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Abstract
Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. The soil bacteria of four typical Chinese rice-growing regions were characterized and compared to those of nonpaddy soils. The paddy soil bacteria were significantly less diverse, with unique taxonomic and functional composition, and harbored distinct cooccurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy samples exhibited a stronger deterministic signature than nonpaddy samples. Compared to other environmental factors, climatic factors such as mean monthly precipitation and mean annual temperature described most of the variance in soil bacterial community structure. Cooccurrence network analysis suggests that the continental biogeographic variance in bacterial community structure was described by the competition between two mutually exclusive bacterial modules in the community. Keystone taxa identified in network models (Anaerolineales, Ignavibacteriae, and Deltaproteobacteria) were more sensitive to changes in environmental factors, leading us to conclude that environmental factors may influence paddy soil bacterial communities via these keystone taxa. Characterizing the uniqueness of bacterial community patterns in paddy soil (compared to nonpaddy soils) at continental scales is central to improving crop productivity and resilience and to sustaining agricultural soils. IMPORTANCE Rice fields provide food for over half of the world’s human population. The ecology of paddy soil microbiomes is shaped by human activities, which can have a profound impact on rice yield, greenhouse gas emissions, and soil health. Investigations of the soil bacteria in four typical Chinese rice-growing regions showed that (i) soil bacterial communities maintain highly modularized species-to-species network structures; (ii) community patterns were shaped by the balance of integrated stochastic and deterministic processes, in which homogenizing selection and dispersal limitation dominate; and (iii) deterministic processes and climatic and edaphic factors influence community patterns mainly by their impact on highly connected nodes (i.e., keystone taxa) in networks. Characterizing the unique ecology of bacterial community patterns in paddy soil at a continental scale may lead to improved crop productivity and resilience, as well as sustaining agricultural soils.
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Uddin M, Chen J, Qiao X, Tian R, Arafat Y, Yang X. Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 167:44-53. [PMID: 30292975 DOI: 10.1016/j.ecoenv.2018.09.101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg-1 of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.
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Affiliation(s)
- Misbah Uddin
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xianliang Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Run Tian
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yasir Arafat
- Key Laboratory of Fujian Province for Agroecological Process and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Xiaojing Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Li HY, Wang H, Wang HT, Xin PY, Xu XH, Ma Y, Liu WP, Teng CY, Jiang CL, Lou LP, Arnold W, Cralle L, Zhu YG, Chu JF, Gilbert JA, Zhang ZJ. The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. MICROBIOME 2018; 6:187. [PMID: 30340631 PMCID: PMC6195703 DOI: 10.1186/s40168-018-0561-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/20/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition. RESULTS We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis. CONCLUSIONS Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.
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Affiliation(s)
- Hong-Yi Li
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Hang Wang
- National Plateau Wetlands Research Center, Southwest Forestry University, 300 Bailongsi, Kunming, 650224 China
| | - Hai-Tiao Wang
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Pei-Yong Xin
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Xin-Hua Xu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Yun Ma
- College of Biological and Environmental Engineering, Zhejiang University of Technology, 18 Chaowang Ave, Hangzhou, 310014 China
| | - Wei-Ping Liu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Chang-Yun Teng
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
| | - Cheng-Liang Jiang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
| | - Li-Ping Lou
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
| | - Wyatt Arnold
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Lauren Cralle
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Ave, Xiamen, 361021 China
| | - Jin-Fang Chu
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Jack A Gilbert
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Zhi-Jian Zhang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108 China
- China Academy of West Region Development, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058 China
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