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Ding J, Wang N, Liu P, Liu B, Zhu Y, Mao J, Wang Y, Ding X, Yang H, Wei Y, Li J, Ding GC. Bacterial wilt suppressive composts: Significance of rhizosphere microbiome. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 169:179-185. [PMID: 37453305 DOI: 10.1016/j.wasman.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Composts are often suppressive to several plant diseases, including the devastating bacterial wilt caused by Ralstonia solanacearum. However, the underlying mechanisms are still unclear. Herein, we carried out an experiment with 38 composts collected from different factories in China to study the interlinking among bacterial wilt suppression, the physicochemical properties and bacterial community of the compost, and bacterial community in the rhizosphere of tomato fertilized by compost. Totally 26 composts were suppressive to bacterial wilt, while six composts stimulated the disease. The control efficiency was neither correlated with physicochemical properties (TC, TN, P and K, pH or GI) nor bacterial community of compost, but with rhizosphere bacterial community (r = 0.17, p = 0.016). The control efficiency was also positive correlated with taxa (Rhizobium, Aeromicrobium) known suppressive to R. solanacearum. The mushroom spent or cow manure, from which the two composts were 100% and 77% in control efficiencies against bacterial wilt respectively were subject to a pilot-scale composting reaction. The reproduced composts from mushroom spent or cow manure were only 57% and 23% effective on the control of bacterial wilt, respectively. The analysis of bacterial communities revealed that the relative abundances of R. solanacearum were 28.4% for the control, but only 7.8%-7.9% for compost fertilized tomatoes. The compost from mushroom spent also exerted a strong effect on rhizosphere bacterial community. Taken together, most composts were suppressive to bacterial wilt possibly also by modifying rhizosphere bacterial community towards inhibiting the colonization of R. solanacearum and selecting for beneficial genera of Proteobacteria, Bacteroidetes and Actinobacteria.
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Affiliation(s)
- Jia Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ning Wang
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Pingping Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Baoju Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yuelin Zhu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Jing Mao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yue Wang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Hefa Yang
- Quzhou Experimental Station, China Agricultural University, 057250 Hebei Province, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China.
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Wahla AQ, Anwar S, Fareed MI, Ikram W, Ali L, Alharby HF, Bamagoos AA, Almaghamsi AA, Iqbal S, Ali S. Immobilization of metribuzin-degrading bacteria on biochar: Enhanced soil remediation and bacterial community restoration. Front Microbiol 2023; 13:1027284. [PMID: 36875536 PMCID: PMC9983365 DOI: 10.3389/fmicb.2022.1027284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/03/2022] [Indexed: 02/17/2023] Open
Abstract
Metribuzin (MB), a triazinone herbicide is extensively sprayed for weed control in agriculture, has been reported to contaminate soil, groundwater, and surface waters. In soil, MB residues can negatively affect not only the germination of subsequent crops but also disturb soil bacterial community. The present study describes the use of biochar as a carrier material to immobilize MB-degrading bacterial consortium, for remediation of MB-contaminated soil and restoration of soil bacterial community in soil microcosms. The bacterial consortium (MB3R) comprised four bacterial strains, i.e., Rhodococcus rhodochrous AQ1, Bacillus tequilensis AQ2, Bacillus aryabhattai AQ3, and Bacillus safensis AQ4. Significantly higher MB remediation was observed in soil augmented with bacterial consortium immobilized on biochar compared to the soil augmented with un-immobilized bacterial consortium. Immobilization of MB3R on biochar resulted in higher MB degradation rate (0.017 Kd-1) and reduced half-life (40 days) compared to 0.010 Kd-1 degradation rate and 68 day half-life in treatments where un-immobilized bacterial consortium was employed. It is worth mentioning that the MB degradation products metribuzin-desamino (DA), metribuzin-diketo (DK), and metribuzin desamino-diketo (DADK) were detected in the treatments where MB3R was inoculated either alone or in combination with biochar. MB contamination significantly altered the composition of soil bacteria. However, soil bacterial community was conserved in response to augmentation with MB3R immobilized on biochar. Immobilization of the bacterial consortium MB3R on biochar can potentially be exploited for remediation of MB-contaminated soil and protecting its microbiota.
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Affiliation(s)
- Abdul Qadeer Wahla
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Samina Anwar
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Irfan Fareed
- Department of Life Sciences, School of Science, University of Management and Technology, Johar Town, Lahore, Pakistan
| | - Wasiq Ikram
- School of Botany, Minhaj University Lahore (MUL), Lahore, Pakistan
| | - Liaqat Ali
- Department of Soil and Environmental Sciences, University of Agriculture Faisalabad, Sub Campus Burewala, Vehari, Pakistan
| | - Hesham F. Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Plant Biology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif A. Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Afaf A. Almaghamsi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Samina Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Shafaqat Ali
- Department of Environmental Science, Government College University, Faisalabad, Pakistan
- Department of Biological Sciences and Technology, China Medical University, Taichung, Taiwan
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Jiang Z, An N, Chu Y, Cao B, Wu F, Zhang Y, Zhang Y, Li Y, Zhang Y. Growth, biofilm formation and atrazine degrading gene (trzN) expression of Arthrobacter sp. DNS10 cultured with montmorillonite, kaolinite and goethite. CHEMOSPHERE 2022; 307:135904. [PMID: 35940415 DOI: 10.1016/j.chemosphere.2022.135904] [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: 05/31/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
The viable and degradation potential of the strains which adhered to soil minerals are essential for eliminating organic pollutants from soil. Herein, the interaction (growth, biofilm formation and survive) of Arthrobacter sp. DNS10, an atrazine degrading strain, with three kinds of typical soil minerals, such as montmorillonite, kaolinite and goethite, as well as the atrazine degradation gene (trzN) expression of the strain in the minerals system were studied. The results showed that montmorillonite had significant promotion effect on the growth of strain DNS10, followed by kaolinite, but goethite significantly inhibited the growth of strain DNS10. In contrast, goethite notably promoted the biofilm formation and there was less biofilm detected in montmorillonite containing system. The percentage of the survival bacteria in the biofilm that formed on montmorillonite, kaolinite and goethite was 53.8%, 40.8% and 28.2%. In addition, there were more reactive oxygen species (ROS) were detected in the cells that exposed to goethite than those of the cells exposed to kaolinite and montmorillonite. These results suggest that the electrostatic repulsion between kaolinite/montmorillonite and strain DNS10 prevents them from contacting each other and facilitates bacterial growth by allowing the strain to obtain more nutrients. Oppositely, the needle-like morphology of goethite might damage the strain DNS10 cell when they were combined by electrostatic attraction, and the goethite induced ROS also aggravate the cytotoxicity of goethite on strain DNS10. In addition, the relative transcription of trzN in the cells contacted with montmorillonite, kaolinite and goethite was 0.94-, 0.27- and 0.20- fold of the no mineral exposure treatment. Briefly, this research suggests that the minerals with different structure and/or physicochemical characteristics might cause various trend for the biofilm formation and degradation potential of the bacteria.
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Affiliation(s)
- Zhao Jiang
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ning An
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yuxin Chu
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Bo Cao
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Fengxue Wu
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yue Zhang
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yuxin Zhang
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yu Li
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ying Zhang
- School of Resources &; Environment, Northeast Agricultural University, Harbin, 150030, PR China; Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130132, PR China.
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4
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Abstract
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~105-fold by mineralogy and ~103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. IMPORTANCE Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.
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5
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Chang X, Song Z, Xu Y, Gao M. Response of soil characteristics to biochar and Fe-Mn oxide-modified biochar application in phthalate-contaminated fluvo-aquic soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112755. [PMID: 34500388 DOI: 10.1016/j.ecoenv.2021.112755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/15/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Biochar (BC) derived from agricultural biomass is effective at immobilizing phthalate in the agricultural soil environment. In this study, we assessed the effects of 0.5%, 1%, and 2% BC and Fe-Mn oxide-modified biochar (FMBC) addition on dibutyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP) residues and biochemical characteristics in the rhizosphere soil of mature wheat polluted with DBP and DEHP using a pot experiment. Scanning electron microscopy showed that the surfaces and pores of BC and FMBC adhered soil mineral particles after remediation. Therefore, DBP and DEHP residues were increased in BC- and FMBC-treated soils. Illumina HiSeq sequencing showed that, compared with the control, BC and FMBC addition significantly enhanced the relative abundance of Firmicutes and reduced Proteobacteria. The abundance of Sphenodons and Pseudomonas, which degrade phthalates, tended to be higher in FMBC-amended soils than in BC-amended and control soils. This result may be related to an increase in available nutrients and organic matter following BC and FMBC application. Subsequently, the changes in soil bacterial abundance and community structure induced an increase in polyphenol oxidase, β-glucosidase, neutral phosphatase, and protease activity in BC and FMBC remediation. In comparison with the BC treatment, FMBC addition had a significantly positive effect on enzyme activity, and the microbial structure and was therefore more effective at immobilizing DBP and DEHP in the soil. Thus, our findings strongly suggest that FMBC is a reliable remediation material for phthalate-contaminated soil.
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Affiliation(s)
- Xipeng Chang
- School of Environmental Science and Engineering, Tiangong University, No. 399 Binshui West Road, Xiqing District, Tianjin 300387, China
| | - Zhengguo Song
- Department of Civil and Environmental Engineering, Shantou University, No. 243 Daxue Road, Shantou, Guangdong Province 515063, China
| | - Yalei Xu
- School of Environmental Science and Engineering, Tiangong University, No. 399 Binshui West Road, Xiqing District, Tianjin 300387, China
| | - Minling Gao
- Department of Civil and Environmental Engineering, Shantou University, No. 243 Daxue Road, Shantou, Guangdong Province 515063, China.
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6
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Tanuwidjaja I, Vogel C, Pronk GJ, Schöler A, Kublik S, Vestergaard G, Kögel-Knabner I, Mrkonjic Fuka M, Schloter M, Schulz S. Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition. MICROBIAL ECOLOGY 2021; 81:897-907. [PMID: 33161521 PMCID: PMC8062357 DOI: 10.1007/s00248-020-01635-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/27/2020] [Indexed: 05/24/2023]
Abstract
Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.
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Affiliation(s)
- Irina Tanuwidjaja
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Cordula Vogel
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute of Soil Science and Site Ecology, Dresden University of Technology, Tharandt, Germany
| | - Geertje J Pronk
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
- KWR Watercycle Research Institute, Nieuwegein, Netherlands
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ingrid Kögel-Knabner
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Mirna Mrkonjic Fuka
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany.
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Jiang H, Huang J, Li L, Huang L, Manzoor M, Yang J, Wu G, Sun X, Wang B, Egamberdieva D, Panosyan H, Birkeland NK, Zhu Z, Li W. Onshore soil microbes and endophytes respond differently to geochemical and mineralogical changes in the Aral Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142675. [PMID: 33077208 DOI: 10.1016/j.scitotenv.2020.142675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
There is limited knowledge about how microbiome develops along the geochemical and mineralogical change in onshore soils derived from continuous desiccation of lakes. In this study, geochemistry and mineralogy were studied in the Aral Sea onshore soils exposed in different periods (from the 1970s to 2018), followed by microbial analyses on the studied soils and the aboveground organs of dominant plants. The soils exhibited an increasing gradient of total soluble salts (TSS: 0.4-0.5 g/L to 71.3 g/L) and evaporite minerals (e.g., gypsum, halite) from the farshore to the nearshore. In the studied soils, microbial diversity decreased with increasing TSS, and microbial community dissimilarities among samples was positively correlated with the contents of gypsum and calcite minerals. Among the measured environmental variables, minerals contributed most to the observed microbial variation. In contrast, the endophytic microbial communities in the aboveground organs of dominant plants were not related to any of the measured variables, indicating that they differed from their soil counterparts with respect to their responses to geochemical and mineralogical variations in soils. In summary, these results help us understand the response of onshore soil microbiome to the decline of lake water caused by continuous desiccation.
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Affiliation(s)
- Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mehvish Manzoor
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Dilfuza Egamberdieva
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany; Faculty of Biology, National University of Uzbekistan, Tashkent, Uzbekistan.
| | - Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025 Yerevan, Armenia
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
| | - Zihua Zhu
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wenjun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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8
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Wahla AQ, Anwar S, Mueller JA, Arslan M, Iqbal S. Immobilization of metribuzin degrading bacterial consortium MB3R on biochar enhances bioremediation of potato vegetated soil and restores bacterial community structure. JOURNAL OF HAZARDOUS MATERIALS 2020; 390:121493. [PMID: 32081488 DOI: 10.1016/j.jhazmat.2019.121493] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Metribuzin (MB) is a triazinone herbicide used for the eradication of weeds in agriculture. Presence of its residues in agricultural soil can potentially harm the establishment of subsequent crops and structure of soil microbial populations. In this study, remediation potential of an MB degrading bacterial consortium MB3R immobilized on biochar was evaluated in potato vegetated soil. In potato vegetated soil augmented with MB3R alone and MB3R immobilized on biochar, 82 and 96% MB degradation was recorded respectively as compared to only 29.3% in un-augmented soil. Kinetic parameters revealed that MB3R immobilized biochar is highly proficient as indicated by significant increase in the rate of biodegradation and decrease in half-life of MB. Enhanced plant growth was observed when augmented with bacterial consortium either alone or immobilized on biochar. Presence of herbicide negatively affected the soil bacterial community structure. However, MB3R immobilized on biochar proved to be helpful for restoration of soil bacterial community structure affected by MB. This is the very first report that reveals improved remediation of contaminated soil and restoration of soil bacterial populations by use of the MB degrading bacterial consortium immobilized on biochar.
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Affiliation(s)
- Abdul Qadeer Wahla
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Samina Anwar
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Jochen A Mueller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, Germany
| | - Muhammad Arslan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, Germany
| | - Samina Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
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Yang J, Jiang H, Sun X, Chen J, Xie Z, Dong H. Minerals play key roles in driving prokaryotic and fungal communities in the surface sediments of the Qinghai-Tibetan lakes. FEMS Microbiol Ecol 2020; 96:5780223. [DOI: 10.1093/femsec/fiaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/02/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
There is limited knowledge of the relative influences of deterministic and stochastic processes on prokaryotic and fungal communities in lake sediments. In this study, we surveyed the prokaryotic and fungal community compositions and their influencing factors in 23 surface sediments from six lakes on the Qinghai-Tibetan Plateau (QTP) with the use of Illumina sequencing. The results showed the distribution of prokaryotic and fungal communities in the studied QTP lake sediments was shaped by different assembly processes, with prokaryotes primarily governed by variable selection and homogenizing dispersal (accounting for 57.9% and 37.3% of the observed variations) and fungi being mainly regulated by variable selection, non-dominant processes and homogenizing dispersal (38.3%, 43.7% and 13.7%, respectively). Regarding the variable selection, mineralogical variables played key roles in shaping prokaryotic and fungal community structures. Collectively, these findings expand current knowledge concerning the influences of deterministic (e.g. variable selection) and stochastic processes (e.g. homogenizing dispersal and non-dominant processes) on the prokaryotic and fungal distribution in the QTP lakes.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Junsong Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, 45056, USA
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10
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Vieira S, Sikorski J, Gebala A, Boeddinghaus RS, Marhan S, Rennert T, Kandeler E, Overmann J. Bacterial colonization of minerals in grassland soils is selective and highly dynamic. Environ Microbiol 2019; 22:917-933. [DOI: 10.1111/1462-2920.14751] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/14/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
| | - Aurelia Gebala
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Runa S. Boeddinghaus
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Sven Marhan
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Thilo Rennert
- Department of Soil Chemistry and PedologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Ellen Kandeler
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
- Braunschweig University of Technology Braunschweig Germany
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11
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Meschewski E, Holm N, Sharma BK, Spokas K, Minalt N, Kelly JJ. Pyrolysis biochar has negligible effects on soil greenhouse gas production, microbial communities, plant germination, and initial seedling growth. CHEMOSPHERE 2019; 228:565-576. [PMID: 31055071 DOI: 10.1016/j.chemosphere.2019.04.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 05/21/2023]
Abstract
Biochar has been promoted as a soil amendment that enhances soil quality and agronomic productivity and reduces greenhouse gas production. However, these benefits are not always realized. A major hurdle to the beneficial use of biochar is our limited knowledge regarding the mechanisms directing its effects on soil systems. This project aimed to eliminate some of this uncertainty by examining the biological responses (plant productivity, greenhouse gas production, soil microbial community structure) of a suite of soils (10) to the addition of biochars produced by different processes (pyrolysis, gasification, burning) from a range of feedstocks (corn stalks, hardwood, grass). Results indicated that these three responses were not significantly impacted by the addition of pyrolysis biochars from different feedstocks at 1 and 5% (w/w) addition levels. On the other hand, both an open-air burned corn stalk (5%) and raw corn stalks (1 and 5%) additions did alter the measured soil functionality. For example, the 5% burnt corn stalks addition reduced total above ground plant biomass (∼30%), increased observed N2O production by an order of magnitude, and altered soil bacterial community structure. The bacterial groups that increased in relative abundance in the burnt corn stalks-amended soils included families associated with cellulose decomposition (Chitinophagaceae), plant pathogens (Xanthomonadaceae), and biochar/charcoal-amended media (Gemmatimonadetes). In contrast, the abundance of these bacterial groups was not impacted by the pyrolysis biochars. Therefore, this research suggests that pyrolysis biochar represents a stabilized form of carbon that is resistant to microbial mineralization and has negligible effects on soil biological responses.
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Affiliation(s)
- Elizabeth Meschewski
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA.
| | - Nancy Holm
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA
| | - Brajendra K Sharma
- Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign, USA
| | - Kurt Spokas
- Agricultural Research Service, United States Department of Agriculture (USDA), USA
| | - Nicole Minalt
- Department of Biology, Loyola University Chicago, USA
| | - John J Kelly
- Department of Biology, Loyola University Chicago, USA
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12
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Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol. Appl Environ Microbiol 2019; 85:AEM.02957-18. [PMID: 30952661 DOI: 10.1128/aem.02957-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO2 emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO2 production.
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13
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Andrés P, Rosell-Melé A, Colomer-Ventura F, Denef K, Cotrufo MF, Riba M, Alcañiz JM. Belowground biota responses to maize biochar addition to the soil of a Mediterranean vineyard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:1522-1532. [PMID: 30743944 DOI: 10.1016/j.scitotenv.2019.01.101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Biochar is a high carbon material resulting from biomass pyrolysis that, when applied to croplands, can increase soil carbon and soil water retention. Both effects are of critical importance in semi-arid regions, where carbon decline and desertification are the main drivers of soil degradation. Since most environmental services provided by soil are mediated by belowground biota, effects of biochar on soil microbial and invertebrate communities must be evaluated under field conditions before its agricultural application can be recommended. We tested maize biochar for its mid-term effect on soil microbes and micro-arthropods of a Mediterranean vineyard. We applied biochar to three field plots with neutral sandy loam soils at a dose of 5 Mg ha-1. During two years, we monitored the abundance of functional groups of soil micro-arthropods and estimated the biomass of soil microbial groups. We also analyzed the δ13C value of microbial PLFA biomarkers to determine biochar-C utilization by each microbial group taking advantage of the δ13C natural abundance differences between the applied biochar and the soil. Biochar addition significantly reduced soil microbial biomass but did not alter the functional microbial diversity nor the abundance or biodiversity of soil micro-arthropods. The contribution of biochar-C to the diet of most microbial groups was very low through the monitoring period. However, two gram-negative bacterial groups increased their biochar-derived carbon uptake under extreme soil dryness, which suggests that biochar-C might help soil microbes to overcome the food shortage caused by drought. The decrease in microbial biomass observed in our experiment and the concomitant decrease of SOM mineralization could contribute to the carbon sequestration potential of Mediterranean soils after biochar addition.
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Affiliation(s)
- Pilar Andrés
- CREAF, Edifici C, Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; ICTA, Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| | - Antoni Rosell-Melé
- ICTA, Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | | | - Karolien Denef
- Central Instrument Facility, Chemistry Department, Colorado State University, 1301 Center Avenue. Campus Delivery 1872. Fort Collins, CO 80523-1872, USA
| | - M Francesca Cotrufo
- Natural Resource Ecology Laboratory, Soil and Crop Sciences Department, Colorado State University, 200 W. Lake. Campus Delivery 1499. Fort Collins, CO 80523-1499, USA
| | - Miquel Riba
- CREAF, Edifici C, Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Department of Animal Biology, Plant Biology and Ecology, Faculty of Sciences, Autonomous University of Barcelona, Edifici C, Campus UAB, 08193, Cerdanyola del Vallès. Barcelona, Spain
| | - Josep M Alcañiz
- CREAF, Edifici C, Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Department of Animal Biology, Plant Biology and Ecology, Faculty of Sciences, Autonomous University of Barcelona, Edifici C, Campus UAB, 08193, Cerdanyola del Vallès. Barcelona, Spain
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14
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Li H, Cai X, Gong J, Xu T, Ding GC, Li J. Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight ( Phytophthora capsici). Front Microbiol 2019; 10:342. [PMID: 30873141 PMCID: PMC6401385 DOI: 10.3389/fmicb.2019.00342] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of organic, integrated, and conventionally managed soils to pepper blight (Phytophthora capsici) was studied in growth chamber experiments. Disease incidence was 41.3 and 34.1% lower in the soil from an organic farming system than in either the soil from the integrated or from the conventional farming systems, respectively. Beta-diversity of rhizospheric microbial communities differed among treatments, with enrichment of Bacillus, Sporosarcina, Acidobacteria Gp5, Gp6, Gp22, and Ignavibacterium by the organic soil. Cultivation-dependent analysis indicated that 50.3% of in vitro antagonists of P. capsici isolated from the rhizosphere of healthy peppers were affiliated to Bacillus. An integration of in vitro antagonists and bacterial diversity analyses indicated that Bacillus antagonists were higher in the rhizosphere of pepper treated by the organic soil. A microbial consortium of 18 in vitro Bacillus antagonists significantly increased the suppressiveness of soil from the integrated farming system against pepper blight. Overall, the soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly owing to Bacillus antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppression under greenhouse conditions.
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Affiliation(s)
- Huixiu Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xiaoxu Cai
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jingyang Gong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guo-chun Ding
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, China
| | - Ji Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, China
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15
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Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana. Braz J Microbiol 2018; 49:757-769. [PMID: 29866608 PMCID: PMC6175736 DOI: 10.1016/j.bjm.2018.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 02/01/2018] [Accepted: 02/14/2018] [Indexed: 11/23/2022] Open
Abstract
Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.
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16
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Sheng Y, Zhu L. Biochar alters microbial community and carbon sequestration potential across different soil pH. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:1391-1399. [PMID: 29890604 DOI: 10.1016/j.scitotenv.2017.11.337] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/29/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
Biochar application to soil has been proposed for soil carbon sequestration and global warming mitigation. While recent studies have demonstrated that soil pH was a main factor affecting soil microbial community and stability of biochar, little information is available for the microbiome across different soil pH and the subsequently CO2 emission. To investigate soil microbial response and CO2 emission of biochar across different pH levels, comparative incubation studies on CO2 emission, degradation of biochar, and microbial communities in a ferralsol (pH5.19) and a phaeozems (pH7.81) with 4 biochar addition rates (0.5%, 1.0%, 2.0%, 5.0%) were conducted. Biochar induced higher CO2 emission in acidic ferralsol, largely due to the higher biochar degradation, while the more drastic negative priming effect (PE) of SOC resulted in decreased total CO2 emission in alkaline phaeozems. The higher bacteria diversity, especially the enrichment of copiotrophic bacteria such as Bacteroidetes, Gemmatimonadetes, and decrease of oligotrophic bacteria such as Acidobacteria, were responsible for the increased CO2 emission and initial positive PE of SOC in ferralsol, whereas biochar did not change the relative abundances of most bacteria at phylum level in phaeozems. The relative abundances of other bacterial taxa (i.e. Actinobacteria, Anaerolineae) known to degrade aromatic compounds were also elevated in both soils. Soil pH was considered to be the dominant factor to affect CO2 emission by increasing the bioavailability of organic carbon and abundance of copiotrophic bacteria after biochar addition in ferralsol. However, the decreased bioavailability of SOC via adsorption of biochar resulted in higher abundance of oligotrophic bacteria in phaeozems, leading to the decrease in CO2 emission.
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Affiliation(s)
- Yaqi Sheng
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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17
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Holmsgaard PN, Dealtry S, Dunon V, Heuer H, Hansen LH, Springael D, Smalla K, Riber L, Sørensen SJ. Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 229:854-862. [PMID: 28734695 DOI: 10.1016/j.envpol.2017.07.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.
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Affiliation(s)
- Peter N Holmsgaard
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Simone Dealtry
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany; Civil Engineering Department, Catholic University of Rio de Janeiro, Rua Marquês de São Vicente 225/301-L, Gávea, 22453-900 Rio de Janeiro, RJ, Brazil
| | - Vincent Dunon
- Division of Soil and Water Management, KULeuven, 3001 Leuven, Belgium
| | - Holger Heuer
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Lars H Hansen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Dirk Springael
- Division of Soil and Water Management, KULeuven, 3001 Leuven, Belgium
| | - Kornelia Smalla
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Leise Riber
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| | - Søren J Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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18
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Ma W, Peng D, Walker SL, Cao B, Gao CH, Huang Q, Cai P. Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides. NPJ Biofilms Microbiomes 2017. [PMID: 28649405 PMCID: PMC5445608 DOI: 10.1038/s41522-017-0013-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid-air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3-16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid-air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.
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Affiliation(s)
- Wenting Ma
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sharon L Walker
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521 USA
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070 China
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19
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Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars. ISME JOURNAL 2017; 11:1087-1101. [PMID: 28169988 DOI: 10.1038/ismej.2016.187] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/17/2016] [Accepted: 12/09/2016] [Indexed: 02/04/2023]
Abstract
Biochar and mineral-enriched biochar (MEB) have been used as soil amendments to improve soil fertility, sequester carbon and mitigate greenhouse gas emissions. Such beneficial outcomes could be partially mediated by soil bacteria, however little is known about how they directly interact with biochar or MEB. We therefore analyzed the diversity and functions of bacterial communities on the surfaces of one biochar and two different MEBs after a 140-day incubation in soil. The results show that the biochar and the MEBs harbor distinct bacterial communities to the bulk soil. Communities on biochar and MEBs were dominated by a novel Gammaproteobacterium. Genome reconstruction combined with electron microscopy and high-resolution elemental analysis revealed that the bacterium generates energy from the oxidation of iron that is present on the surface. Two other bacteria belonging to the genus Thiobacillus and a novel group within the Oxalbacteraceae were enriched only on the MEBs and they had the genetic capacity for thiosulfate oxidation. All three surface-enriched bacteria also had the capacity to fix carbon dioxide, either in a potentially strictly autotrophic or mixotrophic manner. Our results show the dominance of chemolithotrophic processes on the surface of biochar and MEB that can contribute to carbon sequestration in soil.
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20
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Kästner M, Miltner A. Application of compost for effective bioremediation of organic contaminants and pollutants in soil. Appl Microbiol Biotechnol 2016; 100:3433-49. [PMID: 26921182 DOI: 10.1007/s00253-016-7378-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 01/27/2023]
Abstract
Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as 'stimulants' of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a 'metabolic memory' within developing and mature compost materials. Compost addition can thus be considered as a 'super-bioaugmentation' with a complex natural mixture of degrading microorganisms, combined with a 'biostimulation' by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.
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Affiliation(s)
- Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Anja Miltner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
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Uroz S, Kelly LC, Turpault MP, Lepleux C, Frey-Klett P. The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities. Trends Microbiol 2015; 23:751-762. [DOI: 10.1016/j.tim.2015.10.004] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/02/2015] [Accepted: 10/09/2015] [Indexed: 11/17/2022]
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Cébron A, Beguiristain T, Bongoua-Devisme J, Denonfoux J, Faure P, Lorgeoux C, Ouvrard S, Parisot N, Peyret P, Leyval C. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13724-13738. [PMID: 25616383 DOI: 10.1007/s11356-015-4117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.
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Affiliation(s)
- Aurélie Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP 70239, 54506, Vandoeuvre-lès-Nancy Cedex, France,
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23
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Muehe EM, Weigold P, Adaktylou IJ, Planer-Friedrich B, Kraemer U, Kappler A, Behrens S. Rhizosphere microbial community composition affects cadmium and zinc uptake by the metal-hyperaccumulating plant Arabidopsis halleri. Appl Environ Microbiol 2015; 81:2173-81. [PMID: 25595759 PMCID: PMC4345380 DOI: 10.1128/aem.03359-14] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 01/08/2015] [Indexed: 12/07/2022] Open
Abstract
The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a "native" and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, "Candidatus Chloracidobacterium") of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy.
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Affiliation(s)
- E Marie Muehe
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Pascal Weigold
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Irini J Adaktylou
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Ute Kraemer
- Department of Plant Physiology, Ruhr University Bochum, Bochum, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Sebastian Behrens
- Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
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24
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Steinbach A, Schulz S, Giebler J, Schulz S, Pronk GJ, Kögel-Knabner I, Harms H, Wick LY, Schloter M. Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation. ISME JOURNAL 2014; 9:1687-91. [PMID: 25535940 DOI: 10.1038/ismej.2014.243] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 11/12/2014] [Accepted: 11/16/2014] [Indexed: 11/09/2022]
Abstract
Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.
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Affiliation(s)
- Annelie Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stefanie Schulz
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Giebler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schulz
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Geertje J Pronk
- 1] Chair of Soil Science, Technische Universität München, Freising, Germany [2] Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Ingrid Kögel-Knabner
- 1] Chair of Soil Science, Technische Universität München, Freising, Germany [2] Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Hauke Harms
- 1] Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Michael Schloter
- 1] Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany [2] Chair of Soil Science, Technische Universität München, Freising, Germany
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25
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Hemkemeyer M, Pronk GJ, Heister K, Kögel-Knabner I, Martens R, Tebbe CC. Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particle size fractions. FEMS Microbiol Ecol 2014; 90:770-82. [PMID: 25303098 DOI: 10.1111/1574-6941.12436] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 11/30/2022] Open
Abstract
Artificial soils were used in this study to analyse the importance of different mineral compositions for the diversity of soil microorganisms. Variants containing montmorillonite (MT), illite (IL) and illite + ferrihydrite (IL+FH) were compared to each other. Bulk material and their particle size fractions, as obtained by ultracentrifugation and wet-sieving, were characterised for abundance and diversity of Bacteria, Archaea and Fungi. Samples were analysed 6 and 18 months after inoculation with sterilised manure and a soil-extracted microbial community. Generally, IL, and even more pronouncedly IL+FH, supported the growth of more Bacteria, Archaea and Fungi, than MT. This trend was most pronounced in the finest fraction (< 20 μm). The structural diversity of Fungi responded more strongly to the different mineral compositions than the Bacteria, for which particle size fractions were more important. Archaea established a specific community in the finest fraction and showed no response to the different mineral compositions. Overall, this study demonstrates that the mineral composition and the particle size fractions have specific and different selective effects on the three domains and, thus, suggests that these factors strongly contribute to niche separation and the high diversity of microbial communities in natural soils with complex mineral compositions.
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Affiliation(s)
- Michael Hemkemeyer
- Thünen Institute of Biodiversity, Federal Research Institute for Rural Areas, Forestry and Fisheries, Braunschweig, Germany
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26
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Babin D, Vogel C, Zühlke S, Schloter M, Pronk GJ, Heister K, Spiteller M, Kögel-Knabner I, Smalla K. Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils. PLoS One 2014; 9:e106865. [PMID: 25222697 PMCID: PMC4164357 DOI: 10.1371/journal.pone.0106865] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/08/2014] [Indexed: 11/30/2022] Open
Abstract
The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.
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Affiliation(s)
- Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Cordula Vogel
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Sebastian Zühlke
- Institut für Umweltforschung (INFU), Lehrstuhl für Umweltchemie und Analytische Chemie der Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Geertje Johanna Pronk
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Katja Heister
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Michael Spiteller
- Institut für Umweltforschung (INFU), Lehrstuhl für Umweltchemie und Analytische Chemie der Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Ingrid Kögel-Knabner
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- * E-mail:
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27
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Grattepanche JD, Santoferrara LF, McManus GB, Katz LA. Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria. Trends Microbiol 2014; 22:432-7. [PMID: 24814699 DOI: 10.1016/j.tim.2014.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/31/2014] [Accepted: 04/11/2014] [Indexed: 01/05/2023]
Abstract
Recent advances such as high-throughput sequencing (HTS) have changed conceptions about the magnitude of diversity on Earth. This is especially true for microbial lineages, which have seen the discovery of great numbers of rare forms in places such as the human gut as well as diverse environments (e.g., freshwater, marine, and soil). Given the differences in perceptions of diversity for bacterial and eukaryotic microbes, including divergent species concepts, HTS tools used to eliminate errors and population-level variation in bacteria may not be appropriate for microbial eukaryotes and may eliminate valid species from the data. We discuss here how the nature of biodiversity varies among microbial groups and the extent to which HTS tools designed for bacteria are useful for eukaryotes.
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Affiliation(s)
| | | | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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28
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Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 2014; 88:424-35. [PMID: 24597529 DOI: 10.1111/1574-6941.12313] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 11/30/2022] Open
Abstract
The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.
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Affiliation(s)
- Joana M Marques
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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29
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Babin D, Ding GC, Pronk GJ, Heister K, Kögel-Knabner I, Smalla K. Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene. FEMS Microbiol Ecol 2013; 86:3-14. [DOI: 10.1111/1574-6941.12058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/06/2012] [Accepted: 12/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | | | - Katja Heister
- Lehrstuhl für Bodenkunde; Technische Universität München; Freising-Weihenstephan; Germany
| | | | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
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