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Nshimiyimana JB, Zhao K, Wang W, Kong W. Diazotrophic abundance and community structure associated with three meadow plants on the Qinghai-Tibet Plateau. Front Microbiol 2024; 14:1292860. [PMID: 38260880 PMCID: PMC10801153 DOI: 10.3389/fmicb.2023.1292860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Symbiotic diazotrophs form associations with legumes and substantially fix nitrogen into soils. However, grasslands on the Qinghai-Tibet Plateau are dominated by non-legume plants, such as Kobresia tibetica. Herein, we investigated the diazotrophic abundance, composition, and community structure in the soils and roots of three plants, non-legume K. tibetica and Kobresia humilis and the legume Oxytropis ochrocephala, using molecular methods targeting nifH gene. Diazotrophs were abundantly observed in both bulk and rhizosphere soils, as well as in roots of all three plants, but their abundance varied with plant type and soil. In both bulk and rhizosphere soils, K. tibetica showed the highest diazotroph abundance, whereas K. humilis had the lowest. In roots, O. ochrocephala and K. humilis showed the highest and the lowest diazotroph abundance, respectively. The bulk and rhizosphere soils exhibited similar diazotrophic community structure in both O. ochrocephala and K. tibetica, but were substantially distinct from the roots in both plants. Interestingly, the root diazotrophic community structures in legume O. ochrocephala and non-legume K. tibetica were similar. Diazotrophs in bulk and rhizosphere soils were more diverse than those in the roots of three plants. Rhizosphere soils of K. humilis were dominated by Actinobacteria, while rhizosphere soils and roots of K. tibetica were dominated by Verrumicrobia and Proteobacteria. The O. ochrocephala root diazotrophs were dominated by Alphaproteobacteria. These findings indicate that free-living diazotrophs abundantly and diversely occur in grassland soils dominated by non-legume plants, suggesting that these diazotrophs may play important roles in fixing nitrogen into soils on the plateau.
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Affiliation(s)
- Jean Bosco Nshimiyimana
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Kang Zhao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Wenying Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization in Qinghai Tibet Plateau, Xining, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
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2
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Islam W, Ullah A, Zeng F. Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166027. [PMID: 37541502 DOI: 10.1016/j.scitotenv.2023.166027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Sun J, Zhang A, Zhang Z, Liu Y, Zhou H, Cheng H, Chen Z, Li H, Zhang R, Wang Y. Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106082. [PMID: 37429213 DOI: 10.1016/j.marenvres.2023.106082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Aoqi Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Zhongxian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Yang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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4
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Liu N, Hu H, Ma W, Deng Y, Dimitrov D, Wang Q, Shrestha N, Su X, Feng K, Liu Y, Hao B, Zhang X, Feng X, Wang Z. Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships. MICROBIAL ECOLOGY 2023; 85:1013-1027. [PMID: 35364696 DOI: 10.1007/s00248-022-01997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/11/2022] [Indexed: 05/04/2023]
Abstract
Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.
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Affiliation(s)
- Nana Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huifeng Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenhong Ma
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Qinggang Wang
- Department of Ecology and Ecological Engineering, College of Resources and Environmental Sciences, and Key Laboratory of Biodiversity and Organic Farming of Beijing City, China Agricultural University, Beijing, 100193, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Baihui Hao
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Xinying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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5
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Yuan B, Guo M, Wu W, Zhou X, Li M, Xie S. Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship. MICROBIAL ECOLOGY 2023; 85:586-603. [PMID: 35338380 DOI: 10.1007/s00248-022-01999-6] [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: 07/30/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.
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Affiliation(s)
- Bo Yuan
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China.
| | - Mengjing Guo
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Wei Wu
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Xiaode Zhou
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Miaojie Li
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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6
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Wang Y, Dang N, Feng K, Wang J, Jin X, Yao S, Wang L, Gu S, Zheng H, Lu G, Deng Y. Grass-microbial inter-domain ecological networks associated with alpine grassland productivity. Front Microbiol 2023; 14:1109128. [PMID: 36760496 PMCID: PMC9905801 DOI: 10.3389/fmicb.2023.1109128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial β-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.
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Affiliation(s)
- Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China,CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ning Dang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Junbang Wang
- National Ecosystem Science Data Center, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Xin Jin
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Shiting Yao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Linlin Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Hua Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guangxin Lu
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China,*Correspondence: Guangxin Lu ✉
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China,Ye Deng ✉
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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Zhang P, Guan P, Hao C, Yang J, Xie Z, Wu D. Changes in assembly processes of soil microbial communities in forest-to-cropland conversion in Changbai Mountains, northeastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151738. [PMID: 34808170 DOI: 10.1016/j.scitotenv.2021.151738] [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: 04/07/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
In response to human-induced changes in the environment, it is crucial to assess the underlying factors of the impacts of forest conversion on ecosystem function. However, research is limited on bacteria and fungi diversity, functional properties, and community assembly mechanisms in response to forest-to-cropland conversion. We categorized soil bacterial and fungal communities from primary forest, secondary forest, and cropland in Changbai Mountains, China. We found that forest-to-cropland conversion altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that the conversion from forest to cropland enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. Furthermore, ecological drift dominates the ecological processes of cropland fungi. Both edaphic properties (the content of C: N ratio, available phosphorus, nitrate) significantly impacted on soil bacterial and fungal community structures. In addition, there were significant functional variations in the fungal community between forest-to-cropland. The ectomycorrhizal and saprotrophic fungi showed increased abundance in the forest microbial communities, whereas the endophytic and pathogenic fungal abundance was increased in cropland soil. Taken together, our data illustrate the differences in the response of bacteria and fungi to forest-to-cropland conversion in temperate forest areas and deepen our understanding of the effects of forest conversion on microbial functions and community assembly processes.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingting Guan
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Cao Hao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Jingjing Yang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Zhijing Xie
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Donghui Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China; Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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9
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Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station. Int Microbiol 2022; 25:571-586. [DOI: 10.1007/s10123-022-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
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10
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Zhang B, Xue K, Zhou S, Wang K, Liu W, Xu C, Cui L, Li L, Ran Q, Wang Z, Hu R, Hao Y, Cui X, Wang Y. Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas. eLife 2022; 11:70164. [PMID: 35073255 PMCID: PMC8828049 DOI: 10.7554/elife.70164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.
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Affiliation(s)
- Biao Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Kui Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Wenjing Liu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Cong Xu
- Aerospace Information Research Institute, University of Chinese Academy of Sciences
| | - Lizhen Cui
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Linfeng Li
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Qinwei Ran
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Zongsong Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Ronghai Hu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Xiaoyong Cui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, University of Chinese Academy of Sciences
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences
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11
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Duan Y, Lian J, Wang L, Wang X, Luo Y, Wang W, Wu F, Zhao J, Ding Y, Ma J, Li Y, Li Y. Variation in Soil Microbial Communities Along an Elevational Gradient in Alpine Meadows of the Qilian Mountains, China. Front Microbiol 2021; 12:684386. [PMID: 34248904 PMCID: PMC8270674 DOI: 10.3389/fmicb.2021.684386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
Bacterial, archaeal, and eukaryota diversity in mountainous areas varies along elevational gradients, but details remain unclear. Here, we use a next-generation sequencing method based on 16S/18S rRNA to reveal the soil microbial diversity and community compositions of alpine meadow ecosystems along an elevation span of nearly 2,000 m (1,936-3,896 m) in China's Qilian Mountains. Both bacterial and eukaryota diversity increased linearly with increasing elevation, whereas archaeal diversity increased, but not significantly. The diversity patterns of several phyla in the bacterial, archaeal, and eukaryota communities were consistent with the overall elevational trend, but some phyla did not follow this pattern. The soil microbial community compositions were shaped by the coupled effects of regional climate and local soil properties. Intradomain links were more important than interdomain links in the microbial network of the alpine meadows, and these links were mostly positive. The bacteria formed more connections than either archaea or eukaryota, but archaea may be more important than bacteria in building the soil microbial co-occurrence network in this region. Our results provide new visions on the formation and maintenance of soil microbial diversity along an elevational gradient and have implications for microbial responses to climate change in alpine ecosystems.
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Affiliation(s)
- Yulong Duan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Jie Lian
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Lilong Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Xuyang Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yongqing Luo
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Wanfu Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, China.,MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, China.,MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China
| | - Yun Ding
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China
| | - Jun Ma
- Gansu Qilian Mountains National Nature Reserve Authority, Zhangye, China
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuqiang Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China.,University of Chinese Academy of Sciences, Beijing, China
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12
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Lin YP, Wunderlich RF, Lin CM, Uphoff N, Schmeller DS, Shipin OV, Watanabe T, Mukhtar H. Topsoil microbial community structure responds to land cover type and environmental zone in the Western Pacific region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144349. [PMID: 33412402 DOI: 10.1016/j.scitotenv.2020.144349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Soil encompasses diverse microbial communities that are essential for fundamental ecosystem functions such as biogeochemical cycling. To better understand underlying biogeochemical processes, it is necessary to know the structure of soil archaeal and bacterial communities and their responses to edaphic and climate variables within and across various land cover types (LCTs) and environmental zones (ENZs). Here we sampled eighty-nine sites across five ENZs and four LCTs within the Western Pacific region. Through leveraging the second-generation sequencing of topsoil samples, we showed that α-diversity (taxonomic diversity) of archaea strongly varied within LCTs, whereas bacterial α-diversity was significantly controlled by both LCT and ENZ. Soil archaea and bacteria showed global niche differentiation associated with contrasting diversity responses to latitude and differential responses of microbial diversity patterns to edaphic and climate variables within LCTs and ENZs. In contrast to α-diversity, microbial β-diversity (the compositional dissimilarity between sites) was majorly governed by ENZs, particularly for archaea (P < 0.01). Our results highlight the importance of LCTs and ENZs for understanding soil microbial contributions to nutrient dynamics and ecosystem resilience under land-use intensification and climate change.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | - Chiao-Ming Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Norman Uphoff
- SRI International Network and Resources Center (SRI-Rice), Cornell University, USA
| | - Dirk S Schmeller
- Ecolab, Université de Toulouse, UPS, INPT, CNRS, Toulouse, France
| | - Oleg V Shipin
- Environmental Engineering and Management, Asian Institute of Technology, Thailand
| | - Teiji Watanabe
- Faculty of Environmental Earth Science, Hokkaido University, Japan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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13
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. THE ISME JOURNAL 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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14
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The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1546-1559. [PMID: 33439456 DOI: 10.1007/s11427-020-1843-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China. Over a 3,000 km range, community similarity declined with increasing geographic distance (Mantel r=0.62), and community composition was clustered by city (R2=0.50). Within cities (<100 km), the aforementioned biogeographic patterns were weakened. Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales, respectively. Accordingly, the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%, respectively. When the tested samples originated from cities that were more than 1,265 km apart, the soil sources could be identified with nearly 100% accuracy. Overall, this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities. The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.
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15
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Zhang M, Chai L, Huang M, Jia W, Guo J, Huang Y. Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau. BMC Microbiol 2020; 20:235. [PMID: 32738877 PMCID: PMC7395985 DOI: 10.1186/s12866-020-01913-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. RESULTS High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. CONCLUSIONS Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.
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Affiliation(s)
- Mengjun Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Liwei Chai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Jiabao Guo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087.
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16
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Li W, Feng D, Yang G, Deng Z, Rui J, Chen H. Soil water content and pH drive archaeal distribution patterns in sediment and soils of water-level-fluctuating zones in the East Dongting Lake wetland, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:29127-29137. [PMID: 31392608 DOI: 10.1007/s11356-019-06109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Archaea play a vital role in Earth's geochemical cycles, but the factors that drive their distribution between sediments and water-level-fluctuating zones in the East Dongting Lake (EDL) wetland are poorly understood. Here, we used Illumina MiSeq to investigate the variation in the soil archaeal community structure and diversity among sediments and four water-level-fluctuating zones (mudflat, sedge, sedge-Phragmites, and Phragmites) in the EDL wetland. Diverse archaeal assemblages were found in our study, Crenarchaeota, Euryarchaeota, and ammonia-oxidizing and methanogenic subset were the dominant groups, and all their abundances shifted from sediment to water-level-fluctuating zones. The principal coordinates analysis and cluster analysis showed that the overall archaeal community structure was separated into two clusters: cluster I contained nine samples from sediment, mudflat, and sedge zones, whereas cluster II contained six samples from sedge-Phragmites and Phragmites zones. Archaeal diversity was significantly highest in sediment and lowest in Phragmites zone soils. The Mantel test showed that the variation in archaeal community structure was significantly positively correlated with soil water content and pH. The relative abundances of Crenarchaeota and Nitrososphaerales decreased with soil water content, while Euryarchaeota and Methanomicrobiales increased with soil water content. The relative abundance of Methanomicrobiales significantly decreased with pH (R2 = 0.34-0.48). Chao 1, observed operational taxonomic units, Shannon index, and Simpson index all correlated significantly positively with water content (R2 = 0.40-0.60), while Shannon and Simpson indexes both correlated significantly negatively with pH (R2 = 0.20-0.37). Our results demonstrated that the variations in the archaeal community structure were markedly driven by soil water content and pH in the EDL wetland. Our findings suggested that archaeal communities shifted among sediment and four water-level-fluctuating zones, highlighting that the spatiotemporal heterogeneity of greenhouse gas flux in small scale should be taken into account for accurate prediction of greenhouse gas emissions in the Dongting Lake area, especially on the background of climate change and human activities.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, 650091, China
| | - Defeng Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 650224, China
| | - Gang Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhengmiao Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Hunan, 410125, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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17
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Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes. mSystems 2019; 4:4/5/e00442-19. [PMID: 31506265 PMCID: PMC6739103 DOI: 10.1128/msystems.00442-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves. Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms. IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.
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18
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Spatial distribution of prokaryotic communities in hypersaline soils. Sci Rep 2019; 9:1769. [PMID: 30741985 PMCID: PMC6370769 DOI: 10.1038/s41598-018-38339-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/20/2018] [Indexed: 11/29/2022] Open
Abstract
Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.
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19
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Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:6957210. [PMID: 30833827 PMCID: PMC6369511 DOI: 10.1155/2019/6957210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 11/18/2018] [Indexed: 12/29/2022]
Abstract
The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado sensu stricto soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and amoA genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c Thaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher amoA diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.
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20
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Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G. Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China. Front Microbiol 2019; 10:23. [PMID: 30740093 PMCID: PMC6355713 DOI: 10.3389/fmicb.2019.00023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/09/2019] [Indexed: 11/18/2022] Open
Abstract
Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.
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Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia.,Research Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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21
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Huang M, Chai L, Jiang D, Zhang M, Zhao Y, Huang Y. Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:699-707. [PMID: 30092526 DOI: 10.1016/j.scitotenv.2018.07.305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/21/2018] [Accepted: 07/22/2018] [Indexed: 05/15/2023]
Abstract
Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Dalin Jiang
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yanran Zhao
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China.
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22
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Wang Y, Chen X, Guo W, Zhou H. Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean. FEMS Microbiol Lett 2018; 365:5184458. [DOI: 10.1093/femsle/fny273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/13/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
- College of Animal Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, P.R. China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, 410083 Changsha, P.R. China
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23
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Che R, Deng Y, Wang F, Wang W, Xu Z, Hao Y, Xue K, Zhang B, Tang L, Zhou H, Cui X. Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:997-1006. [PMID: 29929338 DOI: 10.1016/j.scitotenv.2018.05.238] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.
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Affiliation(s)
- Rongxiao Che
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yongcui Deng
- Nanjing Normal University, Nanjing 210097, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Weijin Wang
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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24
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Kerfahi D, Tripathi BM, Slik JWF, Sukri RS, Jaafar S, Adams JM. Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest. MICROBIAL ECOLOGY 2018; 76:215-225. [PMID: 29184976 DOI: 10.1007/s00248-017-1118-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors. We sampled soil across several different forest types within Brunei, Northwest Borneo. Soil DNA was extracted, and the 16S rRNA gene of archaea was sequenced using Illumina MiSeq. We found that (1) as hypothesized, there are distinct archaeal communities for each forest type, and community composition significantly correlates with soil parameters including pH, organic matter, and available phosphorous. (2) As hypothesized, the "rare" white sand forest variants kerangas and inland heath had lower archaeal diversity. A nestedness analysis showed that archaeal community in inland heath and kerangas was mainly a less diverse subset of that in dipterocarp forests. However, primary dipterocarp forest had the lowest beta-diversity among the other tropical forest types. (3) Also, as predicted, forest disturbance resulted in lower archaeal alpha-diversity-but increased beta-diversity in contrast with our predictions. (4) Contrary to our predictions, the BetaNTI of the various primary forest types indicated community assembly was mainly stochastic. The possible effects of these habitat and disturbance-related effects on N cycling should be investigated.
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Affiliation(s)
- Dorsaf Kerfahi
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Seestrasse 15, 18119, Rostock, Germany
| | - Binu M Tripathi
- Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - J W Ferry Slik
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S Sukri
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Salwana Jaafar
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Jonathan M Adams
- Division of Agrifood and Environment, Cranfield University, College Rd, Cranfield, MK43 0AL, UK.
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25
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Vera-Gargallo B, Ventosa A. Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain). Genes (Basel) 2018. [PMID: 29518047 PMCID: PMC5867873 DOI: 10.3390/genes9030152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hypersaline environments encompass aquatic and terrestrial habitats. While only a limited number of studies on the microbial diversity of saline soils have been carried out, hypersaline lakes and marine salterns have been thoroughly investigated, resulting in an aquatic-biased knowledge about life in hypersaline environments. To improve our understanding of the assemblage of microbes thriving in saline soils, we assessed the phylogenetic diversity and metabolic potential of the prokaryotic community of two hypersaline soils (with electrical conductivities of ~24 and 55 dS/m) from the Odiel saltmarshes (Spain) by metagenomics. Comparative analysis of these soil databases with available datasets from salterns ponds allowed further identification of unique and shared traits of microbial communities dwelling in these habitats. Saline soils harbored a more diverse prokaryotic community and, in contrast to their aquatic counterparts, contained sequences related to both known halophiles and groups without known halophilic or halotolerant representatives, which reflects the physical heterogeneity of the soil matrix. Our results suggest that Haloquadratum and certain Balneolaeota members may preferentially thrive in aquatic or terrestrial habitats, respectively, while haloarchaea, nanohaloarchaea and Salinibacter may be similarly adapted to both environments. We reconstructed 4 draft genomes related to Bacteroidetes, Balneolaeota and Halobacteria and appraised their metabolism, osmoadaptation strategies and ecology. This study greatly improves the current understanding of saline soils microbiota.
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Affiliation(s)
- Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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26
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Meisner A, Jacquiod S, Snoek BL, Ten Hooven FC, van der Putten WH. Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. Front Microbiol 2018; 9:294. [PMID: 29563897 PMCID: PMC5845876 DOI: 10.3389/fmicb.2018.00294] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden.,Sections of Microbiology and Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | | | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
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27
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Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G. Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China. Front Microbiol 2018; 9:171. [PMID: 29497404 PMCID: PMC5819564 DOI: 10.3389/fmicb.2018.00171] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.
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Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora VIC, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora VIC, Australia
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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28
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Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, Zhang K, Ni Y, Zhu YG, Adams JM, Chu H. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. MICROBIOME 2018; 6:27. [PMID: 29402331 PMCID: PMC5799910 DOI: 10.1186/s40168-018-0409-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND The relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau. RESULTS Our results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%. CONCLUSIONS Our findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Xingjia Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Ruibo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Kaoping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Jonathan M. Adams
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK46 0AL UK
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
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29
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Xie K, Deng Y, Zhang S, Zhang W, Liu J, Xie Y, Zhang X, Huang H. Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils. Sci Rep 2017; 7:13332. [PMID: 29042583 PMCID: PMC5645410 DOI: 10.1038/s41598-017-13608-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/26/2017] [Indexed: 02/01/2023] Open
Abstract
Salinity effects on microbial communities in saline soils is still unclear, and little is known about subsurface soil microbial communities especially in saline or hypersaline ecosystems. Here we presented the survey of the prokaryotic community in saline soils along a salinity gradient (17.3–148.3 dS/m) in surface (0–10 cm) and subsurface (15–30 cm) saline soils of Qarhan Salt Lake, China. Moreover, we compared them with three paired nonsaline normal soils. Using the high-throughput sequencing technology and several statistical methods, we observed no significant community difference between surface soils and subsurface soils. For environmental factors, we found that TOC was the primary driver of the prokaryotic community distribution in surface saline soils, so was pH in subsurface saline soils. Salinity had more effects on the prokaryotic community in subsurface saline soils than in surface saline soils and played a less important role in saline soils than in saline waters or saline sediments. Our research provided references for the prokaryotic community distribution along a salinity gradient in both surface and subsurface saline soils of arid playa areas.
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Affiliation(s)
- Kehui Xie
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Yong Deng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Shaocun Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Wenhao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jianrong Liu
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China
| | - Yulong Xie
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China
| | - Xuze Zhang
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China.
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China.
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30
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Zhao K, Jing X, Sanders NJ, Chen L, Shi Y, Flynn DFB, Wang Y, Chu H, Liang W, He J. On the controls of abundance for soil‐dwelling organisms on the Tibetan Plateau. Ecosphere 2017. [DOI: 10.1002/ecs2.1901] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Ke Zhao
- Department of Ecology College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education Peking University 5 Yiheyuan Road Beijing 100871 China
| | - Xin Jing
- Department of Ecology College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education Peking University 5 Yiheyuan Road Beijing 100871 China
| | - Nathan J. Sanders
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont 05405 USA
| | - Litong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences 23 Xinning Road Xining 810008 China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China
| | - Dan F. B. Flynn
- The Arnold Arboretum of Harvard University 1300 Centre Street Boston Massachusetts 02131 USA
| | - Yonghui Wang
- Department of Ecology College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education Peking University 5 Yiheyuan Road Beijing 100871 China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China
| | - Wenju Liang
- State Key Laboratory of Forest and Soil Ecology Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110164 China
| | - Jin‐Sheng He
- Department of Ecology College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education Peking University 5 Yiheyuan Road Beijing 100871 China
- Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences 23 Xinning Road Xining 810008 China
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31
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Schwob G, Roy M, Manzi S, Pommier T, Fernandez MP. Green alder (
Alnus viridis
) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently. Environ Microbiol 2017; 19:3235-3250. [DOI: 10.1111/1462-2920.13818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/01/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022]
Affiliation(s)
- G. Schwob
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
| | - M. Roy
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 UPS CNRS ENFA IRDToulouse France
| | - S. Manzi
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 UPS CNRS ENFA IRDToulouse France
| | - T. Pommier
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
| | - M. P. Fernandez
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
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