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Guo Y, Cheng S, Fang H, Geng J, Li Y, Shi F, Wang H, Chen L, Zhou Y. Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135626. [PMID: 39197279 DOI: 10.1016/j.jhazmat.2024.135626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/27/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.
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Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulan Cheng
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an 343000, China.
| | - Jing Geng
- School of Geospatial Engineering and Science, Sun Yat-sen University, Zhuhai 519082, China
| | - Yuna Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Chen
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhou
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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Ferrando L, Rariz G, Martínez-Pereyra A, Fernández-Scavino A. Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties. J Appl Microbiol 2024; 135:lxae157. [PMID: 38925647 DOI: 10.1093/jambio/lxae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIM Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Affiliation(s)
- Lucía Ferrando
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Gastón Rariz
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Andrea Martínez-Pereyra
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
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3
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Liu C, Tian J, Chen L, He Q, Liu X, Bian R, Zheng J, Cheng K, Xia S, Zhang X, Wu J, Li L, Joseph S, Pan G. Biochar boosted high oleic peanut production with enhanced root development and biological N fixation by diazotrophs in a sand-loamy Primisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173061. [PMID: 38723970 DOI: 10.1016/j.scitotenv.2024.173061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Peanut yield and quality face significant threats due to climate change and soil degradation. The potential of biochar technology to address this challenge remains unanswered, though biochar is acknowledged for its capacity to enhance the soil microbial community and plant nitrogen (N) supply. A field study was conducted in 2021 on oil peanuts grown in a sand-loamy Primisol that received organic amendments at 20 Mg ha-1. The treatments consisted of biochar amendments derived from poultry manure (PB), rice husk (RB), and maize residue (MB), as well as manure compost (OM) amendment, compared to no organic amendment (CK). In 2022, during the second year after amendment, samples of bulk topsoil, rooted soil, and plants were collected at the peanut harvest. The analysis included the assessment of soil quality, peanut growth traits, microbial community, nifH gene abundance, and biological N fixation (BNF) rate. Compared to the CK, the OM treatment led to an 8 % increase in peanut kernel yield, but had no effect on kernel quality in terms of oil production. Conversely, both PB and MB treatments increased kernel yield by 10 %, whereas RB treatment showed no change in yield. Moreover, all biochar amendments significantly improved oilseed quality by 10-25 %, notably increasing the proportion of oleic acid by up to 70 %. Similarly, while OM amendment slightly decreased root development, all biochar treatments significantly enhanced root development by over 80 %. Furthermore, nodule number, fresh weight per plant, and the nifH gene abundance in rooted soil remained unchanged under OM and PB treatments but was significantly enhanced under RB and MB treatments compared to CK. Notably, all biochar amendments, excluding OM, increased the BNF rate and N-acetyl-glucosaminidase activity. These changes were attributed to alterations in soil aggregation, moisture retention, and phosphorus availability, which were influenced by the diverse physical and chemical properties of biochars. Overall, maize residue biochar contributed synergistically to enhancing soil fertility, peanut yield, and quality while also promoting increased root development, a shift in the diazotrophic community and BNF.
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Affiliation(s)
- Cheng Liu
- Institute of Eco-environmental Research, Zhejiang University of Science and Technology, Hangzhou 310023, Zhejiang, China; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Hangzhou 310023, Zhejiang, China; Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jing Tian
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Lei Chen
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Qunling He
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Rongjun Bian
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shaopan Xia
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jihua Wu
- Institute of Cash Crop, Shangqiu Academy of Agriculture and Forest Sciences, Shangqiu 476002, Henan, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Stephen Joseph
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; School of Materials Science and Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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Cao W, Zhao J, Cai Y, Mo Y, Ma J, Zhang G, Jiang X, Jia Z. Ridge with no-tillage facilitates microbial N 2 fixation associated with methane oxidation in rice soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171172. [PMID: 38402982 DOI: 10.1016/j.scitotenv.2024.171172] [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: 12/16/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.
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Affiliation(s)
- Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, USA
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yongliang Mo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637002, PR China
| | - Jingjing Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xianjun Jiang
- College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China.
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5
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Liu M, Xue R, Han N, Yang S, Wang D, Hu Y, Gu K, Su J. The impact of different preceding crops on soil nitrogen structure and nitrogen cycling in tobacco-planting soil. Sci Rep 2024; 14:1767. [PMID: 38243087 PMCID: PMC10799046 DOI: 10.1038/s41598-024-52285-z] [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: 10/07/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
Soil nitrogen content, structure, and nitrogen cycling play a crucial role in tobacco growth quality, with different preceding crops having varying impacts on tobacco cultivation soil. This study conducted using field experiments, employed three treatments with different preceding crops, namely tobacco, barley, and rapeseed, to investigate the effects of different preceding crops on soil nitrogen structure and the expression levels of soil nitrogen cycling-related functional genes in tobacco cultivation soil. The results indicated that different preceding crops had varying effects on the content of different nitrogen forms in tobacco cultivation soil. Ammonium nitrogen and nitrate nitrogen were the two nitrogen forms which were most influenced by preceding crops, with the ammonium nitrogen content in soils following barley and rapeseed preceding crops increasing by 82.88% and 63.56%, respectively, compared to sole tobacco cultivation. The nitrate nitrogen content in tobacco cultivation soil was 26.97% higher following barley preceding crops and 24.39% higher following rapeseed preceding crops compared to sole tobacco cultivation. Simultaneously, different preceding crops also affected the expression levels of nitrogen cycling-related genes in tobacco cultivation soil. In the nitrification process, amoA was significantly impacted, with its expression reduced by 64.39% and 72.24% following barley and rapeseed preceding crops, respectively, compared to sole tobacco cultivation. In the denitrification process, except for the narG gene, all other genes were subjected to varying degrees of inhibition when preceded by barley and rapeseed crops. Correlation analysis between soil nitrogen structure and the expression levels of nitrogen cycling-related genes revealed that increased nitrogen levels suppressed the expression of Arch-amoA. Additionally, ammonium nitrogen strongly influenced the expression levels of most soil nitrogen cycling functional genes. In conclusion, preceding crops alter soil nitrogen structure, possibly due to changes in soil microorganisms, and different preceding crops modified the expression levels of nitrogen cycling-related genes in tobacco cultivation soil, consequently affecting the proportions of various nitrogen forms in the soil.
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Affiliation(s)
- Ming Liu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Rujun Xue
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Ningbo Han
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Shanqin Yang
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Dexun Wang
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Yanxia Hu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Kaiyuan Gu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Jiaen Su
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China.
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Chen Q, Long C, Bao Y, Men X, Zhang Y, Cheng X. The dominant genera of nitrogenase (nifH) affects soil biological nitrogen fixation along an elevational gradient in the Hengduan mountains. CHEMOSPHERE 2024; 347:140722. [PMID: 37972867 DOI: 10.1016/j.chemosphere.2023.140722] [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: 09/04/2023] [Revised: 11/01/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Biological nitrogen (N) fixation by diazotrophic microbes is an essential process for the N input. However, the patterns of biological N fixation and its biological or environmental mechanism along an elevational gradient in mountain ecosystems are not fully understood. In this study, a field experiment was conducted in the Hengduan Mountains to investigate the biological N fixation associated with the diversity and abundance of the nifH gene. Our results showed that both the abundance of the nifH gene and the biological N fixation displayed hump-shaped trends along an elevation gradient in the wet and dry seasons. However, the diversity of the nifH gene showed an inverse unimodal trend along an elevation gradient. We observed that biological N fixation was jointly associated with the abundance of the nifH gene, especially dominant genera, as well as soil chartacteristics. Among them, clay content played a preeminent role in the regulation of N fixation potentially through the formation of microaggregates and microenvironments. In general, our results revealed that biological N fixation was correlated with the abundance of microorganisms, especially dominant genera, and soil texture. These results highlighted the importance of dominant genera, which should be considered in the modeling and forecasting of N cycling under future environmental change.
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Affiliation(s)
- Qiong Chen
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Chunyan Long
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Yong Bao
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Xiuxian Men
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Yong Zhang
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China
| | - Xiaoli Cheng
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, PR China.
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7
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Yu T, Nie J, Zang H, Zeng Z, Yang Y. Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield. MICROBIAL ECOLOGY 2023; 86:2447-2460. [PMID: 37296336 DOI: 10.1007/s00248-023-02254-2] [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: 12/22/2022] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.
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Affiliation(s)
- Taobing Yu
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Jiangwen Nie
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Huadong Zang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhaohai Zeng
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yadong Yang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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8
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Gruet C, Abrouk D, Börner A, Muller D, Moënne-Loccoz Y. Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere. PLANT, CELL & ENVIRONMENT 2023; 46:1018-1032. [PMID: 36494920 DOI: 10.1111/pce.14508] [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: 08/07/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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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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11
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Zhao Z, Zhang Y, Sun P, Wang Q, Ruan Y. Effects of biochar and chemical fertilizer amendment on diazotrophic abundance and community structure in rhizosphere and bulk soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62361-62370. [PMID: 35397032 DOI: 10.1007/s11356-022-20086-4] [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: 02/10/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Diazotrophs carry out biological nitrogen (N) fixation process that replenishes available soil N; it is unclear how soil diazotrophic communities respond to biochar and chemical fertilizer amendment in agricultural ecosystem. Herein, we studied the impacts of biochar and chemical fertilizer amendment on diazotrophic communities in rhizosphere and bulk soils using nifH gene. The field experiment included four treatments: control (CK), biochar (B), chemical NPK fertilizer (CF), and biochar + chemical fertilizer (B + CF). nifH gene abundance in rhizosphere soils ranged from 9.00 × 107 to 2.57 × 108 copies g-1 dry soil among the different treatments, which was 1.42-2.68 times higher compared with the bulk soils ranging from 5.83 × 107 to 1.19 × 108 copies g-1 dry soil. Single application of biochar increased the abundance of nifH gene, whereas chemical fertilizer addition significantly decreased it in the bulk and rhizosphere soils. Single biochar addition affected diazotrophic community composition in rhizosphere soil, but not in the bulk soil. However, both CF and B + CF treatments obviously changed the community structure of diazotrophs in both soils. Moreover, rhizosphere effect enhanced nifH gene abundance and significantly altered the diazotrophic community structure compared to bulk soil. Phylogenetic analysis showed that all nifH sequences were affiliated to the cyanobacteria, α-, β-, γ-, and δ- subclasses of the proteobacteria group. Soil nutrient availability rather than pH had significant impacts on diazotrophic community structure based on mantel test and redundancy analysis. Overall, biochar improves the diazotrophic abundance, while chemical fertilization negatively affects it by altering nutrient availability, and combined application of biochar and chemical fertilizer does not counteract the adverse influences of chemical fertilizer on nitrogen-fixing microorganisms.
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Affiliation(s)
- Ziting Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yanshu Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Ping Sun
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Qing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
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12
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Arshad M, Naqqash T, Tahir M, Leveau JH, Zaheer A, Tahira SA, Saeed NA, Asad S, Sajjad M. Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.). J Appl Microbiol 2022; 133:3094-3112. [PMID: 35908279 DOI: 10.1111/jam.15751] [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: 05/08/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022]
Abstract
AIMS Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions. METHODS AND RESULTS The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere. CONCLUSION We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants. SIGNIFICANCE OF THE STUDY The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.
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Affiliation(s)
- Muhammad Arshad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Tahir
- Department of Environmental Science, COMSATS University Islamabad, Vehari
| | - Johan H Leveau
- Department of Plant Pathology, One Shield's Avenue, University of California Davis, CA, USA
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | | | - Nasir Ahmad Saeed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Shaheen Asad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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14
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Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains. SUSTAINABILITY 2022. [DOI: 10.3390/su14137910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clarifying the response of soil microbial communities to the change of different vegetation types on a small regional scale is of great significance for understanding the sustainability of grassland development. However, the distribution patterns and driving factors of the microbial community are not well understood in the Qilian Mountains. Therefore, we characterized and compared the soil microbial communities underlying the four vegetation types in a national natural reserve (reseeded grassland, swamp meadow, steppe meadow, and cultivated grassland) using high-throughput sequencing of the 16S rRNA and ITS. Meanwhile, the plant community and soil physicochemical characteristics were also determined. The results showed that bacterial and fungal communities in all vegetation types had the same dominant species, but the relative abundance differed substantially, which caused significant spatial heterogeneities on the small regional scale. Specifically, bacteria showed higher variability among different vegetation types than fungi, among which the bacterial and fungal communities were more sensitive to the changes in soil than to plant characteristics. Furthermore, soil organic carbon affected the widest portion of the microbial community, nitrate-nitrogen was the main factor affecting bacteria, and aboveground plant biomass was the main factor affecting fungi. Collectively, these results demonstrate the value of considering multiple small regional spatial scales when studying the relationship between the soil microbial community and environmental characteristics. Our study may have important implications for grassland management following natural disturbances or human alterations.
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15
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Liu H, Li Y, Pan B, Zheng X, Yu J, Ding H, Zhang Y. Pathways of soil N 2O uptake, consumption, and its driving factors: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:30850-30864. [PMID: 35092587 DOI: 10.1007/s11356-022-18619-y] [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: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N2O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N2O uptake and consumption. N2O emissions at the soil surface are the result of gross N2O production, uptake, and consumption, which are co-occurring processes. Soil N2O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N2O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N2O uptake and consumption and their driving factors and measurement techniques. This systematic review of N2O uptake and consumption will help to further understand N transformations and soil N2O emissions.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China.
| | - Baobao Pan
- School of Agriculture and Food, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China.
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16
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Sun X, Zhang X, Xia Y, Tao R, Zhang M, Mei Y, Qu M. Simulation of the effects of microplastics on the microbial community structure and nitrogen cycle of paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151768. [PMID: 34808183 DOI: 10.1016/j.scitotenv.2021.151768] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/07/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Microplastics (MPs) are ubiquitous in farmland soils. However, few studies have evaluated their effects on the microbial community structure and nitrogen cycle of farmland soils. Here, 0.3% and 1% (mass percentage) of polyethylene terephthalate (PET), polyvinyl chloride (PVC), and polylactic acid (PLA) MPs were added to paddy soil to evaluate their impact on the paddy soil microenvironment. The alpha index of the PLA MP treatment was significantly different from that of the control group (p-value < 0.05). In contrast, the indices of the PET and PVC MP treatments were not different from the control (p-value > 0.05). Among the MP treatments, the alpha index of the PLA MP group was significantly different from the PET and PVC MP groups (p-value < 0.05). PCoA analysis also indicated that there were differences between PLA and other MP groups, and different MP concentrations and exposure times had a great impact on microbial composition. The three MPs affected NH4+ metabolism by changing the abundance of a NH2OH-forming gene (amoA) and an organic nitrogen-forming gene (gdh), as well as the abundances of Thiobacillus, Bradyrhizobium, Anaeromyxobacter, Geobacter, and Desulfobacca. Further, the MPs affected NO3- metabolism by regulating the abundance of the nirS and nirK genes and the abundance of Nitrospirae. In contrast, NO2- metabolism was not significantly affected by the MPs due to the low concentration of NO2-, which was attributed to the high abundance of nirS and nirK in the sample. Taken together, our findings indicated that MP addition may have an inhibitory effect on the nitrogen cycle in paddy soils and that the effect of degradable MPs may be greater than that of their non-degradable counterparts. Given the increasing severity of worldwide MP contamination, additional studies are required to assess their impact on global ecosystems and biogeochemical cycles.
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Affiliation(s)
- Xia Sun
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiaoying Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuxiang Xia
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Ruidong Tao
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Meng Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yunjun Mei
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Mengjie Qu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
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Longepierre M, Feola Conz R, Barthel M, Bru D, Philippot L, Six J, Hartmann M. Mixed Effects of Soil Compaction on the Nitrogen Cycle Under Pea and Wheat. Front Microbiol 2022; 12:822487. [PMID: 35330614 PMCID: PMC8940171 DOI: 10.3389/fmicb.2021.822487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Soil compaction caused by highly mechanized agriculture can constrain soil microbial diversity and functioning. Physical pressure on the soil decreases macropores and thereby limits oxygen diffusion. The associated shift from aerobic to anaerobic conditions can reduce nitrification and promote denitrification processes, leading to nitrogen (N) losses and N depletion that affect plant productivity. High soil moisture content during trafficking can exacerbate the negative effects of soil compaction. However, the extent to which soil moisture amplifies the effects of compaction on the soil microbiome and its control over N cycling is not well understood. Using a controlled greenhouse experiment with two different crops (pea and wheat), we compared the effects of compaction at three different soil moisture levels on soil physicochemical properties, microbial diversity, and the abundance of specific N species and quantification of associated microbial functional groups in the N cycle. Soil compaction increased bulk density from 15% (light compaction) to 25% (severe compaction). Compaction delayed germination in both crops and reduced yield by up to 60% for pea and 40% for wheat. Compaction further induced crop-specific shifts in microbial community structures. After compaction, the relative abundance of denitrifiers increased along with increased nitrate (NO3 -) consumption and elevated nitrous oxide (N2O) concentrations in the soil pores. Conversely, the relative abundance of nitrifiers remained stable under compaction, but potentially decelerated nitrification rates, resulting in ammonium (NH4 +) accumulation in the soil. This study showed that soil compaction effects are proportional to the initial soil moisture content, which could serve as a good indicator of compaction severity on agricultural fields. However, the impact of soil compaction on crop performance and on microbial communities and functions associated with the N cycle were not necessarily aligned. These findings demonstrate that not only the soil physical properties but also various biological indicators need to be considered in order to provide more precise recommendations for developing sustainable farming systems.
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Affiliation(s)
- Manon Longepierre
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Matti Barthel
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - David Bru
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Johan Six
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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Low Frequency of Plants Associated with Symbiotic Nitrogen-Fixers Exhibits High Frequency of Free-Living Nitrogen Fixing Bacteria: A Study in Karst Shrub Ecosystems of Southwest China. FORESTS 2022. [DOI: 10.3390/f13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plants associated with symbiotic nitrogen-fixers and soil free-living nitrogen-fixing bacteria are good indicators for detecting the source of nitrogen in natural ecosystems. However, the community composition and diversity of plants associated with symbiotic nitrogen-fixers and soil free-living nitrogen-fixing bacteria in karst shrub ecosystems remain poorly known. The community composition and diversity of soil free-living nitrogen-fixing bacteria and plants, as well as the soil physical–chemical properties were investigated in 21 shrub plots (including different topographies and plant types). The frequency of plants associated with symbiotic nitrogen-fixers was found to be low in the 21 shrub plots. The soil free-living nitrogen-fixing bacterial community structure varied among the 21 shrub soils. Based on a variance partitioning analysis, topography, plant type, and soil pH explained 48.5% of the observed variation in bacterial community structure. Plant type had a predominant effect on community structure, and topography (aspect and ascent) and soil pH had minor effects. A negative correlation between the abundance of the soil free-living nitrogen-fixing bacterial community and the richness index for plants associated with symbiotic nitrogen-fixers was observed. The result of the low frequency of plants associated with symbiotic nitrogen-fixers highlights the importance of sources of fixed nitrogen by soil free-living nitrogen-fixing bacteria in the nitrogen limitation shrub ecosystem of the karst regions.
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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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Wang H, Li X, Li X, Li F, Su Z, Zhang H. Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China. MICROBIAL ECOLOGY 2021; 82:961-970. [PMID: 33660069 DOI: 10.1007/s00248-021-01716-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.
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Affiliation(s)
- Huanhuan Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China.
| | - Fuli Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
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21
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Sneha GR, Swarnalakshmi K, Sharma M, Reddy K, Bhoumik A, Suman A, Kannepalli A. Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere. World J Microbiol Biotechnol 2021; 37:167. [PMID: 34468874 DOI: 10.1007/s11274-021-03132-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.
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Affiliation(s)
- G R Sneha
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Meenakshi Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kedharnath Reddy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arpan Bhoumik
- ICAR-IndianAgricultural Statistical Research Institute, New Delhi, 110012, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Annapurna Kannepalli
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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22
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Chen S, Xiang X, Ma H, Penttinen P, Zhao J, Li H, Gao R, Zheng T, Fan G. Straw Mulching and Nitrogen Fertilization Affect Diazotroph Communities in Wheat Rhizosphere. Front Microbiol 2021; 12:658668. [PMID: 34093473 PMCID: PMC8175977 DOI: 10.3389/fmicb.2021.658668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/09/2021] [Indexed: 11/30/2022] Open
Abstract
Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N2) replenish biologically available nitrogen (N) in soil and are influenced by the input of inorganic and organic substrates. To date, little is known about the effects of combined organic substrate addition and N fertilization on the diazotroph community composition and structure in purple soils. We investigated the effects of N fertilization and straw mulching on diazotroph communities by quantifying and sequencing the nifH gene in wheat rhizosphere. The abundance and richness of diazotrophs were greater the higher the fertilization level in the mulched treatments, whereas in the nonmulched treatments (NSMs), richness was lowest with the highest N fertilization level. The abundance and α-diversity of diazotrophs correlated with most of the soil properties but not with pH. At the genus level, the relative abundances of Azospirillum, Bacillus, and Geobacter were higher in the NSMs and those of Pseudacidovorax, Skermanella, Azospira, Paraburkholderia, Azotobacter, Desulfovibrio, Klebsiella, and Pelomonas in the mulched treatments. The differences in community composition between the mulched and the NSMs were associated with differences in soil temperature and soil organic carbon and available potassium contents and C:N ratio. Overall, straw mulching and N fertilization were associated with changes in diazotroph community composition and higher abundance of nifH gene in alkaline purple soils.
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Affiliation(s)
- Songhe Chen
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Xiang
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Hongliang Ma
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jiarong Zhao
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Han Li
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Rencai Gao
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Ting Zheng
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Gaoqiong Fan
- Key Laboratory of Crop Eco-Physiology and farming system in Southwest China, Ministry of Agriculture, College of Agronomy, Sichuan Agricultural University, Chengdu, China
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23
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Li Y, Li T, Zhao D, Wang Z, Liao Y. Different tillage practices change assembly, composition, and co-occurrence patterns of wheat rhizosphere diazotrophs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144252. [PMID: 33429279 DOI: 10.1016/j.scitotenv.2020.144252] [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: 09/27/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Tillage has a considerable effect on the soil ecosystem and its services, including microbial communities. Harnessing beneficial microbes is a sustainable way to optimizing crop management and agricultural production. Although diazotrophs play a major role in global biological nitrogen fixation, the effects of tillage on diazotrophic communities in the rhizosphere are not fully understood. In the present study, we investigated the diazotrophic community in wheat rhizosphere soil under different tillage treatments in a long-term experiment, i.e., plow tillage (considered as conventional tillage), chisel plow tillage (considered as conservation tillage), and zero tillage (considered as conservation tillage). Tillage led to a divergent distribution in the rhizosphere diazotrophic community and significant changes in community structure. Tillage caused specific responses from members/modules of the rhizosphere diazotrophic community co-occurrence network, and the relative abundance of keystone taxa was higher under conservation tillage than under conventional tillage. The increased abundance of tillage-sensitive modules under conservation tillage had a broad and significant positive correlation with rhizosphere nutrient availability, whereas the opposite was true for conventional tillage. Differences in nutrients under different tillage practices may lead to different assembly processes of diazotrophs. Overall, our findings indicate that tillage significantly affects the assembly and composition of the rhizosphere diazotrophic community, emphasizing the importance of improved substrate availability for rhizosphere diazotrophic modules under conservation tillage. This knowledge could deepen our understanding of the rhizosphere functional microbial community (e.g., biological nitrogen fixation).
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Affiliation(s)
- Yüze Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Tong Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Deqiang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi 530004, PR China; College of Agronomy, Guangxi University, Nanning, Guangxi 530004, PR China.
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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24
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Chen H, Zheng C, Qiao Y, Du S, Li W, Zhang X, Zhao Z, Cao C, Zhang W. Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142441. [PMID: 33097271 DOI: 10.1016/j.scitotenv.2020.142441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.
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Affiliation(s)
- Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqiang Qiao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shizhou Du
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wei Li
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiangqian Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhu Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chengfu Cao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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25
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Hakim S, Naqqash T, Nawaz MS, Laraib I, Siddique MJ, Zia R, Mirza MS, Imran A. Rhizosphere Engineering With Plant Growth-Promoting Microorganisms for Agriculture and Ecological Sustainability. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.617157] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The rhizosphere is undoubtedly the most complex microhabitat, comprised of an integrated network of plant roots, soil, and a diverse consortium of bacteria, fungi, eukaryotes, and archaea. The rhizosphere conditions have a direct impact on crop growth and yield. Nutrient-rich rhizosphere environments stimulate plant growth and yield and vice versa. Extensive cultivation exhaust most of the soils which need to be nurtured before or during the next crop. Chemical fertilizers are the major source of crop nutrients but their uncontrolled and widespread usage has posed a serious threat to the sustainability of agriculture and stability of an ecosystem. These chemicals are accumulated in the soil, drained in water, and emitted to the air where they persist for decades causing a serious threat to the overall ecosystem. Plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere convert many plant-unavailable essential nutrients e.g., nitrogen, phosphorous, zinc, etc. into available forms. PGPR produces certain plant growth hormones (such as auxin, cytokinin, and gibberellin), cell lytic enzymes (chitinase, protease, hydrolases, etc.), secondary metabolites, and antibiotics, and stress alleviating compounds (e.g., 1-Aminocyclopropane-1- carboxylate deaminase), chelating agents (siderophores), and some signaling compounds (e.g., N-Acyl homoserine lactones) to interact with the beneficial or pathogenic counterparts in the rhizosphere. These multifarious activities of PGPR improve the soil structure, health, fertility, and functioning which directly or indirectly support plant growth under normal and stressed environments. Rhizosphere engineering with these PGPR has a wide-ranging application not only for crop fertilization but developing eco-friendly sustainable agriculture. Due to severe climate change effects on plants and rhizosphere biology, there is growing interest in stress-resilient PGPM and their subsequent application to induce stress (drought, salinity, and heat) tolerance mechanism in plants. This review describes the three components of rhizosphere engineering with an explicit focus on the broader perspective of PGPM that could facilitate rhizosphere engineering in selected hosts to serve as an efficient component for sustainable agriculture.
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26
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Kapili BJ, Dekas AE. PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics 2021; 37:2289-2298. [PMID: 33580675 DOI: 10.1093/bioinformatics/btab100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. RESULTS We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. AVAILABILITY PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
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27
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Xi B, Yu H, Li Y, Dang Q, Tan W, Wang Y, Cui D. Insights into the effects of heavy metal pressure driven by long-term treated wastewater irrigation on bacterial communities and nitrogen-transforming genes along vertical soil profiles. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123853. [PMID: 33264929 DOI: 10.1016/j.jhazmat.2020.123853] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 06/12/2023]
Abstract
Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss.
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Affiliation(s)
- Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hong Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yanping Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yan Wang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China
| | - Dongyu Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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28
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Zhang C, Cao K, Li Y, Zhao J, Peng W, Cao H, Xiao X. Long-term nitrogen fertilization shaped the nifH, nirK, and nosZ gene community patterns in red paddy soil in south China. Can J Microbiol 2020; 67:310-322. [PMID: 33022188 DOI: 10.1139/cjm-2020-0300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To understand the diversities of diazotrophs and denitrifiers in red paddy soil under long-term fertilization conditions, nifH, nirK, and nosZ libraries were constructed by PCR-RFLP. nirK gene diversity proved to be lower than that of nosZ and nifH, and nirK and nosZ genes were more sensitive to different fertilization treatments than the nifH gene was. The 3 libraries were dominated by diverse microbes, including the Alpha, Beta, Gamma, and Delta subclasses of the Proteobacteria. Long-term addition of urea with straw mulch and azophoska increased the abundance of nonsymbiotic diazotrophs, which indicated that nonsymbiotic diazotrophs were responsible for the majority of the nitrogen-fixing ability in paddy soil. In addition, a potential link between nifH and nosZ was found due to the existence of nitrogen fixers, such as Bradyrhizobium and Ralstonia, in the nosZ library. The main chemical factors affecting the 3 genes were identified: pH was the most important factor of the nifH community; the nirK gene was more affected by pH and organic matter; available potassium and the carbon-to-nitrogen ratio significantly influenced the community structure of the nosZ gene.
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Affiliation(s)
- Cunzhi Zhang
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixun Cao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, Anhui 233100, China
| | - Yue Li
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Juan Zhao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wentao Peng
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xin Xiao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, Anhui 233100, China
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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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Diazotrophic Anaeromyxobacter Isolates from Soils. Appl Environ Microbiol 2020; 86:AEM.00956-20. [PMID: 32532868 DOI: 10.1128/aem.00956-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/04/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium.IMPORTANCE Anaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.
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Solanki MK, Wang Z, Wang FY, Li CN, Gupta CL, Singh RK, Malviya MK, Singh P, Yang LT, Li YR. Assessment of Diazotrophic Proteobacteria in Sugarcane Rhizosphere When Intercropped With Legumes (Peanut and Soybean) in the Field. Front Microbiol 2020; 11:1814. [PMID: 32849421 PMCID: PMC7412970 DOI: 10.3389/fmicb.2020.01814] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/10/2020] [Indexed: 12/20/2022] Open
Abstract
Several factors influenced the sugarcane production, and among them, higher use of nitrogen and depletion of soil nutrient constitutes a significant concern in China. Sugarcane-legume intercropping may help to regulate the microbial structure and functions. In the present study, sugarcane rhizosphere soils of three cropping systems: Sugarcane only (S-only), sugarcane with peanut (S + P), and sugarcane + soybean (S + S) were sampled in tillering, elongation, and maturation stages from two different experimental fields. High-throughput sequencing technologies applied to assess the effects of different cropping systems on the structure of nitrogenase (nifH) gene communities. A total of 3818 OTUs (operational taxonomic units) were acquired from all soil samples. Intercropping systems noticeably increased the relative abundance of Proteobacteria in the tillering stage. The increased microbial diversity in the rhizosphere was mainly due to soil organic carbon and total soil N. In contrast, intercropping has no significant negative impact on microbial abundance, but sugarcane growth stages influence it significantly, and two bacteria (Bradyrhizobium and Pseudacidovorax) showed significant shift during plant growth. The results provide insight into the microbial structure of Proteobacteria in the sugarcane legume-intercropping field, and how microbial community behaves in different growth stages. It can boost the microbial activity of the soil, and that could be a new strategy to stimulate soil fertility without causing any negative impact on crop production.
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Affiliation(s)
- Manoj Kumar Solanki
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Zhen Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Fei-Yong Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chang-Ning Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chhedi Lal Gupta
- The Volcani Center, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Rajesh Kumar Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh Kumar Malviya
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Pratiksha Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Yang-Rui Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
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Ji C, Liu Z, Hao L, Song X, Wang C, Liu Y, Li H, Li C, Gao Q, Liu X. Effects of Enterobacter cloacae HG-1 on the Nitrogen-Fixing Community Structure of Wheat Rhizosphere Soil and on Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:1094. [PMID: 32765571 PMCID: PMC7380250 DOI: 10.3389/fpls.2020.01094] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/03/2020] [Indexed: 05/19/2023]
Abstract
The present study investigated the physiological and biochemical characteristics of Enterobacter cloacae HG-1 isolated from saline-alkali soil. We further studied the effect of this strain on the salt tolerance of wheat and on the community structure of nitrogen-fixing bacteria in rhizosphere soil. We determined that the investigated strain had high nitrogen fixation activity and produced iron carriers, 1-aminocyclopropane-1-carboxylic acid deaminase, and plant hormones. The metabolites of this strain contained 2,3-butanediol, [R-(R*, R*)], 2-heptanone, and other growth-promoting and antibacterial substances. The strain was also highly salt-tolerant (10% NaCl). After the inoculation of wheat with the HG-1 strain, we recorded increases in root length, plant height, fresh weight, and dry weight of 19.15%, 18.83%, 16.67%, and 17.96%, respectively, compared with uninoculated plants (P < 0.05). Compared with the leaves of uninoculated plants, the proline concentration in the leaves of inoculated plants increased by 12.43% (P < 0.05), the malondialdehyde level decreased by 27.26% (P < 0.05), K+ increased by 20.69%, Ca2+ increased by 57.53% and Na+ decreased by 31.43% (all P<0.05). Furthermore, we detected that inoculation with the HG-1 strain did not affect the species composition of nitrogen-fixing bacteria in wheat rhizosphere soil at the phylum level. However, the average relative abundance of Proteobacteria was significantly increased, whereas the abundance of Verrucomiorobia was significantly decreased compared with uninoculated plants. At the genus level, we detected 32 genera in control samples and 27 genera in inoculated samples, and the species diversity and relative abundance of samples inoculated with the HG-1 strain decreased compared with uninoculated plants. Inoculated samples had lower abundances of Azospirillum, Rhodomicrobium, and Anabaena. Our study demonstrated that the inoculation of wheat with E. cloacae HG-1 could promote the growth of wheat under salt stress and increase salt stress tolerance. The results of this study investigating the interaction among soil, plants, and microorganisms supplement agricultural microbial databases and could provide a reference for the development of microbial-based saline soil improvement programs.
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Affiliation(s)
- Chao Ji
- College of Forestry, Shandong Agriculture University, Taian, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, China
| | - Zhaoyang Liu
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Liping Hao
- College of Plant Conservation, Shandong Agriculture University, Taian, China
| | - Xin Song
- College of Forestry, Shandong Agriculture University, Taian, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, China
| | - Changdong Wang
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Yue Liu
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Huying Li
- College of Forestry, Shandong Agriculture University, Taian, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, China
| | - Chaohui Li
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Qixiong Gao
- College of Forestry, Shandong Agriculture University, Taian, China
| | - Xunli Liu
- College of Forestry, Shandong Agriculture University, Taian, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, China
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Zou J, Yao Q, Liu J, Li Y, Song F, Liu X, Wang G. Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China. PeerJ 2020; 8:e9550. [PMID: 32742810 PMCID: PMC7368428 DOI: 10.7717/peerj.9550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/24/2020] [Indexed: 11/20/2022] Open
Abstract
Nitrogen-fixing microorganisms play important roles in N cycling. However, knowledge related to the changes in the diazotrophic community in response to cropping systems is still rudimentary. In this study, the nifH gene was used to reveal the abundance and community compositions of diazotrophs in the cropping systems of continuous cropping of corn (CC) and soybean (SS) and soybean-corn rotation for growing corn (CSC) and soybean (SCS) in a black soil of Northeast China. The results showed that the abundance of the nifH gene was significantly higher in cropping soybean than in cropping corn under the same cropping system, while remarkably increased in the rotation system under the same crop. The Shannon index in the CC treatment was significantly higher than that in the other treatments, but the OTU number and Chao1 index had no significant change among the four treatments. Bradyrhizobium japonicum was the dominant diazotrophic species, and its relative abundance was at the lowest value in the CC treatment. In contrast, Skermanella sp. had the highest relative abundance in the CC treatment. A PCoA showed that the diazotrophic communities were separated between different cropping systems, and the variation caused by continuous corn cropping was the largest. Among the tested soil properties, the soil available phosphorus was a primary factor in determining diazotrophic community compositions. Overall, the findings of this study highlighted that the diazotrophic communities in black soils are very sensitive to cropping systems.
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Affiliation(s)
- Jiaxun Zou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.,College of Life Science, Heilongjiang University, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yansheng Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Fuqiang Song
- College of Life Science, Heilongjiang University, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Hu X, Liang A, Yao Q, Liu Z, Yu Z, Wang G, Liu J. Ridge Tillage Improves Soil Properties, Sustains Diazotrophic Communities, and Enhances Extensively Cooperative Interactions Among Diazotrophs in a Clay Loam Soil. Front Microbiol 2020; 11:1333. [PMID: 32714293 PMCID: PMC7344147 DOI: 10.3389/fmicb.2020.01333] [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: 02/24/2020] [Accepted: 05/25/2020] [Indexed: 12/30/2022] Open
Abstract
Reduced tillage practices [such as ridge tillage (RT)] have been potential solutions to the weed pressures of long-term no tillage (NT) and the soil-intensive disturbances caused by conventional tillage [such as moldboard plow (MP) tillage]. Although soil diazotrophs are significantly important in global nitrogen (N) cycling and contribute to the pool of plant-available N in agroecosystems, little is currently known about the responses of diazotrophic communities to different long-term tillage practices. In the current study, we investigated the differences among the effects of NT, RT, and MP on soil properties, diazotrophic communities, and co-occurrence network patterns in bulk and rhizosphere soils under soybean grown in clay loam soil of Northeast China. The results showed that RT and MP led to higher contents of total C, N, and available K compared to NT in both bulk and rhizosphere soils, and RT resulted in higher soybean yield than NT and MP. Compared to NT and RT, MP decreased the relative abundances of free-living diazotrophs, while it promoted the growth of copiotrophic diazotrophs. Little differences of diazotrophic community diversity, composition, and community structure were detected between RT and NT, but MP obviously decreased diazotrophic diversity and changed the diazotrophic communities in contrast to NT and RT in bulk soils. Soil nitrogenous nutrients had negative correlations with diazotrophic diversity and significantly influenced the diazotrophic community structure. Across all diazotrophs' networks, the major diazotrophic interactions transformed into a cooperatively dominated network under RT, with more intense and efficient interactions among species than NT and MP. Overall, our study suggested that RT, with minor soil disturbances, could stabilize diazotrophic diversity and communities as NT and possessed highly positive interactions among diazotrophic species relative to NT and MP.
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Affiliation(s)
- Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Aizhen Liang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhuxiu Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry. mSystems 2020; 5:5/3/e00162-20. [PMID: 32606023 PMCID: PMC7329320 DOI: 10.1128/msystems.00162-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To be effective in predicting future stability of soil functions in the context of various external disturbances, it is necessary to follow the effects of global change on functionally specialized microbes related to C and nutrient cycling. Our study represents an exploratory effort to couple the stoichiometric drivers to microbial populations related with main C, N, and P cycling and their resistances to global change. The abundance of microbial groups involved in cellulose, starch, and xylan degradation, nitrification, N fixation, denitrification, organic P mineralization, and inorganic P dissolution showed a high stoichiometry dependency. Resistance of these microbial populations to global change could be predicted by soil C:N:P stoichiometry. Our work highlights that stoichiometric balance in soil C and nutrients is instrumental in maintaining the stability and adaptability of ecosystem functions under global change. Maintaining stability of ecosystem functions in the face of global change calls for a better understanding regulatory factors of functionally specialized microbial groups and their population response to disturbance. In this study, we explored this issue by collecting soils from 54 managed ecosystems in China and conducting a microcosm experiment to link disturbance, elemental stoichiometry, and genetic resistance. Soil carbon:nitrogen:phosphorus (C:N:P) stoichiometry imparted a greater effect on the abundance of microbial groups associated with main C, N, and P biogeochemical processes in comparison with mean annual temperature and precipitation. Nitrogen cycling genes, including bacterial amoA-b, nirS, narG, and norB, exhibited the highest genetic resistance to N deposition. The amoA-a and nosZ genes exhibited the highest resistance to warming and drying-wetting cycles, respectively. Soil total C, N, and P contents and their ratios had a strong direct effect on the genetic resistance of microbial groups, which was dependent on mean annual temperature and precipitation. Specifically, soil C/P ratio was the main predictor of N cycling genetic resistance to N deposition. Soil total C and N contents and their ratios were the main predictors of P cycling genetic resistance to N deposition, warming, and drying-wetting. Overall, our work highlights the importance of soil stoichiometric balance for maintaining the ability of ecosystem functions to withstand global change. IMPORTANCE To be effective in predicting future stability of soil functions in the context of various external disturbances, it is necessary to follow the effects of global change on functionally specialized microbes related to C and nutrient cycling. Our study represents an exploratory effort to couple the stoichiometric drivers to microbial populations related with main C, N, and P cycling and their resistances to global change. The abundance of microbial groups involved in cellulose, starch, and xylan degradation, nitrification, N fixation, denitrification, organic P mineralization, and inorganic P dissolution showed a high stoichiometry dependency. Resistance of these microbial populations to global change could be predicted by soil C:N:P stoichiometry. Our work highlights that stoichiometric balance in soil C and nutrients is instrumental in maintaining the stability and adaptability of ecosystem functions under global change.
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Han LL, Wang Q, Shen JP, Di HJ, Wang JT, Wei WX, Fang YT, Zhang LM, He JZ. Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China. FEMS Microbiol Ecol 2020; 95:5531308. [PMID: 31295349 DOI: 10.1093/femsec/fiz113] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/10/2019] [Indexed: 11/12/2022] Open
Abstract
Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.
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Affiliation(s)
- Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln 7674, New Zealand
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wen-Xue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Yun-Ting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of the Chinese Academy of Sciences, Beijing 100049, 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 the Chinese Academy of Sciences, Beijing 100049, China.,Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
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Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation. Appl Environ Microbiol 2020; 86:AEM.00195-20. [PMID: 32169937 DOI: 10.1128/aem.00195-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.
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Tu Q, Lin L, Cheng L, Deng Y, He Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 2019; 35:1040-1048. [PMID: 30165481 DOI: 10.1093/bioinformatics/bty741] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/06/2018] [Accepted: 08/23/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families. RESULTS To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways. AVAILABILITY AND IMPLEMENTATION NCycDB database files are available at https://github.com/qichao1984/NCyc. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lei Cheng
- Department of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhili He
- Department of Environmental Science, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Agriculture, College of Agriculture, Hunan Agricultural University, Changsha, China
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Gupta VVSR, Zhang B, Penton CR, Yu J, Tiedje JM. Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil. Front Mol Biosci 2019; 6:115. [PMID: 31750314 PMCID: PMC6848460 DOI: 10.3389/fmolb.2019.00115] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022] Open
Abstract
Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.
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Affiliation(s)
| | - Bangzhou Zhang
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Christopher Ryan Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Julian Yu
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
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Fan K, Delgado-Baquerizo M, Guo X, Wang D, Wu Y, Zhu M, Yu W, Yao H, Zhu YG, Chu H. Suppressed N fixation and diazotrophs after four decades of fertilization. MICROBIOME 2019; 7:143. [PMID: 31672173 PMCID: PMC6824023 DOI: 10.1186/s40168-019-0757-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/02/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization. RESULTS It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp. CONCLUSIONS Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.
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Affiliation(s)
- Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 USA
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, 28933 Móstoles, Spain
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei, 230031 China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei, 230031 China
| | - Yanying Wu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Mo Zhu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Wei Yu
- High School Affiliated to Nanjing Normal University, Nanjing, 210003 China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205 China
| | - Yong-guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
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Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Abstract
With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions. Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.
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Li S, Peng C, Cheng T, Wang C, Guo L, Li D. Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability. J Environ Sci (China) 2019; 76:89-99. [PMID: 30528038 DOI: 10.1016/j.jes.2018.03.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 05/03/2023]
Abstract
Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N2 fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N2 fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.
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Affiliation(s)
- Shuangshuang Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Hebei Engineering Research Center for Water Pollution Control and Water Ecological Remediation, College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Taisheng Cheng
- National University of Tainan, Department of Biological Sciences and Technology, Tainan 70005, China
| | - Chun Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory and State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 10084, China
| | - Liangliang Guo
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Meng H, Zhou Z, Wu R, Wang Y, Gu JD. Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene. Appl Microbiol Biotechnol 2018; 103:995-1005. [PMID: 30474727 DOI: 10.1007/s00253-018-9466-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/17/2018] [Accepted: 10/09/2018] [Indexed: 01/09/2023]
Abstract
Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.
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Affiliation(s)
- Han Meng
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yongfeng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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Ke X, Feng S, Wang J, Lu W, Zhang W, Chen M, Lin M. Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere. Syst Appl Microbiol 2018; 42:248-260. [PMID: 30477902 DOI: 10.1016/j.syapm.2018.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022]
Abstract
Plant growth promoting diazotrophs with the ability to associate with plant roots are in common use as inoculants to benefit crop yield and to mitigate chemical nitrogen fertilization. However, limited information is available in understanding to what extent the plant growth-promoting effect of the inoculum has on the plant's nitrogen acquisition as well as on the impact of inoculation on the indigenous rhizosphere microbial population. Here we reported on experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15N dilution technique under two water regime conditions. The effects of inoculation and different water regimes were also assessed for the maize rhizospheric and surface soil communities by MiSeq community sequencing combined with qPCR of functional genes and transcripts (nifH and amoA) related to nitrogen cycling. Results support maize inoculated with P. stutzeri A1501 grew better and accumulated more nitrogen with a lower δ15N signature after 60 days than did plants inoculated with nifH-mutant and sterilized A1501 cells (non N2-fixing controls). Inoculant contribution to the plant was estimated to range from 0.30 to 0.82g N/plant, depending on water conditions. Inoculation with P. stutzeri A1501 significantly altered the composition of the diazotrophic community that P. stutzeri became dominant in the rhizosphere, and also increased the population of indigenous diazotrophs and ammonia oxidizers and functional genes transcripts. Redundancy analysis revealed that soil compartment and A1501 inoculation treatments were the main factors affecting the distribution of the diazotrophic community.
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Affiliation(s)
- Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Feng
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Draghi WO, Degrossi J, Bialer M, Brelles-Mariño G, Abdian P, Soler-Bistué A, Wall L, Zorreguieta A. Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices. PLoS One 2018; 13:e0200651. [PMID: 30001428 PMCID: PMC6042781 DOI: 10.1371/journal.pone.0200651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/29/2018] [Indexed: 11/19/2022] Open
Abstract
No-tillage crop production has revolutionized the agriculture worldwide. In our country more than 30 Mha are currently cultivated under no-till schemes, stressing the importance of this management system for crop production. It is widely recognized that soil microbiota is altered under different soil managements. In this regard the structure of Burkholderia populations is affected by soils management practices such as tillage, fertilization, or crop rotation. The stability of these structures, however, has not been evaluated under sustainable schemes where the impact of land practices could be less deleterious to physicochemical soils characteristics. In order to assess the structure of Burkholderia spp. populations in no-till schemes, culturable Burkholderia spp. strains were quantified and their biodiversity evaluated. Results showed that Burkholderia spp. biodiversity, but not their abundance, clearly displayed a dependence on agricultural managements. We also showed that biodiversity was mainly influenced by two soil factors: Total Organic Carbon and Total Nitrogen. Results showed that no-till schemes are not per se sufficient to maintain a richer Burkholderia spp. soil microbiota, and additional traits should be considered when sustainability of productive soils is a goal to fulfil productive agricultural schemes.
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Affiliation(s)
- Walter Omar Draghi
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- Instituto de Biotecnología y Biología Molecular–CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail: (AZ); (WOD)
| | - Jose Degrossi
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Magalí Bialer
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | - Graciela Brelles-Mariño
- Center for Research and Development of Industrial Fermentations, (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Patricia Abdian
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | | | - Luis Wall
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- * E-mail: (AZ); (WOD)
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Yu Y, Zhang J, Petropoulos E, Baluja MQ, Zhu C, Zhu J, Lin X, Feng Y. Divergent Responses of the Diazotrophic Microbiome to Elevated CO 2 in Two Rice Cultivars. Front Microbiol 2018; 9:1139. [PMID: 29910783 PMCID: PMC5992744 DOI: 10.3389/fmicb.2018.01139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/14/2018] [Indexed: 01/20/2023] Open
Abstract
The species-specific responses of plant growth to elevated atmospheric CO2 concentration (eCO2) could lead to N limitation and potentially influence the sustainability of ecosystem. Questions remain unanswered with regards to the response of soil N2-fixing community to eCO2 when developing high-yielding agroecosystem to dampen the future rate of increase in CO2 levels and associated climate warming. This study demonstrates the divergent eCO2 influences on the paddy diazotrophic community between weak- and strong-responsive rice cultivars. In response to eCO2, the diazotrophic abundance increased more for the strong-responsive cultivar treatments than for the weak-responsive ones. Only the strong-responsive cultivars decreased the alpha diversity and separated the composition of diazotrophic communities in response to eCO2. The topological indices of the ecological networks further highlighted the different co-occurrence patterns of the diazotrophic microbiome in rice cultivars under eCO2. Strong-responsive cultivars destabilized the diazotrophic community by complicating and centralizing the co-occurrence network as well as by shifting the hub species from Bradyrhizobium to Dechloromonas in response to eCO2. On the contrary, the network pattern of the weak-responsive cultivars was simplified and decentralized in response to eCO2, with the hub species shifting from Halorhodospira under aCO2 to Sideroxydans under eCO2. Collectively, the above information indicates that the strong-responsive cultivars could potentially undermine the belowground ecosystem from the diazotrophs perspective in response to eCO2. This information highlights that more attention should be paid to the stability of the belowground ecosystem when developing agricultural strategies to adapt prospective climatic scenarios by growing high-yielding crop cultivars under eCO2.
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Affiliation(s)
- Yongjie Yu
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | | | - Marcos Q. Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D. Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data. Front Microbiol 2018; 9:703. [PMID: 29760683 PMCID: PMC5936773 DOI: 10.3389/fmicb.2018.00703] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.
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Affiliation(s)
- Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
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Wang Q, Wang J, Li Y, Chen D, Ao J, Zhou W, Shen D, Li Q, Huang Z, Jiang Y. Influence of nitrogen and phosphorus additions on N 2-fixation activity, abundance, and composition of diazotrophic communities in a Chinese fir plantation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:1530-1537. [PMID: 29129329 DOI: 10.1016/j.scitotenv.2017.10.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/19/2017] [Accepted: 10/08/2017] [Indexed: 05/22/2023]
Abstract
Although biological nitrogen (N) fixation (BNF) is an important N input process in subtropical forest ecosystems, how the diazotrophic communities related to this process respond to N and phosphorus (P) inputs is largely unknown. We investigated the effects of exogenous N and/or P inputs on N2-fixation activity, diazotrophic abundance and community composition using a continuous application of fertilizers over 5years experiment in a Chinese fir plantation. The fertilization regimes included control (CK), P treatment (P), low N addition treatment (N1), high N addition treatment (N2), low N and P addition treatment (N1P) and high N with P addition treatment (N2P). N2-fixation activity was determined using the acetylene reduction assay (ARA). Quantitative PCR and Illumina Miseq sequencing of nifH gene were performed to analyze diazotrophic abundance and community composition, respectively. Our results showed that P addition increased N2-fixation activity and nifH gene abundance by 189.07nmol C2H4 and 1.02×107copiesg-1 dry soil, respectively, while were reduced by 1.19nmol C2H4 and 2.04×106copiesg-1 dry soil when N was added. The application of P with low N (N1P) effectively alleviated the inhibitory effect of N input on N2-fixation activity. N-related treatments resulted in significant decreases in operational taxonomic unit (OTU) richness and shifts in diazotrophic community structure. N2-fixation activity and nifH gene abundance were strongly and positively correlated with soil pH and negatively correlated with mineral N (NH4+-N and NO3--N) contents, while mineral N concentrations rather than soil pH appeared to be the main factor altering diazotrophic community structure. These results revealed that P addition played a positive role in regulating biological nitrogen fixation in subtropical forest ecosystems.
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Affiliation(s)
- Qing Wang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Jianlei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuanzheng Li
- School of Resources and Environment, Henan University of Economics and Law, Zhengzhou 450046, China
| | - Diwen Chen
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Junhua Ao
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Wenling Zhou
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Dachun Shen
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Qiwei Li
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Zhenrui Huang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Yong Jiang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China.
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50
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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