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Bai F, You L, Lei H, Li X. Association between increased and decreased gut microbiota abundance and Parkinson's disease: A systematic review and subgroup meta-analysis. Exp Gerontol 2024; 191:112444. [PMID: 38679353 DOI: 10.1016/j.exger.2024.112444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVE The objective of the study was to systematically investigate the association between gut microbiota (GM) abundance and Parkinson's disease (PD). METHODS PubMed, Medline, Cochrane Library and other literature datebase platforms were searched for eligible studies in the English-language from conception to March 1, 2024. Studies evaluating the association between GM and PD were included. The results of the included studies were analyzed using a random effects model with calculation of the mean difference (MD) with the 95 % confidence interval to quantify the incidence of differences in abundance of various bacterial families in PD patients. Continuous models were used to analyze the extracted data. RESULTS A total of 14 studies with 1045 PD cases and 821 healthy controls were included for data extraction and meta-analysis. All the included studies exhibited reasonable quality. The included studies reported the data on the ratios of 10 families of GM. Of these 10 microbiota families, Bifidobacteriaceae, Ruminococcaceae, Rikenellaceae, Lactobacillaceae, Verrucomicrobiaceae and Christensenellaceae were found to have increased ratios according to the pooled ratios, while Prevotellaceae, Lachnospiraceae, Erysipelotrichaceae and Faecalibacterium were decreased in PD cases. CONCLUSION Patients in the PD cohort exhibited distinctive microbiota compositions compared to healthy individuals, with unique differential patterns in gut microbiome abundance at the phylum, family, and genus levels that may be associated wtih PD pathogenesis.
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Affiliation(s)
- Fusheng Bai
- Department of Neurology, Jinqiu Hospital of Liaoning Province, Shenyang 110016, China
| | - Lin You
- Department of Neurology, Jinqiu Hospital of Liaoning Province, Shenyang 110016, China
| | - Hongyan Lei
- Department of Neurology, Jinqiu Hospital of Liaoning Province, Shenyang 110016, China
| | - Xinming Li
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang 110034, China.
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2
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Lin L, Xiong J, Yue T, Xu W, Liu L, Wang F, Yang S, Cao W. Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172575. [PMID: 38641105 DOI: 10.1016/j.scitotenv.2024.172575] [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: 02/03/2024] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.
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Affiliation(s)
- Ling Lin
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Tianchen Yue
- China ASEAN College of Marine Sciences, Xiamen University Malaysia, Jalan Sunsuria Bandar Sunsuria, Sepang 43900, Malaysia
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Shengchang Yang
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiang'an South Road, Xiamen 361102, China.
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3
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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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4
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Wang M, Zhao K, Li X, Xie BB. Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains. Front Microbiol 2023; 14:1308767. [PMID: 38098661 PMCID: PMC10719935 DOI: 10.3389/fmicb.2023.1308767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear. Methods The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology. Results The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential. Discussion This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.
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Affiliation(s)
| | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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5
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Hu X, Huang Y, Gu G, Hu H, Yan H, Zhang H, Zhang R, Zhang D, Wang K. Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China. ENVIRONMENTAL MICROBIOME 2023; 18:75. [PMID: 37805516 PMCID: PMC10560434 DOI: 10.1186/s40793-023-00530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises. RESULTS The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study. CONCLUSIONS Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.
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Affiliation(s)
- Xuya Hu
- 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
| | - Yujie Huang
- 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
| | - Gaoke Gu
- 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
| | - Hanjing Hu
- 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
| | - 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
| | - Huajun 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, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 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, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, 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, 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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6
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Vipindas PV, Jabir T, Venkatachalam S, Yang EJ, Jain A, Krishnan KP. Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. Extremophiles 2023; 27:24. [PMID: 37668803 DOI: 10.1007/s00792-023-01310-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
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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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8
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Zhu J, Chen G, Zhou J, Zeng Y, Cheng K, Cai Z. Dynamic patterns of quorum sensing signals in phycospheric microbes during a marine algal bloom. ENVIRONMENTAL RESEARCH 2022; 212:113443. [PMID: 35550809 DOI: 10.1016/j.envres.2022.113443] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
In the marine environment, the interactions among various species based on chemical signals play critical roles in influencing microbial structure and function. Quorum sensing (QS), the well-known signal-dependent communication autoinducer, is an important regulator in complex microbial communities. Here, we explored the QS gene profiles of phycosphere bacteria during a microcosmic phytoplankton bloom using metagenomic sequence data. More than fifteen subtypes of QS systems and 211,980 non-redundant amino acid sequences were collected and classified for constructing a hierarchical quorum-sensing database. The abundance of the various QS subtypes varied at different bloom stages and showed a strong correlation with phycosphere microorganisms. This suggested that QS is involved in regulating the phycosphere microbial succession during an algal bloom. A neutral community model revealed that the QS functional gene community assemblies were driven by stochastic processes. Co-occurrence model analysis showed that the QS gene networks of phycospheric microbes had similar topological structure and functional composition, which is a potential cornerstone for maintaining signal communication and population stabilization among microorganisms. Overall, QS systems have a strong relationship with the development of algal blooms and participate in regulating algal-associated microbial communities as chemical signals. This research reveals the chemical and ecological behavior of algal symbiotic bacteria and expands the current understanding of microbial dynamics in marine algal blooms.
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Affiliation(s)
- Jianming Zhu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong Province, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong Province, PR China.
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
| | - Yanhua Zeng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
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9
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Co-Occurrence Relationship and Stochastic Processes Affect Sedimentary Archaeal and Bacterial Community Assembly in Estuarine-Coastal Margins. Microorganisms 2022; 10:microorganisms10071339. [PMID: 35889058 PMCID: PMC9318014 DOI: 10.3390/microorganisms10071339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/24/2022] Open
Abstract
Sedimentary microorganisms play crucial roles in maintaining the functional stability of aquatic ecosystems. However, their taxonomic composition and assembly processes are not well known in estuarine−coastal margins because of their complex environment. We investigated microbial communities, co-occurrence relationships, and underlying mechanisms in 33 surface sediment samples collected in the Jiulong River Estuary and the Taiwan Strait to reveal their composition dynamics. The abundance, diversity, and composition of microorganisms demonstrated obvious spatial variables. Methanobacterium and Methanosarcina, as well as Candidatus_Nitrosopumilus and Nitrososphaeraceae were the main methanogenic and ammonia-oxidizing archaea, with an average abundance of more than 5.91% and 4.27%, respectively. Along with a salinity gradient increase, the relative abundance of methanogenic archaea (from 42.9% to 16.6%) contrasted with the trend of ammonia-oxidizing archaea (from 6.04% to 18.7%). The number of methanogenic archaea gradually decreased with increasing geographic distance (p < 0.05), whereas ammonia-oxidizing archaea showed no significant change (p > 0.05). In co-occurrence patterns, closer inter-taxa connections were observed among archaea−archaea and bacteria−bacteria than in archaea−bacteria, which indicated that coexistence within the same kingdom was greater than interaction between different kingdoms in shaping the community structure along the salinity gradient. Furthermore, null model analyses of the microbial community showed that undominated was the most prominent process, explaining over 44.9% of community variation, followed by heterogeneous selection and dispersal limitation, which contributed to 27.7% and 16.3%, respectively. We demonstrated that stochasticity, rather than determinism, regulates community assembly. These results further highlight that intra-kingdom co-occurrence and stochastic processes shape the structure and assembly of microbial communities in estuarine−coastal margins.
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10
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Zhu D, Sethupathy S, Gao L, Nawaz MZ, Zhang W, Jiang J, Sun J. Microbial diversity and community structure in deep-sea sediments of South Indian Ocean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45793-45807. [PMID: 35152353 DOI: 10.1007/s11356-022-19157-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.
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Affiliation(s)
- Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lu Gao
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Zohaib Nawaz
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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11
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Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust’s microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
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Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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12
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Wang B, Liu N, Yang M, Wang L, Liang X, Liu CQ. Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands. ENVIRONMENTAL MICROBIOME 2021; 16:19. [PMID: 34666825 PMCID: PMC8527667 DOI: 10.1186/s40793-021-00388-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/01/2021] [Indexed: 05/26/2023]
Abstract
Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.
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Affiliation(s)
- Baoli Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
- Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin, 300072, China.
| | - Na Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Meiling Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
| | - Lijia Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200244, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
- Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin, 300072, China
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13
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Hou D, Hong M, Wang K, Yan H, Wang Y, Dong P, Li D, Liu K, Zhou Z, Zhang D. Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115756. [PMID: 33162209 DOI: 10.1016/j.envpol.2020.115756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.
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Affiliation(s)
- Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Man Hong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Huizhen Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yanting Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Pengsheng Dong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Daoji Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Kai Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Zhiqiang Zhou
- Xiangshan Fisheries Technology Extension Center, Ningbo, 315700, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
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14
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Seasonality in Spatial Turnover of Bacterioplankton Along an Ecological Gradient in the East China Sea: Biogeographic Patterns, Processes and Drivers. Microorganisms 2020; 8:microorganisms8101484. [PMID: 32992545 PMCID: PMC7600760 DOI: 10.3390/microorganisms8101484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Seasonal succession in bacterioplankton is a common process in marine waters. However, seasonality in their spatial turnover is largely unknown. Here, we investigated spatial turnover of surface bacterioplankton along a nearshore-to-offshore gradient in the East China Sea across four seasons. Although seasonality overwhelmed spatial variability of bacterioplankton composition, we found significant spatial turnover of bacterioplankton along the gradient as well as overall seasonal consistency in biogeographic patterns (including distance-decay relationship and covariation of community composition with distance to shore) with subtle changes. Bacterioplankton assembly was consistently dominated by deterministic mechanisms across seasons, with changes in specific processes. We found overall seasonal consistency in abiotic factors (mainly salinity and nitrogen and phosphorus nutrients) shaping bacterioplankton composition, while phytoplankton showed a similar influence as abiotic factors only in spring. Although key taxa responsible for bacterioplankton spatial turnover showed certain season-specificity, seasonal switching between closely related taxa occurred within most dominant families. Moreover, many close relatives showed different responding patterns to the environmental gradients in different seasons, suggesting their differences in both seasonally climatic and spatially environmental preferences. Our results provide insights into seasonal consistency and variability in spatial turnover of bacterioplankton in terms of biogeographic patterns, ecological processes, and external and internal drivers.
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15
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Liu Y, Li D, Qi J, Peng Z, Chen W, Wei G, Jiao S. Stochastic processes shape the biogeographic variations in core bacterial communities between aerial and belowground compartments of common bean. Environ Microbiol 2020; 23:949-964. [PMID: 32893947 DOI: 10.1111/1462-2920.15227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities among five soil-plant associated compartments of common bean across five sampling sites in China. Neutral and null modelling consistently suggested that stochastic processes dominated the core community assembly processes and escalated from the belowground compartments to the inner tissues of aerial plant parts. The multiple distance-decay relationships also varied and had flattened patterns in the stem endosphere, which were shaped by distinct environmental factors in each compartment. Coexistence patterns also varied in topological features, in addition with the sparsest networks in the stem endosphere resulted from the interaction with the stochastic processes. This study considerably expanded our understanding of various biogeographic patterns, assembly processes, and the underlying mechanisms of core bacterial communities between aerial and belowground compartments of common bean. That will provide a scientific basis for the reasonable regulation of core bacterial consortia to get better plant performance.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
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16
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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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17
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Liu J, Zhu S, Liu X, Yao P, Ge T, Zhang XH. Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. THE ISME JOURNAL 2020; 14:1463-1478. [PMID: 32132664 PMCID: PMC7242467 DOI: 10.1038/s41396-020-0621-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/30/2022]
Abstract
Studies of marine benthic archaeal communities are updating our view of their taxonomic composition and metabolic versatility. However, large knowledge gaps remain with regard to community assembly processes and inter taxa associations. Here, using 16S rRNA gene amplicon sequencing and qPCR, we investigated the spatiotemporal dynamics, assembly processes, and co-occurrence relationships of the archaeal community in 58 surface sediment samples collected in both summer and winter from across ~1500 km of the eastern Chinese marginal seas. Clear patterns in spatiotemporal dynamics in the archaeal community structure were observed, with a more pronounced spatial rather than seasonal variation. Accompanying the geographic variation was a significant distance-decay pattern with varying contributions from different archaeal clades, determined by their relative abundance. In both seasons, dispersal limitation was the most important process, explaining ~40% of the community variation, followed by homogeneous selection and ecological drift, that made an approximately equal contribution (~30%). This meant that stochasticity rather than determinism had a greater impact on the archaeal community assembly. Furthermore, we observed seasonality in archaeal co-occurrence patterns: closer inter-taxa connections in winter than in summer, and unmatched geographic patterns between community composition and co-occurrence relationship. These results demonstrate that the benthic archaeal community was assembled under a seasonal-consistent mechanism but the co-occurrence relationships changed over the seasons, indicating complex archaeal dynamic patterns in coastal sediments of the eastern Chinese marginal seas.
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Affiliation(s)
- Jiwen Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shangqing Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiaoyue Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Studies, Ocean University of China, Qingdao, 266100, China
| | - Tiantian Ge
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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18
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Erratum. Mol Ecol 2020. [DOI: 10.1111/mec.15447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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