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Gupta VVSR, Tiedje JM. Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales. MLIFE 2024; 3:21-41. [PMID: 38827504 PMCID: PMC11139212 DOI: 10.1002/mlf2.12116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 06/04/2024]
Abstract
The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.
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Affiliation(s)
| | - James M. Tiedje
- Centre for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
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2
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Li Y, Gao Y, Chen W, Zhang W, Lu X. Shifts in bacterial diversity, interactions and microbial elemental cycling genes under cadmium contamination in paddy soil: Implications for altered ecological function. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132544. [PMID: 37738847 DOI: 10.1016/j.jhazmat.2023.132544] [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: 06/24/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Cadmium (Cd) contamination has become an emergent environmental issue in agroecosystems worldwide. The impacts of Cd on microbial community and their ecological functional remain unrevealed. This study investigated the response of bacterial community and microbial ecological functions to Cd contamination in paddy soil of East China. Bacterial diversity and community structure significantly changed under Cd contamination. Proteobacteria and Acidobacteria were identified as biomarkers to indicate Cd contamination. The overall elemental cycling genes abundance was negatively correlated to soil Cd content. Acetyl-CoA synthesis, organic N mineralization, N fixation and nitrous reduction genes were especially sensitive to elevated Cd stress, resulting in loss of microbial derived soil C and N pool and increase in N2O emission potential. Bacteria interactions were sparser yet more competitive under Cd contamination. Cd resistant genera Massilia, Burkholderia, Streptomyces and Methylobacterium were essential to bacterial interactions via building connections with non-resistant species. Microbial Cd immobilization potential by urea hydrolysis was enhanced under Cd contamination, with Massilia being the keystone functional taxa involved in this process. Our study elucidated the ecological risks of altered microbial functions under Cd contamination in paddy soil, as well as the significance of Cd resistant bacteria to microbial community and ecological functionality.
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Affiliation(s)
- Yuntao Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Agro-Environment in downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yan Gao
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Agro-Environment in downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Wei Chen
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Agro-Environment in downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Weiguo Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Agro-Environment in downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xin Lu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Agro-Environment in downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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3
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Peng Z, Yang Y, Liu Y, Bu L, Qi J, Gao H, Chen S, Pan H, Chen B, Liang C, Li X, An Y, Wang S, Wei G, Jiao S. The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems. GLOBAL CHANGE BIOLOGY 2024; 30:e16996. [PMID: 37916454 DOI: 10.1111/gcb.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.
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Affiliation(s)
- Ziheng Peng
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yu Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lianyan Bu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiejun Qi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hang Gao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Haibo Pan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Beibei Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunling Liang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yining An
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Hou M, Zhao X, Wang Y, Lv X, Chen Y, Jiao X, Sui Y. Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain. Sci Rep 2023; 13:14555. [PMID: 37666914 PMCID: PMC10477331 DOI: 10.1038/s41598-023-41401-0] [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: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.
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Affiliation(s)
- Meng Hou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xiaorui Zhao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Yao Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xuemei Lv
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China
| | - Yimin Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Xiaoguang Jiao
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China.
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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5
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Lin J, Zhou X, Lu X, Xu Y, Wei Z, Ruan A. Grain size distribution drives microbial communities vertically assemble in nascent lake sediments. ENVIRONMENTAL RESEARCH 2023; 227:115828. [PMID: 37011792 DOI: 10.1016/j.envres.2023.115828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/08/2023]
Abstract
Sediment microbes are crucial for maintaining biogeochemical cycles in aquatic ecosystems, yet the influence of sediment geophysical structure on microbial communities remains unclear. In this study, we collected sediment cores from a nascent reservoir in its initial stage of deposition and utilized the multifractal model to comprehensively characterize the heterogeneity of sediment grain size and pore space. Our results demonstrate that both environmental physiochemistry and microbial community structures varied significantly with depth, with the grain size distribution (GSD) being the key driver of sediment microbial diversity, as revealed by the partial least squares path model (PLS-PM) method. GSD can potentially impact microbial communities and biomass by controlling pore space and organic matter. Overall, this study represents the first attempt to apply soil multifractal models into the integrated description of physical structure in sediment. Our findings provide valuable insights into the vertical distribution of microbial communities.
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Affiliation(s)
- Jie Lin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiaotian Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiang Lu
- Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316 Oslo, Norway
| | - Yaofei Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Zhipeng Wei
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Aidong Ruan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.
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6
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Kim HS, Park K, Jo HY, Kwon MJ. Weathering extents and anthropogenic influences shape the soil bacterial community along a subsurface zonation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162570. [PMID: 36889395 DOI: 10.1016/j.scitotenv.2023.162570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Subsurface environments are composed of various active soil layers with dynamic biogeochemical interactions. We investigated soil bacterial community composition and geochemical properties along a vertical soil profile, which was categorized into surface, unsaturated, groundwater fluctuated, and saturated zones, in a testbed site formerly used as farmland for several decades. We hypothesized that weathering extent and anthropogenic inputs influence changes in the community structure and assembly processes and have distinct contributions along the subsurface zonation. Elemental distribution in each zone was strongly affected by the extent of chemical weathering. A 16S rRNA gene analysis indicated that bacterial richness (alpha diversity) was highest in the surface zone, and also higher in the fluctuated zone, than in unsaturated and saturated zones due to the effects of high organic matter, high nutrient levels, and/or aerobic conditions. Redundancy analysis showed that major elements (P, Na), a trace element (Pb), NO3, and the weathering extent were key driving forces shaping bacterial community composition along the subsurface zonation. Assembly processes were governed by specific ecological niches, such as homogeneous selection, in the unsaturated, fluctuated, and saturated zones, while in the surface zone, they were dominated by dispersal limitation. These findings together suggest that the vertical variation in soil bacterial community assembly is zone-specific and shaped by the relative influences of deterministic vs. stochastic processes. Our results provide novel insights into the relationships between bacterial communities, environmental factors, and anthropogenic influences (e.g., fertilization, groundwater, soil contamination), and into the roles of specific ecological niches and subsurface biogeochemical processes in these relationships.
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Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kanghyun Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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7
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Gao H, Chen J, Wang C, Wang P, Wang R, Hu Y, Pan Y. Diversity and interaction of bacterial and microeukaryotic communities in sediments planted with different submerged macrophytes: Responses to decabromodiphenyl ether. CHEMOSPHERE 2023; 322:138186. [PMID: 36806803 DOI: 10.1016/j.chemosphere.2023.138186] [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: 12/12/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Although various persistent organic pollutants (POPs) can affect microbial communities and functions in aquatic ecosystems, little is known about how bacteria and microeukaryotes respond to the POPs in sediments planted with different submerged macrophytes. Here, a 60-day microcosm experiment was carried out to investigate the changes in the diversity and interaction of bacterial and microeukaryotic communities in sediments collected from Taihu lake, either with decabromodiphenyl ether (BDE-209) own or combined with two common submerged macrophyte species (Vallisneria natans and Hydrilla verticillate). The results showed that BDE-209 significantly decreased the bacterial α-diversity but increased the microeukaryotic one. In sediments planted with submerged macrophytes, the negative effect of BDE-209 on bacterial diversity was weakened, and its positive effect on microeukaryotic one was strengthened. Co-occurrence network analysis revealed that the negative relationship was dominant in bacterial and microeukaryotic communities, while the cooperative relationship between microbial species was increased in planted sediments. Among nine keystone species, one belonging to bacterial family Thermoanaerobaculaceae was enriched by BDE-209, and others were inhibited. Notably, such inhibition was weakened, and the stimulation was enhanced in planted sediments. Together, these observations indicate that the responses of bacteria and microeukaryotes to BDE-209 are different, and their communities under BDE-209 contamination are more stable in sediments planted with submerged macrophytes. Moreover, the effects of plant species on the microbial responses to BDE-209 need to be explored by more specific field studies in the future.
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Affiliation(s)
- Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China
| | - Rong Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China
| | - Yu Hu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, China
| | - Ying Pan
- School of Ecology, Sun Yat-sen University, Shenzhen, 518000, China
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8
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Doane MP, Ostrowski M, Brown M, Bramucci A, Bodrossy L, van de Kamp J, Bissett A, Steinberg P, Doblin MA, Seymour J. Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions. Environ Microbiol 2023. [PMID: 36700447 DOI: 10.1111/1462-2920.16341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high- and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.
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Affiliation(s)
- Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Martin Ostrowski
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mark Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, New South Wales, Australia
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | | | | | - Peter Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Centre for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
| | - Martina A Doblin
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
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9
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Wang YN, Shi H, Wang Q, Wang H, Sun Y, Li W, Bian R. Insights into the landfill leachate properties and bacterial structure succession resulting from the colandfilling of municipal solid waste and incineration bottom ash. BIORESOURCE TECHNOLOGY 2022; 361:127720. [PMID: 35914673 DOI: 10.1016/j.biortech.2022.127720] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Four simulated bioreactors were loaded with only MSW, 5 % BA + MSW, 10 % BA + MSW and 20 % BA + MSW to investigate the leachate property and bacterial community change trends during the colandfilling process. The results showed that with increasing BA addition proportion (5 %∼20 %), the leachate oxidation-reduction potential (ORP) was lower, the leachate pH quickly entered the neutral stage, and the chemical oxygen demand (COD), volatile fatty acids (VFA), NH4+-N, Ca2+ and SO42- presented faster downward trends. The leachate SUVA254 and E300/400 confirmed that BA can accelerate the leachate humification process. BA can quickly increase bacterial diversity, and the higher the addition proportion of BA, the more significant the change in microbial community structure during the landfilling process. The leachate pH and COD greatly influenced the bacterial community structure. A low BA proportion can increase metabolism pathway abundance during the initial stage, but a high BA proportion had an inhibitory effect on the metabolism pathway.
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Affiliation(s)
- Ya-Nan Wang
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
| | - Han Shi
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
| | - Qingzhao Wang
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
| | - Huawei Wang
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China.
| | - Yingjie Sun
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
| | - Weihua Li
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
| | - Rongxing Bian
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, Qingdao University of Technology, School of Environmental and Municipal Engineering, Qingdao, China
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10
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Lyu Q, Luo Y, Liu S, Zhang Y, Li X, Hou G, Chen G, Zhao K, Fan C, Li X. Forest gaps alter the soil bacterial community of weeping cypress plantations by modulating the understory plant diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:920905. [PMID: 36061809 PMCID: PMC9437579 DOI: 10.3389/fpls.2022.920905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Weeping cypress is an endemic tree species that is widely planted in China, and the simple stand structure and fragile ecosystem of its plantation are common issues. Exploring the effect of different gap sizes on the soil bacterial community structure of weeping cypress plantations can provide a theoretical basis for the near-natural management of forest plantations. We, therefore, constructed three kinds of forest gaps with different sizes in weeping cypress plantations, namely, small (50-100 m2), medium (100-200 m2), and large gaps (400-667 m2), for identifying the key factors that affect soil bacterial communities following the construction of forest gaps. The results suggested that the herb layer was more sensitive than the shrub layer, while the Simpson, Shannon, and richness indices of the herb layer in plots with gaps were significantly higher than those of designated sampling plots without any gaps (CK). The presence of large gaps significantly increased the understory plant diversity and the Shannon and Simpson indices of the soil bacterial alpha diversity. There were obvious changes in the community composition of soil bacteria following the construction of forest gaps. The dominant bacterial phyla, orders, and functions were similar across the plots with different gap sizes. Of the indicator bacterial species, the abundance of the nitrogen-fixing bacteria, Lysobacter_ yangpyeongensis, and Ensifer_meliloti, was significantly different across plots with different gap sizes and accounted for a large proportion of the bacterial population of plots with medium and large gaps. The understory plant diversity was mostly related to the soil bacterial community than to other soil factors. The results of structural equation modeling indicated that the understory plant diversity was the most important environmental factor in driving the composition and diversity of bacterial communities. The construction of forest gaps significantly improved the understory plant diversity, physicochemical properties of the soil, and bacterial diversity in weeping cypress plantations, and the results of the comprehensive evaluation were in the order: large gaps > small gaps > medium gaps > CK. Our results suggested that large gaps are beneficial for the diversity of above-ground plant communities and underground soil bacterial communities.
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Affiliation(s)
- Qian Lyu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yan Luo
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Size Liu
- Sichuan Academy of Forestry, Chengdu, China
| | - Yan Zhang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xiangjun Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Guirong Hou
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kuangji Zhao
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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11
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Cao W, Gong J, Zeng G, Qin M, Qin L, Zhang Y, Fang S, Li J, Tang S, Chen Z. Impacts of typical engineering nanomaterials on the response of rhizobacteria communities and rice (Oryza sativa L.) growths in waterlogged antimony-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128385. [PMID: 35152103 DOI: 10.1016/j.jhazmat.2022.128385] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The combined eco-risks of Sb (widely presented in soils, especially nearing mining areas) and the engineering nanomaterials (ENMs) (applied in agriculture and soil remediation) still remain uncovered. The current study investigated the impacts of single and combined exposure of CuO, CeO2 nanoparticles (NPs) and multi-walled carbon nanotube (MWCNTs) with Sb on rice growths and rhizosphere bacterial communities. The results showed that co-exposure of CuO NPs (0.075 wt%) with Sb (III) posed the most adverse impacts on root biomass and branches (up to 66.59% and 70.00% compared to other treatments, respectively). Treatments containing MWCNTs showed insignificant dose-dependent effects, while CeO2 NPs combined with Sb (III) showed significant synergistic stimulating effects on the fresh weights of root and shoot, by 68.30% and 73.48% (p < 0.05) compared to single Sb exposure, respectively. The rice planting increased the percentage of non-specifically sorbed Sb in soils by 1.50-14.49 than the no-planting stage. Analysis on microbial communities revealed that co-exposure of CuO NPs with Sb (III) induced the greatest adverse impacts on rhizobacteria abundances and community structures at both phylum and genus levels. Therein, significant decrease of Bacteroidetes, Acidobacteria and increase of Firmicutes abundance at the phylum level were observed. This study provided information about the risks of different ENMs released to Sb-contaminated soils under flooded condition on both crops and bacterial communities.
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Affiliation(s)
- Weicheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Jilai Gong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; State Environmental Protection Key Laboratory of Monitoring for Heavy Metal Pollutants, Changsha 410082, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Meng Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lei Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Yiqiu Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Siyuan Fang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Juan Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Siqun Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Zengping Chen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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12
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Franco ALC, Guan P, Cui S, de Tomasel CM, Gherardi LA, Sala OE, Wall DH. Precipitation effects on nematode diversity and carbon footprint across grasslands. GLOBAL CHANGE BIOLOGY 2022; 28:2124-2132. [PMID: 34936166 DOI: 10.1111/gcb.16055] [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: 08/06/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Free-living nematodes are one of the most diverse metazoan taxa in terrestrial ecosystems and are critical to the global soil carbon (C) cycling through their role in organic matter decomposition. They are highly dependent on water availability for movement, feeding, and reproduction. Projected changes in precipitation across temporal and spatial scales will affect free-living nematodes and their contribution to C cycling with unforeseen consequences. We experimentally reduced and increased growing season precipitation for 2 years in 120 field plots at arid, semiarid, and mesic grasslands and assessed precipitation controls on nematode genus diversity, community structure, and C footprint. Increasing annual precipitation reduced nematode diversity and evenness over time at all sites, but the mechanism behind these temporal responses differed for dry and moist grasslands. In arid and semiarid sites, there was a loss of drought-adapted rare taxa with increasing precipitation, whereas in mesic conditions increases in the population of predaceous taxa with increasing precipitation may have caused the observed reductions in dominant colonizer taxa and yielded the negative precipitation-diversity relationship. The effects of temporal changes in precipitation on all aspects of the nematode C footprint (respiration, production, and biomass C) were all dependent on the site (significant spatial × temporal precipitation interaction) and consistent with diversity responses at mesic, but not at arid and semiarid, grasslands. These results suggest that free-living nematode biodiversity and their C footprint will respond to climate change-driven shifts in water availability and that more frequent extreme wet years may accelerate decomposition and C turnover in semiarid and arid grasslands.
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Affiliation(s)
- André L C Franco
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Pingting Guan
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, China
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Shuyan Cui
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | | | - Laureano A Gherardi
- School of Life Sciences & Global Drylands Center, Arizona State University, Tempe, Arizona, USA
| | - Osvaldo E Sala
- School of Life Sciences, School of Sustainability & Global Drylands Center, Arizona State University, Tempe, Arizona, USA
| | - Diana H Wall
- Department of Biology & School of Global Environmental Sustainability, Colorado State University, Fort Collins, Colorado, USA
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13
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Cui J, Zhu R, Wang X, Xu X, Ai C, He P, Liang G, Zhou W, Zhu P. Effect of high soil C/N ratio and nitrogen limitation caused by the long-term combined organic-inorganic fertilization on the soil microbial community structure and its dominated SOC decomposition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114155. [PMID: 34861507 DOI: 10.1016/j.jenvman.2021.114155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The application of organic fertilizers, such as straw and manure, is an efficient approach to maintain soil productivity. However, the effect of these organic fertilizers on soil microbial nutrient balance has not yet been established. In this study, the effects of the long-term combined organic-inorganic fertilization on microbial community were investigated by conducting a 30-year-long field test. Overall, the following five fertilizer groups were employed: inorganic NP fertilizer (NP), inorganic NK fertilizer (NK), inorganic NPK fertilizer (NPK), NPK + manure (MNPK), and NPK + straw (SNPK). The results indicated that the mean natural logarithm of the soil C:N:P acquisition enzyme ratio was 1.04:1.11:1.00 under organic-inorganic treatments, which showed a deviation from its overall mean ratio of 1:1:1. This indicates that microbial resources do not have a balance. Vector analysis (vector angle <45°) and threshold elemental ratio analysis (RC:N-TERC:N > 0) further demonstrated that the microbial metabolism was limited by Nitrogen (N) under SNPK and MNPK treatments. N limitation further influenced soil microbial community structure and its dominated SOC decomposition. Specifically, Microbial communities transformed into a more oligotrophic-dominant condition (fungal, Acidobacteria, Chloroflexi) from copiotrophic-dominant (Proteobacteria, Actinobacteria) condition with increasing N limitation. Lysobacter genus and Blastocatellaceae family, in the bacterial communities along with the Mortierella elongata species in fungal communities, were markedly associated with the N limitation, which could be the critical biomarker that represented N limitation. Both correlation analysis and partial least squares path modeling showed significant positive effects of N limitation on the ratio of bacterial functional genes (Cellulase/Amylase), involved in recalcitrant SOC degradation.
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Affiliation(s)
- Jiwen Cui
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ruili Zhu
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Xiya Wang
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Xinpeng Xu
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Chao Ai
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ping He
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Guoqing Liang
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Wei Zhou
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China.
| | - Ping Zhu
- Jilin Academy of Agricultural Sciences, Gongzhuling, 130124, PR China.
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14
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Chao C, Wang L, Li Y, Yan Z, Liu H, Yu D, Liu C. Response of sediment and water microbial communities to submerged vegetations restoration in a shallow eutrophic lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149701. [PMID: 34419912 DOI: 10.1016/j.scitotenv.2021.149701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Submerged macrophytes are the main primary producers in shallow lakes and play an important role in structuring communities. Aquatic microbes are also an important component of aquatic ecosystems and play important roles in maintaining the health and stability of ecosystems. However, little is known about the interactions between macrophytes and microbes during the reintroduction of submerged vegetation. Here, we chose restored zones dominated by four different submerged vegetations and a bare zone in a shallow eutrophic lake to unveil the microbial diversity, composition and structure changes in sediment and water samples after submerged macrophytes were recovered for one and a half years (July 2019) and two years (April 2020). We found that the recovery of submerged vegetations decreased phosphorus content in water and sediments but increased nitrogen and carbon content in sediments. We observed that the transparency of water in the restored zones was significantly higher than that in the bare zone in July. The recovery of submerged vegetations significantly influenced the alpha diversity of bacterial communities in sediments, with higher values observed in restored zones than in bare zones, whereas no significant influence was found in the water samples. In July, the macrophyte species showed strong effects on the bacterial community composition in water and relatively little effect in sediment. However, a strong effect of the macrophyte species on the composition of bacterial communities in sediments was observed in April, which may be related to the decomposition of plant litter and the decay of detritus. Additionally, the dissimilarity of the sedimentary bacterial community may increase more slowly with environmental changes than the planktonic bacterial community dissimilarity. These results suggest that the large-scale restoration of aquatic macrophytes can not only improve water quality and change sediment characteristics but can also affect the diversity and compositions of bacterial communities, and these effects seem to be very long-lasting.
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Affiliation(s)
- Chuanxin Chao
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Ligong Wang
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Yang Li
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Zhiwei Yan
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Huimin Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Dan Yu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Chunhua Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China.
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15
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Kumar A, Dubey A, Malla MA, Dames J. Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100025. [PMID: 34841316 PMCID: PMC8610313 DOI: 10.1016/j.crmicr.2021.100025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/17/2022] Open
Abstract
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities. This work, investigated the changes in bacterial community composition at taxonomic and functional level in rhizosphere soil of sweet sorghum under extensive cultivation practices at three different field sites of South Africa. 16S rRNA amplicon sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8% and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. Overall, this study showed that soil pH, nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in sorghum rhizosphere.
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.
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Affiliation(s)
- Ashwani Kumar
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
- Corresponding author at: Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India.
| | - Anamika Dubey
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Joanna Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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16
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Kim HS, Lee SH, Jo HY, Finneran KT, Kwon MJ. Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148944. [PMID: 34298360 DOI: 10.1016/j.scitotenv.2021.148944] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
The land-use change from natural to managed farmland ecosystems can undergo perturbations and significantly impact soil environment and communities. To understand how anthropogenic land-use alteration determines in-depth relationships among soil environmental factors and soil bacterial communities, high-resolution characterization was performed using soil samples (27 spots × 3 depths; top 10-20 cm, middle 90-100 cm, bottom 180-190 cm) from a natural forest and a 50 year-old farmland. The soil bacterial community abundance (number of OTU's per sample) and diversity (Faith's phylogenetic diversity) was significantly higher in the top layer of farmland soil than in forest soil. However, the differences in bacterial community abundance between farmland and forest decreased with depth, suggesting that the effect of fertilization was limited to top and middle layers. The phyla Acidobacteria and Proteobacteria were distributed distinctively during the land-use change. The subgroups Gp1-3 of Acidobacteria were more abundant in the forest samples (pH 3.5-5), while Gp4-7 and Gp10 were predominant in the farmland (pH 4.5-9.5). Members belonging to α-Proteobacteria and Xanthomonadales in γ-Proteobacteria were dominant in the forest, whereas β-, δ-, and γ-Proteobacteria were relatively abundant in the farmland. Both multivariate and correlation network analyses revealed that Acidobacteria and Proteobacteria communities were significantly affected by soil pH, as well as toxic metals from pesticides (Zn, Cr, Ni, Cu, Cd, As) and terminal electron acceptors (NO3, bioavailable Fe(III), SO4). In line with the long history of anthropogenic fertilization, the farmland site showed high abundance of membrane and ATP-binding cassette transporter genes, suggesting the key for uptake of nutrients and for protection against toxic metals and environmental stresses. This study provides new insights into the use of both Acidobacteria and Proteobacteria community structures as a bacterial indicator for land-use change.
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Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kevin T Finneran
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29643, USA
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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17
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Cao W, Zhu R, Gong J, Yang T, Zeng G, Song B, Li J, Fang S, Qin M, Qin L, Chen Z, Mao X. Evaluating the metabolic functional profiles of the microbial community and alfalfa (Medicago sativa) traits affected by the presence of carbon nanotubes and antimony in drained and waterlogged sediments. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126593. [PMID: 34271448 DOI: 10.1016/j.jhazmat.2021.126593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Antimony (Sb) is the ubiquitous re-emerging contaminant greatly accumulated in sediments which has been revealed risky to ecological environment. However, the impacts of Sb (III/V) on microbes and plants in sediments, under different water management with presence of engineering materials are poorly understood. This study conducted sequential incubation of sediments (flooding, draining and planting) with presence of multiwall carbon nanotubes (MWCNTs) and Sb to explore the influence on microbial functional diversity, Sb accumulation and alfalfa traits. Results showed that water management and planting led to greater impacts of sediment enzyme activities and microbial community metabolic function and bioavailable Sb fractions (defined as sum of acid-soluble fraction and reducible fraction, F1 + F2). Available fractions of Sb (V) showed higher correlation to microbial metabolism (r = 0.933) than that of Sb (III) (r = -0.480) in planting stage. MWCNTs with increasing concentrations (0.011%, w/w) positively correlated to microbial community metabolic function in planting stage whereas resulted in decreasing of Sb (III/V) concentrations in alfalfa, although 0.01% MWCNT led to increase of Sb (V) and decrease of Sb (V) by 50.97% and 32.68% respectively. This study provided information for investigating combined ecological impacts of heavy metal and engineering materials under different water managing sediments.
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Affiliation(s)
- Weicheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Rilong Zhu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
| | - Jilai Gong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; State Environmental Protection Key Laboratory of Monitoring for Heavy Metal Pollutants, Changsha 410082, PR China.
| | - TingYu Yang
- School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Juan Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Siyuan Fang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Meng Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lei Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Zengping Chen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoqian Mao
- Hunan Ecological and Environmental Affairs Center, Changsha 410082, PR China
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18
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Tóthné Bogdányi F, Boziné Pullai K, Doshi P, Erdős E, Gilián LD, Lajos K, Leonetti P, Nagy PI, Pantaleo V, Petrikovszki R, Sera B, Seres A, Simon B, Tóth F. Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review. Microorganisms 2021; 9:2130. [PMID: 34683451 PMCID: PMC8538326 DOI: 10.3390/microorganisms9102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022] Open
Abstract
The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.
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Affiliation(s)
| | - Krisztina Boziné Pullai
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
| | - Pratik Doshi
- ImMuniPot Independent Research Group, H-2100 Gödöllő, Hungary
| | - Eszter Erdős
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Lilla Diána Gilián
- Szent István Campus Dormitories, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Károly Lajos
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Paola Leonetti
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Péter István Nagy
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Vitantonio Pantaleo
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Renáta Petrikovszki
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Bozena Sera
- Department of Environmental Ecology and Landscape Management, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Anikó Seres
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Barbara Simon
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Ferenc Tóth
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
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19
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Wang W, Hu M, Shu X, Li H, Qi W, Yang Y, Zhang Q. Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146552. [PMID: 34030307 DOI: 10.1016/j.scitotenv.2021.146552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/06/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
The reservoir of microbial communities within the soil and the sediment performs many ecological functions and offers many ecosystem services. It has been suggested that its diversity and community structure could be explained by different grain size and heterogeneity. However, most of these conclusions come from studies conducted in terrestrial soil, impermeable marine and freshwater sediment (substrate). It remains to be seen whether these conclusions hold true in permeable substrate, especially in headwater river ecosystems. To address this, a field experiment was aimed to evaluate the link between grain median size and distribution heterogeneity and microbial diversity and community structure. Permeable substrate with gradient grain sizes and heterogeneities was inoculated in a headwater river in central China, while the diversity and community composition of the total microbial community and three denitrifier communities were investigated by high throughput sequencing three months later. The total microbial community was sequenced by 16S rRNA, a marker for taxonomic diversity. Three denitrifier communities were sequenced using three functional gene markers: nirK, nirS, and nosZ. The result showed that both the diversity and community structure of the total microbial community and three denitrifier communities were determined by water chemistry rather than grain size and size distribution heterogeneity, although grain size and heterogeneity positively influenced the nutrient concentrations of the substrate. Compared to the total microbial community, denitrification functional groups had more unique species proportions, indicating that functional genes were more sensitive to environmental change than the 16S rRNA gene. Our study fills a gap in understanding microbial communities in permeable sediment in a headwater river and highlights the less importance of grain size and heterogeneity on mm-scale in shaping the diversity and structure of microbiome.
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Affiliation(s)
- Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Mingming Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 10038, China
| | - Xiao Shu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenhua Qi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yuyi Yang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Quanfa Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
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20
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Li J, Chen Q, Li Q, Zhao C, Feng Y. Influence of plants and environmental variables on the diversity of soil microbial communities in the Yellow River Delta Wetland, China. CHEMOSPHERE 2021; 274:129967. [PMID: 33979943 DOI: 10.1016/j.chemosphere.2021.129967] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/23/2021] [Accepted: 02/09/2021] [Indexed: 05/20/2023]
Abstract
Microorganisms play an important role in the biogeochemical cycle and ecological function regulation of wetlands, have a major impact on global climate change and are critical for maintaining the health of the global ecosystem. In order to investigate the relationships among plants, environmental variables, and microbial communities in coastal wetlands in the Yellow River Delta, we selected soils growing plants such as Suaeda salsa, Tamarix chinensis, Phragmites australis, and cotton etc. The results show that there were differences in microbial diversity among areas with different vegetation cover and the microbial abundance in Phragmites australis and Tamarix chinensis areas was higher than that in mudflat, Suaeda glauca and cotton field, plants increased the diversity of soil microorganisms. The structure and diversity of soil microorganisms were significantly higher than that of endophytes. The Shannon index of soil bacteria was about 4-5.5, while that of endophytes was about 0-4. The soil bacteria were mainly Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria, accounting for more than 90.0% in all samples. The Mn4+, Fe3+ and hydrolytic nitrogen contents in the soil of vegetation covered areas was lower than that of the bare beach, the content of hydrolytic nitrogen in Phragmites australis area was generally higher, and the content of SO42- and NO2- in the area was lowest near oil fields. Redundancy analysis shows that the explanatory rates of environmental factors at the phylum and genus levels were 89.70% and 86.80%, respectively, and K (23.40%), NO2- (11.80%), Mn4+ (9.80%) and Na (8.00%) were the main factors explaining the structural changes and composition of microbial flora at the phylum level. This study provides an ecological perspective for understanding the influence mechanism between wetland microbial diversity and wetland ecosystem function. It is helpful for us to understand the interactions among plants, environmental variables, and microbial communities in the coastal wetland of the Yellow River Delta, and has important guiding significance for the scientific research of soil environmental remediation in the degraded coastal wetland of the Yellow River Delta.
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Affiliation(s)
- Jinye Li
- Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
| | - Qingfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China; College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China.
| | - Qing Li
- Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
| | - Changsheng Zhao
- Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
| | - You Feng
- Key Laboratory for Applied Technology of Sophisticated Analytical Instrument of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
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21
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Xiong W, Jousset A, Li R, Delgado-Baquerizo M, Bahram M, Logares R, Wilden B, de Groot GA, Amacker N, Kowalchuk GA, Shen Q, Geisen S. A global overview of the trophic structure within microbiomes across ecosystems. ENVIRONMENT INTERNATIONAL 2021; 151:106438. [PMID: 33621916 DOI: 10.1016/j.envint.2021.106438] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China; Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia, Spain
| | - Benjamin Wilden
- University of Bielefeld, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany
| | - Gerard Arjen de Groot
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA Wageningen, the Netherlands
| | - Nathalie Amacker
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
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22
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Prada-Salcedo LD, Wambsganss J, Bauhus J, Buscot F, Goldmann K. Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils. Environ Microbiol 2020; 23:1889-1906. [PMID: 32959469 DOI: 10.1111/1462-2920.15244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.
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Affiliation(s)
- Luis Daniel Prada-Salcedo
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,Department of Biology, University of Leipzig, Leipzig, Johannisallee 21, 04103, Germany
| | - Janna Wambsganss
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany.,Chair of Geobotany, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestraße 1, 79104, Germany
| | - Jürgen Bauhus
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Deutscher Platz 5e, 04103, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany
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23
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Lo RKS, Chong KP. Metagenomic data of soil microbial community in relation to basal stem rot disease. Data Brief 2020; 31:106030. [PMID: 32743032 PMCID: PMC7387770 DOI: 10.1016/j.dib.2020.106030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 11/16/2022] Open
Abstract
The oil palm industry, especially in Indonesia and Malaysia is being threatened by Basal Stem Rot (BSR) disease caused by Ganoderma boninense. There is no conclusive remedy in handling this disease effectively. In this study, metagenomics analysis of soil were analyzed for a better understanding of the microbial diversity in relation to BSR disease. Study was conducted in three plantation sites of Sabah, Malaysia which incorporated different disease management and agronomic practices. The estates are located at Sandakan (Kam Cheong Plantation), Lahad Datu (FGV Ladang Sahabat) and Tawau (Warisan Gagah). Soil samples were collected from disease free, high and low BSR incidence plots. Illumina MiSeq metagenomic analysis using V3-V4 region of 16S rRNA gene was employed to study the microbial diversity. Bacteria (97.4%) and Archaea (0.2%) were found majority in kingdom taxonomy level. The most abundant phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia. Higher alpha diversity of all species was observed among all tested soil from each estates. Beta analysis was analyzed using non phylogenetic UnifRac matrix and visualized using Principal Coordinates Analysis (PCoA). The tested soil samples in Kam Cheong Plantation were found to have similar bacterial communities. The data provided is useful as an indicator in developing biology controls against Ganoderma boninense.
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Affiliation(s)
- Racheal Khai Shyen Lo
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 88400 Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Khim Phin Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 88400 Jalan UMS, Kota Kinabalu, Sabah, Malaysia
- FGV Chair of Sustainable Oil Palm Management, Faculty of Agriculture, Universiti Malaysia Sabah, Mile 10, Sg. Batang, 90000 Sandakan, Sabah, Malaysia
- Corresponding author at: Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 88400 Jalan UMS, Kota Kinabalu, Sabah, Malaysia.
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24
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Richter-Heitmann T, Hofner B, Krah FS, Sikorski J, Wüst PK, Bunk B, Huang S, Regan KM, Berner D, Boeddinghaus RS, Marhan S, Prati D, Kandeler E, Overmann J, Friedrich MW. Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland. Front Microbiol 2020; 11:1391. [PMID: 32695081 PMCID: PMC7338559 DOI: 10.3389/fmicb.2020.01391] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/29/2020] [Indexed: 01/15/2023] Open
Abstract
Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
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Affiliation(s)
- Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Benjamin Hofner
- Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franz-Sebastian Krah
- Biodiversity Conservation, Institute for Ecology, Evolution and Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sixing Huang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Doreen Berner
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Runa S Boeddinghaus
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
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25
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Bak F, Nybroe O, Zheng B, Badawi N, Hao X, Nicolaisen MH, Aamand J. Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile. FEMS Microbiol Ecol 2020; 95:5288339. [PMID: 30649315 PMCID: PMC6397044 DOI: 10.1093/femsec/fiz008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below ∼4 m. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of 6 m. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths. Deep fracture communities contained a higher relative abundance of aerobes and plant material decomposers like Nitrospirae, Acidobacteria and Planctomycetes than adjacent matrix sediments. Similarly, analyses of the relative abundances of archaeal amoA, nirK and dsrB genes indicated transition from aerobic to anaerobic nitrogen and sulphur cycling at greater depth in preferential flow paths than in matrix sediments. Preferential flow paths in the top 260 cm contained more indicator operational taxonomic units from the plough layer community than the matrix sediments. This study indicates that the availability of oxygen and organic matter and downward transport of bacteria shape bacterial communities in preferential flow paths, and suggests that their lifestyles differ from those of bacteria in matrix communities.
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Affiliation(s)
- Frederik Bak
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark.,University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen, Denmark
| | - Ole Nybroe
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen, Denmark
| | - Bangxiao Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Nora Badawi
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Xiuli Hao
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen, Denmark.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | | | - Jens Aamand
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
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26
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Song B, Gong J, Tang W, Zeng G, Chen M, Xu P, Shen M, Ye S, Feng H, Zhou C, Yang Y. Influence of multi-walled carbon nanotubes on the microbial biomass, enzyme activity, and bacterial community structure in 2,4-dichlorophenol-contaminated sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136645. [PMID: 31955106 DOI: 10.1016/j.scitotenv.2020.136645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
The rise in manufacture and use of carbon nanotubes has aroused the concern about their potential risks associated with coexisting pollutants in the aquatic environment. 2,4-dichlorophenol (2,4-DCP), with a high toxicity to many aquatic organisms, is a widespread pollutant resulting from the extensive use of pesticides and preservatives. In this article, the adsorption of 2,4-DCP by riverine sediment and the responses of sediment microbial community to 2,4-DCP were studied in the presence of multi-walled carbon nanotubes (MWCNTs). Adding MWCNTs significantly increased the adsorption amount of sediment for 2,4-DCP from 0.541 to 1.44 mg/g as the MWCNT concentration increased from 0 to 15 mg/g. The responses of sediment microbial community were determined after one-month exposure to MWCNTs at different concentrations (0.05, 0.5, 5, and 50 mg/g). The microbial biomass carbon in the sediment contaminated with 2,4-DCP increased in the presence of 5 mg/g of MWCNTs (from 0.06 to 0.11 mg/g), but not significantly changed at other MWCNT concentrations. For the sediments contaminated with 2,4-DCP, the presence of MWCNTs made no difference to urease activity, while the dehydrogenase activity slightly increased with the addition of 5 mg/g of MWCNTs and decreased in the presence of 50 mg/g of MWCNTs. The changes of sediment bacterial communities were further determined by 16S rRNA gene sequencing. Based on the weighted UniFrac distance between communities, the clustering analysis suggested that the contamination of 2,4-DCP affected the bacterial community structure in a greater degree than that caused by MWCNTs at relatively low concentrations (≤5 mg/g). Bacteroidetes, Planctomycetes, and Nitrospirae were feature bacterial phyla to reflect the effects of MWCNTs and 2,4-DCP on sediment bacterial community. These results may contribute to the understanding of microbial community response to co-exposure of MWCNTs and 2,4-DCP and the assessment of associated ecological risks.
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Affiliation(s)
- Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jilai Gong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wangwang Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Ming Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Piao Xu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Maocai Shen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Shujing Ye
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Haopeng Feng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Chengyun Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yang Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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27
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Turley NE, Bell‐Dereske L, Evans SE, Brudvig LA. Agricultural land‐use history and restoration impact soil microbial biodiversity. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13591] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nash E. Turley
- Department of Plant Biology Michigan State University East Lansing MI USA
- Program in Ecology Evolutionary Biology, and Behavior Michigan State University East Lansing MI USA
| | - Lukas Bell‐Dereske
- Kellogg Biological Station Michigan State University East Lansing MI USA
| | - Sarah E. Evans
- Program in Ecology Evolutionary Biology, and Behavior Michigan State University East Lansing MI USA
- Kellogg Biological Station Michigan State University East Lansing MI USA
- Department of Integrative Biology Michigan State University East Lansing MI USA
| | - Lars A. Brudvig
- Department of Plant Biology Michigan State University East Lansing MI USA
- Program in Ecology Evolutionary Biology, and Behavior Michigan State University East Lansing MI USA
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28
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Wang P, Li S, Yang X, Zhou J, Shu W, Jiang L. Mechanisms of soil bacterial and fungal community assembly differ among and within islands. Environ Microbiol 2019; 22:1559-1571. [DOI: 10.1111/1462-2920.14864] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, School of Life Sciences Sun Yat‐sen University Guangzhou 510275 People's Republic of China
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Shao‐Peng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Institute of Eco‐Chongming (IEC) Shanghai 200062 China
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman OK 73019 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing 100084 People's Republic of China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University Guangzhou 510631 People's Republic of China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
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29
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Environmental Filtering Drives Local Soil Fungal beta Diversity More than Dispersal Limitation in Six Forest Types along a Latitudinal Gradient in Eastern China. FORESTS 2019. [DOI: 10.3390/f10100863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biogeographic patterns of soil fungal diversity have been well documented in forest ecosystems, but the underlying mechanisms and processes that shape these patterns remain relatively unknown. This study took soil samples from 300 forest plots spanning six forest types along a latitudinal gradient in eastern China, which ranges from tropical rainforest to boreal forest ecosystems. A null-model analysis was used to compare the observed soil fungal beta diversity (β-diversity) with the β-diversity expected from random sampling of each local species pool. We also compared the relative importance of environmental and spatial variables on soil fungal β-diversity among forest types along the latitudinal gradient. Our results found that observed β-diversity was greater than expected β-diversity in all six forest types, which means that species tend to be more aggregated than expected. We determined that this species aggregation resulted from both environmental filtering and species dispersal limitations. Further, environmental variables had stronger influences on β-diversity than spatial dispersions. Additionally, the co-occurrence network showed that more species interactions occurred in the mid-latitude forests which lead to decreased soil fungal β-diversity and low interpretations of environmental and spatial variables. Study of these processes in different forest types along latitudinal gradients will provide important insights that local differences in the relative importance of different community assembly processes creates different gradients in global biodiversity.
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30
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Matschiavelli N, Kluge S, Podlech C, Standhaft D, Grathoff G, Ikeda-Ohno A, Warr LN, Chukharkina A, Arnold T, Cherkouk A. The Year-Long Development of Microorganisms in Uncompacted Bavarian Bentonite Slurries at 30 and 60 °C. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10514-10524. [PMID: 31369249 DOI: 10.1021/acs.est.9b02670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the multibarrier concept for the deep geological disposal of high-level radioactive waste (HLW), bentonite is proposed as a potential barrier and buffer material for sealing the space between the steel canister containing the HLW and the surrounding host rock. In order to broaden the spectra of appropriate bentonites, we investigated the metabolic activity and diversity of naturally occurring microorganisms as well as their time-dependent evolution within the industrial B25 Bavarian bentonite under repository-relevant conditions. We conducted anaerobic microcosm experiments containing the B25 bentonite and a synthetic Opalinus Clay pore water solution, which were incubated for one year at 30 and 60 °C. Metabolic activity was only stimulated by the addition of lactate, acetate, or H2. The majority of lactate- and H2-containing microcosms at 30 °C were dominated by strictly anaerobic, sulfate-reducing, and spore-forming microorganisms. The subsequent generation of hydrogen sulfide led to the formation of iron-sulfur precipitations. Independent from the availability of substrates, thermophilic bacteria dominated microcosms that were incubated at 60 °C. However, in the respective microcosms, no significant metabolic activity occurred, and there was no change in the analyzed biogeochemical parameters. Our findings show that indigenous microorganisms of B25 bentonite evolve in a temperature- and substrate-dependent manner.
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Affiliation(s)
- Nicole Matschiavelli
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Sindy Kluge
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Carolin Podlech
- University of Greifswald , Institute of Geography and Geology , Friedrich-Ludwig-Jahn-Straße 17a , 17487 Greifswald , Germany
| | - Daniel Standhaft
- University of Greifswald , Institute of Geography and Geology , Friedrich-Ludwig-Jahn-Straße 17a , 17487 Greifswald , Germany
| | - Georg Grathoff
- University of Greifswald , Institute of Geography and Geology , Friedrich-Ludwig-Jahn-Straße 17a , 17487 Greifswald , Germany
| | - Atsushi Ikeda-Ohno
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Laurence N Warr
- University of Greifswald , Institute of Geography and Geology , Friedrich-Ludwig-Jahn-Straße 17a , 17487 Greifswald , Germany
| | | | - Thuro Arnold
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
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31
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Leach WB, Carrier TJ, Reitzel AM. Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis. Ecol Evol 2019; 9:9935-9947. [PMID: 31534705 PMCID: PMC6745676 DOI: 10.1002/ece3.5534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The community of microbes associated with animals can be dynamic depending on the local environment, and factors that influence the composition of the microbiome are essential to our understanding of how microbes may influence the biology of their animal hosts. Regularly repeated changes in the environment, such as diel lighting, can result in two different organismal responses: a direct response to the presence and absence of exogenous light and endogenous rhythms resulting from a molecular circadian clock, both of which can influence the associated microbiota. Here, we report how diel lighting and a potential circadian clock impacts the diversity and relative abundance of bacteria in the model cnidarian Nematostella vectensis using an amplicon-based sequencing approach. Comparisons of bacterial communities associated with anemones cultured in constant darkness and in light:dark conditions revealed that individuals entrained in the dark had a more diverse microbiota. Overall community composition showed little variation over a 24-hr period in either treatment; however, abundances of individual bacterial OTUs showed significant cycling in each treatment. A comparative analysis of genes involved in the innate immune system of cnidarians showed differential expression between lighting conditions in N. vectensis, with significant up-regulation during long-term darkness for a subset of genes. Together, our studies support a hypothesis that the bacterial community associated with this species is relatively stable under diel light conditions when compared with static conditions and that particular bacterial members may have time-dependent abundance that coincides with the diel photoperiod in an otherwise stable community.
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Affiliation(s)
- Whitney B. Leach
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Tyler J. Carrier
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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32
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Dukunde A, Schneider D, Schmidt M, Veldkamp E, Daniel R. Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests. Front Microbiol 2019; 10:1519. [PMID: 31338079 PMCID: PMC6629791 DOI: 10.3389/fmicb.2019.01519] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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Affiliation(s)
- Amélie Dukunde
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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33
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Orland C, Emilson EJS, Basiliko N, Mykytczuk NCS, Gunn JM, Tanentzap AJ. Microbiome functioning depends on individual and interactive effects of the environment and community structure. ISME JOURNAL 2018; 13:1-11. [PMID: 30042502 DOI: 10.1038/s41396-018-0230-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 01/16/2023]
Abstract
How ecosystem functioning changes with microbial communities remains an open question in natural ecosystems. Both present-day environmental conditions and historical events, such as past differences in dispersal, can have a greater influence over ecosystem function than the diversity or abundance of both taxa and genes. Here, we estimated how individual and interactive effects of microbial community structure defined by diversity and abundance, present-day environmental conditions, and an indicator of historical legacies influenced ecosystem functioning in lake sediments. We studied sediments because they have strong gradients in all three of these ecosystem properties and deliver important functions worldwide. By characterizing bacterial community composition and functional traits at eight sites fed by discrete and contrasting catchments, we found that taxonomic diversity and the normalized abundance of oxidase-encoding genes explained as much variation in CO2 production as present-day gradients of pH and organic matter quantity and quality. Functional gene diversity was not linked to CO2 production rates. Surprisingly, the effects of taxonomic diversity and normalized oxidase abundance in the model predicting CO2 production were attributable to site-level differences in bacterial communities unrelated to the present-day environment, suggesting that colonization history rather than habitat-based filtering indirectly influenced ecosystem functioning. Our findings add to limited evidence that biodiversity and gene abundance explain patterns of microbiome functioning in nature. Yet we highlight among the first time how these relationships depend directly on present-day environmental conditions and indirectly on historical legacies, and so need to be contextualized with these other ecosystem properties.
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Affiliation(s)
- Chloé Orland
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK.
| | - Erik J S Emilson
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK.,Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. E., Sault. Ste. Marie, ON, P6A 2E5, Canada
| | - Nathan Basiliko
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - Nadia C S Mykytczuk
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - John M Gunn
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK
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