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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:e0036624. [PMID: 38940511 DOI: 10.1128/msphere.00366-24] [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: 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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Li Z, Xu K, Meng M, Xu Y, Ji D, Wang W, Xie C. Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172692. [PMID: 38663622 DOI: 10.1016/j.scitotenv.2024.172692] [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: 11/19/2023] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/09/2024]
Abstract
The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.
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Affiliation(s)
- Zongtang Li
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Muhan Meng
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
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Zheng Y, Li S, Feng X, He X, Li Y. Seasonality regulates the distinct assembly patterns of microeukaryotic plankton communities in the Three Gorges Reservoir, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:37705-37716. [PMID: 38780846 DOI: 10.1007/s11356-024-33613-2] [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: 01/03/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
The hydrographic and environmental factors along the Three Gorges Reservoir (TGR) have been significantly altered since the Three Gorges Dam (TGD) began working in 2006. Here, we collected 54 water samples, and then measured the environmental factors, followed by sequencing of the 18S rRNA gene and subsequent analysis of community assembly mechanisms. The findings indicated that the majority of environmental variables (such as AN, TP, Chl-a, CODMn, and Cu) exhibited both temporal and spatial variations due to the influences of the TGD. The distribution of different environmental factors and microeukaryotic plankton communities is influenced by the changing seasons. The community structure in TGR showed variations across three seasons, possibly due to variations in their environmental preferences, inherent dissimilarities, and seasonal succession. Furthermore, different communities exhibited a comparable distance-decay trend, suggesting that distinct taxa are likely to exhibit a similar spatial distribution. In addition, the community formation in TGR was influenced by both deterministic and stochastic factors, with the balance between them being mainly controlled by the season. Specifically, deterministic processes could explain 33.9-51.1% of community variations, while stochastic processes could contribute 23.5-32.2%. The findings of this research demonstrated that the varying ecological processes' significance relied on environmental gradients, geographical scale, and ecological conditions. This could offer a fresh outlook on comprehending the composition, assembly mechanisms, and distribution patterns of microeukaryotic plankton in reservoir ecosystems.
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Affiliation(s)
- Yu Zheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Suping Li
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xiao Feng
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xinhua He
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
- School of Biological Sciences, University of Western, Australia, Perth, WA, 6009, Australia
| | - Yong Li
- College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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Fu Y, Qu Z, Wang Y, Sun P, Jiao N, Xu D. Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding. Microbiol Spectr 2024; 12:e0242423. [PMID: 38488393 PMCID: PMC10986530 DOI: 10.1128/spectrum.02424-23] [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: 06/12/2023] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.
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Affiliation(s)
- Yingjun Fu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Zhishuai Qu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Ying Wang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, 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, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Wang D, Huang Y, Jia H, Yang H. Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau. Microorganisms 2023; 12:32. [PMID: 38257859 PMCID: PMC10821157 DOI: 10.3390/microorganisms12010032] [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: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.
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Affiliation(s)
- Dandan Wang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, China
| | - Yuefei Huang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Haichao Jia
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
| | - Haijiao Yang
- School of Civil Engineering and Water Resources, Qinghai University, Xining 810016, China; (D.W.); (H.J.); (H.Y.)
- Key Laboratory of Ecological Protection and High Quality Development in the Upper Yellow River, Qinghai University, Xining 810016, China
- Key Laboratory of Water Ecological Remediation and Protection at Headwater Regions of Big Rivers, Qinghai University, Xining 810016, 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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Xu Z, Chen J, Li Y, Shekarriz E, Wu W, Chen B, Liu H. High Microeukaryotic Diversity in the Cold-Seep Sediment. MICROBIAL ECOLOGY 2023; 86:2003-2020. [PMID: 36973438 DOI: 10.1007/s00248-023-02212-y] [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: 10/29/2022] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.
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Affiliation(s)
- Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yingdong Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Erfan Shekarriz
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenxue Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Bingzhang Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, China.
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Wu J, Zhu Z, Waniek JJ, Niu M, Wang Y, Zhang Z, Zhou M, Zhang R. The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters. MARINE ENVIRONMENTAL RESEARCH 2023; 184:105873. [PMID: 36628821 DOI: 10.1016/j.marenvres.2023.105873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.
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Affiliation(s)
- Jinnan Wu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Zhu Zhu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
| | - Joanna J Waniek
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, 18119, Rostock, Germany
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yuntao Wang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 310000, Hangzhou, Zhejiang, China
| | - Zhaoru Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Meng Zhou
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
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Xiong S, Wang K, Yan H, Hou D, Wang Y, Li M, Zhang D. Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients. Front Microbiol 2022; 13:922580. [PMID: 36406438 PMCID: PMC9669582 DOI: 10.3389/fmicb.2022.922580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/29/2022] [Indexed: 09/17/2023] Open
Abstract
Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.
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Affiliation(s)
- Shangling Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yanting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Meng Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
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10
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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11
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Zhang H, Yan Y, Lin T, Xie W, Hu J, Hou F, Han Q, Zhu X, Zhang D. Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay. Microbiol Spectr 2022; 10:e0148122. [PMID: 35638815 PMCID: PMC9241920 DOI: 10.1128/spectrum.01481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/08/2022] [Indexed: 11/24/2022] Open
Abstract
Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Yi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Weijuan Xie
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Fanrong Hou
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Qingxi Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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12
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Zhang R, Liu Y, Zhao X, Zhang H, Zhao Z, Shang Z, Lan W. Eukaryotic communities in coastal water from Shenzhen in South China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1644-1651. [PMID: 33452970 DOI: 10.1007/s10646-020-02341-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] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Eukaryotic microorganisms are ubiquitous in the marine environment, and have a wide variety of ecosystem functions. Shenzhen is one of the most developed cities in South China, but the eukaryotic communities in the water along its coastlines remain poorly understood. The study applied 18S rRNA gene ITS (internal transcribed spacer) sequencing to identify the eukaryotic community from twenty sites of Shenzhen coast water. The alpha-diversity of the samples between these sites were significantly different, and the seawater of eastern coast had higher alpha-diversity compared to that of the western coast. The abundance of Chlorophyta was notably higher in the seawater of western coast, but Picozoa was relatively depleted. Specifically, Cryptocaryon, Pseudovorticella, and Cyclotella were significantly higher in the water of western coast, while Guinardia, Minutocellus, and Amoebophrya were increased in eastern samples. The spatially variations of eukaryotic microorganism community in the seawater of Shenzhen coast were associated with the water quality. The results have important significance for the understanding of coastal eukaryotic community, their interaction network, and build a foundation for future management and protection of coastal water quality.
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Affiliation(s)
- Rui Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China.
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China.
| | - Yu Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Xianfeng Zhao
- R&D Key Laboratory of Alien Pest Detection Technology, the Shenzhen Academy of Science and Technology for Inspection and Quarantine. Technology Center for Animal and plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China
| | - Honglian Zhang
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Zhihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Zhuangzhuang Shang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Wensheng Lan
- R&D Key Laboratory of Alien Pest Detection Technology, the Shenzhen Academy of Science and Technology for Inspection and Quarantine. Technology Center for Animal and plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China.
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13
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Abdullah Al M, Xue Y, Xiao P, Chen H, Zhang C, Duan M, Yang J. DNA metabarcoding reveals the significant influence of anthropogenic effects on microeukaryotic communities in urban waterbodies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117336. [PMID: 34052609 DOI: 10.1016/j.envpol.2021.117336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/02/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Biological monitoring and assessment are the first and most fundamental steps towards diagnosing ecological or environmental quality. Increasing anthropogenic impact on urban ecosystems has prompted the development of less expensive and more efficient bioassessment approaches. Generally, a morphospecies based approach is effective for plants and large organisms but challenging for the microbial biosphere. To overcome this challenge, we used high-throughput DNA sequencing for predicting anthropogenic effects on microeukaryotic communities in urban waterbodies along a pollution gradient in Wuhan City, central China in summer 2019. Our results indicated that microeukaryotic community structure was distinct between non-urban polluted reservoir and urban polluted waterbodies. The heterogeneity of environmental condition significantly affected the microeukaryotic diversity, community structure, and species interactions. Integrated co-occurring network analysis revealed that the pollution gradient has a significant adverse impact on network complexity and network dissimilarity. These results revealed that the significant variation in anthropogenically-driven environmental condition shaped microeukaryotic communities in urban freshwater ecosystems. Furthermore, we observed that the relative abundance of indicative OTUs were significantly and negatively correlated with pollution level and these indicative OTUs could be used to predict the water quality status with up to 77% success. Thus, our multiple approaches combining 18S rDNA amplicon sequencing, co-occurring network and indicator species analyses suggest that this study gives a novel approach based on microeukaryotic communities to assess and predict the water quality status of urban aquatic environments.
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Affiliation(s)
- Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Institute of Marine Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Chaoshuo Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Ming Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China.
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14
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Zou K, Wang R, Xu S, Li Z, Liu L, Li M, Zhou L. Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence. WATER RESEARCH 2021; 200:117294. [PMID: 34102388 DOI: 10.1016/j.watres.2021.117294] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.
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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
| | - Ruili 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
| | - Shannan Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China
| | - Zhuoying Li
- 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
| | - Li Liu
- 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
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China.
| | - Lei Zhou
- 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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15
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Huang D, Zhang Z, Sun M, Feng Z, Ye M. Characterization and ecological function of bacterial communities in seabed sediments of the southwestern Yellow Sea and northwestern East China Sea, Western Pacific. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143233. [PMID: 33158535 DOI: 10.1016/j.scitotenv.2020.143233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
The marine ecosystems of the marginal seas of the Western Pacific region are frequently disturbed by terrigenous materials. It is of great significance to investigate the ecological functioning of these marine areas, which can be well understood by exploring the microbial communities of sediments. However, the geographical distribution, composition, and genetic functions of sedimentary bacterial communities of the Yellow Sea and East China Sea (YEC Seas) are poorly understood. In this work, sediment samples were collected from YEC Sea areas to investigate bacterial communities by high-throughput sequencing. A total of 1960 genera were determined, with Proteobacteria being the dominant phylum (45.03%), followed by Planctomycetes, Bacteroidetes, Acidobacteria, and Chloroflexi. Correlation analysis indicates that the bacterial composition is influenced by environmental factors, including pressure, depth, seawater density, salinity, organic matter content, nutrient, and heavy metal. Approximately 178 metabolism pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in the bacterial communities, including ones for nutrient metabolism (C, 3.04%; S, 0.70%; N, 0.52%; and P, 0.22%) and exogenous pollutant metabolism (e.g., polycyclic aromatic hydrocarbons (PAHs), chlorobenzene, and benzoate; up to 4.97%). The results demonstrate that the abundant bacterial communities in the sediments of the YEC Seas are important for maintaining marine ecological functioning, especially for elemental biogeochemical cycling and exogenous pollutant transformation.
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Affiliation(s)
- Dan Huang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhongyun Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, PR China
| | - Zhengyao Feng
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan 030024, PR China
| | - Mao Ye
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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16
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Gad M, Hou L, Li J, Wu Y, Rashid A, Chen N, Hu A. Distinct mechanisms underlying the assembly of microeukaryotic generalists and specialists in an anthropogenically impacted river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141434. [PMID: 32814298 DOI: 10.1016/j.scitotenv.2020.141434] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Microeukaryotic communities are sensitive to environmental changes; and are considered essential for microbial food webs and biogeochemical cycles. Therefore, understanding the community responses of microeukaryotes to environmental changes is of great ecological significance. Very little is known about the assembly mechanisms underlying the microeukaryotic communities, especially for the key ecological groups (e.g., habitat generalists/specialists) in the riverine ecosystems. Here, we employed 18S rDNA amplicon sequencing to study the assembly processes governing the microeukaryotic communities and their habitat generalists and specialists across three hydrological seasons in a subtropical river in China. The results showed that deterministic and stochastic processes jointly shaped the microeukaryotic communities, where the relative importance of stochastic processes decreased in the following order: wet > normal > dry seasons. However, deterministic processes played more important role in shaping the microeukaryotic communities than those of prokaryotes. Meanwhile, stochastic and deterministic processes were responsible for structuring the microeukaryotic habitat generalists and specialists, respectively. Generally, the pure effects of physicochemical factors on the microeukaryotic communities and their key ecological groups were ~ 1.7 folds than those of the micropollutants. However, several micropollutants (e.g., acetaminophen, benzophenone-3, bisphenol A, sulfadiazine, triclocarban and triclosan) were found to have a strong effect on the habitat specialists. Altogether, we suggested that the ecological responses of the riverine microeukaryotes to micropollutants may vary among species due to the intrinsic differences in their environmental plasticity.
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Affiliation(s)
- Mahmoud Gad
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Liyuan Hou
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Jiangwei Li
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wu
- Department of Biology and Environmental Engineering, Hefei University, Hefei 230601, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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17
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Du Y, Yang W, Ding X, Zhang J, Zheng Z, Zhu J. High heterogeneity of bacterioplankton community shaped by spatially structured environmental factors in West Lake, a typical urban lake in eastern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:42283-42293. [PMID: 32319051 DOI: 10.1007/s11356-020-08818-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the bacterioplankton spatial distribution patterns and its determinants is a central topic in ecological research. However, research on the distribution patterns of bacterioplankton community composition (BCC) within a small-sized, highly dynamic freshwater lake remains unclear. In this study, we collected surface water samples from West Lake to investigate the spatiotemporal variation of BCC by 16S rRNA gene high-throughput sequencing. Clear spatial heterogeneity in BCC was identified both in summer and winter. The relatively high abundant taxa exhibited greater correlations with environmental factors and other abundant species in summer than in winter. Variation partitioning analysis was used to unravel the relative importance of environmental factors and spatial processes and further explore the underlying mechanism of BCC successions. Our results showed the predominant shared effect of environmental and spatial factors on BCC in summer (68.41%) and winter (57.37%), indicating that spatially structured environmental factors were the key determinants of structuring BCC spatial heterogeneity in West Lake in the two seasons. Furthermore, environmental factors alone explained a higher proportion of the variation in summer whereas spatial factors explained a higher proportion in winter. These divergences may be related to seasonal environmental changes and anthropogenic disturbances. Our study provided knowledge on BCC spatial heterogeneity in small freshwater habitats and their underlying determinants in different seasons.
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Affiliation(s)
- Yi Du
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Xiuying Ding
- Hangzhou West Lake Administration, Hangzhou, 310002, China
| | - Jinjie Zhang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo, 315800, China.
- , Ningbo, China.
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18
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Wang K, Yan H, Peng X, Hu H, Zhang H, Hou D, Chen W, Qian P, Liu J, Cai J, Chai X, Zhang D. Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective. Mol Ecol 2020; 29:3762-3776. [DOI: 10.1111/mec.15600] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/24/2020] [Accepted: 08/12/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Ningbo University Ningbo China
- School of Marine Sciences Ningbo University Ningbo China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Ningbo University Ningbo China
- School of Marine Sciences Ningbo University Ningbo China
| | - Xin Peng
- Zhejiang Mariculture Research Institute Wenzhou China
| | - Hanjing Hu
- School of Marine Sciences Ningbo University Ningbo China
| | - Huajun Zhang
- School of Marine Sciences Ningbo University Ningbo China
| | - Dandi Hou
- School of Marine Sciences Ningbo University Ningbo China
| | - Wei Chen
- School of Marine Sciences Ningbo University Ningbo China
| | - Peng Qian
- School of Marine Sciences Ningbo University Ningbo China
| | - Junfeng Liu
- Zhejiang Mariculture Research Institute Wenzhou China
| | - Jingbo Cai
- Zhejiang Mariculture Research Institute Wenzhou China
| | - Xueliang Chai
- Zhejiang Mariculture Research Institute Wenzhou China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Ningbo University Ningbo China
- School of Marine Sciences Ningbo University Ningbo China
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19
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Zhou L, Liu L, Chen WY, Sun JJ, Hou SW, Kuang TX, Wang WX, Huang XD. Stochastic determination of the spatial variation of potentially pathogenic bacteria communities in a large subtropical river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114683. [PMID: 32388300 DOI: 10.1016/j.envpol.2020.114683] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Understanding the composition and assembly mechanism of waterborne pathogen is essential for preventing the pathogenic infection and protecting the human health. Here, based on 16S rRNA sequencing, we investigated the composition and spatial variation of potentially pathogenic bacteria from different sections of the Pearl River, the most important source of water for human in Southern China. The results showed that the potential pathogen communities consisted of 6 phyla and 64 genera, covering 11 categories of potential pathogens mainly involving animal parasites or symbionts (AniP), human pathogens all (HumPA), and intracellular parasites (IntCelP). Proteobacteria (75.87%) and Chlamydiae (20.56%) were dominant at the phylum level, and Acinetobacter (35.01%) and Roseomonas (8.24%) were dominant at the genus level. Multivariate analysis showed that the potential pathogenic bacterial community was significantly different among the four sections in the Pearl River. Both physicochemical factors (e.g., NO3-N, and suspended solids) and land use (e.g., urban land and forest) significantly shaped the pathogen community structure. However, spatial effects contributed more to the variation of pathogen community based on variation partitioning and path analysis. Null model based normalized stochasticity ratio analysis further indicated that the stochastic process rather than deterministic process dominated the assembly mechanisms by controlling the spatial patterns of potential pathogens. In conclusion, high-throughput sequencing shows great potential for monitoring the potential pathogens, and provided more comprehensive information on the potentially pathogenic community. Our study highlighted the importance of considering the influences of dispersal-related processes in future risk assessments for the prevention and control of pathogenic bacteria.
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Affiliation(s)
- Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wei-Yuan Chen
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Ji-Jia Sun
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shi-Wei Hou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Tian-Xu Kuang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Xiong Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China; School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | - Xian-De Huang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.
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20
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Jeong SY, Choi JY, Kim TG. Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake. MICROBIAL ECOLOGY 2020; 79:801-814. [PMID: 31705158 DOI: 10.1007/s00248-019-01453-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R2 ≥ 0.31), except between Fungi and Metazoa (R2 = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea
| | - Jong-Yun Choi
- Division of Ecological Assessment, National Institute of Ecology, Seocheon, Choongnam, 33657, South Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea.
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21
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Distribution Patterns of Microeukaryotic Community Between Sediment and Water of the Yellow River Estuary. Curr Microbiol 2020; 77:1496-1505. [PMID: 32239287 DOI: 10.1007/s00284-020-01958-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
Water and sediment have always been closely tied in aquatic systems. However, little information regarding the full extent of microeukaryotic composition in both the two habitats did we know especially in estuaries. In the present study, the microeukaryotic abundance, diversity, composition, and their response to environmental factors between sediment and water in the Yellow River Estuary (YRE) were investigated. The microeukaryotic 18S rRNA gene abundance ranged from 1.03 × 106 to 5.48 × 107 copies/g dry for sediment, and 3.01 × 104 to 1.25 × 106 copies/mL for water. The distribution patterns of eukaryotic microorganisms could be clustered into two different branches. And the compositions of microeukaryotes in the two habitats were distinct obviously. Metazoa, Fungi, Streptophyta, Ochrophyta, Cercozoa, and Dinophyta were more abundant in sediment. The dominant phyla in water were Dinophyta, followed by Metazoa, Ochrophyta, Cryptophyta, Chloroplyta, Cercozoa, Fungi, Katablepharidophyta, Choanoflagellida, and Haptophyta. Interestingly, the eukaryotic microorganisms detected in sediment were much less sensitive to environmental variables compared with water. Furthermore, their potential co-occurrence networks in particular were also discovered in the present study. As such, we have provided baseline data to support further research on estuarine microeukaryotes in both sediment and water, which was useful for guiding the practical application of ecosystem management and biodiversity protection.
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22
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Wu PF, Li DX, Kong LF, Li YY, Zhang H, Xie ZX, Lin L, Wang DZ. The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134289. [PMID: 31514034 DOI: 10.1016/j.scitotenv.2019.134289] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/12/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Microeukaryotes are the key ecosystem drivers mediating marine productivity, the food web and biogeochemical cycles. The northwestern Pacific Ocean (NWPO), as one of the world's largest oligotrophic regions, remains largely unexplored regarding diversity and biogeography of microeukaryotes. Here, we investigated the community composition and geographical distribution of microeukaryotes collected from the euphotic zone of three different regions in the NWPO using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors on the distributions of microeukaryotes. The relative abundance of different group taxa, except for Ciliophora, presented distinct patterns in each region, and Metazoa and Dinoflagellata dominated the community, contributing approximately half of reads abundance. Spatial and environmental factors explained 66.01% of community variation in the NWPO. Temperature was the most important environmental factor significantly correlated with community structure. Bacterial biomass was also significantly correlated with microeukaryotic distribution, especially for Dinoflagellata and Diatomea. Network analysis showed strong correlations between microeukaryotic groups and free-living bacteria and different bacterial taxa were correlated with specific microeukaryotic groups, indicating that their interactions enabled microeukaryotic groups to adapt to diverse environments. This study provides a first glance at the diversity and geographical distribution of microeukaryotes in the NWPO and sheds light on the biotic and abiotic factors in shaping the microeukaryotic community in the ocean.
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Affiliation(s)
- Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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23
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Spatharis S, Lamprinou V, Meziti A, Kormas KA, Danielidis DD, Smeti E, Roelke DL, Mancy R, Tsirtsis G. Everything is not everywhere: can marine compartments shape phytoplankton assemblages? Proc Biol Sci 2019; 286:20191890. [PMID: 31662088 DOI: 10.1098/rspb.2019.1890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The idea that 'everything is everywhere, but the environment selects' has been seminal in microbial biogeography, and marine phytoplankton is one of the prototypical groups used to illustrate this. The typical argument has been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative roles of compartmentalization of regional seas and site-specific environmental conditions in shaping assemblage structures have not been specifically examined. We collected data from coastal embayments that fall within two different water compartments within the same regional sea and are characterized by highly localized environmental pressures. We used principal coordinates of neighbour matrices (PCNM) and asymmetric eigenvector maps (AEM) models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our models explained a high percentage of variation in assemblage composition (59-65%) and showed that spatial structure consistent with marine compartmentalization played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalization. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere.
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Affiliation(s)
- Sofie Spatharis
- School of Life Sciences, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vasiliki Lamprinou
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 3844 46 Volos, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 3844 46 Volos, Greece
| | - Daniel D Danielidis
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Panepistimiopolis, Athens 15784, Greece
| | - Evangelia Smeti
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Souniou Avenue, 19013 Anavissos, Attica, Greece
| | - Daniel L Roelke
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77554, USA
| | - Rebecca Mancy
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, University Hill, 81100 Mytilene, Greece
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24
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Mao Y, Liu Y, Li H, He Q, Ai H, Gu W, Yang G. Distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities: Case study of a tributary of the Three Gorges Reservoir, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 682:324-332. [PMID: 31125745 DOI: 10.1016/j.scitotenv.2019.05.172] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Anthropogenic activities can cause serious negative effects on ecosystems. Despite the ecological significance of bacterial communities, the integrated biogeography of planktonic and sedimentary bacterial communities in response to anthropogenic activities is not adequately understood. Here, we examined environmental parameters and the composition of planktonic and sedimentary bacteria in the Yulin River, a tributary of Three Gorges Reservoir, in response to changes in land use and dam construction. The results revealed that human-induced land use changes enhanced the nutrient concentrations in surface water and dam construction reduced the content of carbon and nitrogen in immediately downstream sediments. Intensified human-dominated land use showed a slight impact on sedimentary bacterial communities but largely reduced the diversity of planktonic bacterial communities. Moreover, human-induced land use changes increased the abundance of genes associated with denitrification, nitrification, and anammox in planktonic bacterial communities by 19.04%, 32.40% and 30.45%, respectively. In dam construction regions, the diversity and nutrient-related metabolic activity of sedimentary bacterial communities immediately downstream of the dam were decreased, whereas these changes were not observed in planktonic bacterial communities. Additionally, bacterial community composition was significantly related to nutrient concentrations variability and followed a distance-decay pattern. Furthermore, environmental effects explained more of the variation in planktonic bacterial community composition as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. Our results demonstrated the distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities, and offered new insight for understanding their potential ecological influence on rivers.
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Affiliation(s)
- Yufeng Mao
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Yi Liu
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Hong Li
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Qiang He
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Hainan Ai
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China.
| | - Weikang Gu
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Guofeng Yang
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
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25
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Wang K, Hu H, Yan H, Hou D, Wang Y, Dong P, Zhang D. Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters. Mol Ecol 2019; 28:3101-3118. [PMID: 30993759 DOI: 10.1111/mec.15105] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 01/21/2023]
Abstract
Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. "Selection" was more important than "dispersal limitation" in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of "selection". While "homogenizing dispersal" also considerably governed their biogeography. MGI-Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI-phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII-bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.
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Affiliation(s)
- Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
| | - Hanjing Hu
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
| | - Huizhen Yan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Dandi Hou
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yanting Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Pengsheng Dong
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
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26
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Community Assembly Mechanisms Underlying the Core and Random Bacterioplankton and Microeukaryotes in a River–Reservoir System. WATER 2019. [DOI: 10.3390/w11061127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Whether bacterioplankton are assembled in the same way as microeukaryotes is a key question that has been answered only partially in microbial ecology. In particular, relating distribution patterns to the underlying ecological processes for plankton communities in highly dynamic ecosystems, such as river–reservoirs subjected to anthropogenic impacts, remains largely unstudied. Here, we analyzed taxonomic distribution patterns, and unraveled community assembly processes underlying the core and random bacterioplankton and microeukaryotes from a subtropical river–reservoir system. These plankton domains were modelled using the spatial abundance distributions (SpADs) of the operational taxonomic units (OTUs) as a proxy for abundant and rare taxa delineation. Both bacterioplankton and microeukaryote plankton communities exhibited significant distance–decay relationships, and samples were grouped depending on reservoir or river habitats. The neutral community model showed that 35–45% of the plankton community variation could be explained by neutral processes. The phylogenetic null model revealed that dispersal limitation accounted for the largest percentage of pairwise comparisons (42–68%), followed by environmental selection (18–25%). We concluded that similar prevalence of ecological processes acting on particular subsets of the bacterioplankton and microeukaryotes might have resulted from similar responses to environmental change, potentially induced by human activities in the watershed.
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27
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Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, Nobile CJ. Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California. PLoS One 2019; 14:e0212355. [PMID: 30763377 PMCID: PMC6375613 DOI: 10.1371/journal.pone.0212355] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/31/2019] [Indexed: 11/19/2022] Open
Abstract
Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.
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Affiliation(s)
- Sabah Ul-Hasan
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, United States of America
| | - Robert M. Bowers
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Andrea Figueroa-Montiel
- Department of Biomedical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
| | - Alexei F. Licea-Navarro
- Department of Biomedical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
| | - J. Michael Beman
- Department of Life and Environmental Sciences, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
| | - Tanja Woyke
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
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