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Qin Y, Wu L, Zhang Q, Wen C, Van Nostrand JD, Ning D, Raskin L, Pinto A, Zhou J. Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing. mSystems 2023; 8:e0102523. [PMID: 38038441 PMCID: PMC10734440 DOI: 10.1128/msystems.01025-23] [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: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
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Affiliation(s)
- Yujia Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Qiuting Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Chongqin Wen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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Liu ZD, Song YY, Ma XY, Yuan JB, Lou YJ, Yang C, Tang HR, Song CC. Deep soil microbial carbon metabolic function is important but often neglected: a study on the Songnen Plain reed wetland, Northeast China. FUNDAMENTAL RESEARCH 2023; 3:833-843. [PMID: 38933016 PMCID: PMC11197545 DOI: 10.1016/j.fmre.2022.06.013] [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: 04/29/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022] Open
Abstract
Soil microbial carbon metabolism is critical in wetland soil carbon cycling, and is also a research hotspot at present. However, most studies focus on the surface soil layer in the wetlands and the microorganisms associated with this layer. In this study, 0-75 cm soil profiles were collected from five widely separated reed wetlands in the Songnen Plain, which has a large number of middle-high latitude inland saline-sodic wetlands. The Biolog-ECO method was used to determine the carbon metabolic activity and functional diversity of soil microorganisms. The results showed that soil carbon metabolic activity decreased with increasing soil depth. The carbon metabolic activity of soil microorganisms in the 60-75 cm layer was approximately 57.41%-74.60% of that in the 0-15 cm layer. The soil microbial Shannon index and utilization rate of amines decreased with an increase in soil depth, while the Evenness index and utilization rate of polymers tended to increase with soil depth. Dissolved organic carbon (DOC) is the most important factor affecting microbial carbon source utilization preference, because microorganisms mainly obtain the carbon source from DOC. The result of the correlation analysis showed that the soil microbial carbon metabolic activity, Shannon index, and Evenness index significantly correlated with soil total carbon (TC), microbial biomass carbon (MBC), DOC, total nitrogen (TN), ammonium nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N) contents, and electrical conductivity (EC). This study emphasized the important role of microbial carbon metabolic function in deep soil.
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Affiliation(s)
- Zhen-Di Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Yu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiu-Yan Ma
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jia-Bao Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Jing Lou
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chen Yang
- Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hao-Ran Tang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang-Chun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- School of Hydraulic Engineering, Dalian University of Technology, Dalian 116024, China
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Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming. mBio 2023; 14:e0300922. [PMID: 36786571 PMCID: PMC10127799 DOI: 10.1128/mbio.03009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
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Ai J, Yu T, Liu X, Jiang Y, Hao Z, Zhao X, Wang E, Deng Z. Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii. Front Microbiol 2022; 13:1078208. [PMID: 36532429 PMCID: PMC9751200 DOI: 10.3389/fmicb.2022.1078208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.
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Affiliation(s)
- Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaodong Liu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Yingying Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Ziwei Hao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaoyu Zhao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Entao Wang
- , Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenshan Deng
- College of Life Sciences, Yan’an University, Yan’an, China,*Correspondence: Zhenshan Deng,
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Hao J, Feng Y, Wang X, Yu Q, Zhang F, Yang G, Ren G, Han X, Wang X, Ren C. Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156621. [PMID: 35691356 DOI: 10.1016/j.scitotenv.2022.156621] [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: 03/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.
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Affiliation(s)
- Jiaqi Hao
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Yongzhong Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China.
| | - Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Qi Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Fu Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Gaihe Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Guangxin Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xinhui Han
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaojiao Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
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6
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Lin Y, Ye G, Hu HW, Fan J, He JZ. Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol. Front Microbiol 2022; 13:965293. [PMID: 36033880 PMCID: PMC9412762 DOI: 10.3389/fmicb.2022.965293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.
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Affiliation(s)
- Yongxin Lin
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Guiping Ye
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Jianbo Fan
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
- Ji-Zheng He
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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Koner S, Chen JS, Hsu BM, Rathod J, Huang SW, Chien HY, Hussain B, Chan MWY. Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127266. [PMID: 34600373 DOI: 10.1016/j.jhazmat.2021.127266] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.
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Affiliation(s)
- Suprokash Koner
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
| | - Jagat Rathod
- Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Wei Huang
- Center for environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan; Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung, Taiwan
| | - Hua-Yi Chien
- Environmental Technology Development Department, Taiwan VCM Corporation, Kaohsiung, Taiwan; Department of Environmental Sciences and Engineering, Fooyin University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
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Li Y, Lin H, Gao P, Yang N, Xu R, Sun X, Li B, Xu F, Wang X, Song B, Sun W. Variation in the diazotrophic community in a vertical soil profile contaminated with antimony and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118248. [PMID: 34592324 DOI: 10.1016/j.envpol.2021.118248] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
A nitrogen (N) deficiency will usually hinder bioremediation efforts in mining-derived habitats such as occurring in mining regions. Diazotrophs can provide N to support the growth of plants and microorganisms in these environments. However, diazotrophic communities in mining areas have been not studied frequently and are more poorly understood than those in other environments, such as in agricultural soils or in the presence of legumes. The current study compares the differences in depth-resolved diazotrophic community compositions and interactions in two contrasting sites (to depths of 2 m), including a highly contaminated and a moderately contaminated site. Antimony (Sb) and arsenic (As) co-contamination induced a loosely connected biotic interaction, and a selection of deep soils by diazotrophic communities. Multiple lines of evidence, including the enrichment of diazotrophic taxa in the highly contaminated sites, microbe-microbe interactions, environment-microbe interactions, and a machine learning approach (random forests regression), demonstrated that Rhizobium was the keystone taxon within the vertical profile of contaminated soil and was resistant to the Sb and As contaminant fractions. All of these observations suggest that one diazotroph, Rhizobium, may play an important role in N fixation in the examined contaminated sites.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai, 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; School of Environment, Henan Normal University, China; Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, China.
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10
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Yu GH, Kuzyakov Y, Luo Y, Goodman BA, Kappler A, Liu FF, Sun FS. Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14979-14989. [PMID: 34677955 DOI: 10.1021/acs.est.1c04240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.
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Affiliation(s)
- Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, RUDN University, Moscow 117198, Russia
| | - 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
| | - Bernard A Goodman
- College of Physical Science and Technology, Guangxi University, Nanning 530004, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, Tübingen 72076, Germany
| | - Fei-Fei Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
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11
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Luo Z, Zhong Q, Han X, Hu R, Liu X, Xu W, Wu Y, Huang W, Zhou Z, Zhuang W, Yan Q, He Z, Wang C. Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. MICROBIOME 2021; 9:212. [PMID: 34702367 PMCID: PMC8549172 DOI: 10.1186/s40168-021-01164-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/17/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. RESULTS Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. CONCLUSIONS This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.
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Affiliation(s)
- Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wenjun Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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12
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Ding X, Liu K, Yan Q, Liu X, Chen N, Wang G, He S. Sugar and organic acid availability modulate soil diazotroph community assembly and species co-occurrence patterns on the Tibetan Plateau. Appl Microbiol Biotechnol 2021; 105:8545-8560. [PMID: 34661705 DOI: 10.1007/s00253-021-11629-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 01/03/2023]
Abstract
Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.Key points• Soil metabolites were significantly linked to the diversity of diazotrophic community.• Soil metabolites determined the assembly of diazotrophic community.• Sugars and organic acids were coupled mainly with keystone species in networks.
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Affiliation(s)
- Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Ni Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Guoliang Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Shuai He
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
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13
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Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Nitrogen Fertilization and Native C 4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities. Front Microbiol 2021; 12:675693. [PMID: 34305840 PMCID: PMC8297707 DOI: 10.3389/fmicb.2021.675693] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/14/2021] [Indexed: 01/31/2023] Open
Abstract
Native C4 grasses have become the preferred species for native perennial pastures and bioenergy production due to their high productivity under low soil nitrogen (N) status. One reason for their low N requirement is that C4 grasses may benefit from soil diazotrophs and promote biological N fixation. Our objective was to evaluate the impact of N fertilization rates (0, 67, and 202 kg N ha-1) and grass species (switchgrass [Panicum virgatum] and big bluestem [Andropogon gerardii]) on the abundance, activity, diversity, and community composition of soil diazotrophs over three agricultural seasons (grass green-up, initial harvest, and second harvest) in a field experiment in East Tennessee, United States. Nitrogen fertilization rate had a stronger influence on diazotroph population size and activity (determined by nifH gene and transcript abundances) and community composition (determined by nifH gene amplicon sequencing) than agricultural season or grass species. Excessive fertilization (202 kg N ha-1) resulted in fewer nifH transcripts compared to moderate fertilization (67 kg N ha-1) and decreased both richness and evenness of diazotrophic community, reflecting an inhibitory effect of high N application rates on soil diazotrophic community. Overall, cluster I and cluster III diazotrophs were dominant in this native C4 grass system. Diazotroph population size and activity were directly related to soil water content (SWC) based on structural equation modeling. Soil pH, SWC, and C and N availability were related to the variability of diazotrophic community composition. Our results revealed relationships between soil diazotrophic community and associated soil properties, adding to our understanding of the response of soil diazotrophs to N fertilization and grass species in native C4 grass systems.
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Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jonathan D. Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States
| | - Patrick D. Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States
| | - Lidong Li
- United States Department of Agriculture—Agricultural Research Service, Agroecosystem Management Research Unit, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
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14
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Gao Y, Ding J, Yuan M, Chiariello N, Docherty K, Field C, Gao Q, Gu B, Gutknecht J, Hungate BA, Le Roux X, Niboyet A, Qi Q, Shi Z, Zhou J, Yang Y. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition. NPJ Biofilms Microbiomes 2021; 7:17. [PMID: 33558544 PMCID: PMC7870951 DOI: 10.1038/s41522-021-00187-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.
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Affiliation(s)
- Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Key Laboratory of Dryland Agriculture, Ministry of Agriculture of the People's Republic of China, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Nona Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Chris Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Xavier Le Roux
- Mirobial Ecology Centre LEM, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), Paris, France.,AgroParisTech, Paris, France
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
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15
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Effect of soil chemical fertilization on the diversity and composition of the tomato endophytic diazotrophic community at different stages of growth. Braz J Microbiol 2020; 51:1965-1975. [PMID: 32895888 DOI: 10.1007/s42770-020-00373-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/02/2020] [Indexed: 10/23/2022] Open
Abstract
The aim of this work was to gain a more comprehensive and perspicacious view of the endophytic diazotrophic community (EDC) of tomato plant bacteria and assess the effects of chemical fertilization and the plant phenologic stage on the status of those microbes. When the EDC of stem and roots from tomato plants grown in a greenhouse with and without exogenous chemical fertilization was examined by pyrosequencing the nifH gene during the growth cycle, a high taxonomic and phylogenetic diversity was observed. The abundant taxa were related to ubiquitous endophytes such as Rhizobium or Burkholderia but also involved anaerobic members usually restricted to flooded plant tissues, such as Clostridium, Geobacter, and Desulfovibrio. The EDC composition appeared to be dynamic during the growth phase of the tomato, with the structure of the community at the early stages of growth displaying major differences from the late stages. Inorganic fertilization negatively affected the diversity and modified the profile of the predominant components of the EDC in the different growth stages. Populations such as Burkholderia and Geobacter plus the Cyanobacteria appeared particularly affected by fertilization.Our work demonstrates an extensive endophytic diazotrophic diversity, suggesting a high potential for nitrogen fixation. The effect of the phenologic stage and inorganic-chemical soil fertilization on the community structure indicated a dynamic community that responded to environmental changes. These findings contribute to a better understanding of endophytic associations that could be helpful in assisting to shape the endomicrobiome that provides essential benefits to crops.
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16
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Feng J, Wang C, Lei J, Yang Y, Yan Q, Zhou X, Tao X, Ning D, Yuan MM, Qin Y, Shi ZJ, Guo X, He Z, Van Nostrand JD, Wu L, Bracho-Garillo RG, Penton CR, Cole JR, Konstantinidis KT, Luo Y, Schuur EAG, Tiedje JM, Zhou J. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. MICROBIOME 2020; 8:3. [PMID: 31952472 PMCID: PMC6969446 DOI: 10.1186/s40168-019-0778-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/23/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample). RESULTS We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R2 > 0.725, p < 0.001) with ecosystem respiration or CH4 flux. CONCLUSIONS Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.
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Affiliation(s)
- Jiajie Feng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Cong Wang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Qingyun Yan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Xishu Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Xuanyu Tao
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Mengting M Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhou J Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Xue Guo
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Rosvel G Bracho-Garillo
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - C Ryan Penton
- Center for Fundamental and Applied Microbiomics, Arizona State University, Mesa, AZ, 85212, USA
- College of Integrative Sciences and Arts, Faculty of Science and Mathematics, Arizona State University, Mesa, Arizona, 85212, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, School of Biology, and Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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