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Ochoa-Hueso R, Eldridge DJ, Berdugo M, Trivedi P, Sokoya B, Cano-Díaz C, Abades S, Alfaro F, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Rios A, Durán J, Geisen S, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Singh BK, Teixido AL, Torres-Díaz C, Wang L, Wang J, Wang J, Zaady E, Zhou X, Zhou XQ, Tedersoo L, Delgado-Baquerizo M. Unearthing the soil-borne microbiome of land plants. GLOBAL CHANGE BIOLOGY 2024; 30:e17295. [PMID: 38804108 DOI: 10.1111/gcb.17295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 05/29/2024]
Abstract
Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
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Affiliation(s)
- Raúl Ochoa-Hueso
- Department of Biology, Botany Area, University of Cádiz, Vitivinicultural and Agri-Food Research Institute (IVAGRO), Cádiz, Spain
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of NSW, Sydney, New South Wales, Australia
| | - Miguel Berdugo
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Pankaj Trivedi
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Blessing Sokoya
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Concha Cano-Díaz
- CISAS - Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial Nun'Álvares, Viana do Castelo, Portugal
| | | | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - José L Blanco-Pastor
- Department of Biology, Botany Area, University of Cádiz, Vitivinicultural and Agri-Food Research Institute (IVAGRO), Cádiz, Spain
| | - Asunción de Los Rios
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jorge Durán
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Steven Mamet
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Canada
| | | | - José L Moreno
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | | | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
| | - Alberto L Teixido
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Ling Wang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
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2
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Anthony MA, Tedersoo L, De Vos B, Croisé L, Meesenburg H, Wagner M, Andreae H, Jacob F, Lech P, Kowalska A, Greve M, Popova G, Frey B, Gessler A, Schaub M, Ferretti M, Waldner P, Calatayud V, Canullo R, Papitto G, Marinšek A, Ingerslev M, Vesterdal L, Rautio P, Meissner H, Timmermann V, Dettwiler M, Eickenscheidt N, Schmitz A, Van Tiel N, Crowther TW, Averill C. Fungal community composition predicts forest carbon storage at a continental scale. Nat Commun 2024; 15:2385. [PMID: 38493170 PMCID: PMC10944544 DOI: 10.1038/s41467-024-46792-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.
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Affiliation(s)
- Mark A Anthony
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland.
- Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Bruno De Vos
- Environment & Climate Unit, Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Luc Croisé
- French National Forest Office, Fontainebleau, France
| | | | - Markus Wagner
- Northwest German Forest Research Institute, Göttingen, Germany
| | | | - Frank Jacob
- Sachsenforst State Forest, Pirna OT Graupa, Germany
| | - Paweł Lech
- Forest Research Institute, Sękocin Stary, Poland
| | | | - Martin Greve
- Research Institute for Forest Ecology and Forestry, Trippstadt, Germany
| | - Genoveva Popova
- Executive Environmental Agency at the Ministry of Environment and Water, Sofia, Bulgaria
| | - Beat Frey
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arthur Gessler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Marcus Schaub
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Marco Ferretti
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Peter Waldner
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | | | - Roberto Canullo
- Department of Plant Diversity and Ecosystem Management, University of Camerino, Camerino, Italy
| | - Giancarlo Papitto
- Arma dei Carabinieri Forestry Environmental and Agri-food protection Units, Rome, Italy
| | | | - Morten Ingerslev
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Pasi Rautio
- Natural Resources Institute Finland, Rovaniemi, Finland
| | - Helge Meissner
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Volkmar Timmermann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Mike Dettwiler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Nadine Eickenscheidt
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, Recklinghausen, Germany
| | - Andreas Schmitz
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, Recklinghausen, Germany
- Thuenen Institut of Forest Ecosystems, 16225, Eberswalde, Germany
| | - Nina Van Tiel
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Environmetnal Computational Science and Earth Observation Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas W Crowther
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Colin Averill
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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He L, Sun X, Li S, Zhou W, Yu J, Zhao G, Chen Z, Bai X, Zhang J. Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169905. [PMID: 38190904 DOI: 10.1016/j.scitotenv.2024.169905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jinshuo Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Fu Q, Qiu Y, Zhao J, Li J, Xie S, Liao Q, Fu X, Huang Y, Yao Z, Dai Z, Qiu Y, Yang Y, Li F, Chen H. Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169351. [PMID: 38123079 DOI: 10.1016/j.scitotenv.2023.169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siqi Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Furong Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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Huo C, Mao J, Zhang J, Yang X, Gao S, Li J, He Q, Tang G, Xie X, Chen Z. Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil. Int J Mol Sci 2024; 25:1385. [PMID: 38338664 PMCID: PMC10855151 DOI: 10.3390/ijms25031385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zujing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (C.H.); (J.M.); (J.Z.); (X.Y.); (S.G.); (J.L.); (Q.H.); (G.T.); (X.X.)
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Ji W, Li R, Qian X, Albasher G, Li Z. Microbial nitrogen mineralization is slightly affected by conversion from farmland to apple orchards in thick loess deposits. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168268. [PMID: 37918737 DOI: 10.1016/j.scitotenv.2023.168268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Organic nitrogen mineralization, indispensable to soil carbon and nitrogen cycles, is the largest contributor to nitrate reservoirs in deep vadose zones. The microbial nitrogen mineralization (MNM) within deep soils, particularly in regions with intensive agricultural activities and thick soil horizons, has been largely disregarded. As such, this study aims to address this knowledge gap by investigating the chiA-harboring microbial structure and network within nine 10-m profiles beneath cultivated farmland and two apple orchards. The results showed that apple orchards, compared to farmland, had considerable water deficit and nitrogen accumulation within deeper soil layers due to well-developed root systems and the overuse of chemical fertilizers. However, the chiA-harboring microbial diversity, composition, and abundance all exhibited significant variations with soil depths rather than being influenced by different land use types. Moreover, the diversity indices and gene abundances decreased with soil depths, and the related soil microbes included 19 phyla, 29 classes, 72 orders, 114 families, and 197 genera, with Actinobacteria and Proteobacteria being the two major bacterial phyla. The microbial co-occurrence network was simper beneath apple orchards. The chiA-harboring microorganisms within deep unsaturated zones were greatly influenced by the depth-dependent soil nutrients, such as total nitrogen, organic carbon, and available potassium. The limited plant root biomass and the inhibitory effects of dried soil layers both restricted the availability of carbon sources, which further interfered with the MNM processes within deep soils insignificantly. Therefore, despite the considerable plant-induced ecohydrological consequences, the depth-dependent MNM processes were slightly affected after the transformation from farmland to apple orchards within thick loess deposits. This study offers crucial insights into microbial dynamics of the deep biosphere, thereby contributing to our understanding of depth-dependent biogeochemical cycles within global deep unsaturated zones.
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Affiliation(s)
- Wangjia Ji
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruifeng Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Qian
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gadah Albasher
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zhi Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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7
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Peng Z, Yang Y, Liu Y, Bu L, Qi J, Gao H, Chen S, Pan H, Chen B, Liang C, Li X, An Y, Wang S, Wei G, Jiao S. The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems. GLOBAL CHANGE BIOLOGY 2024; 30:e16996. [PMID: 37916454 DOI: 10.1111/gcb.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.
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Affiliation(s)
- Ziheng Peng
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yu Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lianyan Bu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiejun Qi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hang Gao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Haibo Pan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Beibei Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunling Liang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yining An
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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8
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Sharma S, Bakht A, Jahanzaib M, Kim M, Lee H, Park C, Park D. Characterization of bacterial species and antibiotic resistance observed in Seoul, South Korea's popular Gangnam-gu area. Heliyon 2023; 9:e21751. [PMID: 38053859 PMCID: PMC10694155 DOI: 10.1016/j.heliyon.2023.e21751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
Public transportation facilities, especially road crossings, which raise the pathogenic potential of urban environments, are the most conducive places for the transfer of germs between people and the environment. It is necessary to study the variety of the microbiome and describe its unique characteristics to comprehend these relationships. In this investigation, we used 16 S rRNA gene sample sequencing to examine the biological constituents and inhalable, thoracic, and alveolar particles in aerosol samples collected from busy areas in the Gangnam-gu district of the Seoul metropolitan area using a mobile vehicle. We also conducted a comparison analysis of these findings with the previously published data and tested for antibiotic resistance to determine the distribution of bacteria related to the human microbiome and the environment. Actinobacteria, Cyanobacteria, Bacteriodetes, Proteobacteria, and Firmicutes were the top five phyla in the bacterial 16 S rRNA libraries, accounting for >90 % of all readings across all examined locations. The most prevalent classes among the 12 found bacterial classes were Bacilli (45.812 %), Gammaproteobacteria (25.238 %), Tissierellia (13.078 %), Clostridia (5.697 %), and Alphaproteobacteria (5.142 %). The data acquired offer useful information on the variety of bacterial communities and their resistance to antibiotic drugs on the streets of Gangnam-gu, one of the most significant social centers in the Seoul metropolitan area. This work emphasizes the relevance of biological particles and particulate matter in the air, and it suggests more research is needed to perform biological characterization of the ambient particulate matter.
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Affiliation(s)
- Shambhavi Sharma
- Transportation Environmental Research Division, Korea Railroad Research Institute (KRRI), Chleodobangmulgwan-ro, Uiwang-si, 16105, Republic of Korea
- Transportation System Engineering, University of Science & Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Ahtesham Bakht
- Kumoh National Institute of Technology (KIT), 61 Daehak-ro, Gumi-si, Gyeongsangbuk-do, 39177, Republic of Korea
| | - Muhammad Jahanzaib
- Transportation Environmental Research Division, Korea Railroad Research Institute (KRRI), Chleodobangmulgwan-ro, Uiwang-si, 16105, Republic of Korea
- Transportation System Engineering, University of Science & Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Minkyeong Kim
- Transportation Environmental Research Division, Korea Railroad Research Institute (KRRI), Chleodobangmulgwan-ro, Uiwang-si, 16105, Republic of Korea
| | - Hyunsoo Lee
- Kumoh National Institute of Technology (KIT), 61 Daehak-ro, Gumi-si, Gyeongsangbuk-do, 39177, Republic of Korea
| | - Choonsoo Park
- Transportation Environmental Research Division, Korea Railroad Research Institute (KRRI), Chleodobangmulgwan-ro, Uiwang-si, 16105, Republic of Korea
| | - Duckshin Park
- Transportation Environmental Research Division, Korea Railroad Research Institute (KRRI), Chleodobangmulgwan-ro, Uiwang-si, 16105, Republic of Korea
- Transportation System Engineering, University of Science & Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
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9
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Maisnam P, Jeffries TC, Szejgis J, Bristol D, Singh BK, Eldridge DJ, Horn S, Chieppa J, Nielsen UN. Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands. MICROBIAL ECOLOGY 2023; 86:3097-3110. [PMID: 37878053 PMCID: PMC10640424 DOI: 10.1007/s00248-023-02303-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023]
Abstract
Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.
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Affiliation(s)
- Premchand Maisnam
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Thomas C Jeffries
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Jerzy Szejgis
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Dylan Bristol
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sebastian Horn
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Jeff Chieppa
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute of Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
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10
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Li G, Wilschut RA, Luo S, Chen H, Wang X, Du G, Geisen S. Nematode biomass changes along an elevational gradient are trophic group dependent but independent of body size. GLOBAL CHANGE BIOLOGY 2023; 29:4898-4909. [PMID: 37337363 DOI: 10.1111/gcb.16814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023]
Abstract
Aboveground, large and higher trophic-level organisms often respond more strongly to environmental changes than small and lower trophic-level organisms. However, whether this trophic or size-dependent sensitivity also applies to the most abundant animals, microscopic soil-borne nematodes, remains largely unknown. Here, we sampled an altitudinal transect across the Tibetan Plateau and applied a community-weighted mean (CWM) approach to test how differences in climatic and edaphic properties affect nematode CWM biomass at the level of community, trophic group and taxon mean biomass within trophic groups. We found that climatic and edaphic properties, particularly soil water-related properties, positively affected nematode CWM biomass, with no overall impact of altitude on nematode CWM biomass. Higher trophic-level omnivorous and predatory nematodes responded more strongly to climatic and edaphic properties, particularly to temperature, soil pH, and soil water content than lower trophic-level bacterivorous and fungivorous nematodes. However, these differences were likely not (only) driven by size, as we did not observe significant interactions between climatic and edaphic properties and mean biomasses within trophic groups. Together, our research implies a stronger, size-independent trophic sensitivity of higher trophic-level nematodes compared with lower trophic-level ones. Therefore, our findings provide new insights into the mechanisms underlying nematode body size structure in alpine grasslands and highlight that traits independent of size need to be found to explain increased sensitivity of higher trophic-level nematodes to climatic and edaphic properties, which might affect soil functioning.
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Affiliation(s)
- Guixin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Shuaiwei Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Han Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiangtai Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Guozhen Du
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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11
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Wang X, Morin X, Zhang J, Chen G, Mao L, Chen Y, Song Z, Du Y, Ma K. Geographical patterns and determinants in plant reproductive phenology duration. FRONTIERS IN PLANT SCIENCE 2023; 14:1199316. [PMID: 37396633 PMCID: PMC10309207 DOI: 10.3389/fpls.2023.1199316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/19/2023] [Indexed: 07/04/2023]
Abstract
Biodiversity is and always has been an important issue in ecological research. Biodiversity can reflect niche partitioning among species at several spatial and temporal scales and is generally highest in the tropics. One theory to explain it is that low-latitude tropical ecosystems are dominated by species that are generally only distributed over a narrow area. This principle is known as Rapoport's rule. One previously unconsidered extension of Rapoport's rule may be reproductive phenology, where variation in flowering and fruiting length may reflect a temporal range. Herein, we collected reproductive phenology data for more than 20,000 species covering almost all angiosperm species in China. We used a random forest model to quantify the relative role of seven environmental factors on the duration of reproductive phenology. Our results showed that the duration of reproductive phenology decreased with latitude, although there was no obvious change across longitudes. Latitude explained more of the variation in the duration of flowering and fruiting phases in woody plants than in herbaceous plants. Mean annual temperature and the length of the growing season strongly influenced the phenology of herbaceous plants, and average winter temperature and temperature seasonality were important drivers of woody plant phenology. Our result suggests the flowering period of woody plants is sensitive to temperature seasonality, while it does not influence herbaceous plants. By extending Rapoport's rule to consider the distribution of species in time as well as space, we have provided a novel insight into the mechanisms of maintaining high levels of diversity in low-latitude forests.
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Affiliation(s)
- Xinyang Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou, China
| | - Xavier Morin
- Centre d'Écologie Fonctionnelle et Évolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Ecole Pratique des Hautes Etudes (EPHE), Institut de recherche pour le Développement (IRD), Univ. Paul Valéry Montpellier 3, Montpellier, France
| | - Jian Zhang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Guoke Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuheng Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Zhuqiu Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yanjun Du
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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12
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Wang X, Zhang Q, Zhang Z, Li W, Liu W, Xiao N, Liu H, Wang L, Li Z, Ma J, Liu Q, Ren C, Yang G, Zhong Z, Han X. Decreased soil multifunctionality is associated with altered microbial network properties under precipitation reduction in a semiarid grassland. IMETA 2023; 2:e106. [PMID: 38868425 PMCID: PMC10989785 DOI: 10.1002/imt2.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/20/2023] [Accepted: 04/06/2023] [Indexed: 06/14/2024]
Abstract
Our results reveal different responses of soil multifunctionality to increased and decreased precipitation. By linking microbial network properties to soil functions, we also show that network complexity and potentially competitive interactions are key drivers of soil multifunctionality.
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Affiliation(s)
- Xing Wang
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Qi Zhang
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Zhenjiao Zhang
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Wenjie Li
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Weichao Liu
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Naijia Xiao
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Hanyu Liu
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Leyin Wang
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Zhenxia Li
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Jing Ma
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Quanyong Liu
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Chengjie Ren
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Gaihe Yang
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
| | - Zekun Zhong
- Institute of Soil and Water ConservationNorthwest A&F UniversityYanglingChina
| | - Xinhui Han
- College of AgronomyNorthwest A&F UniversityYanglingChina
- Shaanxi Engineering Research Center of Circular AgricultureYanglingChina
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13
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He L, Sun X, Li S, Zhou W, Chen Z, Bai X. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161754. [PMID: 36709888 DOI: 10.1016/j.scitotenv.2023.161754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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14
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Liang Q, Mod HK, Luo S, Ma B, Yang K, Chen B, Qi W, Zhao Z, Du G, Guisan A, Ma X, Le Roux X. Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition. Mol Ecol 2023. [PMID: 37060060 DOI: 10.1111/mec.16952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.
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Affiliation(s)
- Qingqing Liang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Shuaiwei Luo
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kena Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xavier Le Roux
- INRAE, Université de Lyon, Université Lyon 1, CNRS, vetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, Ecologie Microbienne LEM, Villeurbanne, France
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15
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Shu X, Hu Y, Liu W, Xia L, Zhang Y, Zhou W, Liu W, Zhang Y. Linking between soil properties, bacterial communities, enzyme activities, and soil organic carbon mineralization under ecological restoration in an alpine degraded grassland. Front Microbiol 2023; 14:1131836. [PMID: 37180269 PMCID: PMC10167489 DOI: 10.3389/fmicb.2023.1131836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/17/2023] [Indexed: 04/08/2023] Open
Abstract
Soil organic carbon (SOC) mineralization is affected by ecological restoration and plays an important role in the soil C cycle. However, the mechanism of ecological restoration on SOC mineralization remains unclear. Here, we collected soils from the degraded grassland that have undergone 14 years of ecological restoration by planting shrubs with Salix cupularis alone (SA) and, planting shrubs with Salix cupularis plus planting mixed grasses (SG), with the extremely degraded grassland underwent natural restoration as control (CK). We aimed to investigate the effect of ecological restoration on SOC mineralization at different soil depths, and to address the relative importance of biotic and abiotic drivers of SOC mineralization. Our results documented the statistically significant impacts of restoration mode and its interaction with soil depth on SOC mineralization. Compared with CK, the SA and SG increased the cumulative SOC mineralization but decreased C mineralization efficiency at the 0-20 and 20-40 cm soil depths. Random Forest analyses showed that soil depth, microbial biomass C (MBC), hot-water extractable organic C (HWEOC), and bacterial community composition were important indicators that predicted SOC mineralization. Structural equal modeling indicated that MBC, SOC, and C-cycling enzymes had positive effects on SOC mineralization. Bacterial community composition regulated SOC mineralization via controlling microbial biomass production and C-cycling enzyme activities. Overall, our study provides insights into soil biotic and abiotic factors in association with SOC mineralization, and contributes to understanding the effect and mechanism of ecological restoration on SOC mineralization in a degraded grassland in an alpine region.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Weijia Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Karlsruhe, Baden-Wurttemberg, Germany
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wanling Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Pan J, Shi J, Tian D, Zhang R, Li Y, He Y, Song L, Wang S, He Y, Yang J, Wei C, Niu S, Wang J. Depth-dependent drivers of soil aggregate carbon across Tibetan alpine grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161428. [PMID: 36623644 DOI: 10.1016/j.scitotenv.2023.161428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Elucidating the effects underlying soil organic carbon (SOC) variation is imperative for ascertaining the potential drivers of mitigating climate change. However, the drivers of variations in various SOC fractions (e.g., macroaggregate C, microaggregate C, and silt and clay C) at different soil depths remain poorly understood. Here, we investigated the effects and relative contributions of climatic, plant, edaphic, and microbial factors on soil aggregate C between the topsoil (0-10 cm) and subsoil (20-30 cm) across alpine grasslands on the Tibetan Plateau. Results showed that the C content of macroaggregates, microaggregates, and silt and clay fractions in the topsoil was 128.6 %, 49.6 %, and 242.4 % higher than that in the subsoil, respectively. Overall, plant properties were the most determinants controlling soil macroaggregate, microaggregate, and silt + clay associated C for both two soil depths, accounting for 32.2 %, 37.4 %, and 38.8 % of the variation, respectively, followed by edaphic, microbial, and climatic factors. The aggregate C of both soil depths was significantly related with the climatic, plant, edaphic, and microbial factors, but the relative importance of these determinants was soil-depth dependent. Specifically, the effects of plant root biomass and microbial (e.g., microbial biomass carbon and fungal diversity index) factors on each aggregate C weakened with soil depth, but the importance of edaphic factors (e.g., clay content, pH, and bulk density) strengthened with soil depth, except for the weakened effect of bulk density on the microaggregate C. And the effects of climatic factor (e.g., mean annual precipitation) on macroaggregate and microaggregate C increased with soil depth. Our results highlight differential drivers and their impacts on soil aggregate C between the topsoil and subsoil, which benefits biogeochemical models for more accurately forecasting soil C dynamics and its feedbacks to environmental changes.
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Affiliation(s)
- Junxiao Pan
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jiawei Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Dashuan Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ruiyang Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yang Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yunlong He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lei Song
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Song Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yicheng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jiaming Yang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chunxue Wei
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China.
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Gao L, Wei C, He Y, Tang X, Chen W, Xu H, Wu Y, Wilschut RA, Lu X. Aboveground herbivory can promote exotic plant invasion through intra- and interspecific aboveground-belowground interactions. THE NEW PHYTOLOGIST 2023; 237:2347-2359. [PMID: 36200166 DOI: 10.1111/nph.18520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Aboveground herbivores and soil biota profoundly affect plant invasions. However, how they interactively affect plant invasions through plant-soil feedbacks (PSFs) remains unclear. To explore how herbivory by the introduced beetle Agasicles hygrophila affects Alternanthera philoxeroides invasions in China, we integrated multiyear field surveys and a 2-yr PSF experiment, in which we examined how herbivory affects PSFs on the performance of native and invasive plants and the introduced beetles. Despite increased herbivory from A. hygrophila, A. philoxeroides dominance over co-occurring congeneric native Alternanthera sessilis remained constant from 2014 to 2019. While occurring at lower abundances, A. sessilis experienced similar herbivore damage, suggesting apparent competitive effects. Our experiments revealed that herbivory on A. philoxeroides altered soil microbial communities, prolonged its negative PSF on A. sessilis, and decreased A. hygrophila larvae performance on the next-generation invasive plants. Consequently, A. hygrophila larvae performed better on leaves of natives than those of invasives when grown in soils conditioned by invasive plants defoliated by the introduced beetles. Our findings suggest that aboveground herbivory might promote rather than suppress A. philoxeroides invasion by enhancing its soil-mediated self-reinforcement, providing a novel mechanistic understanding of plant invasions. These findings highlight the need to incorporate an aboveground-belowground perspective during the assessment of potential biocontrol agents.
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Affiliation(s)
- Lunlun Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Hubei Hongshan Laboratory, 430070, Hubei, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, 430070, Hubei, China
| | - Chunqiang Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Guangxi Institute of Botany, Chinese Academy of Science, 540016, Guilin, China
| | - Yifan He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Hubei Hongshan Laboratory, 430070, Hubei, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, 430070, Hubei, China
| | - Xuefei Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
| | - Wei Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Hubei Hongshan Laboratory, 430070, Hubei, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, 430070, Hubei, China
| | - Hao Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Hubei Hongshan Laboratory, 430070, Hubei, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, 430070, Hubei, China
| | - Yuqing Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, 450002, Henan, China
| | - Rutger A Wilschut
- Ecology Group, Department of Biology, University of Konstanz, 78464, Konstanz, Germany
- Department of Nematology, Wageningen University and Research, 6708PB, Wageningen, the Netherlands
| | - Xinmin Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Hubei, China
- Hubei Hongshan Laboratory, 430070, Hubei, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, 430070, Hubei, China
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18
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Tian Q, Jiang Q, Huang L, Li D, Lin Q, Tang Z, Liu F. Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient. MICROBIAL ECOLOGY 2023; 85:628-641. [PMID: 35083529 DOI: 10.1007/s00248-021-01949-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.
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Affiliation(s)
- Qiuxiang Tian
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qinghu Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lin Huang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, China
| | - Qiaoling Lin
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyao Tang
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes, Peking University, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Yang Y, Dou Y, Wang B, Xue Z, Wang Y, An S, Chang SX. Deciphering factors driving soil microbial life-history strategies in restored grasslands. IMETA 2023; 2:e66. [PMID: 38868332 PMCID: PMC10989924 DOI: 10.1002/imt2.66] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/12/2022] [Accepted: 11/06/2022] [Indexed: 06/14/2024]
Abstract
In macroecology, the concept of r- and K-strategy has been widely applied, yet, there have been limited studies on microbial life-history strategies in temperate grasslands using multiple sequencing approaches. Total phospholipid fatty acid (PLFA) analysis, high-throughput meta-genomic sequencing, and GeoChip technologies were used to examine the changes in microbial life-history traits in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration). Grassland restoration increased the relative abundances of Actinobacteria, Proteobacteria, and Bacteroidetes but reduced the relative abundances of Acidobacteria, Planctomycetes, and Chloroflexi. PLFA analysis revealed that grassland restoration reduced the fungi:bacteria and Gram-positive:Gram-negative bacteria ratios. Combined with the meta-genomic data, we found that grassland restoration shifted microorganisms from oligotrophic (K-) to copiotrophic (r-) groups, consistent with the increased rRNA operon copy number of the microbial community. Structural equation modeling showed that soil properties positively (p < 0.05) while plant properties negatively (p < 0.05) affected microbial life-history traits. We built a framework to highlight the importance of plant and soil properties in driving microbial life-history traits during grassland restoration. Finally, by incorporating meta-genomic and other microbiological data, this study showed that microbial life-history traits support the idea that rRNA operon copy number is a trait that reflects resource availability to soil microorganisms.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'anChina
- Chinese Academy of Sciences Center for Excellence in Quaternary Science and Global ChangeXi'anChina
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau in ShaanxiXi'anChina
| | - Yanxing Dou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Zhijing Xue
- College of Geography and TourismShaanxi Normal UniversityXi'anChina
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'anChina
- Chinese Academy of Sciences Center for Excellence in Quaternary Science and Global ChangeXi'anChina
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau in ShaanxiXi'anChina
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Scott X. Chang
- Department of Renewable ResourcesUniversity of AlbertaEdmontonCanada
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20
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Li G, Liu P, Zhao J, Su L, Zhao M, Jiang Z, Zhao Y, Yang X. Correlation of microbiomes in "plant-insect-soil" ecosystem. Front Microbiol 2023; 14:1088532. [PMID: 36793880 PMCID: PMC9922863 DOI: 10.3389/fmicb.2023.1088532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Introduction Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance. Methods Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters. Results and Discussion Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.
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Affiliation(s)
- Guomeng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Peng Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Liangyinan Su
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Mengyu Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Zhengjie Jiang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,*Correspondence: Yang Zhao,
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,Xiping Yang,
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Liao H, Li C, Ai S, Li X, Ai X, Ai Y. A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116672. [PMID: 36343402 DOI: 10.1016/j.jenvman.2022.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.
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Affiliation(s)
- Haijun Liao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China; CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Chaonan Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Shenghao Ai
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Xiaoyan Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
| | - Yingwei Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
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22
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The neglected role of micronutrients in predicting soil microbial structure. NPJ Biofilms Microbiomes 2022; 8:103. [PMID: 36575178 PMCID: PMC9794713 DOI: 10.1038/s41522-022-00363-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9-17% in predicting the structure of soil microbial communities with up to 69-78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.
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Song L, Yang T, Xia S, Yin Z, Liu X, Li S, Sun R, Gao H, Chu H, Ma C. Soil depth exerts stronger impact on bacterial community than elevation in subtropical forests of Huangshan Mountain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158438. [PMID: 36055501 DOI: 10.1016/j.scitotenv.2022.158438] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/12/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
The elevational distribution of bacterial communities in the surface soil of natural mountain forests has been widely studied. However, it remains unknown if microbial communities in surface and sub-surface soils exhibit a similar distribution pattern with elevation. To do so, Illumina HiSeq sequencing was applied to study the alterations in soil bacterial communities of different soil layers, along an altitudinal gradient from 500 to 1100 m on Huangshan Mountain in Anhui Province, China. Our results revealed a significant higher diversity of the bacterial communities in surface soil layers than in subsurface layers. Adonis analysis showed that soil layer had a greater influence on the composition of the bacterial communities than the elevation. The distance-based multivariate linear model suggested that soil labile organic carbon and elevation were the main element influencing the bacterial community composition in surface and subsurface soils, respectively. A remarkable difference appeared between the co-occurrence network structures of bacterial communities in different soil layers. Compared with the subsurface soil, surface soil had more edges, average degree, and much higher clustering coefficient. The two-way ANOVA results highlighted the significant impact of soil layers on the topological properties of the network compared with that of elevation. The keystone species belonged to Rhodospirillaceae in the surface soil, while the OTUs belonged to Actinomycetales in the subsurface soil. Collectively, our results demonstrate that the effects of soil depth on soil bacterial community composition and network properties of subtropical forest in Huangshan Mountain were significantly higher than those of elevation, with different keystone species in different soil layers. These findings can be served as an important basis for better understanding the microbial functions influencing the maintenance of habitat heterogeneity, biodiversity, and ecosystem services in forests ecosystems.
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Affiliation(s)
- Luyao Song
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficicent Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shangguang Xia
- Anhui Huangshan National Positioning Observation and Research Station of Forest Ecosystem, Anhui Academy of Forestry, Hefei 230031, China
| | - Zhong Yin
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficicent Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shaopeng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Ruibo Sun
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficicent Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Hongjian Gao
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficicent Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Chao Ma
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficicent Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
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Li L, Xia T, Yang H. Seasonal patterns of rhizosphere microorganisms suggest carbohydrate-degrading and nitrogen-fixing microbes contribute to the attribute of full-year shooting in woody bamboo Cephalostachyum pingbianense. Front Microbiol 2022; 13:1033293. [PMID: 36523824 PMCID: PMC9745117 DOI: 10.3389/fmicb.2022.1033293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 10/15/2023] Open
Abstract
Compared with the ordinary single-season shooting among woody bamboos in Poaceae, the attribute of full-year shooting in Cephalostachyum pingbianense represents a unique shooting type or mechanism. Nevertheless, except for the overall physiological mechanism, the effect of ecological factors, especially soil microorganisms, on this full-year shooting characteristic remains unclear. In this study, 16S rRNA and ITS rRNA genes were sequenced using the Illumina platform. Our aims were to detect the seasonal changes in rhizospheric microbial communities of C. pingbianense and to discover the correlations of soil microbes with soil properties and bamboo shoot productivity. The results showed that seasonal change had no significant effect on bacterial alpha diversity, but significantly affected bacterial and fungal community structures as well as fungal richness. Among all soil properties examined, soil temperature, soil moisture and organic matter were the predominant factors affecting bacterial community diversity and structure. Soil temperature and soil moisture also significantly influenced fungal community structure, while available phosphorus had the greatest effect on fungal diversity. In each season, bacterial genera Acidothermus, Roseiarcus, and Bradyrhizobium, along with fungal genera Saitozyma, Mortierella, Trichoderma, etc., were dominant in bacterial and fungal communities, respectively. Bacterial community functions in four seasons were dominated by chemoheterotrophy, cellulolysis, and nitrogen fixation. Saprotrophic fungi occupied a high proportion in soil samples of all seasons. In addition, correlation analysis revealed that the bamboo shoot productivity was positively correlated with multiple microbial taxa involved in carbon and nitrogen cycles. It is proposed that highly abundant microbes involved in carbohydrate degradation and nitrogen fixation in the rhizosphere soil may contribute to the attribute of producing bamboo shoots all year round in C. pingbianense. This study is among the few cases revealing the connection between bamboo shooting characteristics and soil microorganisms, and provides new physiological and ecological insights into the forest management of woody bamboos.
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Affiliation(s)
| | | | - Hanqi Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
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Díaz-Martínez P, Panettieri M, García-Palacios P, Moreno E, Plaza C, Maestre FT. Biocrusts Modulate Climate Change Effects on Soil Organic Carbon Pools: Insights From a 9-Year Experiment. Ecosystems 2022; 26:585-596. [PMID: 37179798 PMCID: PMC10167156 DOI: 10.1007/s10021-022-00779-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/14/2022] [Indexed: 11/03/2022]
Abstract
Accumulating evidence suggests that warming associated with climate change is decreasing the total amount of soil organic carbon (SOC) in drylands, although scientific research has not given enough emphasis to particulate (POC) and mineral-associated organic carbon (MAOC) pools. Biocrusts are a major biotic feature of drylands and have large impacts on the C cycle, yet it is largely unknown whether they modulate the responses of POC and MAOC to climate change. Here, we assessed the effects of simulated climate change (control, reduced rainfall (RE), warming (WA), and RE + WA) and initial biocrust cover (low (< 20%) versus high (> 50%)) on the mineral protection of soil C and soil organic matter quality in a dryland ecosystem in central Spain for 9 years. At low initial biocrust cover levels, both WA and RE + WA increased SOC, especially POC but also MAOC, and promoted a higher contribution of carbohydrates, relative to aromatic compounds, to the POC fraction. These results suggest that the accumulation of soil C under warming treatments may be transitory in soils with low initial biocrust cover. In soils with high initial biocrust cover, climate change treatments did not affect SOC, neither POC nor MAOC fraction. Overall, our results indicate that biocrust communities modulate the negative effect of climate change on SOC, because no losses of soil C were observed with the climate manipulations under biocrusts. Future work should focus on determining the long-term persistence of the observed buffering effect by biocrust-forming lichens, as they are known to be negatively affected by warming. Supplementary Information The online version contains supplementary material available at 10.1007/s10021-022-00779-0.
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Affiliation(s)
- Paloma Díaz-Martínez
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Madrid, Spain
- Instituto de Ciencias Agrarias (ICA), CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | - Marco Panettieri
- Instituto de Ciencias Agrarias (ICA), CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | | | - Eduardo Moreno
- Departamento de Química Agrícola y Bromatología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - César Plaza
- Instituto de Ciencias Agrarias (ICA), CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | - Fernando T. Maestre
- Instituto Multidisciplinar Para el Estudio del Medio “Ramón Margalef”, Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
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Li N, Wang B, Huang Y, Huang Q, Jiao F, An S. Response of cbbL-harboring microorganisms to precipitation changes in a naturally-restored grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156191. [PMID: 35618124 DOI: 10.1016/j.scitotenv.2022.156191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The impact of the long-term uneven precipitation distribution model on the diversity and community composition of soil C-fixing microorganisms in arid and semiarid grasslands remains unclear. In 2015, we randomly set up five experimental plots with precipitation gradients on the natural restoration grassland of the Loess Plateau (natural precipitation, NP; ± 40% natural precipitation: decreased precipitation (DP), DP40; increased precipitation (IP), IP40; ± 80% natural precipitation: DP80; IP80). In the third and fifth years after the experimental layout (spanned two years), we explored the cbbL-genes, which are functional genes in the Calvin cycle, harboring microbial diversity and community composition under different precipitation treatments. The results showed that the increase in mean annual precipitation significantly changed the cbbL-harboring microbial alpha diversity, especially when controlling for 40% natural precipitation. The response of the dominant microbial communities to interannual increased precipitation variation shifted from Gammaproteobacteria (Bradyrhizobium) to Betaproteobacteria (Variovorax). The structural equation model showed that precipitation directly affected the cbbL-harboring microbial diversity and community composition and indirectly by affecting soil NO3- (mg N kg -1), soil organic matter, dissolved organic N content, and above- and underground biomass. In conclusion, studying how cbbL-harboring microbial diversity and community composition respond to uneven precipitation variability provides new insights into the ecological processes of C-fixing microbes in semi-arid naturally-restored grasslands dominated by the Calvin cycle.
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Affiliation(s)
- Na Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qian Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Jiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China.
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Pan Y, Kang P, Tan M, Hu J, Zhang Y, Zhang J, Song N, Li X. Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:997292. [PMID: 36119572 PMCID: PMC9471988 DOI: 10.3389/fpls.2022.997292] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.
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Affiliation(s)
- Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Min Tan
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinpeng Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Yaqi Zhang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinlin Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Naiping Song
- Breeding Base for Key Laboratory Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
| | - Xinrong Li
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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Pescador DS, Delgado-Baquerizo M, Fiore-Donno AM, Singh BK, Bonkowski M, Maestre FT. Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210387. [PMID: 35757878 PMCID: PMC9234812 DOI: 10.1098/rstb.2021.0387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022] Open
Abstract
Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.
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Affiliation(s)
- David S. Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Anna Maria Fiore-Donno
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michael Bonkowski
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, San Vicente del Raspeig, Spain
- Departamento de Ecología, Universidad de Alicante, San Vicente del Raspeig, Spain
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29
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Driving Factors of Microbial Community Abundance and Structure in Typical Forest Soils of Sanjiang Plain, Northeast China. SUSTAINABILITY 2022. [DOI: 10.3390/su14138040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Until recently, a comprehensive evaluation of the environmental drivers on the abundance and structure of the microbial community in typical forest soils has not been thoroughly conducted. In this study, the typical forest soils (Mongolian oak (Quercus mongolica) soil, MOS; white birch (Betula platyphylla) soil, WBS; and white poplar (Populus davidiana) soil, WPS) in the Sanjiang Plain were selected to ascertain the differences and the major environmental factors driving soil microbial community abundance and structure. Results indicated that differences existed in the abundance and structure of the bacterial, archaeal, and fungal community. Co-occurrence network analysis showed that the bacterial and fungal networks were more complex than those of archaeal networks. Unclassified Acidobacteria and unclassified Pyrinomonadaceae were the keystone taxa in the bacterial networks, while Pleotrichocladium and Leotia were the keystone taxa in the fungal networks. Among all environmental factors, pH, SOM, and total N exhibited dominant roles in affecting the abundance of bacteria, archaea, and fungi. The redundancy analysis (RDA) showed that pH was the vital environmental factor responsible for driving the structure of the bacterial, archaeal, and fungal community.
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30
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Zhao C, Hu J, Li Q, Fang Y, Liu D, Liu Z, Zhong R. Transfer of Nitrogen and Phosphorus From Cattle Manure to Soil and Oats Under Simulative Cattle Manure Deposition. Front Microbiol 2022; 13:916610. [PMID: 35774448 PMCID: PMC9238326 DOI: 10.3389/fmicb.2022.916610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Simulated cattle manure deposition was used to estimate nutrient transfer to soil and oats and to investigate changes in microbial community composition and functional groups in oat rhizospheres. Nutrient absorption and return efficiency were calculated as a series of standard calculation formulas, and total nutrient transfer efficiency was nutrient absorption efficiency plus nutrient return efficiency. In total, 74.83% of nitrogen (N) and 59.30% of phosphorus (P) in cattle manure were transferred to soil and oats, with 11.79% of N and 7.89% of P in cattle manure absorbed by oats, and the remainder sequestered in the soil for 80 days after sowing. Cattle manure increased oat root length, surface, and volume under 0.2 mm diameter, and improved relative abundance of the microbiome known to be beneficial. In response to cattle manure, several bacteria known to be beneficial, such as Proteobacteria, Bacteroidota, and Firmicutes at phyla the level and Pseudoxanthomonas, Pseudomonas, and Sphingomonas at the genus level, were positively related to oat biomass and nutrient accumulation. For fungal communities, the relative abundance of Ascomycota is the predominant phylum, which varied in a larger range in the control treatment (81.0–63.3%) than the cattle manure deposition treatment (37.0–42.9%) as plant growing days extend. The relevant abundance of Basidiomycota known as decomposer was higher in cattle manure deposition treatment compared to that in control treatment at 15 days after sowing. More importantly, cattle manure deposition inhibited trophic mode within pathotroph like Alternaria and Fusarium fungal genus and promoted saprotroph and symbiotroph.
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Affiliation(s)
- Chengzhen Zhao
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- School of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Juan Hu
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Qiang Li
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Rongzhen Zhong
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- *Correspondence: Rongzhen Zhong,
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Wu K, Wu C, Jiang X, Xue R, Pan W, Li WC, Luo X, Xue S. Remediation of arsenic-contaminated paddy field by a new iron oxidizing strain (Ochrobactrum sp.) and iron-modified biochar. J Environ Sci (China) 2022; 115:411-421. [PMID: 34969469 DOI: 10.1016/j.jes.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 06/14/2023]
Abstract
Iron-oxidizing strain (FeOB) and iron modified biochars have been shown arsenic (As) remediation ability in the environment. However, due to the complicated soil environment, few field experiment has been conducted. The study was conducted to investigate the potential of iron modified biochar (BC-FeOS) and biomineralization by a new found FeOB to remediate As-contaminated paddy field. Compared with the control, the As contents of GB (BC-FeOS), GF (FeOB), GFN (FeOB and nitrogen fertilizer), GBF (BC-FeOS and FeOB) and GBFN (BC-FeOS, FeOB and nitrogen fertilizer) treatments in pore water decreased by 36.53%-80.03% and the microbial richness of iron-oxidizing bacteria in these treatments increased in soils at the rice maturation stage. The concentrations of available As of GB, GF, GFN, GBF and GBFN at the tillering stage were significantly decreased by 10.78%-55.48%. The concentrations of nonspecifically absorbed and specifically absorbed As fractions of GB, GF, GFN, GBF and GBFN in soils were decreased and the amorphous and poorly crystalline hydrated Fe and Al oxide-bound fraction was increased. Moreover, the As contents of GB, GF, GFN, GBF and GBFN in rice grains were significantly decreased (*P < 0.05) and the total As contents of GFN, GBF and GBFN were lower than the standard limit of the National Standard for Food Safety (GB 2762-2017). Compared with the other treatments, GBFN showed the greatest potential for the effective remediation of As-contaminated paddy fields.
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Affiliation(s)
- Kaikai Wu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Chuan Wu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Department of Science and Environmental Studies, The Education University of Hong Kong, Administrative Region, Hong Kong, China.
| | - Xingxing Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Rui Xue
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, China
| | - Weisong Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| | - Wai-Chin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Administrative Region, Hong Kong, China.
| | - Xinghua Luo
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
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Rodriguez V, Moskwa LM, Oses R, Kühn P, Riveras-Muñoz N, Seguel O, Scholten T, Wagner D. Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera. Microorganisms 2022; 10:microorganisms10050847. [PMID: 35630293 PMCID: PMC9143490 DOI: 10.3390/microorganisms10050847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.
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Affiliation(s)
- Victoria Rodriguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Lisa-Marie Moskwa
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Rómulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile;
| | - Peter Kühn
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa #11315, La Pintana, Santiago 8820808, Chile;
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
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Zhang R, Tian X, Xiang Q, Penttinen P, Gu Y. Response of soil microbial community structure and function to different altitudes in arid valley in Panzhihua, China. BMC Microbiol 2022; 22:86. [PMID: 35366810 PMCID: PMC8976301 DOI: 10.1186/s12866-022-02500-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/11/2022] [Indexed: 01/04/2023] Open
Abstract
Background Altitude affects biodiversity and physic-chemical properties of soil, providing natural sites for studying species distribution and the response of biota to environmental changes. We sampled soil at three altitudes in an arid valley, determined the physic-chemical characteristics and microbial community composition in the soils, identified differentially abundant taxa and the relationships between community composition and environmental factors. Results The low, medium and high altitudes were roughly separated based on the physic-chemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents. The contents of organic and microbial biomass C, total and available N and available P, and the richness and diversity of the microbial communities were lowest in the medium altitude. The relative abundances of phyla Proteobacteria, Gemmatimonadetes, Actinobacteria and Acidobacteria were high at all altitudes. The differentially abundant amplified sequence variants (ASVs) were mostly assigned to Proteobacteria and Acidobacteria. The highest number of ASVs characterizing altitude were detected in the high altitude. However, the predicted functions of the communities were overlapping, suggesting that the contribution of the communities to soil processes changed relatively little along the altitude gradient. Conclusions The low, medium and high altitudes were roughly separated based on the physicochemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02500-6.
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Coleine C, Selbmann L, Singh BK, Delgado-Baquerizo M. The poly-extreme tolerant black yeasts are prevalent under high ultraviolet light and climatic seasonality across soils of global biomes. Environ Microbiol 2022; 24:1988-1999. [PMID: 35324062 PMCID: PMC9311647 DOI: 10.1111/1462-2920.15969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
Black yeasts are among the most stress‐tolerant organisms of the planet, thriving under all types of terrestrial habitats and extreme environments. Yet, their global patterns and ecology remain far less studied, limiting our capacity to identify the main environmental drivers of these important organisms across biomes. To fill this knowledge gap, we analysed topsoils from 235 terrestrial ecosystems across and within globally distributed climate groups (i.e. dry, temperate and continental). We found that soils are important repositories of black yeasts, and that ultraviolet light, fine soil texture, and precipitation seasonality are the most consistent environmental factors associated with their diversity across biomes. Finally, we identified Exophiala and Cladophialophora as the most dominant black yeasts genera in soils across the globe. These findings provide novel evidence of global distribution of black yeasts and their key environmental predictors, giving new insights for speculating the evolution and spreading of these extreme‐tolerant organisms throughout both natural and human associated extreme environments.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, 41013, Spain
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35
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Zhang M, Niu Y, Wang W, Bai SH, Luo H, Tang L, Chen F, Xu Z, Guo X. Responses of microbial function, biomass and heterotrophic respiration, and organic carbon in fir plantation soil to successive nitrogen and phosphorus fertilization. Appl Microbiol Biotechnol 2021; 105:8907-8920. [PMID: 34734313 DOI: 10.1007/s00253-021-11663-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Carbon dioxide (CO2) emissions from forest ecosystems originate largely from soil respiration, and microbial heterotrophic respiration plays a critical role in determining organic carbon (C) stock. This study investigated the impacts of successive nitrogen (N) and phosphorus (P) fertilization after 9 years on soil organic C stock; CO2 emission; and microbial biomass, community, and function in a Chinese fir plantation. The annual fertilization rates were (1) CK, control without N or P fertilization; (2) N50, 50 kg N ha-1; (3) N100, 100 kg N ha-1; (4) P50, 50 kg P ha-1; (5) N50P50, 50 kg N ha-1 + 50 kg P ha-1; and (6) N100P50, 100 kg N ha-1 + 50 kg P ha-1. The N100P50 treatment had the highest cumulative soil CO2 emissions, but the CK treatment had the lowest cumulative soil CO2 emissions among all treatments. The declines of soil organic C (SOC) after successive 9-year fertilization were in the order of 100 kg N ha-1 year-1 > 50 kg N ha-1 year-1 > CK. Compared to the CK treatment, successive N fertilization significantly changed soil microbial communities at different application rates and increased the relative gene abundances of glycoside hydrolases, glycosyl transferases, carbohydrate-binding modules, and polysaccharide lyases at 100 kg N ha-1 year-1. Relative to P fertilization alone (50 kg P ha-1 year-1), combined N and P fertilization significantly altered the soil microbial community structure and favored more active soil microbial metabolism. Microbial community and metabolism changes caused by N fertilization could have enhanced CO2 emission from heterotrophic respiration and eventually led to the decrease in organic C stock in the forest plantation soil. KEY POINTS: • N fertilization, alone or with P, favored more active microbial metabolism genes. • 100 kg N ha-1 fertilization significantly changed microbial community and function. • N fertilization led to a "domino effect" on the decrease of soil C stock.
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Affiliation(s)
- Manyun Zhang
- Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China.,Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia
| | - Yun Niu
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia.,Jiangxi Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.,Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Weijin Wang
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia
| | - Shahla Hosseini Bai
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia
| | - Handong Luo
- Jiangxi Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Li Tang
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia
| | - Fusheng Chen
- Jiangxi Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhihong Xu
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, QLD, 4111, Australia. .,Jiangxi Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xiaomin Guo
- Jiangxi Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
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36
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Yu Y, Liu L, Wang J, Zhang Y, Xiao C. Effects of warming on the bacterial community and its function in a temperate steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148409. [PMID: 34146803 DOI: 10.1016/j.scitotenv.2021.148409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
As a significant environmental issue, global warming will have a significant impact on soil microorganisms, especially soil bacteria. However, the effects of warming on the network structure of bacterial communities and the function of ecosystems remain unclear. Therefore, we examined the effects of three-year simulated field warming on the complexity of soil bacterial communities and predicted functions in a temperate steppe of Inner Mongolia. Warming significantly increased the α-diversity of bacteria in 2018 but did not affect it in 2019 and 2020. Warming increased network complexity and stability and keystone taxa, and these bacterial taxa also associated more closely with each other, indicating that the protection of interactions between bacterial taxa is very important for the conservation of biodiversity. Warming significantly increased aerobic chemoheterotrophy, ureolysis, and chemoheterotrophy, suggesting that warming increased the ability of bacteria to decompose organic matter and the emission of greenhouse gases, such as CO2 and CH4. Collectively, warming will alter soil bacterial community structure and its potential functions, further affecting key functions in grassland belowground ecosystems.
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Affiliation(s)
- Yang Yu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Lu Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jing Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yushu Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China.
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37
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Changes in Soil Prokaryotic Diversity in Response to Land-Use Changes in Sub-Saharan Africa. SOIL SYSTEMS 2021. [DOI: 10.3390/soilsystems5040062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Sub-Saharan Africa is one of the most severely affected regions regarding soil degradation, a global issue with the loss of nutrients caused by inappropriate management, leading to low agricultural productivity. Here we asked the question of how soil prokaryotic communities are affected by shifts in land use management and subsequent losses in soil organic carbon. We sampled soils from three sites in Zambia which have neighboring natural and managed sites. After the measurement of soil properties, soil DNA was sequenced, targeting the 16S rRNA gene. As expected, total carbon in soil was decreased in the managed sites, with significant reductions of bacterial biomass. However, the diversity indices in the managed soils were higher than in natural soils. Particularly, the relative abundance of nitrifiers was increased in the managed soils, most likely as a result of fertilization. However also other bacteria, e.g., those which formed tight interactions with the cultivated crops including the genera Balneimonas, and Bacillus, were increased in the managed soils. In contrast bacteria belonging to the family Chloroflexi, which were high in abundance in the natural soil were outcompeted by other prokaryotes in the managed soils most likely as a result of changes in the amount of soil organic carbon. Overall, our results suggest that we need to discuss the trends of prokaryotic diversity separately from those for prokaryotic abundance. Even when bacterial abundances were decreased in the managed soils, nitrifiers’ relative abundance and diversity increased in our experiment, suggesting the possible alteration of the nitrogen cycle in managed soils in sub-Saharan Africa.
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Isolation and Characterization of Biosurfactant-Producing Bacteria from Amapaense Amazon Soils. Int J Microbiol 2021; 2021:9959550. [PMID: 34447438 PMCID: PMC8384547 DOI: 10.1155/2021/9959550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/18/2021] [Accepted: 08/05/2021] [Indexed: 12/05/2022] Open
Abstract
The objective of this research was to perform screening of biosurfactant-producing bacteria from Amapaense Amazon soils. Floodplain- and upland-forest soils of three municipalities of the Amapá state were isolated and identified. The isolates were cultured in nutrient broth with olive oil, and their extracts were evaluated according to drop collapse, oil dispersion, emulsification, and surface tension tests. From three hundred and eighteen isolates, the 43 bacteria were selected and identified by 16S rDNA gene sequencing, indicating the presence of three different genera, Serratia, Paenibacillus, and Citrobacter. The extracellular biosurfactant production pointed out the 15 most efficient bacteria that presented high emulsification capacity (E24 > 48%) and stability (less than 10% of drop after 72 h) and great potential to reduce the surface tension (varying from 49.40 to 34.50 mN·m−1). Cluster analysis classified genetically related isolates in different groups, which can be connected to differences in the amount or the sort of biosurfactants. Isolates from Serratia genus presented better emulsification capacity and produced a more significant surface tension drop, indicating a promising potential for biotechnological applications.
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39
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Beugnon R, Du J, Cesarz S, Jurburg SD, Pang Z, Singavarapu B, Wubet T, Xue K, Wang Y, Eisenhauer N. Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning. ISME COMMUNICATIONS 2021; 1:41. [PMID: 37938251 PMCID: PMC9723754 DOI: 10.1038/s43705-021-00040-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 05/26/2023]
Abstract
Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.
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Affiliation(s)
- Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany.
| | - Jianqing Du
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| | - Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| | - Zhe Pang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Bala Singavarapu
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, Halle (Saale), Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor, Halle, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, Halle (Saale), Germany
| | - Kai Xue
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
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40
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Tian Q, Jiang Y, Tang Y, Wu Y, Tang Z, Liu F. Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient. Front Microbiol 2021; 12:646124. [PMID: 34394018 PMCID: PMC8363232 DOI: 10.3389/fmicb.2021.646124] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.
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Affiliation(s)
- Qiuxiang Tian
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ying Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Tang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyao Tang
- Key Laboratory for Earth Surface Processes, Department of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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41
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Looby CI, Martin PH. Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world. FEMS Microbiol Ecol 2021; 96:5891232. [PMID: 32780840 DOI: 10.1093/femsec/fiaa122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.
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Affiliation(s)
- Caitlin I Looby
- Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, Saint Paul, MN 55108, USA
| | - Patrick H Martin
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
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Wang H, Tian T, Gong Y, Ma S, Altaf MM, Wu H, Diao X. Both environmental and spatial variables affect bacterial functional diversity in mangrove sediments at an island scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:142054. [PMID: 32896729 DOI: 10.1016/j.scitotenv.2020.142054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Sediment microorganisms are influenced by various biotic and abiotic factors. However, information concerning the spatial factors that determine the functional diversity of sediment bacterial communities at an island scale is limited. Here, we conducted an island-scale study to assess the driving forces governing the functional diversity of sediment bacterial communities in different mangroves around the coast of Hainan Island, southern China. For mangrove sediments in Hainan Island, differences in the metabolic activity and functional diversity among four sites were context dependent, while that showed a trend of East > North > West > South. Furthermore, total carbon, nitrite nitrogen, and salinity are important environmental factors that determine the metabolic functional diversity of bacterial communities. This study also provided important insights for explaining the metabolic functional diversity of bacterial communities in tropical mangrove sediments. The metabolic activity had a significantly response to environmental variables (13.2% of pure variance was explained) and spatial variables (12.4%). More importantly, given that spatial variables may contribute to the bacterial functional as important as environmental variables, this spatial variety of bacterial functional provides new insight into studying bacterial functional biogeographic patterns and impacts on sediment-associated function.
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Affiliation(s)
- Haihua Wang
- College of Ecology and Environment, Hainan University, Haikou 570228, People's Republic of China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, People's Republic of China
| | - Tian Tian
- School of Biology, Hainan Normal University, Haikou 571158, People's Republic of China
| | - Ying Gong
- College of Ecology and Environment, Hainan University, Haikou 570228, People's Republic of China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, People's Republic of China
| | - Siyuan Ma
- School of Biology, Hainan Normal University, Haikou 571158, People's Republic of China
| | - Muhammad Mohsin Altaf
- College of Ecology and Environment, Hainan University, Haikou 570228, People's Republic of China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, People's Republic of China
| | - Hongping Wu
- School of Biology, Hainan Normal University, Haikou 571158, People's Republic of China
| | - Xiaoping Diao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, People's Republic of China; School of Biology, Hainan Normal University, Haikou 571158, People's Republic of China.
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43
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Zeng Q, An S. Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau. Microorganisms 2021; 9:139. [PMID: 33435426 PMCID: PMC7827256 DOI: 10.3390/microorganisms9010139] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 01/06/2023] Open
Abstract
High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.
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Affiliation(s)
- Quanchao Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
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44
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Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota. DIVERSITY 2020. [DOI: 10.3390/d12110436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.
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45
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Zhou Y, Yao Q, Zhu H. Soil Organic Carbon Attenuates the Influence of Plants on Root-Associated Bacterial Community. Front Microbiol 2020; 11:594890. [PMID: 33240249 PMCID: PMC7680919 DOI: 10.3389/fmicb.2020.594890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Plant-derived carbon (PDC) released by roots has a strong effect on root-associated bacterial community, which is critical for plant fitness in natural environments. However, the freshly exuded PDC can be diluted by the ancient soil-derived carbon (SDC) at a short distance from root apices. Thus, the rhizosphere C pools are normally dominated by SDC rather than PDC. Yet, how PDC and SDC interact to regulate root-associated bacterial community is largely unknown. In this study, a grass species and a legume species were planted in two contrasting matrixes, quartz sand and soil, to assess the role of PDC and SDC in regulating root-associated bacterial community, and to explore whether SDC affects the influence of PDC on bacterial community in soil. Our results indicated that the legume plant showed significantly positive priming effect on soil organic matter decomposition but the grass plant did not. PDC significantly shaped bacterial community in sand culture as indicated by PCR-DGGE and high-throughput sequencing of bacterial 16S rRNA gene. Intriguingly, we found that dissimilarity of bacterial communities associated with two plant species and the percentage of specific OTUs in quartz sand were significantly higher than those in soil. Moreover, several biomarkers enriched by plants in quartz sand turned to be general taxa in soil, which indicated that SDC attenuated the regulation of bacterial community by PDC. Taken together, these results suggest that SDC interacted with PDC and the root-associated microbial community, thus acted as soil buffering component of biological process contributing to soil resilience. The importance of PDC in structuring rhizosphere bacterial community needs to be reconsidered in the context of wider contribution of other C pool, such as SDC.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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46
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Local community assembly mechanisms shape soil bacterial β diversity patterns along a latitudinal gradient. Nat Commun 2020; 11:5428. [PMID: 33110057 PMCID: PMC7591474 DOI: 10.1038/s41467-020-19228-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/29/2020] [Indexed: 11/29/2022] Open
Abstract
Biodiversity patterns across geographical gradients could result from regional species pool and local community assembly mechanisms. However, little has been done to separate the effects of local ecological mechanisms from variation in the regional species pools on bacterial diversity patterns. In this study, we compare assembly mechanisms of soil bacterial communities in 660 plots from 11 regions along a latitudinal gradient in eastern China with highly divergent species pools. Our results show that β diversity does not co-vary with γ diversity, and local community assembly mechanisms appear to explain variation in β diversity patterns after correcting for variation in regional species pools. The variation in environmental conditions along the latitudinal gradient accounts for the variation in β diversity through mediating the strength of heterogeneous selection. In conclusion, our study clearly illustrates the importance of local community assembly processes in shaping geographical patterns of soil bacterial β diversity. The relative importance of regional species pool and local assembly processes as drivers of beta diversity is unclear. Here the authors investigate soil bacterial diversity patterns along a 3700-km latitudinal gradient in Chinese forests, finding that community assembly processes differ based on environmental heterogeneity.
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How Do Soil Bacterial Diversity and Community Composition Respond under Recommended and Conventional Nitrogen Fertilization Regimes? Microorganisms 2020; 8:microorganisms8081193. [PMID: 32764443 PMCID: PMC7466009 DOI: 10.3390/microorganisms8081193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/17/2022] Open
Abstract
Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N−, RF N+, CF N−, CF N+. No N fertilization was indicated by N− and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.
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48
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Zhou Z, Wang C, Luo Y. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun 2020; 11:3072. [PMID: 32555185 PMCID: PMC7300008 DOI: 10.1038/s41467-020-16881-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Biodiversity on the Earth is changing at an unprecedented rate due to a variety of global change factors (GCFs). However, the effects of GCFs on microbial diversity is unclear despite that soil microorganisms play a critical role in biogeochemical cycling. Here, we synthesize 1235 GCF observations worldwide and show that microbial rare species are more sensitive to GCFs than common species, while GCFs do not always lead to a reduction in microbial diversity. GCFs-induced shifts in microbial alpha diversity can be predominately explained by the changed soil pH. In addition, GCF impacts on soil functionality are explained by microbial community structure and biomass rather than the alpha diversity. Altogether, our findings of GCF impacts on microbial diversity are fundamentally different from previous knowledge for well-studied plant and animal communities, and are crucial to policy-making for the conservation of microbial diversity hotspots under global changes.
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Affiliation(s)
- Zhenghu Zhou
- Center for Ecological Research, Northeast Forestry University, Harbin, 150040, China.,Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Chuankuan Wang
- Center for Ecological Research, Northeast Forestry University, Harbin, 150040, China. .,Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
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49
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Huang M, Tian A, Chen J, Cao F, Chen Y, Liu L. Soil bacterial communities in three rice-based cropping systems differing in productivity. Sci Rep 2020; 10:9867. [PMID: 32555234 PMCID: PMC7300030 DOI: 10.1038/s41598-020-66924-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/26/2020] [Indexed: 11/24/2022] Open
Abstract
Soil microorganisms play an important role in determining productivity of agro-ecosystems. This study was conducted to compare diversity, richness, and structure (relative abundance at the phylum level) of soil bacterial communities among three rice-based cropping systems, namely, a winter fallow-rice-rice (FRR), green manure (Chinese milk vetch)-rice-rice (MRR), and oilseed rape-rice-rice (ORR), in which MRR and ORR had significantly higher productivity than FRR. A 16S rRNA gene sequence analysis showed that no significant differences were observed in diversity and richness indices (observed species, Shannon, Simpson, Chao1, abundance-based coverage estimators, and phylogeny-based metrics) of soil bacterial communities among the three cropping systems. However, relative abundances of dominant phyla in soil bacterial communities, including Proteobacteria, Acidobacteria, Nitrospirae, Gemmatimonadetes, and Verrucomicrobia, were significantly different among the three cropping systems. In particular, a significant reduction in the relative abundance of Nitrospirae was observed in both MRR and ORR compared with FRR. These results indicate that bacterial community structure was affected by cropping systems in the tested paddy soils. Based on the results of our studies and existing knowledge bases, we speculate that benefits to rice yield may be obtained by reducing the relative abundance of Nitrospirae and increasing the ratio of abundances of Proteobacteria/Acidobacteria in paddy soils.
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Affiliation(s)
- Min Huang
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| | - Alin Tian
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Jiana Chen
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Fangbo Cao
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yumei Chen
- Department of Crop Cultivation, Hengyang Academy of Agricultural Sciences, Hengyang, 421101, China
| | - Longsheng Liu
- Department of Crop Cultivation, Hengyang Academy of Agricultural Sciences, Hengyang, 421101, China
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50
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Shen C, Gunina A, Luo Y, Wang J, He JZ, Kuzyakov Y, Hemp A, Classen AT, Ge Y. Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient. Environ Microbiol 2020; 22:3287-3301. [PMID: 32436332 DOI: 10.1111/1462-2920.15090] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/17/2020] [Indexed: 11/28/2022]
Abstract
Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient-bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed-effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.
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Affiliation(s)
- Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Nordbahnhof Strasse 1a, Witzenhausen, 32213, Germany
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jianjun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yakov Kuzyakov
- Department of Environmental Chemistry, University of Kassel, Nordbahnhof Strasse 1a, Witzenhausen, 32213, Germany.,Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, 37077, Germany.,Department of Agricultural Soil Science, University of Göttingen, Göttingen, 37077, Germany.,Institute of Environmental Sciences, Kazan Federal University, Kazan, 420049, Russia.,Agro-Technological Institute, RUDN University, Moscow, 117198, Russia
| | - Andreas Hemp
- Department of Plant Systematics, University of Bayreuth, Universitӓtsstraße 30, Bayreuth, 95440, Germany
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, VT, 05405, USA.,Gund Institute for Environment, University of Vermont, Burlington, VT, 05405, USA
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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