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Xu J, Wang Y, Liu L, Wang X, Xiao S, Chen J, Jiao N, Zheng Q. Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174883. [PMID: 39034013 DOI: 10.1016/j.scitotenv.2024.174883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.
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Affiliation(s)
- Jinxin Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Lu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Xiaomeng Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Shicong Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Jiaxin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, PR China.
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Xian WD, Ding J, Chen J, Qu W, Cao P, Tang C, Liu X, Zhang Y, Li JL, Wang P, Li WJ, Wang J. Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary. MICROBIAL ECOLOGY 2024; 87:42. [PMID: 38356037 DOI: 10.1007/s00248-024-02350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.
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Affiliation(s)
- Wen-Dong Xian
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Junjie Ding
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Jinhui Chen
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Pinglin Cao
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Chunyu Tang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Yiying Zhang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China.
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Qu W, Zuo Y, Zhang Y, Wang J. Structure and assembly process of fungal communities in the Yangtze River Estuary. Front Microbiol 2024; 14:1220239. [PMID: 38260888 PMCID: PMC10800840 DOI: 10.3389/fmicb.2023.1220239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.
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Affiliation(s)
| | | | | | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Lin L, Xiong J, Liu L, Wang F, Cao W, Xu W. Microbial interactions strengthen deterministic processes during community assembly in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167499. [PMID: 37778550 DOI: 10.1016/j.scitotenv.2023.167499] [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: 06/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Systematic studies on the assembly process and driving mechanisms of microbial communities in estuaries with diverse seasonal and spatial scales are still limited. In this study, high-throughput sequencing, and microbial network analysis were combined to decipher the impact of environmental changes and biological interactions on the maintenance of microbial diversity patterns in the Jiulong River Estuary (JRE). The results showed that overall, stochastic processes dominated the bacterioplankton community assembly in the estuary, accounting for 49.66-74.78 % of the total. Additionally, bacterioplankton community diversity varied significantly across seasons and subzones. Specifically, the concentration of soluble reactive phosphorus (SRP) in the estuary steadily reduced from winter to summer, and the corresponding bacterioplankton community interactions gradually shifted from the weakest interaction in winter to the strongest in summer. The deterministic processes contributed more than half (50.34 %) to microbial assembly in the summer, but only 25.22 % in winter. Deterministic processes prevailed in the seaward with low SRP concentrations and strong bacterioplankton community interactions, while stochastic processes contributed 70.14 % to the assembly of microbial communities riverward. Biotic and abiotic factors, such as nutrients and microbial interactions, jointly drove the seasonal and spatial patterns of bacterioplankton community assembly, but overall, nutrients played a dominant role. Nevertheless, the contributions of nutrients and microbial interactions were equivalent in spatial assembly processes, albeit nutrients were the primary seasonal driver of the bacterioplankton community assembly process. This study emphasizes the significance of microbial interactions in the bacterioplankton community assemblage. These findings provide new and comprehensive insights into the microbial communities' organization in estuaries.
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Affiliation(s)
- Ling Lin
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China.
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China.
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Zou K, Zhu Y, Jiang Y, Ma S, Li M, Zhao W, Wang J. Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132161. [PMID: 37523960 DOI: 10.1016/j.jhazmat.2023.132161] [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: 05/15/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
| | - Yiyi Zhu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Yun Jiang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shanshan Ma
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangzhou 510300, Guangdong Province, China
| | - Wencheng Zhao
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Jun Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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Liu J, Wang X, Liu J, Liu X, Zhang XH, Liu J. Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea. Front Microbiol 2022; 13:1003623. [PMID: 36386657 PMCID: PMC9641972 DOI: 10.3389/fmicb.2022.1003623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2022] [Indexed: 10/10/2023] Open
Abstract
Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.
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Affiliation(s)
- Jinmei Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiao Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoyue Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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