | - Yuchun Wang
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China.
| | - Jingjie Feng
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Ran Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yanliang Du
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Dianchang Wang
- Ecological Environment Engineering Research Center of the Yangtze River, China Three Gorges Corporation, Wuhan, 430014, China
| | - Fei Chen
- Ecological Environment Engineering Research Center of the Yangtze River, China Three Gorges Corporation, Wuhan, 430014, China
| | - Shanze Li
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Jie Wen
- State Key Laboratory of Watershed Water Cycle Simulation and Regulation, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Zhuo Chen
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
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Adhikari NP, Adhikari S, Rijal KR. Community composition and co-occurrence of free-living and particle-attached bacteria in the source region of the Ganges and Brahmaputra Rivers. Int Microbiol 2024:10.1007/s10123-024-00607-6. [PMID: 39400629 DOI: 10.1007/s10123-024-00607-6] [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: 08/15/2024] [Revised: 10/06/2024] [Accepted: 10/08/2024] [Indexed: 10/15/2024]
Abstract
Bacteria have two trophic lifestyles in aquatic ecosystems, i.e., free-living (FL) and particle-attached (PA), with different but essential ecological roles. However, relevant knowledge is still dearth in the upstream source region of the Himalayan Rivers. Thus, we emphasized a comparative study on community composition, co-occurrence, and geographic distribution of the FL and PA bacteria and the effect of environmental factors in the source region of the Ganges and Brahmaputra Rivers. PA bacteria relative to FL harbored a significantly higher local diversity, richness, and evenness. A significantly higher abundance of Betaproteobacteria, Verrucomicrobiota, and Planctomycetota in PA trophic lifestyle and Gammaproteobacteria and Actinomycetota in FL tropic lifestyle and indicator OTUs belonging to related taxa were observed. The spatial variation of the FL and PA bacterial communities was most significantly impacted by dispersal limitation as a discrete factor. Among the environmental parameters, the total nitrogen (TN) was found to be a significant (P < 0.001) driver of the variation in PA communities. Meanwhile, particulate organic carbon (POC) and TN considerably explained the variation of FL communities. A significant correlation (P < 0.001) of TN with dominant bacterial taxa (Pseudomonadota, Actinomycetota, and Verrucomicrobiota) and FL and PA indicator OTUs associated with these taxa further confirmed nitrogen as the limiting nutrient in the source region of the Ganges and Brahmaputra Rivers. The co-occurrence network topological characteristics showed that the PA network was more stable than the FL network, which was more complicated and unstable. Thus, it can be speculated that FL communities relative to PA are more vulnerable to shifting upon disturbances.
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Affiliation(s)
- Namita Paudel Adhikari
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Subash Adhikari
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Komal Raj Rijal
- Central Department of Microbiology, Tribhuvan University, Kirtipur, 44613, Kathmandu, Nepal
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Radford EJ, Whitworth DE. The genetic basis of predation by myxobacteria. Adv Microb Physiol 2024; 85:1-55. [PMID: 39059819 DOI: 10.1016/bs.ampbs.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Myxobacteria (phylum Myxococcota) are abundant and virtually ubiquitous microbial predators. Facultatively multicellular organisms, they are able to form multicellular fruiting bodies and swarm across surfaces, cooperatively hunting for prey. Myxobacterial communities are able to kill a wide range of prey microbes, assimilating their biomass to fuel population growth. Their mechanism of predation is exobiotic - hydrolytic enzymes and toxic metabolites are secreted into the extracellular environment, killing and digesting prey cells from without. However, recent observations of single-cell predation and contact-dependent prey killing challenge the dogma of myxobacterial predation being obligately cooperative. Regardless of their predatory mechanisms, myxobacteria have a broad prey range, which includes Gram-negative bacteria, Gram-positive bacteria and fungi. Pangenome analyses have shown that their extremely large genomes are mainly composed of accessory genes, which are not shared by all members of their species. It seems that the diversity of accessory genes in different strains provides the breadth of activity required to prey upon such a smorgasbord of microbes, and also explains the considerable strain-to-strain variation in predatory efficiency against specific prey. After providing a short introduction to general features of myxobacterial biology which are relevant to predation, this review brings together a rapidly growing body of work into the molecular mechanisms and genetic basis of predation, presenting a summary of current knowledge, highlighting trends in research and suggesting strategies by which we can potentially exploit myxobacterial predation in the future.
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Affiliation(s)
- Emily J Radford
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - David E Whitworth
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
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Wang S, Zhuang Y, Gao L, Huang H, Zhang X, Jia S, Shi P, Zhang XX. Deciphering the dynamics and driving mechanisms of high-risk antibiotic resistome in size-fractionated bacterial community during drinking water chlorination via metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133572. [PMID: 38280321 DOI: 10.1016/j.jhazmat.2024.133572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/03/2024] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
To reveal the impact of chlorination on the high-risk resistome in size-fractionated bacterial community, we employed metagenomic approaches to decipher dynamics of high-risk antibiotic resistance genes (ARGs) and driving mechanisms in the free-living and particle-associated fractions within a full-scale drinking water treatment system. Our results revealed that chlorination significantly increased the relative abundance of high-risk ARGs in the free-living fraction to 0.33 ± 0.005 copies/cell (cpc), bacitracin and chloramphenicol resistance types were major contributors. Furthermore, chlorination significantly increased the relative abundance of mobile genetic elements (MGEs) in the free-living fraction, while decreasing it in the particle-associated fraction. During chlorination, size-fractionated bacterial communities varied considerably. Multiple statistical analyses highlighted the pivotal role of the bacterial community in altering high-risk ARGs in both the free-living and particle-associated fractions, while MGEs had a more pronounced impact on high-risk ARGs in the free-living fraction. Specifically, the enrichment of pathogenic hosts, such as Comamonas and Pseudomonas, led to an increase in the abundance of high-risk ARGs. Concurrently, MGEs exhibited significant correlations with high-risk ARGs, indicating the potential of horizontal transfer of high-risk ARGs. These findings provide novel insights for mitigating antibiotic resistance risk by considering different bacterial fractions and respective risk ranks in drinking water.
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Affiliation(s)
- Shuya Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Zhuang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Linjun Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongbin Huang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xian Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuyu Jia
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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Izabel-Shen D, Höger AL, Jürgens K. Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles. Front Microbiol 2021; 12:690712. [PMID: 34262550 PMCID: PMC8273345 DOI: 10.3389/fmicb.2021.690712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/25/2021] [Indexed: 01/23/2023] Open
Abstract
Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Anna-Lena Höger
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
- Department of Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Klaus Jürgens
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
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