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Singh A, T V A, Singh S, Saxena AK, Nain L. Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism. Int Microbiol 2024:10.1007/s10123-024-00570-2. [PMID: 39138687 DOI: 10.1007/s10123-024-00570-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/01/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024]
Abstract
Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Kushmaur, UP, India
- ICAR-Central Soil Salinity Research Institute, RRS Lucknow, Lucknow, UP, India
| | - Abiraami T V
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Kushmaur, UP, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Liu B, Xia H, Jiang C, Jiang C, Riaz M, Yang L, Chen Y, Fan X, Zhang Z, Duan X, Wu M, Xia X. Straw Addition Enhances Crop Yield, Soil Aggregation, and Soil Microorganisms in a 14-Year Wheat-Rice Rotation System in Central China. PLANTS (BASEL, SWITZERLAND) 2024; 13:985. [PMID: 38611514 PMCID: PMC11013638 DOI: 10.3390/plants13070985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Straw return utilizes waste resources to reduce the use of chemical fertilizers worldwide. However, information is still lacking on the relative impact of straw return on soil fertility, the nutrient composition of different soil aggregates, and soil microbial communities. Therefore, this study aimed to understand the effects of different management practices on the crop yield, soil fertility, and soil community composition in a 14-year wheat-rice rotation system. The treatments included a control (without fertilizer and straw addition), chemical fertilization (NPK), straw return without fertilizer (S), and straw addition with chemical fertilizer (NPKS). The results showed that NPKS improved the wheat and rice yield by 185.12% and 88.02%, respectively, compared to the CK treatment. Additionally, compared to the CK treatment, the N, P, and K contents of the wheat stem were increased by 39.02%, 125%, and 20.23% under the NPKS treatment. Compared to the CK treatment, SOM, TN, TP, AN, AP, AK, CEC, AFe, AMn, ACu, and AZn were increased by 49.12%, 32.62%, 35.06%, 22.89%, 129.36%, 48.34%, 13.40%, 133.95%, 58.98%, 18.26% and 33.33% under the NPKS treatment, respectively. Moreover, straw addition promoted the creation and stabilization of macro-aggregates in crop soils. The relative abundance of macro-aggregates (0.25-2 mm) increased from 37.49% to 52.97%. Straw addition was associated with a higher proportion of aromatic and carbonyl carbon groups in the soil, which, in turn, promoted the formation of macro-aggregates. Redundancy analysis showed that straw return significantly increased the microbial community diversity. These findings demonstrate that straw addition together with chemical fertilizer could increase the crop yield by improving soil fertility, soil aggregate stability, and the diversity of fungi.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Hao Xia
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Chaoqiang Jiang
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Riaz
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Li Yang
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Yunfeng Chen
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Xianpeng Fan
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Zhiyi Zhang
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Xiaoli Duan
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Maoqian Wu
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
| | - Xiange Xia
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, National Station for Qianjiang Agro-Environment, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China (Y.C.); (M.W.)
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Kong L, Zhang L, Wang Y, Huang Z. Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils. Microorganisms 2023; 12:41. [PMID: 38257868 PMCID: PMC10818615 DOI: 10.3390/microorganisms12010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.
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Affiliation(s)
| | | | | | - Zhanbin Huang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China; (L.K.); (L.Z.); (Y.W.)
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Świątczak J, Kalwasińska A, Szabó A, Brzezinska MS. The effect of seed bacterization with Bacillus paralicheniformis 2R5 on bacterial and fungal communities in the canola rhizosphere. Microbiol Res 2023; 275:127448. [PMID: 37453237 DOI: 10.1016/j.micres.2023.127448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Bacillus sp. is one of the best-studied plant growth-promoting rhizobacteria (PGPR). However, more detailed studies targeting its effect on the rhizosphere microbial community are required for improving management practices regarding its commercial application in the field. Our earlier study showed that PGPR Bacillus paralicheniformis 2R5 stimulated canola growth. Hence, this study aimed to assess the time-course impact of B. paralicheniformis 2R5 on bacterial and fungal community structure and diversity. The results showed that inoculation with B. paralicheniformis 2R5 initially significantly decreased the observed bacterial richness compared to the control, while after 44 days of treatment this alpha diversity metrics increased. A linear discriminant analysis effect size showed that B. paralicheniformis 2R5 altered the soil bacterial and fungal community structure by increasing the abundance of plants' beneficial microorganisms such as Nitrospira, Ramlibacter, Sphingomonas, Massilia, Terrimonas as well as Solicoccozyma, Schizothecium, Cyphellophora, Fusicolla, Humicola. B. paralicheniformis 2R5 seems to be a promising alternative to chemical pesticides and can be considered for practical application in the field. Its ability to alter the rhizosphere microbiome by increasing the diversity and composition of bacterial communities and increasing plants' beneficial groups of fungi, appears to be important in terms of improving canola development. However, further studies on these increased microbial taxa are necessary to confirm their function in promoting canola growth.
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Affiliation(s)
- Joanna Świątczak
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Attila Szabó
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, SE-75007 Uppsala, Sweden
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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Kumar R, Choudhary JS, Naik SK, Mondal S, Mishra JS, Poonia SP, Kumar S, Hans H, Kumar S, Das A, Kumar V, Bhatt BP, Chaudhari SK, Malik RK, Craufurd P, McDonald A, Sherpa SR. Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India. Front Microbiol 2023; 14:1181317. [PMID: 37485518 PMCID: PMC10356824 DOI: 10.3389/fmicb.2023.1181317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied. Methods Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods. Results and Discussion Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50-23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2-13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.
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Affiliation(s)
- Rakesh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Jaipal Singh Choudhary
- ICAR Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, Jharkhand, India
| | - Sushanta Kumar Naik
- ICAR Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, Jharkhand, India
| | - Surajit Mondal
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | | | - Shish Pal Poonia
- Cereal Systems Initiative for South Asia (CSISA)-CIMMYT, Patna, India
| | - Saurabh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Hansraj Hans
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Sanjeev Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Anup Das
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Virender Kumar
- International Rice Research Institute, Los Banos, Philippines
| | | | | | - Ram Kanwar Malik
- Cereal Systems Initiative for South Asia (CSISA)-CIMMYT, Patna, India
| | | | - Andrew McDonald
- Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
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Hereira-Pacheco SE, Estrada-Torres A, Dendooven L, Navarro-Noya YE. Shifts in root-associated fungal communities under drought conditions in Ricinus communis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Zhu X, Guo Z, Wang N, Liu J, Zuo Y, Li K, Song C, Song Y, Gong C, Xu X, Yuan F, Zhang L. Environmental stress stimulates microbial activities as indicated by cyclopropane fatty acid enhancement. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162338. [PMID: 36813189 DOI: 10.1016/j.scitotenv.2023.162338] [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: 11/01/2022] [Revised: 01/24/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Soil microbial responses to environmental stress remain a critical question in microbial ecology. The content of cyclopropane fatty acid (CFA) in cytomembrane has been widely used to evaluate environmental stress on microorganisms. Here, we used CFA to investigate the ecological suitability of microbial communities and found a stimulating impact of CFA on microbial activities during wetland reclamation in Sanjiang Plain, Northeastern China. The seasonality of environmental stress resulted in the fluctuation of CFA content in the soil, which suppressed microbial activities due to nutrient loss upon wetland reclamation. After land conversion, the aggravation of temperature stress to microbes increased the CFA content by 5 % (autumn) to 163 % (winter), which led to the suppression of microbial activities by 7 %-47 %. By contrast, the warmer soil temperature and permeability decreased the CFA content by 3 % to 41 % and consequently aggravated the microbial reduction by 15 %-72 % in spring and summer. Complex microbial communities of 1300 CFA-produced species were identified using a sequencing approach, suggesting that soil nutrients dominated the differentiation in these microbial community structures. Further analysis with structural equation modeling highlighted the important function of CFA content to environmental stress and the stimulating influence of CFA induced by environmental stress on microbial activities. Our study shows the biological mechanisms of seasonal CFA content for microbial adaption to environmental stress under wetland reclamation. It advances our knowledge of microbial physiology affecting soil element cycling caused by anthropogenic activities.
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Affiliation(s)
- Xinhao Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Ziyu Guo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nannan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China
| | - Jianzhao Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunjiang Zuo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kexin Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China
| | - Yanyu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China
| | - Chao Gong
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China
| | - Xiaofeng Xu
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Fenghui Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, China; Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Lihua Zhang
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, Beijing 100081, China.
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Bertola M, Righetti L, Gazza L, Ferrarini A, Fornasier F, Cirlini M, Lolli V, Galaverna G, Visioli G. Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines. FRONTIERS IN PLANT SCIENCE 2023; 14:1172857. [PMID: 37223792 PMCID: PMC10200949 DOI: 10.3389/fpls.2023.1172857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/06/2023] [Indexed: 05/25/2023]
Abstract
Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.
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Affiliation(s)
- Marta Bertola
- Department of Food and Drugs, University of Parma, Parma, Italy
| | - Laura Righetti
- Department of Food and Drugs, University of Parma, Parma, Italy
- Wageningen Food Safety Research, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
| | - Laura Gazza
- Council for Agricultural Research and Economics, Research Centre for Engineering and Agro-Food Processing, Rome, Italy
| | - Andrea Ferrarini
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Flavio Fornasier
- Council for Agricultural Research and Economics (CREA) Research Centre for Viticulture and Enology, Unit of Gorizia, Gorizia, Italy
| | - Martina Cirlini
- Department of Food and Drugs, University of Parma, Parma, Italy
| | - Veronica Lolli
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Land-use change alters the bacterial community structure, but not forest management. Folia Microbiol (Praha) 2022; 68:277-290. [PMID: 36273059 DOI: 10.1007/s12223-022-01009-9] [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: 02/12/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
Deforestation has a large impact on soil fertility, especially on steep slopes, but by applying sustainable management practices, local communities in Oaxaca (Mexico) have tried to avoid the most negative effects on the forest ecosystems they manage. In this study, the characteristics and bacterial community structure were investigated from soil sampled in triplicate (n = 3) with different land use, i.e., arable, natural forest, sustainable managed, and reforested soil. The pH was significantly higher in the arable (6.2) than in the forest soils (≤ 5.3), while the organic matter was > 2 times higher in the natural forest (80.4 g/kg) and sustainable managed soil (86.3 g/kg) than in the arable (36.8 g/kg) and cleared and reforested soil (39.3 g/kg). The higher organic matter content in the first two soils was due to leaf litter, absent in the other soils. The species richness (q = 0), the typical (q = 1) and dominant bacteria (q = 2) were not affected significantly by land use. The beta diversity, however, showed a significant effect of land use on species richness (p = 0.0029). Proteobacteria (40.135%) and Actinobacteria (20.15%) were the dominant bacterial phyla, and Halomonas (14.50%) and the Verrucomicrobia DA101 (3.39%) were the dominant genera. The bacterial communities were highly significantly different in soil with different land use considering the taxonomic level of genus and OTUs (p ≤ 0.003). It was found that the sustainable managed forest provided the local community with sellable wood while maintaining the soil organic matter content, i.e., sequestered C and without altering the bacterial community structure.
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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Tagg AS, Sperlea T, Labrenz M, Harrison JP, Ojeda JJ, Sapp M. Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth. Microorganisms 2022; 10:microorganisms10091775. [PMID: 36144377 PMCID: PMC9506493 DOI: 10.3390/microorganisms10091775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.
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Affiliation(s)
- Alexander S. Tagg
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
- Correspondence:
| | - Theodor Sperlea
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Matthias Labrenz
- Leibniz-Institut für Ostseeforschung Warnemünde, Seestraße 15, 18119 Rostock, Germany
| | - Jesse P. Harrison
- CSC—IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Jesús J. Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, UK
| | - Melanie Sapp
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany
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12
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Sennett LB, Goyer C, Burton DL, Zebarth BJ, Whitney S. Chemical fumigation and biofumigation alter soil bacterial community diversity and composition. FEMS Microbiol Ecol 2022; 98:fiac026. [PMID: 35441686 DOI: 10.1093/femsec/fiac026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Chemical fumigation and biofumigation are used to reduce soil-borne diseases in agricultural production systems; however, non-targeted soil microorganisms may also be affected. This study compared the effects of chemical fumigation, either used alone or combined with an organic amendment, and biofumigation on soil bacterial community diversity and composition under controlled conditions over 160 days. Treatments included: fumigation with chloropicrin (CP), fumigation with metam sodium used alone (MS) or combined with barley plant residues (MSBR); biofumigation with mustard plant residues; addition of barley plant residues; and untreated control. Biofumigation had a greater impact on bacterial diversity at early time points, transiently decreasing species evenness and yielding the most dissimilar β-diversity after 3 days. MS fumigation did not affect bacterial diversity indices; however, MSBR transiently decreased species evenness after 8 days. CP-treated soil had decreased species evenness that did not recover over time and had the most dissimilar β-diversity at the end of the incubation compared to all other treatments. This study demonstrated that CP fumigation had the greatest and most persistent impact on bacterial diversity, whereas MS fumigation and biofumigation led to transient decreases in bacterial diversity.
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Affiliation(s)
- Louise B Sennett
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Claudia Goyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - David L Burton
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Sean Whitney
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
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Singh U, Choudhary AK, Sharma S. A 3-year field study reveals that agri-management practices drive the dynamics of dominant bacterial taxa in the rhizosphere of Cajanus cajan. Symbiosis 2022. [DOI: 10.1007/s13199-022-00834-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices. Microbiol Spectr 2022; 10:e0183421. [PMID: 35254138 PMCID: PMC9049951 DOI: 10.1128/spectrum.01834-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage. IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.
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15
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Nazir S, Zaman QU, Abbasi A, Komal N, Riaz U, Ashraf K, Ahmad N, Agarwal S, Nasir R, Chen Y. Bioresource Nutrient Recycling in the Rice-Wheat Cropping System: Cornerstone of Organic Agriculture. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112323. [PMID: 34834686 PMCID: PMC8625801 DOI: 10.3390/plants10112323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
This study evaluated the impact of conventional practices (fertilizer alone) and diverse farming approaches (such as green manuring, farmyard manure application, rice-residue incorporation, residue mulching, residue removal and residue burning) on soil attributes. A total of thirty-five farm sites were selected, with five sites (replications) for each farming approach system, which were used over the past three years in the study farms. Characterization of rice residues of all cultivars, green manure crop (sesbenia: Sesbania sesban) and decomposed farmyard manure samples showed differential behaviours for macronutrients and micronutrients. Continuous application of inorganic fertilizers significantly influenced soil attributes, especially electrical conductivity, nutrient contents, bacterial and fungal population and soil enzymatic attributes. The crop residue treatments favourably influenced the soil parameters over the control. Crop residue incorporation or burning significantly increased soil available potassium, microbial biomass, enzymatic activities and organic carbon when compared with applications of chemical fertilizer alone, while total nitrogen content was increased by residue incorporation. However, green manuring and farmyard manure applications showed inferior responses compared with residue management treatment. It is therefore recommended that bioresources should be managed properly to warrant improvements in soil properties, nutrient recycling and the sustainability for crop productivity, in order to achieve sustainable development goals for climate action.
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Affiliation(s)
- Saba Nazir
- Department of Environmental Sciences, The University of Lahore, Lahore 54590, Pakistan; (S.N.); (N.K.); (R.N.)
| | - Qamar uz Zaman
- Department of Environmental Sciences, The University of Lahore, Lahore 54590, Pakistan; (S.N.); (N.K.); (R.N.)
| | - Asim Abbasi
- Department of Zoology, Punjab Group of College, University of Central Punjab, Bahawalpur 63100, Pakistan;
| | - Nayab Komal
- Department of Environmental Sciences, The University of Lahore, Lahore 54590, Pakistan; (S.N.); (N.K.); (R.N.)
| | - Umair Riaz
- Soil and Water Testing Laboratory for Research, Agriculture Department, Government of Punjab, Bahawalpur 63100, Pakistan;
| | - Kamran Ashraf
- Department of Food Science and Nutrition, Faisalabad Sahiwal Campus, Government College University, Sahiwal 57000, Pakistan;
| | - Nabeel Ahmad
- Department of Public Health, Torrens University, Melbourne 3000, Australia;
| | - Shweta Agarwal
- Department of Business, Torrens University, Melbourne 3000, Australia;
| | - Rabiya Nasir
- Department of Environmental Sciences, The University of Lahore, Lahore 54590, Pakistan; (S.N.); (N.K.); (R.N.)
| | - Yinglong Chen
- The UWA Institute of Agriculture, School of Agriculture and Environment, The University of Western Australia, Perth 6009, Australia
- Institute of Soil and Water Conservation, Chinese Academy of Sciences, Northwest A&F University, Yangling 712100, China
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Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety. Microorganisms 2021; 9:microorganisms9071400. [PMID: 34203506 PMCID: PMC8308033 DOI: 10.3390/microorganisms9071400] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023] Open
Abstract
Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.
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17
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Hereira-Pacheco SE, Navarro-Noya YE, Dendooven L. The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content. Sci Rep 2021; 11:2173. [PMID: 33500437 PMCID: PMC7838207 DOI: 10.1038/s41598-021-81551-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 01/25/2023] Open
Abstract
Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.
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Affiliation(s)
| | - Yendi E Navarro-Noya
- Cátedras CONACYT, Centro Tlaxcala de Biología de La Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico.
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18
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Choudhary M, Jat HS, Datta A, Sharma PC, Rajashekar B, Jat ML. Topsoil Bacterial Community Changes and Nutrient Dynamics Under Cereal Based Climate-Smart Agri-Food Systems. Front Microbiol 2020; 11:1812. [PMID: 32849419 PMCID: PMC7399647 DOI: 10.3389/fmicb.2020.01812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/10/2020] [Indexed: 02/01/2023] Open
Abstract
Soil microorganisms play a critical role in soil biogeochemical processes, nutrient cycling, and resilience of agri-food systems and are immensely influenced by agronomic management practices. Understanding soil bacterial community and nutrient dynamics under contrasting management practices is of utmost importance for building climate-smart agri-food systems. Soil samples were collected at 0–15 cm soil depth from six management scenarios in long-term conservation agriculture (CA) and climate-smart agriculture (CSA) practices. These scenarios (Sc) involved; ScI-conventional tillage based rice-wheat rotation, ScII- partial CA based rice-wheat-mungbean, ScIII- partial CSA based rice-wheat-mungbean, ScIV is partial CSA based maize-wheat-mungbean, ScV and ScVI are CSA based scenarios, were similar to ScIII and ScIV respectively, layered with precision water & nutrient management. The sequencing of soil DNA results revealed that across the six scenarios, a total of forty bacterial phyla were observed, with Proteobacteria as dominant in all scenarios, followed by Acidobacteria and Actinobacteria. The relative abundance of Proteobacteria was 29% higher in rice-based CSA scenarios (ScIII and ScV) and 16% higher in maize-based CSA scenarios (ScIV and ScVI) compared to conventional-till practice (ScI). The relative abundance of Acidobacteria and Actinobacteria was respectively 29% and 91% higher in CT than CSA based rice and 27% and 110% higher than maize-based scenarios. Some taxa are present relatively in very low abundance or exclusively in some scenarios, but these might play important roles there. Three phyla are exclusively present in ScI and ScII i.e., Spirochaetes, Thermi, and Euryarchaeota. Shannon diversity index was 11% higher in CT compared to CSA scenarios. Maize based CSA scenarios recorded higher diversity indices than rice-based CSA scenarios. Similar to changes in soil bacterial community, the nutrient dynamics among the different scenarios also varied significantly. After nine years of continuous cropping, the soil organic carbon was improved by 111% and 31% in CSA and CA scenarios over the CT scenario. Similarly, the available nitrogen, phosphorus, and potassium were improved by, respectively, 38, 70, and 59% in CSA scenarios compared to the CT scenario. These results indicate that CSA based management has a positive influence on soil resilience in terms of relative abundances of bacterial groups, soil organic carbon & available plant nutrients and hence may play a critical role in the sustainability of the intensive cereal based agri-food systems.
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Affiliation(s)
- Madhu Choudhary
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - Hanuman S Jat
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India.,International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Ashim Datta
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - Parbodh C Sharma
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | | | - Mangi L Jat
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
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Zenteno-Rojas A, Martínez-Romero E, Castañeda-Valbuena D, Rincón-Molina CI, Ruíz-Valdiviezo VM, Meza-Gordillo R, Villalobos-Maldonado JJ, Vences-Guzmán MÁ, Rincón-Rosales R. Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls. AMB Express 2020; 10:124. [PMID: 32651884 PMCID: PMC7351888 DOI: 10.1186/s13568-020-01058-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/02/2020] [Indexed: 11/20/2022] Open
Abstract
Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (HS and HP) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L−1 PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for HS and HP soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.
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Changes in soil organic carbon fractions and microbial community under rice straw return in Northeast China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00962] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Piazza G, Ercoli L, Nuti M, Pellegrino E. Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area. Front Microbiol 2019; 10:2047. [PMID: 31551981 PMCID: PMC6737287 DOI: 10.3389/fmicb.2019.02047] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/20/2019] [Indexed: 01/20/2023] Open
Abstract
Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.
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Degrune F, Boeraeve F, Dufrêne M, Cornélis JT, Frey B, Hartmann M. The Pedological Context Modulates the Response of Soil Microbial Communities to Agroecological Management. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rieke EL, Moorman TB, Soupir ML, Yang F, Howe A. Assessing Pathogen Presence in an Intensively Tile Drained, Agricultural Watershed. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1033-1042. [PMID: 30272801 DOI: 10.2134/jeq2017.12.0500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Increases in swine production and concomitant manure application provide beneficial nutrients for crops but also include the potential to spread pathogenic bacteria in the environment. While manure is known to contain a variety of pathogens, little is known regarding the long-term effect of manure application on fate and transport of this diverse set of pathogens into surrounding waterways. We report on the use of 16S-rRNA gene sequencing to detect pathogen-containing genera in the agriculturally dominated South Fork Iowa River watershed, home to approximately 840,000 swine in the 76,000-ha basin. DNA was extracted from monthly grab samples collected from three surface water sites and two main artificial drainage outlets. DNA sequences from water samples were matched with sequences from genera known to contain pathogens using targeted 16S rRNA amplicon sequencing. The specific genera known to contain pathogens were quantified by combining percentage of genera sequence matches with 16S rRNA gene quantitative polymerase chain reaction results. Specifically, abundances of , , and significantly increased in surface water after typical fall manure application. Additionally, the likely transport pathways for specific genera known to contain pathogens were identified. Surface water concentrations were influenced mainly by artificial drainage, whereas was primarily transported to surface waters by runoff events. The results of this study will help us to understand environmental pathways that may be useful for mitigation of the diverse set of pathogenic genera transported in agroecosystems and the capability of manure application to alter existing microbial community structures.
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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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25
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Choudhary M, Sharma PC, Jat HS, Dash A, Rajashekar B, McDonald AJ, Jat ML. Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains. 3 Biotech 2018; 8:304. [PMID: 30002994 DOI: 10.1007/s13205-018-1317-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
In Indo-Gangetic plains (IGP) of India, natural resources (soil, water, and environment) are degrading under the conventional-till (CT)-based management practices in rice-wheat cropping system. A long-term field experiment was conducted to understand the soil bacterial diversity and abundance under different sets of management scenarios (Sc). The study comprised of four scenarios, namely, -Sc.I CT-based rice-wheat system (farmers' practice); Sc.II, partial conservation agriculture (CA) based in which rice is under CT-wheat and mungbean under zero-tillage (ZT); Sc.III, full CA-based in which rice-wheat-mungbean are under ZT and Sc.IV, where maize-wheat-mungbean are under ZT. These scenarios varied in cropping system, tillage, and crop residue management practices. Using Illumina MiSeq sequencing technology, the variable regions V3-V4 of 16S rRNA were sequenced and the obtained reads were analyzed to study the diversity patterns in the scenarios. Results showed the presence of 53 bacterial phyla across scenarios. The predominant phyla in all scenarios were Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes which accounted for more than 70% of the identified phyla. However, the rice-based systems (Sc.I, Sc.II, and Sc.III) were dominated by phylum Proteobacteria; however, maize-based system (Sc.IV) was dominated by Acidobacteria. The class DA052 and Acidobacteriia of Acidobacteria and Bacteroidetes of Bacteroidia were exceptionally higher in Sc.IV. Shannon diversity index was 8.8% higher in Sc.I, 7.5% in Sc.II, and 2.7% in Sc.III compared to Sc.IV. The findings revealed that soil bacterial diversity and abundance are influenced by agricultural management practices as bacterial diversity under full CA-based management systems (Sc.III and Sc.IV) was lower when compared to farmer's practice (Sc.I) and partial CA (Sc.II) scenarios.
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Affiliation(s)
- Madhu Choudhary
- 1Division of Soil and Crop Management, ICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal, Haryana 132001 India
| | - Parbodh C Sharma
- 1Division of Soil and Crop Management, ICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal, Haryana 132001 India
| | - Hanuman S Jat
- International Maize and Wheat Improvement Centre (CIMMYT), New Delhi, India
| | | | | | - Andrew J McDonald
- International Maize and Wheat Improvement Centre (CIMMYT), Kathmandu, Nepal
| | - Mangi L Jat
- International Maize and Wheat Improvement Centre (CIMMYT), New Delhi, India
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26
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Yang Y, Dou Y, An S. Testing association between soil bacterial diversity and soil carbon storage on the Loess Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:48-58. [PMID: 29335174 DOI: 10.1016/j.scitotenv.2018.01.081] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/20/2017] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
Bacteria are widely distributed and play an important role in soil carbon (C) cycling. The impact of soil bacterial diversity on soil C storage has been well established, yet little is known about the underlying mechanisms and the interactions among them. Here, we examined the association between soil bacterial diversity and soil C storage in relation to vegetation restoration on the Loess Plateau. The dominant phyla among land use types (artificial forest, Af; natural shrubland, Ns; artificial grassland, Ag; natural grassland, Ng; slope cropland, Sc) were Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria, which transited from Acidobacteria-dominant to Actinobacteria-dominant community due to vegetation restoration. Soil C storage and the Shannon diversity index of soil bacterial community (HBacteria) showed the order Ns > Ng > Af > Ag > Sc, whereas no significant difference was found in Good's coverage (p > .05). Further, a strong relationship was observed between the relative abundance of dominant bacterial groups and soil C storage (p < .05). Additionally, soil bacterial diversity was closely related to soil C storage based on the structural equation model (SEM) and generalized additive models (GAMs). Specifically, soil C storage had the largest deterministic effects, explaining >70% of the variation and suggesting a strong association between soil C storage and soil bacterial diversity. Overall, we propose that further studies are necessary with a focus on the soil bacterial groups with specific functions in relation to soil C storage on the Loess Plateau.
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Affiliation(s)
- Yang Yang
- College of Natural Resource and Environment, Northwest A&F University, Yangling 712100, China
| | - Yanxing Dou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| | - Shaoshan An
- College of Natural Resource and Environment, Northwest A&F University, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China.
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27
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Anderson C, Beare M, Buckley HL, Lear G. Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils. PeerJ 2017; 5:e3930. [PMID: 29062604 PMCID: PMC5649590 DOI: 10.7717/peerj.3930] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/26/2017] [Indexed: 01/13/2023] Open
Abstract
In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
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Affiliation(s)
| | - Mike Beare
- Plant and Food Research, Lincoln, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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28
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Degrune F, Theodorakopoulos N, Colinet G, Hiel MP, Bodson B, Taminiau B, Daube G, Vandenbol M, Hartmann M. Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes. Front Microbiol 2017; 8:1127. [PMID: 28674527 PMCID: PMC5474472 DOI: 10.3389/fmicb.2017.01127] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/01/2017] [Indexed: 12/01/2022] Open
Abstract
Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.
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Affiliation(s)
- Florine Degrune
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- TERRA-AgricultureIsLife, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Nicolas Theodorakopoulos
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Gilles Colinet
- Exchanges Ecosystems – Atmosphere, Department of BIOSE, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Marie-Pierre Hiel
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Bernard Bodson
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | | | - Georges Daube
- Food Microbiology, University of LiègeLiège, Belgium
| | - Micheline Vandenbol
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Research Institute for Forest, Snow and Landscape Research WSLBirmensdorf, Switzerland
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de León-Lorenzana AS, Delgado-Balbuena L, Domínguez-Mendoza C, Navarro-Noya YE, Luna-Guido M, Dendooven L. Reducing Salinity by Flooding an Extremely Alkaline and Saline Soil Changes the Bacterial Community but Its Effect on the Archaeal Community Is Limited. Front Microbiol 2017; 8:466. [PMID: 28396654 PMCID: PMC5366314 DOI: 10.3389/fmicb.2017.00466] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 03/07/2017] [Indexed: 11/13/2022] Open
Abstract
Regular flooding of the soil to reduce salinity will change soil characteristics, but also the microbial community structure. Soil of the former lake Texcoco with electrolytic conductivity (EC) 157.4 dS m-1 and pH 10.3 was flooded monthly in the laboratory under controlled conditions for 10 months while soil characteristics were determined and the archaeal and bacterial community structure monitored by means of 454 pyrosequencing of the 16S rRNA gene. The EC of the soil dropped from 157.8 to 1.7 dS m-1 and the clay content decreased from 430 to 270 g kg-1 after ten floodings, but the pH (10.3) did not change significantly over time. Flooding the soil had a limited effect on the archaeal community structure and only the relative abundance of Haloferax-like 16S rRNA phylotypes changed significantly. Differences in archaeal population structure were more defined by the initial physicochemical properties of the soil sample than by a reduction in salinity. Flooding, however, had a stronger effect on bacterial community structure than on the archaeal community structure. A wide range of bacterial taxa was affected significantly by changes in the soil characteristics, i.e., four phyla, nine classes, 17 orders, and 28 families. The most marked change occurred after only one flooding characterized by a sharp decrease in the relative abundance of bacterial groups belonging to the Gammaproteobacteria, e.g., Halomonadaceae (Oceanospirillales), Pseudomonadaceae, and Xanthomonadaceae and an increase in that of the [Rhodothermales] (Bacteroidetes), Nitriliruptorales (Actinobacteria), and unassigned Bacteria. It was found that flooding the soil sharply reduced the EC, but also the soil clay content. Flooding the soil had a limited effect on the archaeal community structure, but altered the bacterial community structure significantly.
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Affiliation(s)
- Arit S de León-Lorenzana
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | - Laura Delgado-Balbuena
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | | | - Yendi E Navarro-Noya
- Centro Tlaxcala de Biología de la Conducta, Cátedras CONACYT, Universidad Autónoma de Tlaxcala Tlaxcala, Mexico
| | - Marco Luna-Guido
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | - Luc Dendooven
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
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30
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De la Cruz-Barrón M, Cruz-Mendoza A, Navarro-Noya YE, Ruiz-Valdiviezo VM, Ortíz-Gutiérrez D, Ramírez-Villanueva DA, Luna-Guido M, Thierfelder C, Wall PC, Verhulst N, Govaerts B, Dendooven L. The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices. MICROBIAL ECOLOGY 2017; 73:135-152. [PMID: 27538875 DOI: 10.1007/s00248-016-0807-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.
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Affiliation(s)
| | | | - Yendi E Navarro-Noya
- Cátedras CONACYT-Universidad Autónoma de Tlaxcala, Av. Universidad 1, C.P., 90062, Tlaxcala, Mexico
| | | | | | | | - Marco Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico
| | - Cristian Thierfelder
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Patrick C Wall
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico.
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31
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Liu X, Zhang S, Jiang Q, Bai Y, Shen G, Li S, Ding W. Using community analysis to explore bacterial indicators for disease suppression of tobacco bacterial wilt. Sci Rep 2016; 6:36773. [PMID: 27857159 PMCID: PMC5114674 DOI: 10.1038/srep36773] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 10/20/2016] [Indexed: 12/20/2022] Open
Abstract
Although bacterial communities play important roles in the suppression of pathogenic diseases and crop production, little is known about the bacterial communities associated with bacterial wilt. Based on 16S rRNA gene sequencing, statistical analyses of microbial communities in disease-suppressive and disease-conducive soils from three districts during the vegetation period of tobacco showed that Proteobacteria was the dominant phylum, followed by Acidobacteria. Only samples from September were significantly correlated to disease factors. Fifteen indicators from taxa found in September (1 class, 2 orders, 3 families and 9 genera) were identified in the screen as being associated with disease suppression, and 10 of those were verified for potential disease suppression in March. Kaistobacter appeared to be the genus with the most potential for disease suppression. Elucidating microbially mediated natural disease suppression is fundamental to understanding microecosystem responses to sustainable farming and provides a possible approach for modeling disease-suppressive indicators. Here, using cluster analysis, MRPP testing, LEfSe and specific filters for a Venn diagram, we provide insight into identifying possible indicators of disease suppression of tobacco bacterial wilt.
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Affiliation(s)
- Xiaojiao Liu
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Shuting Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Qipeng Jiang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Yani Bai
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Guihua Shen
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Shili Li
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
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32
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Smith CR, Blair PL, Boyd C, Cody B, Hazel A, Hedrick A, Kathuria H, Khurana P, Kramer B, Muterspaw K, Peck C, Sells E, Skinner J, Tegeler C, Wolfe Z. Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem. Ecol Evol 2016; 6:8075-8084. [PMID: 27878079 PMCID: PMC5108259 DOI: 10.1002/ece3.2553] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022] Open
Abstract
The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.
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Affiliation(s)
- Chris R Smith
- Department of Biology Earlham College Richmond IN USA
| | - Peter L Blair
- Department of Biology Earlham College Richmond IN USA
| | - Charlie Boyd
- Department of Biology Earlham College Richmond IN USA
| | - Brianne Cody
- Department of Biology Earlham College Richmond IN USA
| | - Alexander Hazel
- Department of Biology Earlham College Richmond IN USA; Present address: Department of Entomology University of Illinois Urbana Champaign IL USA
| | | | - Hitesh Kathuria
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Parul Khurana
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Brent Kramer
- Department of Biology Earlham College Richmond IN USA
| | | | - Charles Peck
- Department of Computer Science Earlham College Richmond IN USA
| | - Emily Sells
- Department of Biology Earlham College Richmond IN USA
| | - Jessica Skinner
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Cara Tegeler
- School of Natural Science and Mathematics Indiana University East Richmond IN USA
| | - Zoe Wolfe
- Department of Biology Earlham College Richmond IN USA
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Delgado-Balbuena L, Bello-López JM, Navarro-Noya YE, Rodríguez-Valentín A, Luna-Guido ML, Dendooven L. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils. PLoS One 2016; 11:e0160991. [PMID: 27727277 PMCID: PMC5058544 DOI: 10.1371/journal.pone.0160991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/28/2016] [Indexed: 01/13/2023] Open
Abstract
Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure.
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Affiliation(s)
| | | | | | | | | | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, D.F., Mexico
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Myer PR, Wells JE, Smith TPL, Kuehn LA, Freetly HC. Microbial community profiles of the jejunum from steers differing in feed efficiency. J Anim Sci 2016; 94:327-38. [PMID: 26812338 DOI: 10.2527/jas.2015-9839] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Research regarding the association between the microbial community and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when determining the interplay between host and nonhost factors affecting feed efficiency. The objective of this study was to characterize the microbial communities of the jejunum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual ADFI and ADG were determined from animals fed the same diet. At the end of each feeding period, steers were ranked based on their standardized distance from the bivariate mean (ADG and ADFI). Four steers with the greatest deviation within each Cartesian quadrant were sampled ( = 16/group; 2 groups). Bacterial 16S rRNA gene amplicons were sequenced from the jejunum content using next-generation sequencing technology. The phylum Firmicutes accounted for up to 90% of the populations within all samples and was dominated by the families Clostridiaceae and Ruminococcaceae. UniFrac principal coordinate analyses did not indicate any separation of microbial communities within the jejunum based on feed efficiency phenotype, and no significant changes were indicated by bacterial diversity or richness metrics. The relative abundances of microbial populations and operational taxonomic units did reveal significant differences between feed efficiency groups ( < 0.05), including the phylum Proteobacteria ( = 0.030); the families Lachnospiraceae ( = 0.035), Coriobacteriaceae ( = 0.012), and Sphingomonadaceae ( = 0.035); and the genera ( = 0.019), ( = 0.018), and ( = 0.022). The study identified jejunal microbial associations with feed efficiency, ADG, and ADFI. This study suggests the association of the jejunum microbial community as a factor influencing feed efficiency at the 16S level.
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Rothrock M, Locatelli A, Glenn T, Thomas J, Caudill A, Kiepper B, Hiett K. Assessing the microbiomes of scalder and chiller tank waters throughout a typical commercial poultry processing day. Poult Sci 2016; 95:2372-82. [DOI: 10.3382/ps/pew234] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022] Open
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Jiménez-Bueno NG, Valenzuela-Encinas C, Marsch R, Ortiz-Gutiérrez D, Verhulst N, Govaerts B, Dendooven L, Navarro-Noya YE. Bacterial indicator taxa in soils under different long-term agricultural management. J Appl Microbiol 2016; 120:921-33. [PMID: 26808352 DOI: 10.1111/jam.13072] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 12/22/2022]
Abstract
AIMS In this study, the species indicator test was used to identify key bacterial taxa affected by changes in the soil environment as a result of conservation agriculture or conventional practices. METHODS AND RESULTS Soils cultivated with wheat (Triticum spp. L.) and maize (Zea mays L.) under different raised bed planting systems for 20 years, that is, varying crop residue and fertilizer management, were used. Taxonomic- and divergence-based 16S-metagenomics, and IndVal analysis were used to study the bacterial communities and identify indicator taxa (genus and OTU97 ) affected by agricultural practices. Although, some phyla were affected significantly by different treatments, the taxonomic assemblages at phylum level were similar. Bacterial taxa related to different processes of the N-cycle were indicators of different fertilization rates, for example, Azorhizobium, Nostoc and Nitrosomonas. A large number of OTU97 were indicators for conventionally tilled beds and their distribution was defined by soil organic carbon. IndVal analysis identified different taxa in each of the residue management systems. This suggests that although the same organic material remains in the field, crop residue management affects specific taxa. The taxa indicator of the burned residues belonged mainly to the order SBR1031 (Anaerolineae, Chloroflexi), and the genera Bacillus and Alicyclobacillus. CONCLUSIONS N-fertilizer application rates affected N-cycling taxa. Tillage affected Actinobacteria members and organic matter decomposers. Although the same crop residue was retained in the field, organic material management was important for specific taxa. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, we report that agricultural practice affected soil bacterial communities. We also identified distinctive taxa and related their distribution to changes in the soil environment resulting from different agricultural practices.
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Affiliation(s)
| | | | - R Marsch
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico
| | | | - N Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF, Mexico
| | - B Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF, Mexico
| | - L Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico, DF, Mexico
| | - Y E Navarro-Noya
- CONACYT Research Fellow - Research Center of Biological Sciences, Tlaxcala Autonomous University, Tlaxcala, Tlaxcala, Mexico
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Salaheen S, Chowdhury N, Hanning I, Biswas D. Zoonotic bacterial pathogens and mixed crop-livestock farming. Poult Sci 2015; 94:1398-1410. [DOI: 10.3382/ps/peu055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Bonilla N, Vida C, Martínez-Alonso M, Landa BB, Gaju N, Cazorla FM, de Vicente A. Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities. Appl Environ Microbiol 2015; 81:3405-18. [PMID: 25769825 PMCID: PMC4407234 DOI: 10.1128/aem.03787-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/01/2015] [Indexed: 11/20/2022] Open
Abstract
One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.
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Affiliation(s)
- Nuria Bonilla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga, Consejo Superior de Investigaciones Científicas, and Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Carmen Vida
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga, Consejo Superior de Investigaciones Científicas, and Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Maira Martínez-Alonso
- Departamento de Genética y Microbiología, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Spain
| | - Blanca B Landa
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Finca Alameda del Obispo, Córdoba, Spain
| | - Nuria Gaju
- Departamento de Genética y Microbiología, Facultad de Biociencias, Universidad Autónoma de Barcelona, Bellaterra, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga, Consejo Superior de Investigaciones Científicas, and Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga, Consejo Superior de Investigaciones Científicas, and Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Figuerola ELM, Guerrero LD, Türkowsky D, Wall LG, Erijman L. Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale. Environ Microbiol 2015; 17:678-88. [PMID: 24803003 DOI: 10.1111/1462-2920.12497] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/28/2014] [Indexed: 11/28/2022]
Abstract
The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyse bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on β-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower β-diversity and narrower breadth compared with distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of β-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region was likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity.
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Affiliation(s)
- Eva L M Figuerola
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI-CONICET), Buenos Aires, Argentina
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Bacterial colonization of a fumigated alkaline saline soil. Extremophiles 2014; 18:733-43. [PMID: 24846742 DOI: 10.1007/s00792-014-0653-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/27/2014] [Indexed: 10/25/2022]
Abstract
After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.
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Prado B, Fuentes M, Verhulst N, Govaerts B, De León F, Zamora O. Fate of atrazine in a soil under different agronomic management practices. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2014; 49:844-855. [PMID: 25190559 DOI: 10.1080/03601234.2014.938555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Agricultural management affects the movement of atrazine in soil and leaching to groundwater. The objective of this study was to determine atrazine adsorption in a soil after 20 years of atrazine application under agronomic management practices differing in tillage practice (conventional and zero tillage), residue management (with and without residue retention) and crop rotation (wheat-maize rotation and maize monoculture). Atrazine sorption was determined using batch and column experiments. In the batch experiment, the highest distribution coefficient Kd (1.1 L kg(-1)) at 0-10 cm soil depth was observed under zero tillage, crop rotation and residue retention (conservation agriculture). The key factor in adsorption was soil organic matter content and type. This was confirmed in the column experiment, in which the highest Kd values were observed in treatments with residue retention, under either zero or conventional tillage (0.81 and 0.68 L kg(-1), respectively). Under zero tillage, the fact that there was no soil movement helped to increase the Kd. The increased soil organic matter content with conservation agriculture may be more important than preferential flow due to higher pore connectivity in the same system. The soil's capacity to adsorb 2-hydroxyatrazine (HA), an important atrazine metabolite, was more important than its capacity to adsorb atrazine, and was similar under all four management practices (Kd ranged from 30 to 40 L kg(-1)). The HA adsorption was attributed to the type and amount of clay in the soil, which is unaffected by agronomic management. Soils under conservation agriculture had higher atrazine retention potential than soils under conventional tillage, the system that predominates in the study area.
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Affiliation(s)
- B Prado
- a Instituto de Geología, UNAM , Ciudad Universitaria , México , D.F. , Mexico
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Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo. Appl Environ Microbiol 2013; 79:7290-7. [PMID: 24056463 DOI: 10.1128/aem.02541-13] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
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Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Appl Environ Microbiol 2013; 79:5450-7. [PMID: 23793630 DOI: 10.1128/aem.00268-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.
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Bissett A, Brown MV, Siciliano SD, Thrall PH. Microbial community responses to anthropogenically induced environmental change: towards a systems approach. Ecol Lett 2013; 16 Suppl 1:128-39. [DOI: 10.1111/ele.12109] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/17/2012] [Accepted: 02/26/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Andrew Bissett
- CSIRO Plant Industry; PO Box 1600; Canberra; 2601; Australia
| | - Mark V. Brown
- School of Biotechnology and Biomolecular Sciences and Ecology and Evolution Research Center; University of New South Wales; Sydney; 2052; Austraila
| | | | - Peter H. Thrall
- CSIRO Plant Industry; PO Box 1600; Canberra; 2601; Australia
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Takenaka S, Nomura R, Minegishi A, Yoshida KI. Enrichment and characterization of a bacterial culture that can degrade 4-aminopyridine. BMC Microbiol 2013; 13:62. [PMID: 23517195 PMCID: PMC3637104 DOI: 10.1186/1471-2180-13-62] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/11/2013] [Indexed: 11/23/2022] Open
Abstract
Background The agrichemical 4-aminopyridine is used as a bird repellent in crop fields and has an epileptogenic action in a variety of animals, including man and mouse. 4-Aminopyridine is biodegraded in the environment through an unknown mechanism. Results A 4-aminopyridine-degrading enrichment culture utilized 4-aminopyridine as a carbon, nitrogen, and energy source, generating 4-amino-3-hydroxypyridine, 3,4-dihydroxypyridine, and formate as intermediates. 4-Amino-3-hydroxypyridine could not be further metabolized and probably accumulated as a dead-end product in the culture. Biodegradability tests and partial sequence analysis of the enrichment culture indicated that 4-aminopyridine was mainly degraded via 3,4-dihydroxypyridine and that the metabolite is probably cleaved by 3-hydroxy-4-pyridone dioxygenase. Seven culturable predominant bacterial strains (strains 4AP-A to 4AP-G) were isolated on nutrient agar plates. Changes in the bacterial populations of 4-aminopyridine, 3,4-dihydroxypyridine, or formate/ammonium chloride enrichment cultures were monitored by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Sequence analysis of the 16S rRNA gene fragments derived from predominant DGGE bands indicated that Pseudomonas nitroreducens 4AP-A and Enterobacter sp. 4AP-G were predominant in the three tested enrichment cultures and that the unculturable strains Hyphomicrobium sp. 4AP-Y and Elizabethkingia sp. 4AP-Z were predominant in 4-aminopyridine and formate/ammonium chloride enrichment cultures and in the 3,4-dihydroxypyridine enrichment culture, respectively. Among the culturable strains, strain 4AP-A could utilize 3,4-dihydroxypyridine as a growth substrate. Although we could not isolate strain 4AP-Y on several media, PCR-DGGE analysis and microscopy indicated that the unique bi-polar filamentous bacterial cells gradually became more dominant with increasing 4-aminopyridine concentration in the medium. Conclusions Hyphomicrobium sp. 4AP-Y, P. nitroreducens 4AP-A, and Elizabethkingia sp. 4AP-Z probably play important roles in 4-aminopyridine degradation in crop fields. In the enrichment culture, 3,4-dihydroxypyridine and its metabolites including formate might be shared as growth substrates and maintain the enrichment culture, including these indispensable strains.
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Affiliation(s)
- Shinji Takenaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics. Microbiol Res 2012; 168:165-73. [PMID: 23083746 DOI: 10.1016/j.micres.2012.09.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/20/2012] [Accepted: 09/17/2012] [Indexed: 12/22/2022]
Abstract
Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.
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Cross-site soil microbial communities under tillage regimes: fungistasis and microbial biomarkers. Appl Environ Microbiol 2012; 78:8191-201. [PMID: 22983972 DOI: 10.1128/aem.02005-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy.
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Ng JP, Hollister EB, González-Chávez MDCA, Hons FM, Zuberer DA, Aitkenhead-Peterson JA, Loeppert R, Gentry TJ. Impacts of Cropping Systems and Long-Term Tillage on Soil Microbial Population Levels and Community Composition in Dryland Agricultural Setting. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/487370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Few studies have used molecular methods to correlate the abundance of specific microbial taxonomic groups with changes in soil properties impacted by long-term agriculture. Community qPCR with 16S rRNA gene sequencing to examine the effects of long-term crop-management practices (no-till vs. conventional tillage, and continuous wheat (Triticum aestivum L.) vs. sorghum-wheat-soybean rotation (Sorghum bicolor L. Moench-Triticum aestivum L.-Glycine max L. Merr) on bacterial and fungal relative abundances and identify the dominant members of the soil microbial community. The qPCR assays revealed that crop rotation decreased bacterial copy numbers, but no-till practices did not significantly alter bacteria or fungi relative to conventional tillage. Cyanobacteria were more abundant while Actinobacteria were less numerous under continuous wheat. Acidobacteria and Planctomycetes were positively correlated with soil microbial biomass C and N. This study highlights ways cropping systems affect microbial communities and aids the development of sustainable agriculture.
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Affiliation(s)
- Justin P. Ng
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
- Programa de Edafología, Colegio de Postgraduados en Ciencias Agrícolas, Campus Montecillo, Carr. México-Texcoco, 56230 Montecillo, MEX, Mexico
| | - Emily B. Hollister
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - Ma. del Carmen A. González-Chávez
- Programa de Edafología, Colegio de Postgraduados en Ciencias Agrícolas, Campus Montecillo, Carr. México-Texcoco, 56230 Montecillo, MEX, Mexico
| | - Frank M. Hons
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - David A. Zuberer
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | | | - Richard Loeppert
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - Terry J. Gentry
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
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