1
|
Zhou J, Liu J, Wang D, Ruan Y, Gong S, Gou J, Zou X. Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes. Appl Microbiol Biotechnol 2024; 108:88. [PMID: 38194134 DOI: 10.1007/s00253-023-12882-w] [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: 06/22/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]
Abstract
Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.
Collapse
Affiliation(s)
- Jiaxi Zhou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China
- Postdoctoral Research Workstation of China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jing Liu
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Dongfei Wang
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Yibin Ruan
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Shuang Gong
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jianyu Gou
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Xiao Zou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China.
| |
Collapse
|
2
|
Qin L, Ni B, Zou Y, Freeman C, Peng X, Yang L, Wang G, Jiang M. Deciphering soil environmental regulation on reassembly of the soil bacterial community during wetland restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176586. [PMID: 39349191 DOI: 10.1016/j.scitotenv.2024.176586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/17/2024] [Accepted: 09/26/2024] [Indexed: 10/02/2024]
Abstract
Soil bacteria are vital to regulate biogeochemical processes in wetlands, however, little is known about the patterns and mechanisms of soil bacterial re-organization during wetland restoration. Here, we used a space-for-time substitution approach and examined the ecological processes that drive soil bacterial assembly from cultivated to restored to natural wetlands. Results showed a decrease of soil bacterial α diversity and increase of bacterial community similarity and bacterial interaction (cooperation vs. competition) with years of restoration, which was dominantly influenced by deterministic processes. Identified bacterial keystone taxa (e.g. Variibacter, Acidibacter) with nutrient metabolism capacity exerted strong positive effect on bacterial interaction. Furthermore, changes of soil water condition and nutrient status showed dominantly direct positive effects on soil bacterial reassembly, while falling soil pH significantly promoted bacterial reassembly by increasing keystone taxa and bacterial interaction during wetland restoration. Overall, findings highlighted the crucial role of environmental filtering and its pathway in influencing keystone bacterial taxa that promotes the reassembly of bacterial community during wetland restoration. Our work thus provides a new crucial and timely insight for improving the management of soil bacterial community assembly within the plethora of current and future wetland restoration projects.
Collapse
Affiliation(s)
- Lei Qin
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Bingbo Ni
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanchun Zou
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Xiaojun Peng
- Heilongjiang Provincial Hydrology and Water Resources Center, Jixi 158100, China
| | - Liang Yang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Guodong Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Ming Jiang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Wetland Ecology and Environment, Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| |
Collapse
|
3
|
Wang X, Wang H, Liang Y, McMinn A, Wang M. Community organization and network complexity and stability: contrasting strategies of prokaryotic versus eukaryotic microbiomes in the Bohai Sea and Yellow Sea. mSphere 2024; 9:e0039524. [PMID: 39136485 PMCID: PMC11423591 DOI: 10.1128/msphere.00395-24] [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: 05/28/2024] [Accepted: 07/08/2024] [Indexed: 09/26/2024] Open
Abstract
Unraveling the effects of spatial gradients on microbiome assembly and association is a challenging topic that remains understudied in the coastal ecosystem. Here, we aimed to investigate the effects of spatial variation on the network complexity and stability of plankton microbiomes in the Bohai Sea and Yellow Sea. These seas serve as spawning and nursery grounds for economically important fisheries valued at billions of dollars annually. Environmental heterogeneity structures microbial communities into distinct spatial patterns, leading to complex direct/indirect relationships and broader ecological niches of bacterioplankton compared to microeukaryotic communities. Interestingly, salinity gradients positively influenced the richness of rare subgroups of bacterioplankton, while the rare microeukaryotic subgroups showed an opposite trend. Abundant subgroups of prokaryotic/eukaryotic microbiomes exhibited greater environmental niche breadth and lower phylogenetic distance compared to the rare subgroups. Stochastic processes contributed greatly to microbiome dynamics, and deterministic processes governed the bacterioplankton organization with a lower phylogenetic turnover rate. Compared to microeukaryotes, bacterioplankton exhibit higher network modularity, complexity, and robustness and lower fragmentation, and vulnerability. These observations offer vital insights into the anti-interference ability and resistance of plankton microbiomes in response to environmental gradients in terms of organization and survival strategy as well as their adaptability to environmental disturbances.IMPORTANCEAn in-depth understanding of community organization and stability of coastal microbiomes is crucial to determining the sustainability of marine ecosystems, such as the Bohai Sea and Yellow Sea. Distinct responses between prokaryotic and eukaryotic microbiomes to spatial heterogeneity were observed in terms of geographical distribution, phylogenetic distance, niche breadth, and community assembly process. Environmental variations are significantly correlated with the dynamics of rare eukaryotic plankton subcommunities compared to prokaryotic plankton subcommunities. Deterministic processes shaped prokaryotic plankton community organization with a lower phylogenic turnover rate. Rare subgroups had noticeably higher phylogenetic distance and lower niche breadth than the corresponding abundant subgroups. Prokaryotic microbiomes had higher molecular network complexity and stability compared to microeukaryotes. Results presented here show how environmental gradients alter both the geographical characteristics of the microbial organization in coastal seas and also their co-occurrence network complexity and stability and thus have critical implications for nutrient and energy cycling.
Collapse
Affiliation(s)
- Xiaoxiao Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| |
Collapse
|
4
|
Wei J, Chen W, Wen D. Rare biosphere drives deterministic community assembly, co-occurrence network stability, and system performance in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2024; 190:108887. [PMID: 39024826 DOI: 10.1016/j.envint.2024.108887] [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: 03/30/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Bacterial community is strongly associated with activated sludge performance, but there still remains a knowledge gap regarding the rare bacterial community assembly and their influence on the system performance in industrial wastewater treatment plants (IWWTPs). Here, we investigated bacterial communities in 11 full-scale IWWTPs with similar process designs, aiming to uncover ecological processes and functional traits regulating abundant and rare communities. Our findings indicated that abundant bacterial community assembly was governed by stochastic processes; thereby, abundant taxa are generally present in wastewater treatment compartments across different industrial types. On the contrary, rare bacterial taxa were primarily driven by deterministic processes (homogeneous selection 61.9%-79.7%), thus they only exited in specific IWWTPs compartments and wastewater types. The co-occurrence networks analysis showed that the majority of keystone taxa were rare bacterial taxa, with rare taxa contributing more to network stability. Furthermore, rare bacteria rather than abundant bacteria in the oxic compartment contributed more to the degradation of xenobiotics compounds, and they were main potential drivers of pollutant removal. This study demonstrated the irreplaceable roles of rare bacterial taxa in maintaining system performance of IWWTPs, and called for environmental engineers and microbial ecologists to increase their attention on rare biosphere.
Collapse
Affiliation(s)
- Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
5
|
Ding Y, Pan B, Han X, Guo S, Feng Z, Sun H, Wang X. Habitat selection drives diatom community assembly and network complexity in sediment-laden riverine environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:172983. [PMID: 38744389 DOI: 10.1016/j.scitotenv.2024.172983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/15/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Microbial communities assemble stochastically and deterministically, but how different assembly processes shape diatom community structure across riverine habitats is unclear, especially in sediment-laden environments. In this study, we deciphered the mechanisms of riverine diatom community assembly in the water column and riverbed substrate with varying sediment concentrations. Water and sediment samples were collected from 44 sampling sites along the Yellow River mainstream during two seasons. Diatom communities were characterized based on high-throughput sequencing of the 18S ribosomal RNA genes coupled with multivariate statistical analyses. A total of 198 diatom species were taxonomically assigned, including 182 free-living and particle-attached species and 184 surface-sediment species. Planktonic communities were structurally different from benthic communities, with Cyclotella being dominant mainly in the middle and lower reaches of the river with higher sediment concentrations. Both stochastic and deterministic processes affected diatom community assembly in different habitats. Species dispersal was more important in the water than in the substrate, and this process was strengthened by increased sediment concentration across habitats. Diatom communities exhibited lower network complexity and enhanced antagonistic or competitive interactions between species in response to higher sediment concentrations compared with lower sediment concentrations mainly in the source region of the river. Differences in the species composition and community diversity of planktonic diatoms were closely correlated with the proportion of bare land area, nitrogen nutrients, precipitation, and sediment concentration. In particular, particle-attached diatoms responded sensitively to environmental factors. These findings provide strong evidence for sediment-mediated assembly and interactions of riverine diatom communities.
Collapse
Affiliation(s)
- Yitong Ding
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China.
| | - Xu Han
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Shansong Guo
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Zhiyuan Feng
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - He Sun
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Xinyuan Wang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| |
Collapse
|
6
|
Xi M, Wang Y, Yang J, Bi X, Zhong S, Duan T, He Y, Tu T, Qian X. Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems. Fungal Biol 2024; 128:1815-1826. [PMID: 38876534 DOI: 10.1016/j.funbio.2024.05.001] [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: 01/09/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024]
Abstract
Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.
Collapse
Affiliation(s)
- Meijuan Xi
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Juanjuan Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohui Bi
- Shangqiu Institute of Quality Inspection and Technical Research, Shangqiu, China
| | - Shengen Zhong
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Duan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yimin He
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tieyao Tu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- Fujian Agriculture and Forestry University, Fuzhou, China.
| |
Collapse
|
7
|
Li S, Luo N, Li C, Mao S, Huang H. Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106451. [PMID: 38492505 DOI: 10.1016/j.marenvres.2024.106451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/04/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2-2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.
Collapse
Affiliation(s)
- Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Ningjian Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Chuang Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shuoqian Mao
- Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
8
|
Yang S, Hou Q, Li N, Wang P, Zhao H, Chen Q, Qin X, Huang J, Li X, Liao N, Jiang G, Dong K, Zhang T. Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries. Front Microbiol 2024; 15:1365546. [PMID: 38706965 PMCID: PMC11066265 DOI: 10.3389/fmicb.2024.1365546] [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: 01/04/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.
Collapse
Affiliation(s)
- Shu Yang
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, China
| | - Qinghua Hou
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
| | - Nan Li
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
| | - Pengbin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Re-sources, Hangzhou, China
| | - Huaxian Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, China
| | - Qingxiang Chen
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
| | - Xinyi Qin
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, China
| | | | - Xiaoli Li
- School of Agriculture, Ludong University, Yantai, China
| | - Nengjian Liao
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, China
| | - Gonglingxia Jiang
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Republic of Korea
| | - Tianyu Zhang
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, China
| |
Collapse
|
9
|
Wu P, Hu D, Guo J, Li J, Zhong Q, Cheng D. Unraveling the spatial-temporal distribution patterns of soil abundant and rare bacterial communities in China's subtropical mountain forest. Front Microbiol 2024; 15:1323887. [PMID: 38410396 PMCID: PMC10895375 DOI: 10.3389/fmicb.2024.1323887] [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: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria. Methods Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community. Results and discussion Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations.
Collapse
Affiliation(s)
- Panpan Wu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dandan Hu
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jiaheng Guo
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Jinlong Li
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Quanlin Zhong
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
| | - Dongliang Cheng
- Institute of Geography, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Plant Ecophysiology, Fujian Normal University, Fuzhou, China
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fuzhou, China
| |
Collapse
|
10
|
Li J, Fan M, Wei Z, Zhang K, Ma X, Shangguan Z. Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration. ENVIRONMENTAL RESEARCH 2024; 242:117720. [PMID: 37996008 DOI: 10.1016/j.envres.2023.117720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.
Collapse
Affiliation(s)
- Jiajia Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Miaochun Fan
- Department of Grassland Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Zhenhao Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Kang Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xing Ma
- Department of Grassland Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| |
Collapse
|
11
|
Li Y, Sun X, Zhang M, Khan A, Sun W. Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132807. [PMID: 37879275 DOI: 10.1016/j.jhazmat.2023.132807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.
Collapse
Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Ajmal Khan
- Department of Environmental Sciences, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
12
|
Wang K, Huang Y, Zhang M, Xiao H, Zhang G, Zhang T, Wang X. Pressure of different level PFOS on aerobic granule sludge: Insights on performance, AGS structure, community succession, and microbial interaction responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167682. [PMID: 37820810 DOI: 10.1016/j.scitotenv.2023.167682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Perfluorooctane sulfonic acid (PFOS) has received much attention due to its potential environmental risks. However, the response of aerobic granular sludge (AGS) to PFOS exposure, particularly the microbial interactions, remains unclear. In this study, we investigated the particle structure of AGS, pollutant removal performance, community succession, and microbial interaction in the AGS system under different PFOS concentrations (0.1 and 1 mg/L). The mass balance showed that PFOS was mainly removed by adsorption with a removal rate of >85 %. PFOS caused some particles to break up and decreased the average particle size from 3.37 mm to 2.64 mm. It also significantly decreased the total nitrogen and total phosphorus removal rates, which was consistent with the deterioration of microbial activity, such as denitrification rate (25 % inhibition), phosphorus uptake rate (73.19 % inhibition), and phosphorus release rate (73.33 % inhibition). PFOS promoted the secretion of extracellular polymer (EPS) in AGS, especially proteins, leading to poor particle hydrophobicity. The network analysis illustrated that PFOS slowed down the information transfer between microorganisms, and increased the competition between them, which may be responsible for the deterioration of the system performance. Connections related to rare species accounted for >75 % of the network, suggesting that rare species have an indispensable role in community information exchange. In addition, rare species acted as seed banks for microorganisms, and under PFOS stress, they transformed into keystone species, which could contribute to system stabilization. This study provides new insights into the effects of PFOS on microbial interactions in AGS systems and the roles of rare species in the AGS microbial community.
Collapse
Affiliation(s)
- Kening Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yan Huang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Minglu Zhang
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Haihe Xiao
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Gengyi Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tingting Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
13
|
Huang Y, Zhang J, Liu J, Gao X, Wang X. Effect of C/N on the microbial interactions of aerobic granular sludge system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119505. [PMID: 37992659 DOI: 10.1016/j.jenvman.2023.119505] [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: 04/01/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
The main focus of this study was to evaluate the operational stability and changes in microbial interactions of aerobic granular sludge (AGS) systems at reduced C/N (16, 8 and 4). The results showed that the removal efficiency of total nitrogen and total phosphorus decreased from 95.99 ± 0.93% and 84.44 ± 0.67% to 48.46 ± 1.92% and 50.93 ± 2.67%, respectively, when C/N was reduced from 16 to 4. The granule settling performance and stability also deteriorated. Molecular ecological network analysis showed that the reduction of the C/N ratio made the overall network as well as the subnetworks of the Proteobacteria and Bacteroidota more complex and tightly connected. Similarly, the subnetworks of two dominant genera (Thiothrix and Defluviicoccus) became more complex as the C/N decreased. Meanwhile, the decreased C/N ratio might promote competition among microbes in these overall networks and subnetworks. In conclusion, reduced C/N added complexity and tightness to microbial linkages within the AGS system, while increased competition between species might have contributed to the deterioration in pollutant removal performance. This study adds a new dimension to our understanding of the effects of C/N on the microbial community of AGS using a molecular ecological network approach.
Collapse
Affiliation(s)
- Yan Huang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Junqi Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Junyu Liu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoping Gao
- Fuzhou Planning Design Research Institute, Fuzhou, 350108, China.
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
14
|
Lyu Y, Zhang J, Chen Y, Li Q, Ke Z, Zhang S, Li J. Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119240. [PMID: 37837767 DOI: 10.1016/j.jenvman.2023.119240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/05/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.
Collapse
Affiliation(s)
- Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhixin Ke
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Si Zhang
- 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
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| |
Collapse
|
15
|
Sun J, Zhou H, Cheng H, Chen Z, Yang J, Wang Y, Jing C. Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts. MICROBIAL ECOLOGY 2023; 86:3027-3042. [PMID: 37792089 DOI: 10.1007/s00248-023-02305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023]
Abstract
Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.
Collapse
Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, People's Republic of China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China.
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China.
| | - Chunlei Jing
- National Deepsea Center, Ministry of Natural Resources, Qingdao, 266237, Shandong, People's Republic of China.
| |
Collapse
|
16
|
Yan Y, Lin T, Xie W, Zhang D, Jiang Z, Han Q, Zhu X, Zhang H. Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay. MICROBIAL ECOLOGY 2023; 86:1575-1588. [PMID: 36697746 DOI: 10.1007/s00248-023-02175-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.
Collapse
Affiliation(s)
- Yi Yan
- 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
| | - Tenghui Lin
- 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
| | - Weijuan Xie
- School of Marine Sciences, Ningbo University, Ningbo, 315211, 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
| | - Zhibing Jiang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Qingxi Han
- 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
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Huajun 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.
| |
Collapse
|
17
|
Sun J, Zhang A, Zhang Z, Liu Y, Zhou H, Cheng H, Chen Z, Li H, Zhang R, Wang Y. Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106082. [PMID: 37429213 DOI: 10.1016/j.marenvres.2023.106082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.
Collapse
Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Aoqi Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Zhongxian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Yang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
| |
Collapse
|
18
|
Mohapatra M, Manu S, Kim JY, Rastogi G. Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163109. [PMID: 36996988 DOI: 10.1016/j.scitotenv.2023.163109] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.
Collapse
Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500048, India
| | - Ji Yoon Kim
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
| |
Collapse
|
19
|
Tang Y, Zhang H, Yan J, Luo N, Fu X, Wu X, Wu J, Liu C, Zhang D. Assessing the efficacy of bleaching powder in disinfecting marine water: Insights from the rapid recovery of microbiomes. WATER RESEARCH 2023; 241:120136. [PMID: 37295228 DOI: 10.1016/j.watres.2023.120136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Single-bleaching powder disinfection is a highly prevalent practice to disinfect source water for marine aquaculture to prevent diseases. However, due to the decay of active chlorine and the presence of disinfectant resistance bacteria (DRB), the effects of bleaching powder on prokaryotic community compositions (PCCs) and function in marine water remain unknown. In the present study, the source water in a canvas pond was treated with the normal dose of bleaching powder, and the impact on PCCs and functional profiles was investigated using 16S rRNA gene amplicon sequencing. The bleaching powder strongly altered the PCCs within 0.5 h, but they began to recover at 16 h, eventually achieving 76% similarity with the initial time at 72 h. This extremely rapid recovery was primarily driven by the decay of Bacillus and the regrowth of Pseudoalteromonas, both of which are DRB. Abundant community not only help PCCs recover but also provide larger functional redundancy than rare community. During the recovery of PCCs, stochastic processes drove the community assembly. After 72 h, five out of seven identified disinfectant resistance genes related to efflux pump systems were highly enriched, primarily in Staphylococcus and Bacillus. However, 15 out of the 16 identified antibiotic resistance genes (ARGs) remained unchanged compared to the initial time, indicating that bleaching powder does not contribute to ARGs removal. Overall, the findings demonstrate that single-bleaching powder disinfection cannot successfully meet the objective of disease prevention in marine aquaculture water due to the extremely rapid recovery of PCCs. Hence, secondary disinfection or novel disinfection strategies should be explored for source water disinfection.
Collapse
Affiliation(s)
- Yawen Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jiaojiao Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Nan Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xuezhi Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaoyu Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jialin Wu
- Ningbo Haiwei Ecological Technology Co., Ltd., Ningbo 315141, China
| | - Changjun Liu
- Xiangshan Fisheries Technical 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; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
20
|
Zhu X, Deng Y, Huang T, Han C, Chen L, Zhang Z, Liu K, Liu Y, Huang C. Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau. Front Microbiol 2023; 14:1118892. [PMID: 36970704 PMCID: PMC10031068 DOI: 10.3389/fmicb.2023.1118892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated β-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated β-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of β-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in β-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.
Collapse
Affiliation(s)
- Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- *Correspondence: Yongcui Deng, ; Tao Huang,
| | - Tao Huang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- *Correspondence: Yongcui Deng, ; Tao Huang,
| | - Cheng Han
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Lei Chen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Zhigang Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Changchun Huang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| |
Collapse
|
21
|
Bai S, Zhang J, Qi X, Zeng J, Wu S, Peng X. Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period. Microorganisms 2023; 11:microorganisms11020536. [PMID: 36838501 PMCID: PMC9964997 DOI: 10.3390/microorganisms11020536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical-chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea.
Collapse
Affiliation(s)
- Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Correspondence: (S.B.); (X.P.)
| | - Jian Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- The State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijun Wu
- The State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Xiaotong Peng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Correspondence: (S.B.); (X.P.)
| |
Collapse
|
22
|
Li C, Jin L, Zhang C, Li S, Zhou T, Hua Z, Wang L, Ji S, Wang Y, Gan Y, Liu J. Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress. IMETA 2023; 2:e79. [PMID: 38868331 PMCID: PMC10989821 DOI: 10.1002/imt2.79] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 06/14/2024]
Abstract
Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.
Collapse
Affiliation(s)
- Changchao Li
- Environment Research InstituteShandong UniversityQingdaoChina
- Department of Civil and Environmental Engineering and State Key Laboratory of Marine PollutionThe Hong Kong Polytechnic UniversityKowloonHong Kong SARChina
| | - Ling Jin
- Department of Civil and Environmental Engineering and State Key Laboratory of Marine PollutionThe Hong Kong Polytechnic UniversityKowloonHong Kong SARChina
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityKowloonHong Kong SARChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
| | - Chao Zhang
- Environment Research InstituteShandong UniversityQingdaoChina
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Zhongyi Hua
- National Resource Center for Chinese Materia MedicaChinese Academy of Chinese Medical SciencesBeijingChina
| | - Lifei Wang
- Environment Research InstituteShandong UniversityQingdaoChina
| | - Shuping Ji
- Environment Research InstituteShandong UniversityQingdaoChina
| | - Yanfei Wang
- College of Computer Science and TechnologyShanghai University of Electric PowerShanghaiChina
| | - Yandong Gan
- School of Life SciencesQufu Normal UniversityQufuChina
| | - Jian Liu
- Environment Research InstituteShandong UniversityQingdaoChina
| |
Collapse
|
23
|
Tian L, Zhang Y, Zhang L, Zhang L, Gao X, Feng B. Biogeographic Pattern and Network of Rhizosphere Fungal and Bacterial Communities in Panicum miliaceum Fields: Roles of Abundant and Rare Taxa. Microorganisms 2023; 11:microorganisms11010134. [PMID: 36677426 PMCID: PMC9863577 DOI: 10.3390/microorganisms11010134] [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: 11/07/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Unraveling how microbial interactions and assembly process regulate the rhizosphere abundant and rare taxa is crucial for determining how species diversity affects rhizosphere microbiological functions. We assessed the rare and abundant taxa of rhizosphere fungal and bacterial communities in proso millet agroecosystems to explore their biogeographic patterns and co-occurrence patterns based on a regional scale. The taxonomic composition was significantly distinct between the fungal and bacterial abundant and rare taxa. Additionally, the rare taxa of bacteria and fungi exhibited higher diversity and stronger phylogenetic clustering than those of the abundant ones. The phylogenetic turnover rate of abundant taxa of bacteria was smaller than that of rare ones, whereas that of fungi had the opposite trend. Environmental variables, particularly mean annual temperature (MAT) and soil pH, were the crucial factors of community structure in the rare and abundant taxa. Furthermore, a deterministic process was relatively more important in governing the assembly of abundant and rare taxa. Our network analysis suggested that rare taxa of fungi and bacteria were located at the core of maintaining ecosystem functions. Interestingly, MAT and pH were also the important drivers controlling the main modules of abundant and rare taxa. Altogether, these observations revealed that rare and abundant taxa of fungal and bacterial communities showed obvious differences in biogeographic distribution, which were based on the dynamic interactions between assembly processes and co-occurrence networks.
Collapse
Affiliation(s)
- Lixin Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yuchuan Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Liyuan Zhang
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng 024031, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (X.G.); (B.F.)
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (X.G.); (B.F.)
| |
Collapse
|
24
|
Sun R, Wang X, Alhaj Hamoud Y, Lu M, Shaghaleh H, Zhang W, Zhang C, Ma C. Dynamic variation of bacterial community assemblage and functional profiles during rice straw degradation. Front Microbiol 2023; 14:1173442. [PMID: 37125169 PMCID: PMC10140369 DOI: 10.3389/fmicb.2023.1173442] [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: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Bacteria is one of the most important drivers of straw degradation. However, the changes in bacterial community assemblage and straw-decomposing profiles during straw decomposition are not well understood. Based on cultivation-dependent and independent technologies, this study revealed that the "common species" greatly contributed to the dynamic variation of bacterial community during straw decomposition. Twenty-three functional strains involved in straw decomposition were isolated, but only seven were detected in the high-throughput sequencing data. The straw decomposers, including the isolated strains and the agents determined by functional prediction, constituted only 0.024% (on average) of the total bacterial community. The ecological network showed that most of the identified decomposers were self-existent without associations with other species. These results showed that during straw composition, community assembly might be greatly determined by the majority, but straw decomposition functions might be largely determined by the minority and emphasized the importance of the rare species in community-specific functions.
Collapse
Affiliation(s)
- Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Xin Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | | | - Mengxing Lu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Hiba Shaghaleh
- College of Environment, Hohai University, Nanjing, China
| | - Wenjie Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Chaochun Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- *Correspondence: Chaochun Zhang, ; Chao Ma,
| | - Chao Ma
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
- *Correspondence: Chaochun Zhang, ; Chao Ma,
| |
Collapse
|
25
|
Zhu J, Tang S, Cheng K, Cai Z, Chen G, Zhou J. Microbial community composition and metabolic potential during a succession of algal blooms from Skeletonema sp. to Phaeocystis sp. Front Microbiol 2023; 14:1147187. [PMID: 37138603 PMCID: PMC10149697 DOI: 10.3389/fmicb.2023.1147187] [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: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Elucidating the interactions between algal and microbial communities is essential for understanding the dynamic mechanisms regulating algal blooms in the marine environment. Shifts in bacterial communities when a single species dominates algal blooms have been extensively investigated. However, bacterioplankton community dynamics during bloom succession when one algal species shift to another is still poorly understood. In this study, we used metagenomic analysis to investigate the bacterial community composition and function during algal bloom succession from Skeletonema sp. to Phaeocystis sp. The results revealed that bacterial community structure and function shifted with bloom succession. The dominant group in the Skeletonema bloom was Alphaproteobacteria, while Bacteroidia and Gammaproteobacteria dominated the Phaeocystis bloom. The most noticeable feature during the successions was the change from Rhodobacteraceae to Flavobacteriaceae in the bacterial communities. The Shannon diversity indices were significantly higher in the transitional phase of the two blooms. Metabolic reconstruction of the metagenome-assembled genomes (MAGs) showed that dominant bacteria exhibited some environmental adaptability in both blooms, capable of metabolizing the main organic compounds, and possibly providing inorganic sulfur to the host algae. Moreover, we identified specific metabolic capabilities of cofactor biosynthesis (e.g., B vitamins) in MAGs in the two algal blooms. In the Skeletonema bloom, Rhodobacteraceae family members might participate in synthesizing vitamin B1 and B12 to the host, whereas in the Phaeocystis bloom, Flavobacteriaceae was the potential contributor for synthesizing vitamin B7 to the host. In addition, signal communication (quorum sensing and indole-3-acetic acid molecules) might have also participated in the bacterial response to bloom succession. Bloom-associated microorganisms showed a noticeable response in composition and function to algal succession. The changes in bacterial community structure and function might be an internal driving factor for the bloom succession.
Collapse
Affiliation(s)
- Jianming Zhu
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shandong, China
| | - Si Tang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 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, Guangdong, 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, Guangdong, China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shandong, China
- *Correspondence: Guofu Chen,
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
- Jin Zhou,
| |
Collapse
|
26
|
Yun HS, Lee JH, Choo YS, Pak JH, Kim HS, Kim YS, Yoon HS. Environmental Factors Associated with the Eukaryotic Microbial Diversity of Ulleungdo Volcanic Island in South Korea. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261721100568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
27
|
Ma K, Tu Q. Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly. Front Microbiol 2022; 13:1011269. [PMID: 36312987 PMCID: PMC9598869 DOI: 10.3389/fmicb.2022.1011269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022] Open
Abstract
Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.
Collapse
Affiliation(s)
- Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- *Correspondence: Qichao Tu,
| |
Collapse
|
28
|
Xie W, Yan Y, Hu J, Dong P, Hou D, Zhang H, Yao Z, Zhu X, Zhang D. Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China. MICROBIAL ECOLOGY 2022; 84:746-758. [PMID: 34665286 DOI: 10.1007/s00248-021-01899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.
Collapse
Affiliation(s)
- Weijuan Xie
- 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, 315832, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Jian Hu
- 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, 315832, China
| | - Pengsheng Dong
- 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, 315832, China
| | - 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, 315832, China
| | - Huajun 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, 315832, China.
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, 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, 315832, China.
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Zhang H, Yan Y, Lin T, Xie W, Hu J, Hou F, Han Q, Zhu X, Zhang D. Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay. Microbiol Spectr 2022; 10:e0148122. [PMID: 35638815 PMCID: PMC9241920 DOI: 10.1128/spectrum.01481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/08/2022] [Indexed: 11/24/2022] Open
Abstract
Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.
Collapse
Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Yi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Weijuan Xie
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Fanrong Hou
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Qingxi Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| |
Collapse
|
31
|
Zhao G, He H, Wang H, Liang Y, Guo C, Shao H, Jiang Y, Wang M. Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas. Microorganisms 2022; 10:microorganisms10061204. [PMID: 35744722 PMCID: PMC9228619 DOI: 10.3390/microorganisms10061204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.
Collapse
Affiliation(s)
- Guihua Zhao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- Correspondence: (H.H.); (M.W.)
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- OUC-UMT Joint Academic Centre for Marine Studies, Qingdao 266003, China
- Correspondence: (H.H.); (M.W.)
| |
Collapse
|
32
|
Meng Y, Wang D, Wang P, Yu Z, Yuan S, Xia L, Meng F. The counteraction of anammox community to long-term nitrite stress: Crucial roles of rare subcommunity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153062. [PMID: 35031357 DOI: 10.1016/j.scitotenv.2022.153062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/02/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Understanding the temporal dynamics and recovery of anammox community under nitrite stress is critical for successful application of anammox-related processes. Here, the response behaviors of anammox community were investigated to characterize the reactor performance and ecological function under varied levels of nitrite stress (changing from 0, 50, 100, 200 to 0 mg-N/L) across a large temporal scale (588 days). The nitrogen removal rates decreased from 0.51 ± 0.02 to 0.16 ± 0.04 kg-N/(m3·d) under nitrite stress from 0 to 200 mg-N/L, while it was recovered to 0.29 ± 0.06 kg-N/(m3·d) as nitrite stress terminated. A strong community succession was driven by the initial nitrite stress of 50 mg-N/L, while the community dissimilarity mainly resulted from the increased beta diversity of rare subcommunity. Meanwhile, the rare subcommunity with high functional redundancy likely warranted the functional resilience of anammox community across the nitrite stress gradients. Moreover, the increased positive interactions between anammox bacteria and side populations supported the resilience of anammox after discontinuing nitrite stress, which facilitated the recovery of nitrogen removal efficiency. This study deciphers the interspecies interactions and functional redundancy of rare subcommunity in shaping the robustness and resilience of anammox-related processes when treating nitrite fluctuated wastewater.
Collapse
Affiliation(s)
- Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Lichao Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
| |
Collapse
|
33
|
Yan Q, Liu Y, Hu A, Wan W, Zhang Z, Liu K. Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes. Environ Microbiol 2022; 24:4153-4166. [PMID: 35590455 DOI: 10.1111/1462-2920.16044] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
Microbial metacommunities normally comprise generalists and specialists. Uncovering the mechanisms underlying the diversity patterns of these two sub-communities is crucial for aquatic biodiversity maintenance. However, little is known about the ecological assembly processes and co-occurrence patterns of the habitat generalists and specialists across large spatial scales in plateau lake sediments, particularly regarding their environmental adaptations. Here, we investigated assembly processes of the habitat generalists and specialists in sediment of Tibetan lakes and their role in the stability of metacommunity co-occurrence network. Our results showed that the habitat generalists exhibited broader environmental thresholds and closer phylogenetic clustering than specialist counterparts. In contrast, the specialists exhibited stronger phylogenetic signals of ecological preferences compared with the habitat generalists. Stochastic processes dominated the habitat generalist (63.2%) and specialist (81.3%) community assembly. Sediment pH was the major factor mediating the balance between stochastic and deterministic processes in the habitat generalists and specialists. In addition, revealed by network analysis, the habitat specialists played a greater role in maintaining the stability of metacommunity co-occurrence network. The insights gained from this study can be helpful to understand the mechanisms underlying maintenance of sediment microbial diversity in plateau lakes. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Qi Yan
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Anyu Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhihao Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
34
|
Hilal MG, Zhou R, Yu Q, Wang Y, Feng T, Li X, Li H. Successions of rare and abundant microbial subcommunities during fish carcass decomposition in a microcosm under the influence of variable factors. FEMS Microbiol Lett 2022; 369:6554547. [DOI: 10.1093/femsle/fnac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/08/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Animal carcasses are hotspots of ecological activity. The study of the role of microbes in carcass decomposition has been exclusively focused on microbes with higher abundance. The comparative study of abundant and rare subcommunities associated with decomposition needs in-depth exploration. The current experiment has been conducted on the decomposition of a fish carcass in a microcosm. We conducted 16S rRNA gene sequencing of the microbial communities. The correlation of the physicochemical properties of tap and Yellow river water with the microbial communities was evaluated. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were found to be the dominant phyla in both abundant and rare subcommunities. Among bacteria, the Acidobacteria, Planctomycetes, and Cyanobacteria were found only in the rare subcommunity. In both subcommunities, the abundance of Proteobacteria was found to increase over time, and that of Firmicutes to decrease. The rare subcommunity shows higher alpha diversity than the abundant one. The variation in the abundant subcommunity was influenced by time and water type, and that in the rare subcommunity was influenced by pH and water type. These results have implications for future research on the ecological role of rare and abundant subcommunities in the decomposition of carcasses in the aquatic ecosystem.
Collapse
Affiliation(s)
- Mian Gul Hilal
- MOE, Key laboratory of Cell activities and stress adaptations, School of life science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Rui Zhou
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiangkai Li
- MOE, Key laboratory of Cell activities and stress adaptations, School of life science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Huan Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
35
|
Su Y, Hu Y, Zi H, Chen Y, Deng X, Hu B, Jiang Y. Contrasting assembly mechanisms and drivers of soil rare and abundant bacterial communities in 22-year continuous and non-continuous cropping systems. Sci Rep 2022; 12:3264. [PMID: 35228617 PMCID: PMC8885686 DOI: 10.1038/s41598-022-07285-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
Despite many studies on the influence of cropping practices on soil microbial community structure, little is known about ecological patterns of rare and abundant microbial communities in response to different tobacco cropping systems. Here, using the high-throughput sequencing technique, we investigated the impacts of two different cropping systems on soil biochemical properties and the microbial community composition of abundant and rare taxa and its driving factors in continuous and rotational tobacco cropping systems in the mountain lands of Yunnan, China. Our results showed that distinct co-occurrence patterns and driving forces for abundant and rare taxa across the different cropping systems. The abundant taxa were mainly constrained by stochastic processes in both cropping systems. In contrast, rare taxa in continuous cropping fields were mainly influenced by environmental perturbation (cropping practice), while governed by deterministic processes under rotational cropping. The α-diversity indices of rare taxa tended to be higher than those of the abundant ones in the two cropping systems. Furthermore, the network topologies of rare taxa were more complex than those of the abundant taxa in the two cropping systems. These results highlight that rare taxa rather than abundant ones play important roles in maintaining ecosystem diversity and sustaining the stability of ecosystem functions, especially in continuous cropping systems.
Collapse
Affiliation(s)
- Yan Su
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yanxia Hu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Haiyun Zi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Binbin Hu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
| |
Collapse
|
36
|
Stock W, Willems A, Mangelinckx S, Vyverman W, Sabbe K. Selection constrains lottery assembly in the microbiomes of closely related diatom species. ISME COMMUNICATIONS 2022; 2:11. [PMID: 37938731 PMCID: PMC9723743 DOI: 10.1038/s43705-022-00091-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 04/25/2023]
Abstract
It is generally recognised that interactions between microalgae and bacteria play an important role in the functioning of marine ecosystems. In this context, increasing attention is paid to the processes that shape microalga-associated microbiomes. In recent years, conflicting evidence has been reported with respect to the relative importance of selective vs neutral processes in the assembly process. Whereas some studies report strong selection imposed by the host, others propose a more neutral, lottery-like assembly model according to which the chance of bacteria becoming part of the microbiome is proportional to their abundance in the environment and not driven by the selectional pressure created by the host. In the present study, we investigated to what degree selective vs neutral assembly processes constrain taxonomic, phylogenetic and functional variation within and between microbiomes associated with 69 isolates belonging to the Cylindrotheca closterium benthic marine diatom complex. The diatom cultures were initiated from non-axenic clonal isolates from different marine environments and geographic locations, and were then reared in a common garden (lab) environment. An important environmental imprint, likely due to in situ lottery dynamics, was apparent in the diatom microbiomes. However, microbiome assembly was also phylogenetically and functionally constrained through selective filtering related to the host microhabitat. Randomised microbiome assembly simulations revealed evidence for phylogenetic overdispersion in the observed microbiomes, reflecting an important role in the assembly process for competition between bacteria on the one hand and predominantly genetically driven differences between the hosts on the other hand. Our study thus shows that even between closely related diatom strains, host selection affects microbiome assembly, superimposing the predominantly stochastically driven recruitment process.
Collapse
Affiliation(s)
- Willem Stock
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium.
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium.
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium
| |
Collapse
|
37
|
Zhang W, Wan W, Lin H, Pan X, Lin L, Yang Y. Nitrogen rather than phosphorus driving the biogeographic patterns of abundant bacterial taxa in a eutrophic plateau lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150947. [PMID: 34655620 DOI: 10.1016/j.scitotenv.2021.150947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Eutrophication of freshwater lakes is an important cause of global water pollution. In this study, the composition and biogeographic distribution of both abundant and rare sedimentary bacterial taxa and their relationship with nutrients were assessed in Erhai Lake, a subtropical plateau lake. Proteobacteria (48.3%) and Nitrospirae (11.7%) dominated the composition of abundant taxa, while the rare taxa were dominated by Proteobacteria (25.8%) and Chloroflexi (14.1%). The abundant bacterial taxa had strong energy metabolism, whereas the rare bacterial taxa had strong xenobiotics biodegradation and metabolism. These results indicated different compositions and functions existed between abundant and rare taxa. Total nitrogen (TN) was the most influential factor shaping the biogeographic patterns of both abundant and rare taxa. Phosphorus was not the deterministic factor, although nitrogen and phosphorus were the main contributors to eutrophication. Total organic carbon and pH also contributed to the biogeographic patterns of both abundant and rare taxa. In the eutrophic plateau lake sediments, abundant taxa, rather than rare taxa, played a dominant role in maintaining the community structure and ecological function of the bacterial community. The TN gradient was an important factor that affected the biogeographic distribution and assembly processes of abundant taxa. This study sheds light on the role of TN in shaping the biogeographic distribution and assembly processes of abundant taxa in eutrophic lakes.
Collapse
Affiliation(s)
- Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Lin
- The Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiong Pan
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan 430014, China
| | - Li Lin
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan 430014, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
38
|
Chen Y, Liu Y, Liu K, Ji M, Li Y. Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau. Front Microbiol 2022; 12:784273. [PMID: 35154026 PMCID: PMC8829297 DOI: 10.3389/fmicb.2021.784273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/27/2021] [Indexed: 12/05/2022] Open
Abstract
Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.
Collapse
Affiliation(s)
- Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yang Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| |
Collapse
|
39
|
Du S, Chen W, Yao Z, Huang X, Chen C, Guo H, Zhang D. Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival. Anim Microbiome 2021; 3:88. [PMID: 34952650 PMCID: PMC8710032 DOI: 10.1186/s42523-021-00152-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut. RESULTS We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio. CONCLUSIONS Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota.
Collapse
Affiliation(s)
- Shicong Du
- 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.,School of Energy and Environment, City University of Hong Kong, Hong Kong, SAR, China
| | - Wei Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhiyuan Yao
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China. .,School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China.
| | - Xiaolin Huang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Zhejiang Mariculture Research Institute, Wenzhou, 325099, China
| | - Chen Chen
- Zhejiang Mariculture Research Institute, Wenzhou, 325099, China
| | - Haipeng Guo
- 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
| | - 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.
| |
Collapse
|
40
|
Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil. mSystems 2021; 6:e0104021. [PMID: 34636665 PMCID: PMC8510535 DOI: 10.1128/msystems.01040-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Soil microorganisms, which intricately link to ecosystem functions, are pivotal for the ecological restoration of heavy metal-contaminated soil. Despite the importance of rare and abundant microbial taxa in maintaining soil ecological function, the taxonomic and functional changes in rare and abundant communities during in situ chemical stabilization of cadmium (Cd)-contaminated soil and their contributions to the restoration of ecosystem functions remain elusive. Here, a 3-year field experiment was conducted to assess the effects of five soil amendments (CaCO3 as well as biochar and rice straw, individually or in combination with CaCO3) on rare and abundant microbial communities. The rare bacterial community exhibited a narrower niche breadth to soil pH and Cd speciation than the abundant community and was more sensitive to environmental changes altered by different soil amendments. However, soil amendments had comparable impacts on rare and abundant fungal communities. The assemblies of rare and abundant bacterial communities were dominated by variable selection and stochastic processes (dispersal limitation and undominated processes), respectively, while assemblies of both rare and abundant fungal communities were governed by dispersal limitation. Changes in soil pH, Cd speciation, and soil organic matter (SOM) by soil amendments may play essential roles in community assembly of rare bacterial taxa. Furthermore, the restored ecosystem multifunctionality by different amendments was closely related to the recovery of specific keystone species, especially rare bacterial taxa (Gemmatimonadaceae and Haliangiaceae) and rare fungal taxa (Ascomycota). Together, our results highlight the distinct responses of rare and abundant microbial taxa to soil amendments and their linkage with ecosystem multifunctionality. IMPORTANCE Understanding the ecological roles of rare and abundant species in the restoration of soil ecosystem functions is crucial to remediation of heavy metal-polluted soil. Our study assessed the efficiencies of five commonly used soil amendments on recovery of ecosystem multifunctionality and emphasized the relative contributions of rare and abundant microbial communities to ecosystem multifunctionality. We found great discrepancies in community composition, assembly, niche breadth, and environmental responses between rare and abundant communities during in situ chemical stabilization of Cd-contaminated soil. Application of different soil amendments triggered recovery of specific key microbial species, which were highly related to ecosystem multifunctionality. Together, our results highlighted the importance of rare bacterial as well as rare and abundant fungal communities underpinning restoration of soil ecosystem multifunctionality during the Cd stabilization process.
Collapse
|
41
|
Zhang W, Lu Y, Li X, Li Y, Wang L, Niu L, Zhang H. Effects of black carbon-based thin-layer capping for nitrogen-overloaded sediment remediation on microbial community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147888. [PMID: 34134363 DOI: 10.1016/j.scitotenv.2021.147888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Black carbon is considered as a promising material for thin-layer capping for sediment remediation. However, the effects of black carbon-based thin-layer capping on microbial communities have not been thoroughly studied. Here, the preparation conditions of capping material were optimized, and the interaction and assembly mechanisms of the microbial community in sediment under black carbon capping were studied. The results showed that concentration of NH4+-N in the overlying water was stably lower than 0.5 mg/L after capping. The abundance of key genes related to nitrogen transformation in the sediment was increased. Denitrification was the dominant nitrogen removal pathway under coarse granule capping, while aromatic compound degradation was dominant under fine granule capping and dissimilatory N reduction to ammonium was regarded as the dominant nitrogen removal pathway. Community assembly was mainly driven by deterministic processes (≥ 80%). Interactions between rare and common operational taxonomic units were most frequent. The functional zoning of nitrogen transformation in the vertical aerobic, hypoxic, and anaerobic zones of the sediment was strengthened because of black carbon capping. Overall, these results expand our current understanding of the ecological significance of black carbon capping for remediating contaminated sediment.
Collapse
Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yumiao Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Xinyi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| |
Collapse
|
42
|
Zhou L, Zhou Y, Tang X, Zhang Y, Jeppesen E. Biodegradable dissolved organic carbon shapes bacterial community structures and co-occurrence patterns in large eutrophic Lake Taihu. J Environ Sci (China) 2021; 107:205-217. [PMID: 34412783 DOI: 10.1016/j.jes.2021.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/07/2021] [Accepted: 02/07/2021] [Indexed: 06/13/2023]
Abstract
Interactions between dissolved organic matter (DOM) and bacteria are central in the biogeochemical cycles of aquatic ecosystems; however, the relative importance of biodegradable dissolved organic carbon (BDOC) compared with other environmental variables in structuring the bacterial communities needs further investigation. Here, we investigated bacterial communities, chromophoric DOM (CDOM) characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu, China, to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns. We found that the proportion of BDOC (%BDOC) correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM (BIX). %BDOC, further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity, indicating that autochthonous production of protein-like CDOM was an important source of BDOC. The richness of the bacterial communities correlated negatively with %BDOC, indicating an enhanced number of species in the refractory DOC environments. %BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network, suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake. Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities. Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.
Collapse
Affiliation(s)
- Lei Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlin Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg 8600, Denmark; Sino-Danish Centre for Education and Research, Beijing 100049, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| |
Collapse
|
43
|
Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
Collapse
Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
44
|
High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments. Appl Environ Microbiol 2021; 87:e0092821. [PMID: 34190611 DOI: 10.1128/aem.00928-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungi are key components of microbial communities in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi and seldom on the structure and driving factors of entire fungal communities. The compositions, community assembly, and interaction patterns of mangrove fungal communities on a large scale remain elusive. Here, biogeography, assembly, and co-occurrence patterns of fungal communities in mangroves across eastern to southern China were systematically analyzed by targeting the entire internal transcribed spacer (ITS) region with high-throughput Pacific Biosciences single-molecule real-time sequencing. The analysis revealed a high level of fungal diversity, including a number of basal fungal lineages not previously reported in mangroves, such as Rozellomycota and Chytridiomycota. Beta nearest-taxon index analyses suggested a determinant role of dispersal limitation on fungal community in overall and most individual mangroves, with support from the strong distance-decay patterns of community similarity. Further, nonmetric multidimensional scaling analyses revealed similar biogeographies of dominant and rare fungal communities. A minor role of environmental selection on the fungal community was noted, with geographical location and sediment depth as crucial factors driving the distribution of both, the dominant and rare taxa. Finally, network analysis revealed high modularized co-occurrence patterns of fungal community in mangrove sediments, and the keystone taxa might play important roles in microbial interactions and ecological functions. The investigation expands our understanding of biogeography, assembly patterns, driving factors, and co-occurrence relationships of mangrove fungi and will spur the further functional exploration and protection of fungal resources in mangroves. IMPORTANCE As key components of microbial community in mangroves, fungi have important ecological functions. However, the fungal community in mangroves on a large scale is generally elusive, and mangroves are declining rapidly due to climate change and anthropogenic activities. This work provides an overview of fungal community structure and biogeography in mangrove wetlands along a >9,000-km coastline across eastern to southern China. Our study observed a high number of basal fungal lineages, such as Rozellomycota and Chytridiomycota, in mangrove sediments. In addition, our results highlight a crucial role of dispersal limitation and a minor role of environmental selections on fungal communities in mangrove sediments. These novel findings add important knowledge about the structure, assembly processes, and driving factors of fungal communities in mangrove sediments.
Collapse
|
45
|
Dong Y, Wu S, Deng Y, Wang S, Fan H, Li X, Bai Z, Zhuang X. Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses. Front Microbiol 2021; 12:689762. [PMID: 34276621 PMCID: PMC8283415 DOI: 10.3389/fmicb.2021.689762] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.
Collapse
Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
46
|
Zhang N, Liang C, Liu X, Yao Z, Zhu DZ, Du S, Zhang H. Divergent Temporal Response of Abundant and Rare Bacterial Communities to Transient Escherichia coli O157:H7 Invasion. Front Microbiol 2021; 12:665380. [PMID: 34163444 PMCID: PMC8215281 DOI: 10.3389/fmicb.2021.665380] [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: 02/08/2021] [Accepted: 04/22/2021] [Indexed: 11/24/2022] Open
Abstract
The release of Escherichia coli (E. coli) O157:H7 has been widely found in various environments, but little is known about the probable influence of the transient E. coli O157:H7 invasion on the native microbial community. Here, we investigated the temporal response of two bacterial biospheres (abundant and rare) of two marsh sediments against E. coli O157:H7 during a 60-day incubation. The diversity of both biospheres showed no evident response to O157:H7 invasion. Temporal factor exhibited greater effects on bacterial variation than O157:H7 invasion. We found that O157:H7 invasion led to an increase in the niche breadth of the bacterial community while decreasing the efficiency of bacterial interaction of the abundant taxa. Moreover, the rare biosphere exhibited enhanced stability against O157:H7 invasion compared with the abundant biosphere, acting as the backbone in resisting external disturbance. Furthermore, each subcommunity assembly showed different randomness levels. The stochastic events were relatively more important in constraining the abundant taxa assembly after invasion. Collectively, E. coli O157:H7 exhibited diverse tangible impact on both biospheres, which unearthed differential responses of abundant and rare biosphere against transient microbial invasion.
Collapse
Affiliation(s)
- Nan Zhang
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, China.,Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Chunling Liang
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, China
| | - Xiangjun Liu
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, China
| | - David Z Zhu
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, China.,Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Shicong Du
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
| |
Collapse
|
47
|
Zhang Y, Yao P, Sun C, Li S, Shi X, Zhang XH, Liu J. Vertical diversity and association pattern of total, abundant and rare microbial communities in deep-sea sediments. Mol Ecol 2021; 30:2800-2816. [PMID: 33960545 PMCID: PMC8251536 DOI: 10.1111/mec.15937] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.
Collapse
Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chuang Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Sanzhong Li
- Key Laboratory of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaochong Shi
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| |
Collapse
|
48
|
Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
Collapse
Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
| |
Collapse
|
49
|
Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient. mSystems 2020; 5:5/6/e01150-20. [PMID: 33361326 PMCID: PMC7762797 DOI: 10.1128/msystems.01150-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata. Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes. IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.
Collapse
|
50
|
Zhang H, Xie W, Hou F, Hu J, Yao Z, Zhao Q, Zhang D. Response of microbial community to the lysis of Phaeocystis globosa induced by a biological algicide, prodigiosin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:115047. [PMID: 32585552 DOI: 10.1016/j.envpol.2020.115047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/14/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
Terminating harmful algal blooms by using algicidal agents is a strong disturbance event in marine environment, which has powerful structural influences on microbial ecosystems. But, the response of microbial ecosystem to algicidal agent is largely unknown. Here, we conducted Phaeocystis globosa microcosms to investigate the dynamics, assembly processes, and co-occurrence patterns of microbial communities in response to algicidal process induced by a highly efficient algicidal agent, prodigiosin, by using 16S rRNA gene amplicon sequencing. The α-diversity of microbial community showed no obvious changes during the algicidal process in P. globosa microcosm treated with prodigiosin (group PD). Rhodobacteraceae increased significantly (P < 0.05) during algicidal process in PD, and this was mainly due to the lysis of P. globosa cells. Compared to the control group, the temporal turnover rates of common and rare taxa in PD were significantly higher because of the lysis of P. globosa induced by prodigiosin. Neutral processes mainly drove the assembly of microbial communities in all microcosms, even though the algicidal process induced by prodigiosin had no effect on the assembly processes. In addition, the time-decay relationship and co-occurrence network analysis indicate that rare taxa play important roles in maintaining microbial community stability in response to the algicidal process, rather than prodigiosin. These findings suggest that prodigiosin cannot affect the dynamics of microbial communities directly; however, future investigations into the function of microbial communities in response to prodigiosin remain imperative.
Collapse
Affiliation(s)
- Huajun 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
| | - Weijuan Xie
- 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
| | - Fanrong 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
| | - Jian Hu
- 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
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Qunfen Zhao
- 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
| | - 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.
| |
Collapse
|