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Sun QW, Chen JZ, Liao XF, Huang XL, Liu JM. Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171952. [PMID: 38537823 DOI: 10.1016/j.scitotenv.2024.171952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.
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Affiliation(s)
- Qing-Wen Sun
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China
| | - Jing-Zhong Chen
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China.
| | | | | | - Ji-Ming Liu
- College of Forestry, Guizhou University, Guiyang 550025, 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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Wu Y, Zhou S, Li Y, Niu L, Wang L. Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168968. [PMID: 38042190 DOI: 10.1016/j.scitotenv.2023.168968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.
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Affiliation(s)
- Yunyu Wu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China
| | - Shubu Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China.
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210024, PR China
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Lin L, Xiong J, Liu L, Wang F, Cao W, Xu W. Microbial interactions strengthen deterministic processes during community assembly in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167499. [PMID: 37778550 DOI: 10.1016/j.scitotenv.2023.167499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Systematic studies on the assembly process and driving mechanisms of microbial communities in estuaries with diverse seasonal and spatial scales are still limited. In this study, high-throughput sequencing, and microbial network analysis were combined to decipher the impact of environmental changes and biological interactions on the maintenance of microbial diversity patterns in the Jiulong River Estuary (JRE). The results showed that overall, stochastic processes dominated the bacterioplankton community assembly in the estuary, accounting for 49.66-74.78 % of the total. Additionally, bacterioplankton community diversity varied significantly across seasons and subzones. Specifically, the concentration of soluble reactive phosphorus (SRP) in the estuary steadily reduced from winter to summer, and the corresponding bacterioplankton community interactions gradually shifted from the weakest interaction in winter to the strongest in summer. The deterministic processes contributed more than half (50.34 %) to microbial assembly in the summer, but only 25.22 % in winter. Deterministic processes prevailed in the seaward with low SRP concentrations and strong bacterioplankton community interactions, while stochastic processes contributed 70.14 % to the assembly of microbial communities riverward. Biotic and abiotic factors, such as nutrients and microbial interactions, jointly drove the seasonal and spatial patterns of bacterioplankton community assembly, but overall, nutrients played a dominant role. Nevertheless, the contributions of nutrients and microbial interactions were equivalent in spatial assembly processes, albeit nutrients were the primary seasonal driver of the bacterioplankton community assembly process. This study emphasizes the significance of microbial interactions in the bacterioplankton community assemblage. These findings provide new and comprehensive insights into the microbial communities' organization in estuaries.
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Affiliation(s)
- Ling Lin
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China.
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China.
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Liu L, Zhong KX, Chen Q, Wang Y, Zhang T, Jiao N, Zheng Q. Selective cell lysis pressure on rare and abundant prokaryotic taxa across a shelf-to-slope continuum in the Northern South China Sea. Appl Environ Microbiol 2023; 89:e0139323. [PMID: 38014961 PMCID: PMC10734510 DOI: 10.1128/aem.01393-23] [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: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
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Affiliation(s)
- Lu Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Junger PC, Sarmento H, Giner CR, Mestre M, Sebastián M, Morán XAG, Arístegui J, Agustí S, Duarte CM, Acinas SG, Massana R, Gasol JM, Logares R. Global biogeography of the smallest plankton across ocean depths. SCIENCE ADVANCES 2023; 9:eadg9763. [PMID: 37939185 PMCID: PMC10631730 DOI: 10.1126/sciadv.adg9763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones. We found that selection decreased, while dispersal limitation increased with depth, possibly due to differences in habitat heterogeneity and dispersal barriers such as water masses and bottom topography. Picoplankton β-diversity positively correlated with environmental heterogeneity and water mass variability, but this relationship tended to be weaker for eukaryotes than for prokaryotes. Community patterns were more pronounced in the Mediterranean Sea, probably because of its cross-basin environmental heterogeneity and deep-water isolation. We conclude that different combinations of ecological mechanisms shape the biogeography of the ocean microbiome across depths.
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Affiliation(s)
- Pedro C. Junger
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
- Programa de Pós-Graduação em Ecologia e Recursos Naturais, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
| | - Caterina R. Giner
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Mireia Mestre
- Centro COPAS-COASTAL, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Xosé Anxelu G. Morán
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Asturias 33212, Spain
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria 35214, Spain
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M. Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Silvia G. Acinas
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
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Yuan Z, Zeng Z, Liu F. Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve. Sci Rep 2023; 13:17127. [PMID: 37816825 PMCID: PMC10564911 DOI: 10.1038/s41598-023-44447-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.
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Affiliation(s)
- Zongsheng Yuan
- College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Zhihao Zeng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Li F, Mai Z, Qiu C, Long L, Hu A, Huang S. Dissemination of antibiotic resistance genes from the Pearl River Estuary to adjacent coastal areas. MARINE ENVIRONMENTAL RESEARCH 2023; 188:105978. [PMID: 37087846 DOI: 10.1016/j.marenvres.2023.105978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 05/03/2023]
Abstract
The spread of antibiotic resistance genes (ARGs) is a growing concern over the world's various environments. Coastal environments may receive pollutants from land runoffs via estuaries. However, the impact of ARG contamination from estuarine regions to coastal areas is rarely reported. This study used high-throughput quantitative PCR to examine the diversity and abundance of ARGs in Pearl River Estuary (PRE) and adjacent coastal areas. We found that the distribution of ARGs in seawater exhibited the distance-decay phenomenon from the estuary to coastal areas, while the sediment samples did not exhibit an obvious distribution pattern. The estuarine water was found to be the hotspot of ARGs, with 74 ARG species detected and absolute abundance being 5.93 × 105 copies per mL, on average, while less species and lower abundance of ARGs were detected in coastal waters. Ordination analysis showed that estuarine ARG communities were significantly different from coastal ARG communities for water samples. SourceTracker analysis revealed that ARGs from the estuarine environment contributed only a minor fraction of ARG contamination to downstream coastal areas (1.5%-7.4% for water samples, and 0.7-1.8% for sediment samples), indicating the strong dilution effect of seawater. Mantel tests, redundancy analysis and random forest model analysis identified salinity, nutrients, microbial community structure and mobile genetic elements (MGEs) as important factors influencing ARG distribution. Partial least squares-path model revealed that, among all environmental factors, MGEs directly affected the distribution of ARGs, while other factors indirectly contributed by affecting the MGEs assemblage. Our study provides insight into the dissemination of ARGs from the PRE to adjacent coastal areas.
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Affiliation(s)
- Furun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Huairou, Beijing, 101400, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Chen Qiu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Huairou, Beijing, 101400, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Sijun Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean. mSystems 2023; 8:e0001323. [PMID: 36847533 PMCID: PMC10134807 DOI: 10.1128/msystems.00013-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 μm) and particle-associated (PA; >3 μm) bacteria and protists (0.22 to 200 μm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.
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Wang B, Ma B, Stirling E, He Z, Zhang H, Yan Q. Freshwater trophic status mediates microbial community assembly and interdomain network complexity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120690. [PMID: 36403871 DOI: 10.1016/j.envpol.2022.120690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Freshwater microorganisms and their interactions are important drivers of nutrient cycling that are in turn affected by nutrient status, causing shifts in microbial community diversity, composition, and interactions. However, the impact of water trophic status on bacterial-archaeal interdomain interactions remains poorly understood. This study focused on the impact of trophic status, as characterized by trophic state index (TSI), on the interdomain interactions of freshwater microbial communities from 45 ponds in Hangzhou. Our results showed that the mesotrophic wetland bordering on lightly eutrophic (Hemu: TSI of 49; lightly eutrophic is defined as 50 ≤ TSI <60) harbored a much more complex bacterial-archaeal interdomain network, which showed significantly (P < 0.05) higher connectivity than the wetlands with lower (TSI of 38) or higher (TSI of 57) trophic levels. Notably, light eutrophication strengthened the network modules' negative associations with organic carbon through some network hubs, which could trigger carbon loss in wetlands. We also detected a non-linear response of interdomain network complexity to the increasing of nutrients with a turning point of approximately TSI 50. Quantitative estimates of community assembly processes and structural equation modelling analysis indicated that chlorophyll-a, total nitrogen, and total phosphorus could regulate interdomain network complexity (50% of the variation explanation rate) by driving microbial community assembly. This study demonstrates that microbial interdomain network complexity could be used as a bioindicator for ecological changes, which would helpful for improving ecological assessment of the freshwater eutrophication.
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Affiliation(s)
- Binhao Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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Zhu W, Zhu M, Liu X, Xia J, Yin H, Li X. Different Responses of Bacteria and Microeukaryote to Assembly Processes and Co-occurrence Pattern in the Coastal Upwelling. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02093-7. [PMID: 35927589 DOI: 10.1007/s00248-022-02093-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Upwelling may generate unique hydrological and environmental heterogeneity, leading to enhanced diffusion to reshape microbial communities. However, it remains largely unknown how different microbial taxa respond to highly complex and dynamic upwelling systems. In the present study, geographic patterns and co-occurrence network of different microbial communities in response to upwelling were examined. Our results showed that coastal upwelling shaped prokaryotic and eukaryotic microbial community and decreased their diversity. In addition, bacteria and microeukaryote had similar biogeographical patterns with distinct assembly mechanisms. The impact of stochastic processes on bacteria was significantly stronger compared with microeukaryote in upwelling. Lower network complexity but more frequent interaction was found in upwelling microbial co-occurrence. However, the upwelling environment increased the robustness and modularity of bacterial network, while eukaryotic network was just the opposite. Co-occurrence networks of bacteria and microeukaryote showed significant distance-decay patterns, while the bacterial network had a stronger spatial variation. Temperature and salinity were the strongest environmental factors affecting microbial coexistence, whereas the topological characteristics of bacterial and eukaryotic networks had different responses to the upwelling environment. These findings expanded our understanding of biogeographic patterns of microbial community and ecological network and the underlying mechanisms of different microbial taxa in upwelling.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China
| | - Ming Zhu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China
- College of Marine Science, Hainan University, Haikou, China
| | - Xiangbo Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China
- College of Marine Science, Hainan University, Haikou, China
| | - Jingquan Xia
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China
| | - Hongyang Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China
- College of Marine Science, Hainan University, Haikou, China
| | - Xiubao Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Road, Haikou, 570228, Hainan, China.
- College of Marine Science, Hainan University, Haikou, China.
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