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Gao W, Zhao J, Guo X, Wang F, Chen X, Zhu Z, Ge T, Wang L, Kuzyakov Y, Wu J, Jia Z. Intensive N 2 fixation accelerates microbial turnover in cropland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170081. [PMID: 38220009 DOI: 10.1016/j.scitotenv.2024.170081] [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: 11/23/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Biological nitrogen fixation (BNF) is strongly affected by the carbon (C) and nitrogen (N) stoichiometry in soil and depends on the input of organic C. Due to the high metabolic costs of nitrogenase activity, however, the response of BNF to organic C input and its impact on microbial turnover remain unclear. To address this knowledge gap, we combined 15N2 tracing with high-throughput sequencing by adding glucose or glucose plus mineral N fertilizer for a 12-day incubation in three cropland soils. Glucose addition alone strongly changed the BNF activity (0.76-2.51 mg N kg-1 d-1), while BNF was completely absent after mineral N fertilization. This switch-on of BNF by glucose addition supported equally high rates of microbial growth and organic C mineralization compared with the direct mineral N assimilation by microorganisms. Glucose-induced BNF was predominantly catalyzed by Azotobacter-affiliated free-living diazotrophs (>50 % of the total nifH genes), which increased with diverse nondiazotrophs such as Nitrososphaera, Bacillus and Pseudoxanthomonas. Structural equation models (SEMs) and random forest (RF) analyses consistently revealed that the soil C:N ratio and Azotobacter-affiliated diazotrophic abundances were the key factors affecting glucose-induced BNF. Our findings emphasize the importance of free-living diazotrophs for microbial turnover of organic C in soil.
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Affiliation(s)
- Wei Gao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jun Zhao
- Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, Institute for Food and Agricultural Sciences (IFAS), University of Florida, Davie, FL 33314, USA
| | - Xiaobin Guo
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xiangbi Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Zhenke Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Lianfeng Wang
- College of Environmental and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, PR China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen 37077, Germany; Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia; Institute of Environmental Sciences, Kazan Federal University, Kazan 420049, Russia
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China.
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2
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Zeng JY, Wang XS, Liu XH, Li QR, Feng J, Zhang XZ. Light-driven biohybrid system utilizes N 2 for photochemical CO 2 reduction. Natl Sci Rev 2023; 10:nwad142. [PMID: 37426486 PMCID: PMC10325001 DOI: 10.1093/nsr/nwad142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/03/2023] [Accepted: 05/11/2023] [Indexed: 07/11/2023] Open
Abstract
Attempting to couple photochemical CO2 reduction with N2 fixation is usually difficult, because the reaction conditions for these two processes are typically incompatible. Here, we report that a light-driven biohybrid system can utilize abundant, atmospheric N2 to produce electron donors via biological nitrogen fixation, to achieve effective photochemical CO2 reduction. This biohybrid system is constructed by incorporating molecular cobalt-based photocatalysts into N2-fixing bacteria. It is found that N2-fixing bacteria can convert N2 into reductive organic nitrogen and create a localized anaerobic environment, which allows the incorporated photocatalysts to continuously perform photocatalytic CO2 reduction under aerobic conditions. Specifically, the light-driven biohybrid system displays a high formic acid production rate of over 1.41 × 10-14 mol h-1 cell-1 under visible light irradiation, and the organic nitrogen content undergoes an over-3-fold increase within 48 hours. This work offers a useful strategy for coupling CO2 conversion with N2 fixation under mild and environmentally benign conditions.
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Affiliation(s)
| | | | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, and Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Qian-Ru Li
- Key Laboratory of Biomedical Polymers of Ministry of Education, and Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jun Feng
- Key Laboratory of Biomedical Polymers of Ministry of Education, and Department of Chemistry, Wuhan University, Wuhan 430072, China
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3
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Yadav A, Boruah JLH, Geed SR, Sharma RK, Saikia R. Occurrence, identification and characterization of diazotrophic bacteria from aerial roots of Rhynchostylis retusa (L.) Blume for plant growth-promoting activity. Arch Microbiol 2023; 205:131. [PMID: 36947279 DOI: 10.1007/s00203-023-03458-3] [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: 11/12/2022] [Revised: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 03/23/2023]
Abstract
In this study, the diversity of diazotrophic bacteria of orchid Rhynchostylis retusa (L.) Blume and its potential application in plant growth promotion were evaluated. About 183 nitrogen-fixing bacteria were isolated to screen various plant growth-promoting traits viz. phosphate solubilization,IAA, siderophore, HCN, biofilm and ammonia production. Based on 16S rRNA gene sequencing analysis Achromobacter, Arthrobacter, Acinetobacter, Bacillus, Brevibacterium, Curtobacterium, Erwinia, Kosakonia, Lysinibacillus, Klebseilla, Microbacterium, Mixta, Pantoea, Pseudomonas and Stenotrophomonas isolates were selected and showed positive results for PGP traits. Overall, genus Pantoea, Brevibacterium, Achromobacter, Arthrobacter, Klebsiella, Mixta, Bacillus, and Pseudomonas had the most pronounced PGP characteristics and acetylene reduction among the screened isolates. BOX PCR fingerprinting analysis showed variation in polymorphic banding patterns among diazotrophic strains. PCR amplification of nifH gene and the presence of 37 kDa nitrogenase reductase enzyme band in western blot indicated presence of nitrogenase activity. Our study showed that orchid R. retusa diazotroph interaction helps orchid plant to fix nitrogen, essential nutrients, and control pathogen entry. To the best of our knowledge, this is the first report on characterization of diazotrophic bacterial community from aerial roots of R. retusa.
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Affiliation(s)
- Archana Yadav
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.
- Department of Applied Biology, University of Science and Technology, Baridua, Meghalaya, India.
| | - Jyoti Lakshmi Hati Boruah
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Sachin Rameshrao Geed
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Rabin K Sharma
- Department of Applied Biology, University of Science and Technology, Baridua, Meghalaya, India
| | - Ratul Saikia
- Microbial Biotechnology Laboratory, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
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Rosado-Porto D, Ratering S, Wohlfahrt Y, Schneider B, Glatt A, Schnell S. Elevated atmospheric CO 2 concentrations caused a shift of the metabolically active microbiome in vineyard soil. BMC Microbiol 2023; 23:46. [PMID: 36809988 PMCID: PMC9942357 DOI: 10.1186/s12866-023-02781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, 080002, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Yvette Wohlfahrt
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366, Geisenheim, Germany
| | - Bellinda Schneider
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Andrea Glatt
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany.
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5
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Guo DJ, Singh RK, Singh P, Li DP, Sharma A, Xing YX, Song XP, Yang LT, Li YR. Complete Genome Sequence of Enterobacter roggenkampii ED5, a Nitrogen Fixing Plant Growth Promoting Endophytic Bacterium With Biocontrol and Stress Tolerance Properties, Isolated From Sugarcane Root. Front Microbiol 2020; 11:580081. [PMID: 33072048 PMCID: PMC7536287 DOI: 10.3389/fmicb.2020.580081] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Sugarcane is the leading economic crop in China, requires huge quantities of nitrogen in the preliminary plant growth stages. However, the use of an enormous amount of nitrogen fertilizer increases the production price, and have detrimental results on the environment, causes severe soil and water pollution. In this study, a total of 175 endophytic strains were obtained from the sugarcane roots, belonging to five different species, i.e., Saccharum officinarum, Saccharum barberi, Saccharum robustum, Saccharum spontaneum, and Saccharum sinense. Among these, only 23 Enterobacter strains were chosen based on nitrogen fixation, PGP traits, hydrolytic enzymes production, and antifungal activities. Also, all selected strains were showed diverse growth range under different stress conditions, i.e., pH (5–10), temperature (20–45°C), and NaCl (7–12%) and 14 strains confirmed positive nifH, and 12 strains for acdS gene amplification, suggested that these strains could fix nitrogen along with stress tolerance properties. Out of 23 selected strains, Enterobacter roggenkampii ED5 was the most potent strain. Hence, this strain was further selected for comprehensive genome analysis, which includes a genome size of 4,702,851 bp and 56.05% of the average G + C content. Genome annotations estimated 4349 protein-coding with 83 tRNA and 25 rRNA genes. The CDSs number allocated to the KEGG, COG, and GO database were 2839, 4028, and 2949. We recognized a total set of genes that are possibly concerned with ACC deaminase activity, siderophores and plant hormones production, nitrogen and phosphate metabolism, symbiosis, root colonization, biofilm formation, sulfur assimilation and metabolism, along with resistance response toward a range of biotic and abiotic stresses. E. roggenkampii ED5 strain was also a proficient colonizer in sugarcane (variety GT11) and enhanced growth of sugarcane under the greenhouse. To the best of our knowledge, this is the first information on the whole-genome sequence study of endophytic E. roggenkampii ED5 bacterium associated with sugarcane root. And, our findings proposed that identification of predicted genes and metabolic pathways might describe this strain an eco-friendly bioresource to promote sugarcane growth by several mechanisms of actions under multi-stresses.
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Affiliation(s)
- Dao-Jun Guo
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
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Hsu TK, Chen JS, Hsu BM, Chen YP, Leu TH, Huang TY, Hsu YW, Wu SF. Application of modified JDP-DGGE-based molecular genotyping method to predict Acanthamoeba genotype and to analyse community diversity in aquatic environments. Parasitol Res 2017; 117:437-446. [PMID: 29248979 DOI: 10.1007/s00436-017-5719-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Acanthamoeba spp. are ubiquitous, opportunistic potential human pathogens, causing granulomatous amoebic encephalitis and keratitis. They are classified as protozoa, and they include at least 20 different genotypes (T1-T20) based on variation in the 18S rRNA gene. Acanthamoeba spp. are diverse in their production of toxins and in their ability to resist environmental factors. Therefore, it is necessary to develop a rapid genotyping method for Acanthamoeba spp. in aquatic environments. Although the denaturing gradient gel electrophoresis (DGGE) method for analysing microbial genotypes is potentially useful for rapid identification of aquatic environmental species, the technique has been compromised by artificial DGGE profiles in which many DNA fragments of identical sequences are segregated and displayed as different bands. The results indicate that PCR-DGGE genotyping with a GC clamp results in many segregated weaker bands of identical DNA sequences. In contrast, PCR-DGGE genotyping without a GC clamp displays genotype-dependent patterns in the major bands. Thus, DGGE without a GC clamp was performed to compare genotyping efficiency for Acanthamoeba in 21 water samples from rivers and reservoirs in Taiwan. Among them, four samples were found to demonstrate a banding pattern with more than one major band, and these band profiles of major bands were identical to those of positive controls. DNA cloning further confirmed that the sequences of the major bands were identical. In conclusion, more than two genotypes of Acanthamoeba in the four samples were identified by this method, suggesting that PCR-DGGE genotyping without a GC clamp is a useful approach for studying the diversity of Acanthamoeba communities. Graphical abstract.
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Affiliation(s)
- Tsui-Kang Hsu
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, 62102, Taiwan.,Department of Ophthalmology, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Jung-Sheng Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, Taiwan.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, Taiwan.
| | - Yu-Pin Chen
- Department of Orthopaedic Surgery, Taipei Medical University-Wan Fang Hospital, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsai-Hsueh Leu
- Department of Orthopaedic Surgery, Taipei Medical University-Wan Fang Hospital, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tung-Yi Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, Taiwan
| | - Yu-Wen Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, Taiwan
| | - Shu-Fen Wu
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Minhsiung Township, Chiayi County, 62102, Taiwan.
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Li HB, Singh RK, Singh P, Song QQ, Xing YX, Yang LT, Li YR. Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere. Front Microbiol 2017; 8:1268. [PMID: 28769881 PMCID: PMC5509769 DOI: 10.3389/fmicb.2017.01268] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/23/2017] [Indexed: 01/09/2023] Open
Abstract
The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL-1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg-1 h-1. For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C2H2 h-1 mL-1). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 (Pseudomonas koreensis) and CN11 (Pseudomonas entomophila) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog phenotypic profiling, which comprised utilization of C and N sources, and tolerance to osmolytes and pH, revealed the metabolic versatility of the selected strains. The colonization ability of the selected strains was evaluated by genetically tagging them with a constitutively expressing GFP-pPROBE-pTetr-OT plasmid. qRT-PCR results showed that both strains had the ability to express the nifH gene at 90 and 120 days, as compared to a control, in both sugarcane varieties GT11 and GXB9. Therefore, our isolated strains, P. koreensis and P. entomophila may be used as inoculums or in biofertilizer production for enhancing growth and nutrients, as well as for improving nitrogen levels, in sugarcane and other crops. The present study, to the best of our knowledge, is the first report on the diversity of Pseudomonas spp. associated with sugarcane in Guangxi, China.
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Affiliation(s)
- Hai-Bi Li
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Rajesh K Singh
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Pratiksha Singh
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Qi-Qi Song
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Yong-Xiu Xing
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Li-Tao Yang
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China
| | - Yang-Rui Li
- Agricultural College, State Key Laboratory of Subtropical Bioresources Conservation and Utilization, Guangxi UniversityNanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement Guangxi, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Sugarcane Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
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8
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Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling. Appl Environ Microbiol 2015. [PMID: 26209674 DOI: 10.1128/aem.01382-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.
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9
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da Silva MDCS, Paula TDA, Moreira BC, Carolino M, Cruz C, Bazzolli DMS, Silva CC, Kasuya MCM. Nitrogen-fixing bacteria in Eucalyptus globulus plantations. PLoS One 2014; 9:e111313. [PMID: 25340502 PMCID: PMC4207822 DOI: 10.1371/journal.pone.0111313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/23/2014] [Indexed: 11/23/2022] Open
Abstract
Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.
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Affiliation(s)
| | | | - Bruno Coutinho Moreira
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Manuela Carolino
- Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Lisboa, Campo Grande, Portugal
| | - Cristina Cruz
- Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Lisboa, Campo Grande, Portugal
| | | | - Cynthia Canedo Silva
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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10
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Effect of abandonment on diversity and abundance of free-living nitrogen-fixing bacteria and total bacteria in the cropland soils of Hulun Buir, Inner Mongolia. PLoS One 2014; 9:e106714. [PMID: 25268844 PMCID: PMC4182089 DOI: 10.1371/journal.pone.0106714] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 08/09/2014] [Indexed: 11/19/2022] Open
Abstract
In Inner Mongolia, steppe grasslands face desertification or degradation because of human over activity. One of the reasons for this condition is that croplands have been abandoned after inappropriate agricultural management. The soils in these croplands present heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, we assessed the molecular ecology of total and free-living nitrogen-fixing bacterial communities in soils from steppe grasslands and croplands that were abandoned for different periods (1, 5, and 25 years) and compared the degree of recovery. The abandoned croplands included in the study were natural restoration areas without human activity. Denaturing gradient gel electrophoresis and quantitative PCR (qPCR) were used to analyze the nifH and 16S rRNA genes to study free-living diazotrophs and the total bacterial community, respectively. The diversities of free-living nitrogen fixers and total bacteria were significantly different between each site (P<0.001). Neither the total bacteria nor nifH gene community structure of a cropland abandoned for 25 years was significantly different from those of steppe grasslands. In contrast, results of qPCR analysis of free-living nitrogen fixers and total bacteria showed significantly high abundance levels in steppe grassland (P<0.01 and P<0.03, respectively). In this study, the microbial communities and their gene abundances were assessed in croplands that had been abandoned for different periods. An understanding of how environmental factors and changes in microbial communities affect abandoned croplands could aid in appropriate soil management to optimize the structures of soil microorganisms.
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11
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Fernandes GDC, Trarbach LJ, de Campos SB, Beneduzi A, Passaglia LMP. Alternative nitrogenase and pseudogenes: unique features of the Paenibacillus riograndensis nitrogen fixation system. Res Microbiol 2014; 165:571-80. [PMID: 24956360 DOI: 10.1016/j.resmic.2014.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Biological nitrogen fixation (BNF) is a tightly regulated process that is carried out by diazotrophic microorganisms. The regulatory mechanisms of BNF-related genes are well characterized in Gram-negative models, but they are poorly understood in Gram-positive bacteria. Paenibacillus riograndensis SBR5(T) is a Gram-positive, endospore-forming facultative aerobic diazotroph. Three clusters of BNF-related genes with dissimilar phylogenetic histories were identified in the P. riograndensis genome, and no regulatory genes were recognized. P. riograndensis nifH2 was considered inactive based on transcript and promoter analyses, whereas transcripts of nifH1 and anfH were induced upon nitrogen-limited conditions. The functionality of the alternative nitrogenase system was also validated by enzymatic activity analysis. Fragments upstream of the two active clusters seem to harbor primary functional promoter sequences, producing a constitutive expression pattern in Escherichia coli. Sequences upstream of the anf genes were not recognized by this heterologous host, indicating a very distinct promoter pattern. These results shed light upon the evolutionary history of nitrogen fixation genes in this Gram-positive bacterium and highlight the presence of novel regulatory elements that are yet to be described.
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Affiliation(s)
- Gabriela de C Fernandes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
| | - Laura J Trarbach
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
| | - Samanta B de Campos
- Department of Genetics of Prokaryotes, Bielefeld University, Universitätsstraße 25, 33594 Bielefeld, Germany.
| | - Anelise Beneduzi
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060, Porto Alegre, RS, Brazil.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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12
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Szilagyi-Zecchin VJ, Ikeda AC, Hungria M, Adamoski D, Kava-Cordeiro V, Glienke C, Galli-Terasawa LV. Identification and characterization of endophytic bacteria from corn (Zea mays L.) roots with biotechnological potential in agriculture. AMB Express 2014; 4:26. [PMID: 24949261 PMCID: PMC4052694 DOI: 10.1186/s13568-014-0026-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 01/23/2014] [Indexed: 12/02/2022] Open
Abstract
Six endophytic bacteria of corn roots were identified as Bacillus sp. and as Enterobacter sp, by sequencing of the 16S rRNA gene. Four of the strains, CNPSo 2476, CNPSo 2477, CNPSo 2478 and CNPSo 2480 were positive for the nitrogen fixation ability evaluated through the acetylene reduction assay and amplification of nifH gene. Two Bacillus strains (CNPSo 2477 and CNPSo 2478) showed outstanding skills for the production of IAA, siderophores and lytic enzymes, but were not good candidates as growth promoters, because they reduced seed germination. However, the same strains were antagonists against the pathogenic fungi Fusarium verticillioides, Colletotrichum graminicola, Bipolaris maydis and Cercospora zea-maydis. As an indication of favorable bacterial action, Enterobacter sp. CNPSo 2480 and Bacillus sp. CNPSo 2481 increased the root volume by 44% and 39%, respectively, and the seed germination by 47% and 56%, respectively. Therefore, these two strains are good candidates for future testing as biological inoculants for corn.
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13
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Hara S, Desyatkin R, Hashidoko Y. Investigation of the mechanisms underlying the high acetylene-reducing activity exhibited by the soil bacterial community from BC2 horizon in the permafrost zone of the East Siberian larch forest bed. J Appl Microbiol 2014; 116:865-76. [DOI: 10.1111/jam.12424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/02/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022]
Affiliation(s)
- S. Hara
- Graduate School and Research Faculty of Agriculture; Hokkaido University; Sapporo Hokkaido Japan
| | - R.V. Desyatkin
- Institute of Biological Problems of Cryolithzone; Russian Academy of Sciences; Yakutsk Russia
| | - Y. Hashidoko
- Graduate School and Research Faculty of Agriculture; Hokkaido University; Sapporo Hokkaido Japan
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Kumar V, Kayasth M, Chaudhary V, Gera R. Diversity of diazotrophs in arid and semi-arid regions of Haryana and evaluation of their plant growth promoting potential on Bt-cotton and pearl millet. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0774-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Chen MH, Sheu SY, James EK, Young CC, Chen WM. Azoarcus
olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2013; 63:3755-3761. [DOI: 10.1099/ijs.0.050609-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing strain, designated DQS-4T, was isolated from oil-contaminated soil in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain DQS-4T stained Gram-negative, contained poly-β-hydroxybutyrate granules and were motile rods, surrounded by a thin capsule. Cells displayed a strictly aerobic type of metabolism and fixed nitrogen microaerobically. Growth occurred at 10–45 °C (optimum, 35–40 °C), at pH 7.0–8.0 (optimum, pH 7.0) and with 0–2 % NaCl (optimum, 0.5–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DQS-4T belonged to the genus
Azoarcus
, and its closest neighbours were
Azoarcus indigens
VB32T and
Azoarcus communis
SWub3T, with sequence similarities of 97.4 and 96.4 %, respectively. The major cellular fatty acids of strain DQS-4T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 64.5 mol%. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The mean level of DNA–DNA relatedness between strain DQS-4T and
A. indigens
LMG 9092T was 27.4 %. On the basis of the genotypic and phenotypic data, strain DQS-4T represents a novel species in the genus
Azoarcus
, for which the name
Azoarcus
olearius sp. nov. is proposed. The type strain is DQS-4T ( = BCRC 80407T = KCTC 23918T = LMG 26893T).
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Affiliation(s)
- Ming-Hui Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Euan K. James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil & Environmental Sciences, National Chung Hsing University, Taichung City 402, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd Nan-Tzu, Kaohsiung City 811, Taiwan
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Morales-Jiménez J, Vera-Ponce de León A, García-Domínguez A, Martínez-Romero E, Zúñiga G, Hernández-Rodríguez C. Nitrogen-fixing and uricolytic bacteria associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae). MICROBIAL ECOLOGY 2013; 66:200-210. [PMID: 23525792 DOI: 10.1007/s00248-013-0206-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 02/28/2013] [Indexed: 06/02/2023]
Abstract
The bark beetles of the genus Dendroctonus feed on phloem that is a nitrogen-limited source. Nitrogen fixation and nitrogen recycling may compensate or alleviate such a limitation, and beetle-associated bacteria capable of such processes were identified. Raoultella terrigena, a diazotrophic bacteria present in the gut of Dendroctonus rhizophagus and D. valens, exhibited high acetylene reduction activity in vitro with different carbon sources, and its nifH and nifD genes were sequenced. Bacteria able to recycle uric acid were Pseudomonas fluorescens DVL3A that used it as carbon and nitrogen source, Serratia proteomaculans 2A CDF and Rahnella aquatilis 6-DR that used uric acid as sole nitrogen source. Also, this is the first report about the uric acid content in whole eggs, larvae, and adults (male and female) samples of the red turpentine beetle (Dendroctonus valens). Our results suggest that the gut bacteria of these bark beetles could contribute to insect N balance.
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Affiliation(s)
- Jesús Morales-Jiménez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. De Carpio y Plan de Ayala, Col. Sto. Tomas, Mexico, Distrito Federal, 11340, Mexico
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17
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Derxia lacustris sp. nov., a nitrogen-fixing bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2013; 63:965-970. [DOI: 10.1099/ijs.0.041186-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing strain, designated HL-12T, was isolated from a freshwater lake in Taiwan. Cells of strain HL-12T were aerobic, Gram-negative, motile rods that were surrounded by a thick capsule, contained poly-β-hydroxybutyrate granules, and formed light-yellow to brownish-red colonies. Growth occurred at 15–40 °C (optimum 25–35 °C), at pH 6.0–7.0 (optimum pH 6.0) and with 0–4 % NaCl (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HL-12T belonged to the genus
Derxia
and exhibited 99.1 and 98.8 % 16S rRNA gene sequence similarity, respectively, with
Derxia gummosa
IAM 14990 and
D. gummosa
IAM 13946T. The major fatty acids (>10 %) of strain HL-12T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The cellular hydroxy fatty acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The isoprenoid quinone was Q-8 and the DNA G+C content was 72.0 mol%. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unknown aminophospholipids and phospholipids. DNA–DNA relatedness between strain HL-12T and LMG 3975 and LMG 3977T was <70 %. On the basis of the genotypic and phenotypic data, strain HL-12T represents a novel species in the genus
Derxia
, for which the name Derxia lacustris sp. nov. is proposed. The type strain is HL-12T ( = BCRC 80208T = KCTC 23311T).
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18
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van Overbeek LS, Wellington EMH, Egan S, Smalla K, Heuer H, Collard JM, Guillaume G, Karagouni AD, Nikolakopoulou TL, van Elsas JD. Prevalence of streptomycin-resistance genes in bacterial populations in European habitats. FEMS Microbiol Ecol 2012; 42:277-88. [PMID: 19709288 DOI: 10.1111/j.1574-6941.2002.tb01018.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The prevalence of selected streptomycin (Sm)-resistance genes, i.e. aph (3''), aph (6)-1d, aph (6)-1c, ant (3'') and ant (6), was assessed in a range of pristine as well as polluted European habitats. These habitats included bulk and rhizosphere soils, manure from farm animals, activated sludge from wastewater treatment plants and seawater. The methods employed included assessments of the prevalence of the genes in habitat-extracted DNA by PCR, followed by hybridisation with specific probes, Sm-resistant culturable bacteria and exogenous isolation of plasmids carrying Sm-resistance determinants. The direct DNA-based analysis showed that aph (6)-1d genes were most prevalent in the habitats examined. The presence of the other four Sm-modifying genes was demonstrated in 58% of the tested habitats. A small fraction of the bacterial isolates (8%) did not possess any of the selected Sm-modifying genes. These isolates were primarily obtained from activated sludge and manure. The presence of Sm-modifying genes in the isolates often coincided with the presence of IncP plasmids. Exogenous isolation demonstrated the presence of plasmids of 40-200 kb in size harbouring Sm-resistance genes from all the environments tested. Most plasmids were shown to carry the ant (3'') gene, often in combination with other Sm-resistance genes, such as aph (3'') and aph (6)-1d. The most commonly found Sm-modifying gene on mobile genetic elements was ant (3''). Multiple Sm-resistance genes on the same genetic elements appeared to be the rule rather than the exception. It is concluded that Sm-resistance genes are widespread in the environmental habitats studied and often occur on mobile genetic elements and ant (3'') was most often encountered.
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Affiliation(s)
- Leo S van Overbeek
- Plant Research International B.V., P.O. Box 16, 6700 AA Wageningen, The Netherlands.
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19
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Percival SL, Hill KE, Williams DW, Hooper SJ, Thomas DW, Costerton JW. A review of the scientific evidence for biofilms in wounds. Wound Repair Regen 2012; 20:647-57. [DOI: 10.1111/j.1524-475x.2012.00836.x] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Katja E. Hill
- School of Dentistry; Cardiff University; Cardiff; United Kingdom
| | | | - Samuel J. Hooper
- School of Dentistry; Cardiff University; Cardiff; United Kingdom
| | - Dave W. Thomas
- School of Dentistry; Cardiff University; Cardiff; United Kingdom
| | - John W. Costerton
- Center for Genomic Sciences; Allegheny-Singer Research Institute; Pittsburgh; Pennsylvania
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20
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He M, Tian G, Semenov AM, van Bruggen AHC. Short-term fluctuations of sugar beet damping-off by Pythium ultimum in relation to changes in bacterial communities after organic amendments to two soils. PHYTOPATHOLOGY 2012; 102:413-420. [PMID: 22150210 DOI: 10.1094/phyto-07-11-0189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Previously, oscillations in beet seedling damping-off by Pythium ultimum, measured as area under the disease progress curve (AUDPC), were demonstrated after incorporation of organic materials into organic and conventional soils. These periodic fluctuations of P. ultimum infections were cross-correlated with oscillations of copiotrophic CFU at lags of 2 to 4 days. For this article, we investigated whether bacterial communities and microbial activities fluctuated after a disturbance from incorporation of organic materials, and whether these fluctuations were linked to the short-term oscillations in AUDPC of beet seedling damping-off and bacterial populations (CFU) in soil. Soil microbial communities studied by polymerase chain reaction-DGGE analysis of 16S DNA after isolation of total DNA from soil and microbial activities measured as CO(2) emission rates were monitored daily for 14 days after addition of grass-clover (GC) or composted manure (CM) into organic versus conventional soils. Similar to our previous findings, AUDPC and density of copiotrophic bacteria oscillated with time. Fluctuations in species richness (S), Shannon diversity index (H), and individual amplicons on DGGE gels were also detected. Oscillations in AUDPC were positively cross-correlated with copiotrophic CFU in all soils. Oscillations in AUDPC were also positively cross-correlated with 19 to 35% of the high-intensity DNA fragments in soils amended with GC but only 2 to 3% of these fragments in CM-amended soils. AUDPC values were negatively cross-correlated with 13 to 17% of the amplicons with low average intensities in CM-amended soils, which were not correlated with densities of copiotrophic CFU. CO(2) emission rates had remarkable variations in the initial 7 days after either of the soil amendments but were not associated with daily changes in AUDPC. The results suggest that infection by P. ultimum is hampered by competition from culturable copiotrophic bacteria and some high-intensity DGGE amplicons, because AUDPC is cross-correlated with these variables at lags of 1 to 4 days. However, negative cross-correlations with low-intensity DNA fragments indicate that P. ultimum infection could also be suppressed by antagonistic bacteria with low densities that may be nonculturable species, especially in CM amended soil. The organic soil generally had lower AUDPC values, higher bacterial diversity, and negative cross-correlations between AUDPC and low-intensity DNA fragments (after CM amendment), indicating that specific bacteria that do not attain high densities may contribute to P. ultimum suppression in organic soils.
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Affiliation(s)
- Miaomiao He
- Department of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China
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21
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Loiacono ST, Meyer-Dombard DR, Havig JR, Poret-Peterson AT, Hartnett HE, Shock EL. Evidence for high-temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin, Yellowstone National Park. Environ Microbiol 2012; 14:1272-83. [PMID: 22404902 DOI: 10.1111/j.1462-2920.2012.02710.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genes encoding nitrogenase (nifH) were amplified from sediment and photosynthetic mat samples collected in the outflow channel of Mound Spring, an alkaline thermal feature in Yellowstone National Park. Results indicate the genetic capacity for nitrogen fixation over the entire range of temperatures sampled (57.2°C to 80.2°C). Amplification of environmental nifH transcripts revealed in situ expression of nifH genes at temperatures up to 72.7°C. However, we were unable to amplify transcripts of nifH at the higher-temperature locations (> 72.7°C). These results indicate that microbes at the highest temperature sites contain the genetic capacity to fix nitrogen, yet either do not express nifH or do so only transiently. Field measurements of nitrate and ammonium show fixed nitrogen limitation as temperature decreases along the outflow channel, suggesting nifH expression in response to the downstream decrease in bioavailable nitrogen. Nitrogen stable isotope values of Mound Spring sediment communities further support geochemical and genetic data. DNA and cDNA nifH amplicons form several unique phylogenetic clades, some of which appear to represent novel nifH sequences in both photosynthetic and chemosynthetic microbial communities. This is the first report of in situ nifH expression in strictly chemosynthetic zones of terrestrial (non-marine) hydrothermal systems, and sets a new upper temperature limit (72.7°C) for nitrogen fixation in alkaline, terrestrial hydrothermal environments.
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Affiliation(s)
- Sara T Loiacono
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, Chicago, IL, USA
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22
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Jin HJ, Tu R, Xu F, Chen SF. Identification of nitrogen-fixing Paenibacillus from different plant rhizospheres and a novel nifH gene detected in the P. stellifer. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711010097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Mandic-Mulec I, Prosser JI. Diversity of Endospore-forming Bacteria in Soil: Characterization and Driving Mechanisms. SOIL BIOLOGY 2011. [DOI: 10.1007/978-3-642-19577-8_2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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26
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Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils. Appl Environ Microbiol 2010; 77:911-9. [PMID: 21131514 DOI: 10.1128/aem.01250-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agricultural soils are heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, the molecular ecology of the total bacterial and free-living nitrogen-fixing communities in soils from the Nafferton Factorial Systems Comparison (NFSC) study in northeast England were examined. The field experiment was factorial in design, with organic versus conventional crop rotation, crop protection, and fertility management factors. Soils were sampled on three dates (March, June, and September) in 2007. Total RNA was extracted from all soil samples and reverse transcribed. Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were used to analyze nifH and 16S rRNA genes in order to study free-living diazotrophs and the total bacterial community, respectively. Crop rotation was shown to have a significant effect on total bacterial diversity (and that of free-living N fixers) (P ≤ 0.001). On all three dates, nifH activity was higher in the conventional crop rotation. In contrast, qPCR analysis of free-living N fixers indicated significantly higher levels of activity in conventionally fertilized plots in June (P = 0.0324) and in plots with organic crop protection in September (P = 0.0143). To our knowledge, the effects of organic and conventional farming systems on free-living diazotrophs have never been studied. An increased understanding of the impacts of management practices on free-living N fixers could allow modifications in soil management practices to optimize the activity of these organisms.
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28
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Lin C, Gan L, Chen ZL. Biodegradation of naphthalene by strain Bacillus fusiformis (BFN). JOURNAL OF HAZARDOUS MATERIALS 2010; 182:771-7. [PMID: 20643503 DOI: 10.1016/j.jhazmat.2010.06.101] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 05/15/2023]
Abstract
Bacterial strains isolated from oil refining wastewater sludge (Fuzhou, China) were used to biodegrade naphthalene in cultured medium. Bacillus fusiformis (BFN) strain was identified using 16S rDNA gene sequence analysis. Optimal conditions for the biodegradation of naphthalene included: temperature of 30 degrees C, pH 7.0, 0.2% inoculum size and a C/N ratio of 1.0. Under these conditions and initial naphthalene concentration of 50 mg/L, more than 99.1% was removed within 96 h. Of those factors influencing the biodegradation of naphthalene, salinity and inoculum concentration were of greatest importance. Furthermore, the biodegradation kinetics of naphthalene corresponded with the first-order rate model. Degradation metabolites identified using GC-MS, included o-phthalic acid and benzoic acid, suggesting possible metabolic pathways. Finally, given these metabolites are water-soluble and non-toxic, the findings suggest a potential bioremediation role of Bacillus fusiformis (BFN) in the removal of naphthalene from wastewaters.
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Affiliation(s)
- Chen Lin
- School of Chemistry and Material Sciences, Fujian Normal University, Fuzhou, 350007, China
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29
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Hrčková K, Simek M, Hrouzek P, Lukešová A. Biological dinitrogen fixation by selected soil cyanobacteria as affected by strain origin, morphotype, and light conditions. Folia Microbiol (Praha) 2010; 55:467-73. [PMID: 20941582 DOI: 10.1007/s12223-010-0078-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 05/11/2010] [Indexed: 10/19/2022]
Abstract
The potential for N(2) fixation by heterocystous cyanobacteria isolated from soils of different geographical areas was determined as nitrogenase activity (NA) using the acetylene reduction assay. Morphology of cyanobacteria had the largest influence on NA determined under light conditions. NA was generally higher in species lacking thick slime sheaths. The highest value (1446 nmol/h C(2)H(4) per g fresh biomass) was found in the strain of branched cyanobacterium Hassalia (A Has1) from the polar region. A quadratic relationship between NA and biomass was detected in the Tolypothrix group under light conditions. The decline of NA in dark relative to light conditions ranged from 37 to 100 % and differed among strains from distinct geographical areas. Unlike the NA of temperate and tropical strains, whose decline in dark relative to light was 24 and 17 %, respectively, the NA of polar strains declined to 1 % in the dark. This difference was explained by adaptation to different light conditions in temperate, tropical, and polar habitats. NA was not related to the frequency of heterocysts in strains of the colony-forming cyanobacterium Nostoc. Colony morphology and life cycle are therefore more important for NA then heterocyst frequency. NA values probably reflect the environmental conditions where the cyanobacterium was isolated and the physiological and morphological state of the strain.
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Affiliation(s)
- K Hrčková
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
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Baudoin E, Couillerot O, Spaepen S, Moënne-Loccoz Y, Nazaret S. Applicability of the 16S-23S rDNA internal spacer for PCR detection of the phytostimulatory PGPR inoculant Azospirillum lipoferum CRT1 in field soil. J Appl Microbiol 2010; 108:25-38. [PMID: 19583800 DOI: 10.1111/j.1365-2672.2009.04393.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AIMS To assess the applicability of the 16S-23S rDNA internal spacer regions (ISR) as targets for PCR detection of Azospirillum ssp. and the phytostimulatory plant growth-promoting rhizobacteria seed inoculant Azospirillum lipoferum CRT1 in soil. METHODS AND RESULTS Primer sets were designed after sequence analysis of the ISR of A. lipoferum CRT1 and Azospirillum brasilense Sp245. The primers fAZO/rAZO targeting the Azospirillum genus successfully yielded PCR amplicons (400-550 bp) from Azospirillum strains but also from certain non-Azospirillum strains in vitro, therefore they were not appropriate to monitor indigenous Azospirillum soil populations. The primers fCRT1/rCRT1 targeting A. lipoferum CRT1 generated a single 249-bp PCR product but could also amplify other strains from the same species. However, with DNA extracts from the rhizosphere of field-grown maize, both fAZO/rAZO and fCRT1/rCRT1 primer sets could be used to evidence strain CRT1 in inoculated plants by nested PCR, after a first ISR amplification with universal ribosomal primers. In soil, a 7-log dynamic range of detection (10(2)-10(8) CFU g(-1) soil) was obtained. CONCLUSIONS The PCR primers targeting 16S-23S rDNA ISR sequences enabled detection of the inoculant A. lipoferum CRT1 in field soil. SIGNIFICANCE AND IMPACT OF THE STUDY Convenient methods to monitor Azospirillum phytostimulators in the soil are lacking. The PCR protocols designed based on ISR sequences will be useful for detection of the crop inoculant A. lipoferum CRT1 under field conditions.
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Affiliation(s)
- E Baudoin
- IRD, UMR 113, LSTM, Campus International de Baillarguet, TA-A82/J, 34398 Montpellier cedex5, France
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van Overbeek LS, Franz E, Semenov AV, de Vos OJ, van Bruggen AHC. The effect of the native bacterial community structure on the predictability of E. coli O157:H7 survival in manure-amended soil. Lett Appl Microbiol 2010; 50:425-30. [PMID: 20184674 DOI: 10.1111/j.1472-765x.2010.02817.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The survival capability of pathogens like Escherichia coli O157:H7 in manure-amended soil is considered to be an important factor for the likelihood of crop contamination. The aim of this study was to reveal the effects of the diversity and composition of soil bacterial community structure on the survival time (ttd) and stability (irregularity, defined as the intensity of irregular dynamic changes in a population over time) of an introduced E. coli O157:H7 gfp-strain were investigated for 36 different soils by means of bacterial PCR-DGGE fingerprints. METHODS AND RESULTS Bacterial PCR-DGGE fingerprints made with DNA extracts from the different soils using bacterial 16S-rRNA-gene-based primers were grouped by cluster analysis into two clusters consisting of six and 29 soils and one single soil at a cross-correlation level of 16% among samples per cluster. Average irregularity values for E. coli O157:H7 survival in the same soils differed significantly between clusters (P = 0.05), whereas no significant difference was found for the corresponding average ttd values (P = 0.20). The irregularity was higher for cluster 1, which consisted primarily of soils that had received liquid manure and artificial fertilizer and had a significant higher bacterial diversity and evenness values (P < 0.001). CONCLUSIONS Bacterial PCR-DGGE fingerprints of 36 manure-amended soils revealed two clusters which differed significantly in the stability (irregularity) of E. coli O157 decline. The cluster with the higher irregularity was characterized by higher bacterial diversity and evenness. SIGNIFICANCE AND IMPACT OF THE STUDY The consequence of a high temporal irregularity is a lower accuracy of predictions of population behaviour, which results in higher levels of uncertainty associated with the estimates of model parameters when modelling the behaviour of E. coli O157:H7 in the framework of risk assessments. Soil community structure parameters like species diversity and evenness can be indicative for the reliability of predictive models describing the fate of pathogens in (agricultural) soil ecosystems.
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Affiliation(s)
- L S van Overbeek
- Plant Research International BV, Wageningen University and Research Centre, Wageningen, the Netherlands
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Rastogi G, Stetler LD, Peyton BM, Sani RK. Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA. J Microbiol 2009; 47:371-84. [PMID: 19763410 DOI: 10.1007/s12275-008-0249-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 04/10/2009] [Indexed: 11/29/2022]
Abstract
A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.
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Affiliation(s)
- Gurdeep Rastogi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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Andreote FD, Azevedo JL, Araújo WL. Assessing the diversity of bacterial communities associated with plants. Braz J Microbiol 2009; 40:417-32. [PMID: 24031382 PMCID: PMC3768544 DOI: 10.1590/s1517-83822009000300001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 10/27/2008] [Accepted: 02/15/2009] [Indexed: 12/20/2022] Open
Abstract
Plant-bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants.
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Affiliation(s)
- Fernando Dini Andreote
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo , Piracicaba, SP , Brasil ; Laboratório de Microbiologia Ambiental, Embrapa Meio Ambiente , Jaguariúna, SP , Brasil
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Martínez-Iñigo MJ, Pérez-Sanz A, Ortiz I, Alonso J, Alarcón R, García P, Lobo MC. Bulk soil and rhizosphere bacterial community PCR-DGGE profiles and beta-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke. CHEMOSPHERE 2009; 75:1376-1381. [PMID: 19345981 DOI: 10.1016/j.chemosphere.2009.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 03/05/2009] [Accepted: 03/05/2009] [Indexed: 05/27/2023]
Abstract
The biological quality of two heavy metal contaminated soils (soil C: Typic Calcixerept, pH 8.3 and soil H: Typic Haploxeraf, pH 7.3) was investigated after growing the metal-tolerant plant Silene vulgaris (Moench) Garcke for two vegetative periods. The activity of the enzyme beta-galactosidase, which is sensitive to the presence of contaminants in soil, and the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of 16S rRNA gene fragments of culturable bacteria from bulk soil and rhizosphere were determined. The microbial enzymatic activity was higher in planted soils than in bare soils at the contamination level of 600 mg of total heavy metals kg(-1) soil. After growing S. vulgaris, beta-galactosidase activity was almost recovered in the calcareous soil. In this soil new bands appeared in the PCR-DGGE profiles of the rhizosphere bacterial community as a response to the exposure to heavy metals.
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Affiliation(s)
- M J Martínez-Iñigo
- Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario, IMIDRA, Km, 38.2 A-II, 28800 Madrid, Spain.
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Coelho M, Carneiro N, Marriel I, Seldin L. Molecular detection ofnifHgene-containingPaenibacillusin the rhizosphere of sorghum (Sorghum bicolor) sown in Cerrado soil. Lett Appl Microbiol 2009; 48:611-7. [DOI: 10.1111/j.1472-765x.2009.02578.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mohania D, Nagpal R, Kumar M, Bhardwaj A, Yadav M, Jain S, Marotta F, Singh V, Parkash O, Yadav H. Molecular approaches for identification and characterization of lactic acid bacteria. J Dig Dis 2008; 9:190-8. [PMID: 18959589 DOI: 10.1111/j.1751-2980.2008.00345.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The last few years have produced a revolution in the development of very sensitive, rapid, automated, molecular detection methods for a variety of various species of lactic acid bacteria (LAB) associated with food and dairy products. Nowadays many such strains of LAB are considered probiotics. The genome-based methods are useful in identifying bacteria as a complementary or alternative tool to phenotypical methods. Over the years, identification methodologies using primers that target different sequences, such as the 16S ribosomal RNA (rRNA)-encoding gene, the 16S-23S rRNA intergenic spacer region, the 23S rRNA-encoding, recA and ldhD genes; randomly amplified polymorphic DNA, restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, amplification rDNA restriction analysis, restriction enzyme analysis, rRNA, pulse field gel electrophoresis and amplification fragment length polymorphism have played a significant role in probiotic bacteriology. Hence, the aim of this review is to provide an overview of some rapid and reliable polymerase chain reaction-based molecular methods used for identifying and differentiating closely related species and strains of LAB associated with food and industry.
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Affiliation(s)
- Dheeraj Mohania
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
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de Oliveira VM, Sette LD, Simioni KCM, Dos Santos Neto EV. Bacterial diversity characterization in petroleum samples from Brazilian reservoirs. Braz J Microbiol 2008; 39:445-52. [PMID: 24031244 PMCID: PMC3768447 DOI: 10.1590/s1517-83822008000300007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 11/22/2008] [Accepted: 07/14/2008] [Indexed: 11/22/2022] Open
Abstract
This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments.
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Affiliation(s)
- Valéria Maia de Oliveira
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas , Campinas, SP , Brasil
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TAYLOR DLEE, BOOTH MICHAELG, MCFARLAND JACKW, HERRIOTT IANC, LENNON NIALLJ, NUSBAUM CHAD, MARR THOMASG. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Mol Ecol Resour 2008; 8:742-52. [DOI: 10.1111/j.1755-0998.2008.02094.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Betancourt DA, Loveless TM, Brown JW, Bishop PE. Characterization of diazotrophs containing Mo-independent nitrogenases, isolated from diverse natural environments. Appl Environ Microbiol 2008; 74:3471-80. [PMID: 18378646 PMCID: PMC2423014 DOI: 10.1128/aem.02694-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/22/2008] [Indexed: 11/20/2022] Open
Abstract
Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium Azotobacter vinelandii and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Mo-independent nitrogenases from aquatic environments. In the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, "paraffin dirt," and sediments from mangrove swamps. Mo-deficient, N-free media under both aerobic and anaerobic conditions were used for the isolations. A total of 26 isolates were genetically and physiologically characterized. Their phylogenetic placement was determined using 16S rRNA gene sequence analysis. Most of the isolates are members of the gamma subdivision of the class Proteobacteria and appear to be specifically related to fluorescent pseudomonads and azotobacteria. Two other isolates, AN1 and LPF4, are closely related to Enterobacter spp. and Paenibacillus spp., respectively. PCR and/or Southern hybridization were used to detect the presence of nitrogenase genes in the isolates. PCR amplification of vnfG and anfG was used to detect the genetic potential for the expression of the vanadium-containing nitrogenase and the iron-only nitrogenase in the isolates. This study demonstrates that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments.
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Affiliation(s)
- Doris A Betancourt
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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Opelt K, Chobot V, Hadacek F, Schönmann S, Eberl L, Berg G. Investigations of the structure and function of bacterial communities associated with Sphagnum mosses. Environ Microbiol 2008; 9:2795-809. [PMID: 17922763 DOI: 10.1111/j.1462-2920.2007.01391.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High acidity, low temperature and extremely low concentration of nutrients form Sphagnum bogs into extreme habitats for organisms. Little is known about the bacteria associated with living Sphagnum plantlets, especially about their function for the host. Therefore, we analysed the endo- and ectophytic bacterial populations associated with two widely distributed Sphagnum species, Sphagnum magellanicum and Sphagnum fallax, by a multiphasic approach. The screening of 1222 isolates for antagonistic activity resulted in 326 active isolates. The bacterial communities harboured a high proportion of antifungal (26%) but a low proportion of antibacterial isolates (0.4%). Members of the genus Burkholderia (38%) were found to be the most dominant group of antagonistic bacteria. The finding that a large proportion (89%) of the antagonistic bacteria produced antifungal compounds may provide an explanation for the well-known antimicrobial activity of certain Sphagnum species. The secondary metabolites of the Sphagnum species themselves were analysed by HPLC-PDA. The different spectra of detected compounds may not only explain the antifungal activity but also the species specificity of the microbial communities. The latter was analysed using cultivation-independent single-stranded conformation polymorphism (SSCP) analysis. Using Burkholderia-specific primers we found a high diversity of Burkholderia isolates in the endophytic and ectophytic habitats of Sphagnum. Furthermore, a high diversity of nitrogen-fixing bacteria was detected by using nifH-specific primers, especially inside Sphagnum mosses. In conclusion, this study provides evidence that both Sphagnum species were colonized by characteristic bacterial populations, which appear to be important for pathogen defence and nitrogen fixation.
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Affiliation(s)
- Katja Opelt
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, A-8010 Graz, Austria
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Chou JH, Jiang SR, Cho JC, Song J, Lin MC, Chen WM. Azonexus hydrophilus sp. nov., a nifH gene-harbouring bacterium isolated from freshwater. Int J Syst Evol Microbiol 2008; 58:946-51. [DOI: 10.1099/ijs.0.65434-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR–denaturing gradient gel electrophoresis. Arch Microbiol 2008; 190:19-28. [DOI: 10.1007/s00203-008-0359-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 02/28/2008] [Accepted: 03/03/2008] [Indexed: 11/27/2022]
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Teixeira R, von der Weid I, Seldin L, Rosado AS. Differential expression of nifH and anfH genes in Paenibacillus durus analysed by reverse transcriptase-PCR and denaturing gradient gel electrophoresis. Lett Appl Microbiol 2008; 46:344-9. [DOI: 10.1111/j.1472-765x.2008.02322.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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TAYLOR DLEE, BOOTH MICHAELG, MCFARLAND JACKW, HERRIOTT IANC, LENNON NIALLJ, NUSBAUM CHAD, MARR THOMASG. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Mol Ecol Resour 2008. [DOI: 10.1111/j.1471-8286.2008.02094.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol 2008. [PMID: 18245263 DOI: 10.1128/aem.01720‐07] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.
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Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol 2008; 74:1922-31. [PMID: 18245263 DOI: 10.1128/aem.01720-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.
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Franz E, Semenov AV, Termorshuizen AJ, de Vos OJ, Bokhorst JG, van Bruggen AHC. Manure-amended soil characteristics affecting the survival of E. coli O157:H7 in 36 Dutch soils. Environ Microbiol 2008; 10:313-27. [DOI: 10.1111/j.1462-2920.2007.01453.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Humphry DR, Andrews M, Santos SR, James EK, Vinogradova LV, Perin L, Reis VM, Cummings SP. Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia. Antonie van Leeuwenhoek 2007; 91:105-13. [PMID: 17013548 DOI: 10.1007/s10482-006-9100-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
The taxonomic position of "Agrobacterium radiobacter strain 204," used in Russia as a cereal crop growth promoting inoculant, was derived by a polyphasic approach. The phenotypic analyses gave very similar biochemical profiles for strain 204, Rhizobium radiobacter NCIMB 9042 (formerly the A. radiobacter type strain) and R. radiobacter NCIMB 13307 (formerly the Agrobacterium tumefaciens type strain). High percentage similarities, above the species separation level, were observed between the 16S rRNA, fusA and rpoB housekeeping gene sequences of these three strains, and the genomic DNA-DNA hybridisation of strain 204 against the type strain of R. radiobacter NCIMB 9042 was over 70%. Strain 204 is not phytopathogenic and it does not fix atmospheric N2 or form a physical association with the roots of barley. Strain 204 culture and culture supernatant stimulated the rate of mobilisation of seed reserves of barley in darkness and promoted its shoot growth in the light. Gibberellic acid (GA) concentration was 1.3 microM but indole acetic acid was undetectable (< 50 nM) in cultures of strain 204. It is concluded that strain 204 is phenotypically and genotypically very similar to the current R. radiobacter type strain and that the mechanism of its effect on growth of cereals is via the production of plant growth promoting substances. GA is likely to play an important role in the strain 204 stimulation of early growth of barley.
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MESH Headings
- Agrobacterium tumefaciens/classification
- Agrobacterium tumefaciens/genetics
- Agrobacterium tumefaciens/physiology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Crops, Agricultural/growth & development
- Crops, Agricultural/microbiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA-Directed RNA Polymerases/genetics
- Genes, rRNA
- Gibberellins/biosynthesis
- Hordeum/growth & development
- Hordeum/microbiology
- Indoleacetic Acids/metabolism
- Molecular Sequence Data
- Nitrogen Fixation/genetics
- Nucleic Acid Hybridization
- Oxidoreductases/genetics
- Peptide Elongation Factor G/genetics
- Phylogeny
- Plant Diseases/microbiology
- Plant Shoots/growth & development
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Russia
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Solanum tuberosum/microbiology
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Affiliation(s)
- David R Humphry
- Department of Biology, University of York, P.O. Box 373, University Road, Heslington, York, UK
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Nocker A, Lepo JE, Martin LL, Snyder RA. Genotypic microbial community profiling: a critical technical review. MICROBIAL ECOLOGY 2007; 54:532-42. [PMID: 17351811 DOI: 10.1007/s00248-007-9236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 10/23/2006] [Accepted: 11/23/2006] [Indexed: 05/04/2023]
Abstract
Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
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Affiliation(s)
- Andreas Nocker
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514, USA
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