51
|
Bai F, Guo W, Li P, Qiao D, Du Z, Qi X. Different responses of abundant and rare bacterial composition to groundwater depth and reduced nitrogen application in summer maize field. Front Microbiol 2023; 14:1220731. [PMID: 37901810 PMCID: PMC10613034 DOI: 10.3389/fmicb.2023.1220731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction It is well known that reduced nitrogen application and groundwater depth can change soil microbial communities, but the associated difference in the response of abundant and rare bacterial composition to these local environmental changes remains unclear. Methods In this study a lysimeter experiment was carried out to examine the impact of reduced nitrogen and groundwater depth on the composition of abundant and rare bacteria. Results and discussion Our results demonstrated that the summer maize field soil species composition of rare bacterial sub-communities was significantly regulated by reduced nitrogen application, groundwater depth change and their interactions. However, only reduced nitrogen application had a significant influence on the species composition of abundant bacterial sub-communities. The structural equation model (SEM) indicated that reduced nitrogen application and groundwater depth change also could indirectly regulate the species composition of abundant and rare bacteria by altering soil attributes. The changes in soil pH and TSN had the most significant effects on the community composition of abundant and rare bacteria, respectively. More importantly, rare bacterial sub-communities were more sensitive to the changes in nitrogen input, groundwater depth and soil factors. Collectively, our study first demonstrated that abundant and rare microbial sub-communities responded differently to reduced nitrogen application and groundwater depth change. This study highlights that summer maize farmland production management should take nitrogen input and groundwater depth into consideration to maintain the compositional stability of soil rare microbial sub-communities.
Collapse
Affiliation(s)
- Fangfang Bai
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Wei Guo
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Ping Li
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Agricultural Water Soil Environmental Field Research Station of Xinxiang, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Dongmei Qiao
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Zhenjie Du
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Xuebin Qi
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| |
Collapse
|
52
|
Zhang ZF, Mao J, Cai L. Dispersal Limitation Controlling the Assembly of the Fungal Community in Karst Caves. J Fungi (Basel) 2023; 9:1013. [PMID: 37888269 PMCID: PMC10608104 DOI: 10.3390/jof9101013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
As a unique ecosystem, Karst caves harbor an impressive diversity of specific fungi. However, the factors and mechanisms that shape fungal biodiversity in caves remain elusive. In this study, we explored the assembly patterns of fungal communities based on our previous research in eight representative Karst caves in Southwest China. Our results indicated that dispersal limitation plays a crucial role in shaping the overall fungal community as well as specific communities in rock, sediment, and water samples. However, "Undominated" processes contributed more than dispersal limitation in air samples. Interestingly, the dominant assembly processes varied between caves. Consistently, environmental selection had a minor impact on the assembly of fungal communities. Among the examined spatial and environmental variables, latitude, longitude, altitude, and temperature were found to significantly influence fungal communities irrespective of substrate type. These findings provide valuable insights into the ecological factors governing fungal community assembly in Karst caves.
Collapse
Affiliation(s)
- Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
| | - Jian Mao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
53
|
Huang XR, Neilson R, Yang LY, Deng JJ, Zhou SYD, Li H, Zhu YG, Yang XR. Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil. CHEMOSPHERE 2023; 338:139533. [PMID: 37459932 DOI: 10.1016/j.chemosphere.2023.139533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/23/2023]
Abstract
Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.
Collapse
Affiliation(s)
- Xin-Rong Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jing-Jun Deng
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China.
| |
Collapse
|
54
|
Rui J, Zhao Y, Cong N, Wang F, Li C, Liu X, Hu J, Ling N, Jing X. Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities. Front Microbiol 2023; 14:1280011. [PMID: 37808282 PMCID: PMC10557256 DOI: 10.3389/fmicb.2023.1280011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.
Collapse
Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Nan Cong
- Lhasa Plateau Ecosystem Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Fuxin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
55
|
Chen C, Yin G, Hou L, Jiang Y, Sun D, Liang X, Han P, Zheng Y, Liu M. Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality. ENVIRONMENT INTERNATIONAL 2023; 179:108151. [PMID: 37603994 DOI: 10.1016/j.envint.2023.108151] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.
Collapse
Affiliation(s)
- Cheng Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yinghui Jiang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022 Jiangxi, China
| | - Dongyao Sun
- School of Geography Science and Geomatics Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai 200241, China.
| |
Collapse
|
56
|
Liu Y, Ge W, Dong C, Shao Q, Zhang Z, Zou X, Hu H, Han Y. The Analysis of Microbial Community Characteristics Revealed that the Pathogens of Leaf Spot of Rosa roxburghii Originated from the Phyllosphere. Indian J Microbiol 2023; 63:324-336. [PMID: 37781006 PMCID: PMC10533460 DOI: 10.1007/s12088-023-01093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 08/13/2023] [Indexed: 10/03/2023] Open
Abstract
Members of the plant mycobiota are all associated to varying degrees with the development of plant diseases. Although many reports on the plant mycobiota are well documented, the relationships between mycobiota of Rosa roxburghii and plant diseases are poorly understood. Mutual interactions and extent of the roles of microbial communities associated with R. roxburghii and the source of pathogens are still unclear, and more research is needed on the health benefits of this ecologically important population. Using high-throughput sequencing, we analyzed the mycobiota composition and ecological guilds of the rhizosphere, root, and phyllosphere of healthy and diseased R. roxburghii from the Tianfu R. roxburghii Industrial Park in Panzhou city, Guizhou province. Analysis of community composition showed that the relative abundance of pathogens of leaf spot, including Alternaria, Pestalotiopsis and Neofusicoccum in the phyllosphere of diseased plant (LD), were 1.15%, 0.15% and 0.06%, and the relative abundance of Alternaria and Pestalotiopsis were 0.96% and 0.58% in healthy plant (LH). The alpha diversity indices indicated that fungal diversity was higher in healthy plants compared to diseased plants in each compartment. The alpha diversity index of fungi in the phyllosphere (LH) of healthy R. roxburghii, including Shannon, Chao-1, and Faith-pd indices, was 1.02, 81.50 and 10.42 higher than that of the diseased (LD), respectively. The fungi in the rhizosphere of healthy was 1.03, 59.00 and 5.56 higher than the diseased, respectively. The Shannon index of fungi in the root of healthy was 0.29 higher than that of diseased. Principal Coordinate analysis and ANOSIM results showed that there were significant differences in mycobiota composition between healthy and diseased phyllospheres (P < 0.05), as well as rhizosphere fungal community, while there was no significant difference between healthy and diseased roots (P > 0.05). Linear discriminant analysis effect size revealed that, at different taxonomic levels, there were significantly different taxa between the healthy and diseased plants in each compartment. The ecological guilds differed between healthy and diseased plants according to the FUNGuild analysis. For example, of healthy compared to diseased plants, the percentages of "lichenized-undefined saprotroph" were increased by 2.34%, 0.44%, and 1.54% in the phyllosphere, root, and rhizosphere, respectively. In addition, the plant pathogens existed in each compartment of R. roxburghii, but the percentages of "plant pathogen" were increased by 1.16% in the phyllosphere of diseased compared to healthy plants. Together, the ecological guild and co-occurrence network indicated that the potential pathogens of leaf spot were mainly found in the phyllosphere. This study explained one of pathogen origin of leaf spots of R. roxburghii by the microbial community ecology, which will provide the new insights for identification of plant pathogens.
Collapse
Affiliation(s)
- Yuxing Liu
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Zhiyuan Zhang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Xiao Zou
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Haiyan Hu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081 Guizhou China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| |
Collapse
|
57
|
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
|
58
|
Yang Y, Zhang W, Liu W, He D, Wan W. Irreversible community difference between bacterioplankton generalists and specialists in response to lake dredging. WATER RESEARCH 2023; 243:120344. [PMID: 37482008 DOI: 10.1016/j.watres.2023.120344] [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: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Understanding response of bacterioplankton community responsible for maintaining ecological functions of aquatic ecosystems to environmental disturbance is an important subject. However, it remains largely unclear how bacterioplankton generalists and specialists respond to dredging disturbance. Illumina MiSeq sequencing and statistical analyses were used to evaluate landscape patterns, evolutionary potentials, environmental adaptability, and community assembly processes of generalists and specialists in response to dredging in eutrophic Lake Nanhu. The Proteobacteria and Actinobacteria dominated bacterioplankton communities of generalists and specialists, and abundances of Proteobacteria decreased and Actinobacteria increased after dredging. The generalists displayed higher phylogenetic distance, richness difference, speciation rate, extinction rate, and diversification rate as well as stronger environmental adaptation than that of specialists. In contrast, the specialists rather than generalists showed higher community diversity, taxonomic distance, and species replacement as well as closer phylogenetic clustering. Stochastic processes dominated community assemblies of generalists and specialists, and stochasticity exhibited a larger effect on community assembly of generalists rather than specialists. Our results emphasized that lake dredging could change landscape patterns of bacterioplankton generalists and specialists, whereas the short-term dredging conducted within one year was unable to reverse community difference between generalists and specialists. Our findings extend our understanding of how bacterioplankton generalists and specialists responding to dredging disturbance, and these findings might in turn call on long-term dredging for better ecological restoration of eutrophic lakes.
Collapse
Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Donglan He
- College of Life Science, South-Central Minzu University, Wuhan 430070, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China.
| |
Collapse
|
59
|
Qin Z, Zhao Z, Xia L, Yu G, Miao A, Liu Y. Significant roles of core prokaryotic microbiota across soil profiles in an organic contaminated site: Insight into microbial assemblage, co-occurrence patterns, and potentially key ecological functions. ENVIRONMENTAL RESEARCH 2023; 231:116195. [PMID: 37207735 DOI: 10.1016/j.envres.2023.116195] [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: 03/30/2023] [Revised: 05/06/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
Extreme environmental disturbances induced by organic contaminated sites impose serious impacts on soil microbiomes. However, our understanding of the responses of the core microbiota and its ecological roles in organic contaminated sites is limited. In this study, we took a typical organic contaminated site as an example and investigated the composition and structure, assembly mechanisms of core taxa and their roles in key ecological functions across soil profiles. Results presented that core microbiota with a considerably lower number of species (7.93%) than occasional taxa presented comparatively high relative abundances (38.04%) yet, which was mainly comprised of phyla Proteobacteria (49.21%), Actinobacteria (12.36%), Chloroflexi (10.63%), and Firmicutes (8.21%). Furthermore, core microbiota was more influenced by geographical differentiation than environmental filtering, which possessed broader niche widths and stronger phylogenetic signals for ecological preferences than occasional taxa. Null modelling suggested that stochastic processes dominated the assembly of the core taxa and maintained a stable proportion along soil depths. Core microbiota had a greater impact on microbial community stability and possessed higher functional redundancy than occasional taxa. Additionally, the structural equation model illustrated that core taxa played pivotal roles in degrading organic contaminants and maintaining key biogeochemical cycles potentially. Overall, this study deepens our knowledge of the ecology of core microbiota under complicated environmental conditions in organic contaminated sites, and provides a fundamental basis for preserving and potentially utilizing core microbiota to maintain soil health.
Collapse
Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing, 210016, China
| | - Guangwen Yu
- China National Chemical Civil Engineering Co., Ltd, Nanjing, 210031, China
| | - Aihua Miao
- China National Chemical Civil Engineering Co., Ltd, Nanjing, 210031, China
| | - Yuhong Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.
| |
Collapse
|
60
|
Zhong S, Hou B, Zhang J, Wang Y, Xu X, Li B, Ni J. Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater. Front Microbiol 2023; 14:1111383. [PMID: 37560528 PMCID: PMC10407230 DOI: 10.3389/fmicb.2023.1111383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.
Collapse
Affiliation(s)
- Sining Zhong
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bowen Hou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jinzheng Zhang
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yichu Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bin Li
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| |
Collapse
|
61
|
Ramond P, Siano R, Sourisseau M, Logares R. Assembly processes and functional diversity of marine protists and their rare biosphere. ENVIRONMENTAL MICROBIOME 2023; 18:59. [PMID: 37443126 PMCID: PMC10347826 DOI: 10.1186/s40793-023-00513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential. RESULTS Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions. CONCLUSIONS Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.
Collapse
Affiliation(s)
- Pierre Ramond
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain.
| | - Raffaele Siano
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Marc Sourisseau
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain
| |
Collapse
|
62
|
Tang Y, Fan D, Guo W, Kong W. Controls on diversity of core and indicative microbial subcommunities in Tibetan Plateau grassland soils. FEMS Microbiol Ecol 2023; 99:fiad059. [PMID: 37237437 DOI: 10.1093/femsec/fiad059] [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: 11/27/2022] [Revised: 05/10/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023] Open
Abstract
Core subcommunity represents the less diversity but high abundance, while indicative subcommunity is highly diverse but low abundance in soils. The core subcommunity fundamentally maintains ecosystem stability, while the indicative plays important roles in vital ecosystem functions and is more sensitive to environmental change. However, their environmental driving factors and responses to human disturbances remain less defined. Herein, we explored the patterns of core and indicative soil microbes and their responses to animal grazing in dry grasslands across the Tibetan Plateau, using the Illumina sequencing of 16S rRNA gene. The results revealed that the core subcommunity diversity and richness were lower than the indicative in soils. The indicative subcommunity diversity exhibited substantially stronger correlations with nutrient-associated factors than the core diversity, including soil organic carbon, nitrogen, and plant biomass. The core and indicative microbial subcommunities both strongly varied with grassland ecosystems, while the latter was also significantly influenced by grazing. The variation partitioning analysis revealed that indicative microbial subcommunity was explained less by environmental factors than core subcommunity (34.5% vs 73.0%), but more influenced by grazing (2.6% vs 0.1%). Our findings demonstrated that the indicative microbes were particularly sensitive to soil nutrient-associated factors and human disturbances in alpine dry grasslands.
Collapse
Affiliation(s)
- Yazhou Tang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| |
Collapse
|
63
|
Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
Collapse
Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
64
|
Liu H, Han H, Zhang R, Xu W, Wang Y, Zhang B, Yin Y, Cao H. Biogeographic Patterns of Fungal Sub-Communities under Different Land-Use Types in Subtropical China. J Fungi (Basel) 2023; 9:646. [PMID: 37367582 DOI: 10.3390/jof9060646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Revealing the regional distribution and diversity of fungal sub-communities under different land management practices is essential to conserve biodiversity and predict microbial change trends. In this study, a total of 19 tilled and 25 untilled soil samples across different land-use types were collected from subtropical China to investigate the differences between the spatial distribution patterns, diversity, and community assembly of fungal sub-communities using high-throughput sequencing technology. Our results found that anthropogenic disturbances significantly reduced the diversity of abundant taxa but significantly increased the diversity of rare taxa, suggesting that the small-scale intensive management of land by individual farmers is beneficial for fungal diversity, especially for the conservation of rare taxa. Abundant, intermediate, and rare fungal sub-communities were significantly different in tilled and untilled soils. Anthropogenic disturbances both enhanced the homogenization of fungal communities and decreased the spatial-distance-decay relationship of fungal sub-communities in tilled soils. Based on the null model approach, the changes in the assembly processes of the fungal sub-communities in tilled soils were found to shift consistently to stochastic processes, possibly as a result of the significant changes in the diversity of those fungal sub-communities and associated ecological niches in different land-use types. Our results provide support for the theoretical contention that fungal sub-communities are changed by different land management practices and open the way to the possibility of predicting those changes.
Collapse
Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Heming Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruoling Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weidong Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuwei Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
65
|
Guo S, Zhang S, Wang S, Lv X, Chen H, Hu X, Ma Y. Potamogeton crispus restoration increased the epiphytic microbial diversity and improved water quality in a micro-polluted urban river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121485. [PMID: 36958656 DOI: 10.1016/j.envpol.2023.121485] [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: 01/15/2023] [Revised: 03/03/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Special characterization and assembly of epiphytic microbial communities remain unclear in micro-polluted water column during submersed macrophytes restoration. In this study, an in-situ enclosure area sowing with turions of Potamogeton crispus (P. crispus) was conducted in a micro-polluted urban river to investigate the characterization of P. crispus and epiphytic microbial communities and their response to water environment under different water depths. Turions completely germinated in water column with <90 cm water depth and the germination speed decreased with increasing water depth within 18 days. There were obvious differences in morphological characteristics of P. crispus between deep and shallow water layers. P. crispus restoration decreased by 12-32%, 13-36%, 9-43% and 5-36% of COD, NH4+-N, TN and TP concentration, respectively, in enclosed overlying water compared to the river (P < 0.05) during 5 months of experiment. Illumina sequencing was employed to explore the epiphytic bacterial and microeukayotic communities at water depth 25-35 cm (shallow area) and 80-90 cm (deep area). A total of 9 bacterial and 12 microeukayotic dominant phyla were obtained in eight samples. It should be noted that the algae abundances were higher in shallow area than deep area but a reverse trend was observed for methanotrophs. Null model analysis revealed that dispersal limitation and undominated process was the most important assembly process, whereas stochastic processes gained more importance in shallow area than deep one. According to cooccurrence analysis (|r| > 0.6, P < 0.05), there were more strongly correlated edges in shallow area (456 edges) than deep area (340 edges). These results highlight that submerged macrophytes restoration can increase microbial diversity and improve water quality, and provide a "summer disease cured in winter" way by using could-resistant P. crispus for water purification in micro-polluted rivers in low-temperature season.
Collapse
Affiliation(s)
- Shaozhuang Guo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Songhe Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Supeng Wang
- College of Environment, Hohai University, Nanjing, 210098, PR China; CCCC National Engineering Research Center of Dredging Technology and Equipment Co., Ltd, Shanghai, PR China
| | - Xin Lv
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Hezhou Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Xiuren Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yu Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| |
Collapse
|
66
|
Wen T, Ding Z, Thomashow LS, Hale L, Yang S, Xie P, Liu X, Wang H, Shen Q, Yuan J. Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil. THE NEW PHYTOLOGIST 2023; 238:2634-2650. [PMID: 36932631 DOI: 10.1111/nph.18886] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information needs to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH• ) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system, and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a 'cry for help' case, wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.
Collapse
Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhexu Ding
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164, USA
| | - Lauren Hale
- US Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Avenue, Parlier, CA, 93648, USA
| | - Shengdie Yang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Penghao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Liu
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Heqi Wang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
67
|
Qiang W, Gunina A, Kuzyakov Y, Luo R, Zhang Y, Liu B, Pang X. Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118119. [PMID: 37207458 DOI: 10.1016/j.jenvman.2023.118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.
Collapse
Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Department of Soil Biology and Biochemistry, Dokuchaev Soil Science Institute, Russian Federation; Tyumen State University, 625003, Tyumen, Russia
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia
| | - Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Yan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; Department of Environment and Geography, University of York, Heslington, York, North Yorkshire, UK
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
| |
Collapse
|
68
|
Li Y, Gao W, Wang C, Gao M. Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162413. [PMID: 36842601 DOI: 10.1016/j.scitotenv.2023.162413] [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: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.
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, PR China
| | - Wenlong Gao
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, PR China; Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, PR 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, PR China
| | - Caixia Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Miao Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China.
| |
Collapse
|
69
|
Zhu M, Qi X, Yuan Y, Zhou H, Rong X, Dang Z, Yin H. Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131080. [PMID: 36842200 DOI: 10.1016/j.jhazmat.2023.131080] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.
Collapse
Affiliation(s)
- Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Heyang Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xufa Rong
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
| |
Collapse
|
70
|
Zhang X, Zhao W, Kou Y, Fang K, Liu Y, He H, Liu Q. The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region. Front Microbiol 2023; 14:1177239. [PMID: 37250033 PMCID: PMC10213230 DOI: 10.3389/fmicb.2023.1177239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.
Collapse
Affiliation(s)
- Xiaoying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yongping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yanjiao Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Heliang He
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
71
|
Cui W, Li R, Fan Z, Wu L, Zhao X, Wei G, Shu D. Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162063. [PMID: 36746286 DOI: 10.1016/j.scitotenv.2023.162063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R2 = 0.15, P < 0.001) and rare (R2 = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R2bacteria = 0.03, P < 0.05; R2fungi = 0.05, P < 0.05) and nitrogen (R2bacteria = 0.03, P < 0.05; R2fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.
Collapse
Affiliation(s)
- Weili Cui
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruochen Li
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Fan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Likun Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shaanxi, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
72
|
Liu L, Zhu L, Yan R, Yang Y, Adams JM, Liu J. Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162178. [PMID: 36775144 DOI: 10.1016/j.scitotenv.2023.162178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO3--N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.
Collapse
Affiliation(s)
- Lei Liu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Zhu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rong Yan
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Yang
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Jinshan Liu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
73
|
Gong X, Liu X, Li Y, Ma K, Song W, Zhou J, Tu Q. Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling. Appl Environ Microbiol 2023; 89:e0209622. [PMID: 36815790 PMCID: PMC10056974 DOI: 10.1128/aem.02096-22] [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: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated. The significant spatial scaling of biodiversity could be observed across all microbial domains, including archaea, bacteria, fungi, and protists. Among them, archaea and fungi were found with much stronger DDR slopes than those observed in bacteria and protists. For both TAR and DDR, rare subcommunities were mainly responsible for the observed spatial scaling patterns, except for the DDR of protists and bacteria. This was also evidenced by extending the TAR and DDR diversity metrics to Hill numbers. Further statistical analyses demonstrated that different microbial domains were influenced by different environmental factors and harbored distinct local community assembly processes. Of these, drift was mainly responsible for the compositional variations of bacteria and protists. Archaea were shaped by strong homogeneous selection, whereas fungi were more affected by dispersal limitation. Such differing ecological processes resulted in the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling and provides novel mechanistic insights into the diversity patterns of microbes that belong to different trophic levels. IMPORTANCE As the most diverse and numerous life form on Earth, microorganisms play indispensable roles in natural ecological processes. Revealing their diversity patterns across space and through time is of essential importance to better understand the underlying ecological mechanisms controlling the distribution and assembly of microbial communities. However, the diversity patterns and their underlying ecological mechanisms for different microbial domains and/or trophic levels require further exploration. In this study, the spatial scaling of different microbial domains and their associated ecological processes in a mudflat intertidal zone were investigated. The results showed different spatial scaling patterns for different microbial domains. Different ecological processes underlie the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling to provide novel mechanistic insights into the diversity patterns of microorganisms that belong to different trophic levels.
Collapse
Affiliation(s)
- Xiaofan Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- 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
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
| |
Collapse
|
74
|
Pu H, Yuan Y, Qin L, Liu X. pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments. Microorganisms 2023; 11:microorganisms11030676. [PMID: 36985249 PMCID: PMC10056738 DOI: 10.3390/microorganisms11030676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
As microorganisms are very sensitive to changes in the lake environment, a comprehensive and systematic understanding of the structure and diversity of lake sediment microbial communities can provide feedback on sediment status and lake ecosystem protection. Xiao Xingkai Lake (XXL) and Xingkai Lake (XL) are two neighboring lakes hydrologically connected by a gate and dam, with extensive agricultural practices and other human activities existing in the surrounding area. In view of this, we selected XXL and XL as the study area and divided the area into three regions (XXLR, XXLD, and XLD) according to different hydrological conditions. We investigated the physicochemical properties of surface sediments in different regions and the structure and diversity of bacterial communities using high-throughput sequencing. The results showed that various nutrients (nitrogen, phosphorus) and carbon (DOC, LOC, TC) were significantly enriched in the XXLD region. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla in the sediments, accounting for more than 60% of the entire community in all regions. Non-metric multidimensional scaling analysis and analysis of similarities confirmed that β-diversity varied among different regions. In addition, the assembly of bacterial communities was dominated by a heterogeneous selection in different regions, indicating the important influence of sediment environmental factors on the community. Among these sediment properties, the partial least squares path analysis revealed that pH was the best predictor variable driving differences in bacterial communities in different regions, with higher pH reducing beta diversity among communities. Overall, our study focused on the structure and diversity of bacterial communities in lake sediments of the Xingkai Lake basin and revealed that high pH causes the β-diversity of bacterial communities in the sediment to decrease. This provides a reference for further studies on sediment microorganisms in the Xingkai Lake basin in the future.
Collapse
Affiliation(s)
- Haiguang Pu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxiang Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiaohui Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- Correspondence:
| |
Collapse
|
75
|
Liu L, Wang N, Liu M, Guo Z, Shi S. Assembly processes underlying bacterial community differentiation among geographically close mangrove forests. MLIFE 2023; 2:73-88. [PMID: 38818341 PMCID: PMC10989747 DOI: 10.1002/mlf2.12060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 06/01/2024]
Abstract
Bacterial communities play pivotal roles in nutrient cycling in mangrove forests. The assembly of mangrove microbial communities has been found to be influenced by complex factors, such as geographic distance, physicochemical conditions, and plant identity, but the relative importance of these factors and how these factors shape the assembling process remain elusive. We analyzed the bacterial communities sampled from three mangrove species (Aegiceras corniculatum, Bruguiera sexangula, and Kandelia obovata) at three locations along the estuarine Dongzhai Harbor in Hainan, China. We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species, indicated by differences in diversity, composition, and interaction networks. We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations. Following the phylogenetic-bin-based null model analysis (iCAMP) framework, we also found dispersal limitation and homogeneous selection showing dominance in some bins. The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance. We also found that beta diversity was positively correlated with environmental distances, implying that the more similar environmental conditions (such as rich carbon and nitrogen contents) among plant species may have shaped similar bacterial communities. We concluded that the geographic distances, which are associated with dispersal limitation, played a key role in assembling mangrove rhizosphere bacterial communities, while physicochemical conditions and plant identity contributed less.
Collapse
Affiliation(s)
- Lu Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Nan Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Min Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| |
Collapse
|
76
|
Luziatelli F, Melini F, Ficca AG, Melini V, Nardilli F, Ruzzi M. Core microbiome and bacterial diversity of the Italian Mediterranean river buffalo milk. Appl Microbiol Biotechnol 2023; 107:1875-1886. [PMID: 36773061 DOI: 10.1007/s00253-023-12415-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023]
Abstract
Milk is one of the most nutritionally complete foods and plays an important role in the human diet. Buffalo milk represents 15% of worldwide milk production and is an important source of bioactive compounds. Buffalo milk has a great market in the Mediterranean area, and dairy products, such as Mozzarella and Ricotta di Bufala Campana, obtained with the Italian Mediterranean buffalo milk, are acknowledged with the Protected Designation of Origin (PDO). This study aimed to characterize, using high-throughput sequencing of the 16S rRNA gene, the milk core microbiome of water buffalo rises in the Amaseno Valley included in the Mozzarella PDO region. The principal features of the core and the auxiliary buffalo milk microbiome are the predominance of Firmicutes and Lactococcus, one of the most important lactic acid bacteria (LAB) taxa in the dairy industry. The comparative analysis of the core microbiomes indicated that the milk of the Italian Mediterranean Buffalo and other mammals share the presence of Streptococcus-affiliated OTUs (operational taxonomic units). Our data also demonstrated that the core microbiome of milk samples collected from PDO and non-PDO regions differ in the number and type of taxa. KEY POINTS: • Buffalo milk and their derivate products are becoming more popular worldwide. • Dairy locations and practice management affect the structure of the milk microbiota. • Next-generation sequencing (NGS) analysis allows to identify the features of the Italian Buffalo milk microbiome.
Collapse
Affiliation(s)
- Francesca Luziatelli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy.
| | - Francesca Melini
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy.,Council for Agricultural Research and Economics (CREA), Research Centre for Food and Nutrition, Rome, Italy
| | - Anna Grazia Ficca
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Valentina Melini
- Council for Agricultural Research and Economics (CREA), Research Centre for Food and Nutrition, Rome, Italy
| | - Francesca Nardilli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Maurizio Ruzzi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| |
Collapse
|
77
|
New Inonotus Polysaccharides: Characterization and Anticomplementary Activity of Inonotus rheades Mycelium Polymers. Polymers (Basel) 2023; 15:polym15051257. [PMID: 36904498 PMCID: PMC10007321 DOI: 10.3390/polym15051257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Inonotus is a small genus of xylotrophic basidiomycetes and a source of bioactive fungochemicals among which a special place is occupied by polymeric compounds. In this study, polysaccharides that are widespread in Europe, Asia, and North America and a poorly understood fungal species, I. rheades (Pers.) Karst. (fox polypore), were investigated. Water-soluble polysaccharides of I. rheades mycelium were extracted, purified, and studied using chemical reactions, elemental and monosaccharide analysis, UV-Vis and FTIR spectroscopy, gel permeation chromatography, and linkage analysis. Five homogenic polymers (IRP-1-IRP-5) with molecular weights of 110-1520 kDa were heteropolysaccharides that consist mainly of galactose, glucose, and mannose. The dominant component, IRP-4, was preliminary concluded to be a branched (1→3,6)-linked galactan. Polysaccharides of I. rheades inhibited the hemolysis of sensitized sheep erythrocytes by complement from human serum, signifying anticomplementary activity with the greatest effects for the IRP-4 polymer. These findings suggest that I. rheades mycelium is a new source of fungal polysaccharides with potential immunomodulatory and anti-inflammatory properties.
Collapse
|
78
|
Ye F, Hong Y, Yi X, Sun Z, Wu J, Wang Y. Stochastic processes drive the soil fungal communities in a developing mid-channel bar. Front Microbiol 2023; 14:1104297. [PMID: 36814566 PMCID: PMC9939660 DOI: 10.3389/fmicb.2023.1104297] [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: 11/21/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
Intricate associations between rhizosphere microbial communities and plants play a critical role in developing and maintaining of soil ecological functioning. Therefore, understanding the assembly patterns of rhizosphere microbes in different plants and their responses to environmental changes is of great ecological implications for dynamic habitats. In this study, a developing mid-channel bar was employed in the Yangtze River to explore the assembly processes of rhizosphere fungal communities among various plant species using high-throughput sequencing-based null model analysis. The results showed a rare significant variation in the composition and alpha diversity of the rhizosphere fungal community among various plant species. Additionally, the soil properties were found to be the primary drivers instead of plant species types. The null model analysis revealed that the rhizosphere fungal communities were primarily driven by stochastic processes (i.e., undominated processes of ecological drift), and the predominance varied with various plant species. Moreover, the assembly processes of rhizosphere fungal communities were significantly related to the changes in soil properties (i.e., soil total carbon, total nitrogen, organic matter, and pH). The co-occurrence network analysis revealed that many keystone species belonged to unclassified fungi. Notably, five network hubs were almost unaffected by the measured soil properties and aboveground plant traits, indicating the effect of stochastic processes on the rhizosphere fungal community assembly. Overall, these results will provide insights into the underlying mechanisms of fungal community assembly in the rhizosphere soils, which are significant for maintaining the functional stability of a developing ecosystem.
Collapse
Affiliation(s)
- Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Xuemei Yi
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Zhaohong Sun
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China,*Correspondence: Yu Wang,
| |
Collapse
|
79
|
Zhou X, Liu L, Zhao J, Zhang J, Cai Z, Huang X. High carbon resource diversity enhances the certainty of successful plant pathogen and disease control. THE NEW PHYTOLOGIST 2023; 237:1333-1346. [PMID: 36305241 DOI: 10.1111/nph.18582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The host-associated microbiome highly determines plant health. Available organic resources, such as food for microbes, are important in shaping microbial community structure and multifunctionality. However, how using organic resources precisely manipulates the soil microbiome and makes it supportive of plant health remains unclear. Here, we experimentally tested the influence of carbon resource diversity on the microbial trophic network and pathogen invasion success in a microcosm study. We further explored how resource diversity affects microbial evenness, community functions, and plant disease outcomes in systems involving tomato plants and the in vivo soil microbiome. Increasing available resource diversity altered trophic network architecture, increased microbial evenness, and thus increased the certainty of successful pathogen control. By contrast, the invasion resistance effects of low resource diversity were less effective and highly varied. Accordingly, increases in the evenness and connection of dominant species induced by high resource diversity significantly contributed to plant disease suppression. Furthermore, high carbohydrate diversity upregulated plant immune system regulation-related microbial functions. Our results deepen the biodiversity-invasion resistance theory and provide practical guidance for the control of plant pathogens and diseases by using organic resource-mediated approaches, such as crop rotation, intercropping, and organic amendments.
Collapse
Affiliation(s)
- Xing Zhou
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
| | - Liangliang Liu
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Xinqi Huang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| |
Collapse
|
80
|
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
|
81
|
Zhao H, Brearley FQ, Huang L, Tang J, Xu Q, Li X, Huang Y, Zou S, Chen X, Hou W, Pan L, Dong K, Jiang G, Li N. Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient. MICROBIAL ECOLOGY 2023; 85:495-507. [PMID: 35195737 DOI: 10.1007/s00248-022-01976-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.
Collapse
Affiliation(s)
- Huaxian Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Francis Q Brearley
- Department of Natural Sciences, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, UK
| | - Liangliang Huang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, China
| | - Jinli Tang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Qiangsheng Xu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Xiaoli Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Yuqing Huang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Shuqi Zou
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-guGyeonggi-do, Suwon-si, 16227, South Korea
| | - Xing Chen
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China
| | - Weiguo Hou
- State Key Laboratory of Biogeosciences and Environmental Geology, Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China
| | - Lianghao Pan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Centre, Guangxi Academy of Sciences, Beihai, 536000, Guangxi, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-guGyeonggi-do, Suwon-si, 16227, South Korea
| | - Gonglingxia Jiang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China.
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, Guangxi, China.
| |
Collapse
|
82
|
Plant Community Associates with Rare Rather than Abundant Fungal Taxa in Alpine Grassland Soils. Appl Environ Microbiol 2023; 89:e0186222. [PMID: 36602328 PMCID: PMC9888191 DOI: 10.1128/aem.01862-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The importance of the rare microbial biosphere in maintaining biodiversity and ecological functions has been highlighted recently. However, the current understanding of the spatial distribution of rare microbial taxa is still limited, with only a few investigations for rare prokaryotes and virtually none for rare fungi. Here, we investigated the spatial patterns of rare and abundant fungal taxa in alpine grassland soils across 2,000 km of the Qinghai-Tibetan plateau. We found that most locally rare fungal taxa remained rare (13.07%) or were absent (82.85%) in other sites, whereas only a small proportion (4.06%) shifted between rare and abundant among sites. Although they differed in terms of diversity levels and compositions, the distance decay relationships of both the rare and the abundant fungal taxa were valid and displayed similar turnover rates. Moreover, the community assemblies of both rare and abundant fungal taxa were predominantly controlled by deterministic rather than stochastic processes. Notably, the community composition of rare rather than abundant fungal taxa associated with the plant community composition. In summary, this study advances our understanding of the biogeographic features of rare fungal taxa in alpine grasslands and highlights the concordance between plant communities and rare fungal subcommunities in soil. IMPORTANCE Our current understanding of the ecology and functions of rare microbial taxa largely relies on research conducted on prokaryotes. Despite the key ecological roles of soil fungi, little is known about the biogeographic patterns and drivers of rare and abundant fungi in soils. In this study, we investigated the spatial patterns of rare and abundant fungal taxa in Qinghai-Tibetan plateau (QTP) alpine grassland soils across 2,000 km, with a special concentration on the importance of the plant communities in shaping rare fungal taxa. We showed that rare fungal taxa generally had a biogeographic pattern that was similar to that of abundant fungal taxa in alpine grassland soils on the QTP. Furthermore, the plant community composition was strongly related to the community composition of rare taxa but not abundant taxa. In summary, this study significantly increases our biogeographic and ecological knowledge of rare fungal taxa in alpine grassland soils.
Collapse
|
83
|
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
|
84
|
Wang R, Cui L, Li J, Li W. Factors driving the halophyte rhizosphere bacterial communities in coastal salt marshes. Front Microbiol 2023; 14:1127958. [PMID: 36910212 PMCID: PMC9992437 DOI: 10.3389/fmicb.2023.1127958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Root-associated microorganisms promote plant growth and provide protection from stresses. Halophytes are the fundamental components maintaining ecosystem functions of coastal salt marshes; however, it is not clear how their microbiome are structured across large spatial scales. Here, we investigated the rhizosphere bacterial communities of typical coastal halophyte species (Phragmites australis and Suaeda salsa) in temperate and subtropical salt marshes across 1,100 km in eastern China. Methods The sampling sites were located from 30.33 to 40.90°N and 119.24 to 121.79°E across east China. A total of 36 plots were investigated in the Liaohe River Estuary, the Yellow River Estuary, Yancheng, and Hangzhou Bay in August 2020. We collected shoot, root, and rhizosphere soil samples. the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. The soil properties, plant functional traits, the genome sequencing, and metabolomics assay were detected. Results The results showed that soil nutrients (total organic carbon, dissolved organic carbon, total nitrogen, soluble sugars, and organic acids) are high in the temperate marsh, while root exudates (measured by metabolite expressions) are significantly higher in the subtropical marsh. We observed higher bacterial alpha diversity, more complex network structure, and more negative connections in the temperate salt marsh, which suggested intense competition among bacterial groups. Variation partitioning analysis showed that climatic, edaphic, and root exudates had the greatest effects on the bacteria in the salt marsh, especially for abundant and moderate subcommunities. Random forest modeling further confirmed this but showed that plant species had a limited effect. Conclutions Taken together, the results of this study revealed soil properties (chemical properties) and root exudates (metabolites) had the greatest influence on the bacterial community of salt marsh, especially for abundant and moderate taxa. Our results provided novel insights into the biogeography of halophyte microbiome in coastal wetlands and can be beneficial for policymakers in decision-making on the management of coastal wetlands.
Collapse
Affiliation(s)
- Rumiao Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Lijuan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Wei Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| |
Collapse
|
85
|
Ge W, Ren Y, Dong C, Shao Q, Bai Y, He Z, Yao T, Zhang Y, Zhu G, Deshmukh SK, Han Y. New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria. Front Microbiol 2023; 14:1074468. [PMID: 36876069 PMCID: PMC9978014 DOI: 10.3389/fmicb.2023.1074468] [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: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.
Collapse
Affiliation(s)
- Wei Ge
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yulian Ren
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yanmin Bai
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Zhaoying He
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan, China
| | - Yanwei Zhang
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, China
| | - Guosheng Zhu
- Guizhou Key Laboratory of Edible Fungi Breeding, Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| |
Collapse
|
86
|
Cao H, Li S, He H, Sun Y, Wu Y, Huang Q, Cai P, Gao CH. Stronger linkage of diversity-carbon decomposition for rare rather than abundant bacteria in woodland soils. Front Microbiol 2023; 14:1115300. [PMID: 36937304 PMCID: PMC10017465 DOI: 10.3389/fmicb.2023.1115300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
Soil microbial diversity is important for maintaining ecosystem functions. However, the linkage between microbial diversity, especially rare and abundant bacterial diversity, and carbon decomposition remains largely unknown. In this study, we assessed the establishment and maintenance of rare and abundant bacterial α-diversities at the taxonomic and phylogenetic levels and their linkages with soil carbon decomposition separately in four Chinese woodlands. Compared to abundant bacteria, rare bacteria showed higher community diversity, tighter phylogenetic clustering, wider environmental breadth, stronger phylogenetic signals, and higher functional redundancy. The assembly of the abundant bacterial subcommunity was governed by stochastic (59.2%) and deterministic (41.8%) processes, whereas the assembly of the rare bacterial subcommunity was mainly dominated by deterministic processes (85.8%). Furthermore, total phosphorus, soil pH, and ammonium nitrogen balanced stochastic and deterministic processes in both rare and abundant bacterial subcommunities. Our results reveal that rare bacteria displayed stronger environmental adaptability and environmental constraint. Importantly, the α-diversities of rare taxa, rather than abundant taxa, were significantly related to carbon decomposition. This study provides a holistic understanding of biogeographic patterns of abundant and rare bacteria and their α-diversities in relation to carbon decomposition, thus helping us better predict and regulate carbon dynamics under the background of global climate change.
Collapse
|
87
|
Ye F, Sun Z, Moore SS, Wu J, Hong Y, Wang Y. Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02152-z. [PMID: 36502425 DOI: 10.1007/s00248-022-02152-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.
Collapse
Affiliation(s)
- Fei Ye
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Zhaohong Sun
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Selina Sterup Moore
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Yu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| |
Collapse
|
88
|
Lin X, Li Y, Xu G, Tian C, Yu Y. Biodegradable microplastics impact the uptake of Cd in rice: The roles of niche breadth and assembly process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158222. [PMID: 36028027 DOI: 10.1016/j.scitotenv.2022.158222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Biodegradable microplastics (MPs) can impact the accumulation of cadmium (Cd) by plants, however, its mechanisms have not been fully understood. In this study, two biodegradable MPs, polypropylene carbonate (PPC) and polylactic acid (PLA), were used to examine their influences on the uptake of Cd in rice plants. Results showed that PPC significantly reduced the accumulation of Cd in rice root and aerial part, whereas PLA increased the Cd concentrations in rice root. The random forest analysis revealed that the bacterial biomarkers enriched by two MPs were different at genus level. Niche breadths were significantly reduced under Cd stress, and PPC alleviated this environmental pressure for entire bacterial community, whereas PLA reduced the niche breadth for whole community and abundant taxa, which was further verified by co-occurrence network and normalized stochasticity ratio model. The abundant taxa of group PPC were primarily governed by deterministic process while rare taxa were more driven by stochastic process. Structural equation model and Mantel analysis identified that the niche breadth imposed a strong selection on Cd accumulation after co-exposure. This study reveals the underlying mechanism of assembly process and niche breadth of rice rhizosphere microbiome on Cd accumulation by rice plants.
Collapse
Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chunjie Tian
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| |
Collapse
|
89
|
Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
Collapse
Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| |
Collapse
|
90
|
Xiang Q, Chen QL, Yang XR, Li G, Zhu D. Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157820. [PMID: 35932868 DOI: 10.1016/j.scitotenv.2022.157820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.
Collapse
Affiliation(s)
- Qian Xiang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Gang Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Dong Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China.
| |
Collapse
|
91
|
Zhang S, Hu W, Xu Y, Zhong H, Kong Z, Wu L. Linking bacterial and fungal assemblages to soil nutrient cycling within different aggregate sizes in agroecosystem. Front Microbiol 2022; 13:1038536. [DOI: 10.3389/fmicb.2022.1038536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Soil aggregates provide spatially heterogeneous microhabitats that support the coexistence of soil microbes. However, there remains a lack of detailed assessment of the mechanism underlying aggregate-microbiome formation and impact on soil function. Here, the microbial assemblages within four different aggregate sizes and their correlation with microbial activities related to nutrient cycling were studied in rice fields in Southern China. The results show that deterministic and stochastic processes govern bacterial and fungal assemblages in agricultural soil, respectively. The contribution of determinism to bacterial assemblage improved as aggregate size decreased. In contrast, the importance of stochasticity to fungal assemblage was higher in macroaggregates (>0.25 mm in diameter) than in microaggregates (<0.25 mm). The association between microbial assemblages and nutrient cycling was aggregate-specific. Compared with microaggregates, the impacts of bacterial and fungal assemblages on carbon, nitrogen, and phosphorus cycling within macroaggregates were more easily regulated by soil properties (i.e., soil organic carbon and total phosphorus). Additionally, soil nutrient cycling was positively correlated with deterministic bacterial assemblage but negatively correlated with stochastic fungal assemblage in microaggregates, implying that bacterial community may accelerate soil functions when deterministic selection increases. Overall, our study illustrates the ecological mechanisms underlying the association between microbial assemblages and soil functions in aggregates and highlights that the assembly of aggregate microbes should be explicitly considered for revealing the ecological interactions between agricultural soil and microbial communities.
Collapse
|
92
|
Cuartero J, Pascual JA, Vivo JM, Özbolat O, Sánchez-Navarro V, Weiss J, Zornoza R, Martínez-Mena M, García E, Ros M. Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa. Front Microbiol 2022; 13:1004593. [PMID: 36419434 PMCID: PMC9676475 DOI: 10.3389/fmicb.2022.1004593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.
Collapse
Affiliation(s)
- Jessica Cuartero
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Jose Antonio Pascual
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Juana-María Vivo
- Department of Statistics and Operations Research, CMN & IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | - Onurcan Özbolat
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Virginia Sánchez-Navarro
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Julia Weiss
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Raúl Zornoza
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
- Department of Agricultural Science, Polytechnic University of Cartagena, Cartagena, Spain
| | - María Martínez-Mena
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Eloisa García
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Margarita Ros
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
- *Correspondence: Margarita Ros
| |
Collapse
|
93
|
Zhao Y, Lin H, Liu Y, Jiang Y, Zhang W. Abundant bacteria shaped by deterministic processes have a high abundance of potential antibiotic resistance genes in a plateau river sediment. Front Microbiol 2022; 13:977037. [DOI: 10.3389/fmicb.2022.977037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.
Collapse
|
94
|
Liu K, Hu A, Hou L, Zhang L, Zeng Q, Yan Q, Wang F, Zhang Z, Xiao X, Junzhi L, Liu Y. Effects of land-use patterns on the biogeography of the sediment bacteria in the Yarlung Tsangpo River. FEMS Microbiol Ecol 2022; 98:6764718. [PMID: 36264286 DOI: 10.1093/femsec/fiac125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/08/2022] [Accepted: 10/18/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteria communities, as key drivers of energy flow and nutrient recycling in rivers, usually consist of a few abundant taxa and many rare taxa. During the last decades, rivers on the Tibetan Plateau have experienced dramatic land surface changes under climate change and anthropogenic disturbances. However, the responses of abundant and rare taxa to such changes and disturbances still remains unclear. In this study, we explored the biogeography and drivers of the abundant and rare bacteria in Yarlung Tsangpo River sediments on the Tibetan Plateau. Our study demonstrated that changes in surrounding land-use patterns, especially in forest land, bare land and cropland, had profound influences on the distribution of the abundant and rare sediment bacteria in the Yarlung Tsangpo River. Although both communities exhibited significant distance-decay patterns, dispersal limitation was the dominant process in the abundant community, while the rare community was mainly driven by heterogeneous selection. Our results also revealed that the abundant bacteria exhibited stronger adaptation across environmental gradients than the rare bacteria. The similar biogeographic patterns but contrasting assembly processes in abundant and rare communities may result from the differences in their environmental adaptation processes. This work provides valuable insights into the importance of land surface changes in influencing the biogeographic patterns of bacteria in fluvial sediments, which helps to predict their activities and patterns in Tibetan rivers under future global climate change and anthropogenic disturbances.
Collapse
Affiliation(s)
- Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Liyuan Hou
- Utah Water Research Laboratory, Utah State University, Logan, Utah 84322, United States
| | - Lanping Zhang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoting Zeng
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qi Yan
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China.,School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Feng Wang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Xiao
- College of Geographic Science, Hunan Normal University, Changsha 410081, China
| | - Liu Junzhi
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
95
|
Liu B, Yao J, Ma B, Li S, Duran R. Disentangling biogeographic and underlying assembly patterns of fungal communities in metalliferous mining and smelting soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157151. [PMID: 35798111 DOI: 10.1016/j.scitotenv.2022.157151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Elucidating community assembly and their relevance to environmental variables are fundamental for understanding microbial diversity and functioning in terrestrial ecosystems, yet the geographical diversity and assembly patterns of the fungal community in metalliferous ecospheres associated with mining and smelting activities have received penurious understandings. Here, the fungal communities collected from three groups of soils around the mining and smelting sites were profiled by Internal Transcribed Spacer (ITS) sequencing, in order to understand the geographical distributions of fungal community diversities, structures, compositions, assembly processes and the occurrence patterns. The results suggested obvious biogeographic distribution patterns of fungal compositions among the three groups of soils. Among them, 15 fungal phyla including Ascomycota, Basidiomycota and Mortierellomycota were recognized across the samples. 12 abundant classes showing significantly different in relative abundances among the three groups of soils. Total metal(loid)s and level significantly decreased the fungal abundances and diversities. The community similarity demonstrated distance-decay pattern among the three sites. Metal(loid)s explained relatively higher fungal community variations (4.16 %) relative to other factors (1.89 %) and geography (1.21 %), though 83.32 % of the variations could not be explained. Stochastic dispersal limitation and undominated fraction were dominated relative to deterministic heterogeneous selection in total and individual site, respectively. These results highlighted the stochastic processes in governing the biogeography of fungal communities in mining and smelting ecospheres.
Collapse
Affiliation(s)
- Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China.
| | - Bo Ma
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, People's Republic of China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China; Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| |
Collapse
|
96
|
Jiao S, Qi J, Jin C, Liu Y, Wang Y, Pan H, Chen S, Liang C, Peng Z, Chen B, Qian X, Wei G. Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems. GLOBAL CHANGE BIOLOGY 2022; 28:6653-6664. [PMID: 36002985 DOI: 10.1111/gcb.16387] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Agricultural ecosystems are facing increasing environmental changes. Revealing ecological stability of belowground organisms is key to developing management strategies that maintain agricultural ecosystem services in a changing world. Here, we collected soils from adjacent pairs of maize and rice fields along large spatial scale across Eastern and Southeast China to investigate the importance of core microbiota as a predictor of resistance of soil microbiome (e.g. bacteria, fungi and protist) to climate changes and nutrient fertilization, and their effect on multiple ecosystem functions, representing key services for crop growth and health in agro-ecosystems. Soil microbiome in maize soils exhibited stronger resistance than that in rice soils, by considering multiple aspects of the resistance index, for example, community, phylogenetic conservation and network complexity. Community resistance of soil microbiome showed a geographic pattern, with higher resistance at lower latitudes, suggesting their stronger resistance in warmer regions. Particularly, we highlighted the role of core phylotypes in enhancing the community resistance of soil microbiome, which was essential for the maintenance of multifunctionality in agricultural ecosystems. Our results represent a significant advance in linking core phylotypes to community resistance and ecosystem functions, and therefore forecasting agro-ecosystems dynamics in response to ongoing environmental changes. These suggest that core phylotypes should be considered a key factor in enhancing agricultural sustainability and crop productivity under global change scenarios.
Collapse
Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Chujie Jin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Yu Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Yang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Shi Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Chunling Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Beibei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Xun Qian
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, P. R. China
| |
Collapse
|
97
|
Feng SW, Lu JL, Liang JL, Wu ZH, Yi X, Wen P, Li FL, Liao B, Jia P, Shu WS, Li JT. Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02121-6. [PMID: 36205737 DOI: 10.1007/s00248-022-02121-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.
Collapse
Affiliation(s)
- Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Zhuo-Hui Wu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Ping Wen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Feng-Lin Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Bin Liao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| |
Collapse
|
98
|
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
|
99
|
Wang Y, Wang J, Zou X, Qu M, Li J. Groundwater depth regulates assembly processes of abundant and rare bacterial communities across arid inland river basin. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115767. [PMID: 35982567 DOI: 10.1016/j.jenvman.2022.115767] [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: 04/19/2022] [Revised: 06/18/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Although numerous studies on bacterial biogeographic patterns in dryland have been conducted, bacterial community assembly across arid inland river basins is unclear. Here, we assessed the ecological drivers that regulate the assembly processes of abundant (ABS) and rare (RBS) bacterial subcommunities based on 162 soil samples collected in an arid inland river basin of China. The results showed that: (1) ABS exhibited a steeper distance-decay slope, and were more strongly affected by dispersal limitation (75.5% and 84.5%), than RBS in surface and subsurface soil. RBS were predominantly controlled by variable selection (54.6% and 50.2%). (2) Soil electric conductivity played a decisive role in mediating the balance between deterministic and stochastic processes of ABS and RBS in surface soil, increasing soil electric conductivity increased the importance of deterministic process. For subsurface soil, soil available phosphorus (SAP) and soil pH drove the balance in the assembly processes of ABS and RBS, respectively. The RBS shifted from determinism to stochasticity with decreased pH, while the dominance of deterministic processes was higher in low-SAP sites. (3) Groundwater depth seasonality had substantial effects on the assembly processes of ABS and RBS, but groundwater depth seasonality affected them indirectly mainly by regulating soil properties. Collectively, our study provides robust evidence that groundwater-driven variations in soil properties mediates the community assembly process of soil bacteria in arid inland river basins. This finding is of importance for forecasting the dynamics of soil microbial community and soil process in response to current and future depleted groundwater.
Collapse
Affiliation(s)
- Yin Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Jianming Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Xuge Zou
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Mengjun Qu
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Jingwen Li
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| |
Collapse
|
100
|
Chen W, Wei J, Su Z, Wu L, Liu M, Huang X, Yao P, Wen D. Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2022; 168:107486. [PMID: 36030743 DOI: 10.1016/j.envint.2022.107486] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.
Collapse
Affiliation(s)
- Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing China
| | - Min Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoxuan Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Pengcheng Yao
- Zhejiang Institute of Hydraulics and Estuary, Hangzhou 310017, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|