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Beta Diversity of Arbuscular Mycorrhizal Communities Increases in Time after Crop Establishment of Peruvian Sacha Inchi ( Plukenetia volubilis). J Fungi (Basel) 2023; 9:jof9020194. [PMID: 36836309 PMCID: PMC9966307 DOI: 10.3390/jof9020194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
(1) Background: Beta diversity, i.e., the variance in species compositions across communities, has been pointed out as a main factor for explaining ecosystem functioning. However, few studies have directly tested the effect of crop establishment on beta diversity. We studied beta diversity patterns of arbuscular mycorrhizal (AM) fungal communities associated to sacha inchi (Plukenetia volubilis) after crop establishment. (2) Methods: We molecularly characterized the AM fungal communities associated to roots of sacha inchi in plots after different times of crop establishment, from less than one year to older than three. We analyzed the patterns of alpha, beta, and phylogenetic diversity, and the sources of variation of AM fungal community composition. (3) Results: Beta diversity increased in the older plots, but no temporal effect in alpha or phylogenetic diversity was found. The AM fungal community composition was driven by environmental factors (altitude and soil conditions). A part of this variation could be attributed to differences between sampled locations (expressed as geographic coordinates). Crop age, in turn, affected the composition with no interactions with the environmental conditions or spatial location. (4) Conclusions: These results point out towards a certain recovery of the soil microbiota after sacha inchi establishment. This fact could be attributed to the low-impact management associated to this tropical crop.
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Barathi S, Sabapathi N, Aruljothi KN, Lee JH, Shim JJ, Lee J. Regulatory Small RNAs for a Sustained Eco-Agriculture. Int J Mol Sci 2023; 24:ijms24021041. [PMID: 36674558 PMCID: PMC9863784 DOI: 10.3390/ijms24021041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Small RNA (sRNA) has become an alternate biotechnology tool for sustaining eco-agriculture by enhancing plant solidity and managing environmental hazards over traditional methods. Plants synthesize a variety of sRNA to silence the crucial genes of pests or plant immune inhibitory proteins and counter adverse environmental conditions. These sRNAs can be cultivated using biotechnological methods to apply directly or through bacterial systems to counter the biotic stress. On the other hand, through synthesizing sRNAs, microbial networks indicate toxic elements in the environment, which can be used effectively in environmental monitoring and management. Moreover, microbes possess sRNAs that enhance the degradation of xenobiotics and maintain bio-geo-cycles locally. Selective bacterial and plant sRNA systems can work symbiotically to establish a sustained eco-agriculture system. An sRNA-mediated approach is becoming a greener tool to replace xenobiotic pesticides, fertilizers, and other chemical remediation elements. The review focused on the applications of sRNA in both sustained agriculture and bioremediation. It also discusses limitations and recommends various approaches toward future improvements for a sustained eco-agriculture system.
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Affiliation(s)
- Selvaraj Barathi
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Nadana Sabapathi
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Kandasamy Nagarajan Aruljothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, India
- Correspondence: (K.N.A.); (J.L.); Tel.: +91-995-235-8239 (K.N.A.); +82-53-810-2533 (J.L.); Fax: +82-53-810-4631 (J.L.)
| | - Jin-Hyung Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jae-Jin Shim
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Correspondence: (K.N.A.); (J.L.); Tel.: +91-995-235-8239 (K.N.A.); +82-53-810-2533 (J.L.); Fax: +82-53-810-4631 (J.L.)
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Chen X, Yang C, Palta JA, Li Y, Fan X. An Enterobacter cloacae strain NG-33 that can solubilize phosphate and promote maize growth. Front Microbiol 2022; 13:1047313. [PMID: 36439855 PMCID: PMC9685795 DOI: 10.3389/fmicb.2022.1047313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/25/2022] [Indexed: 09/06/2023] Open
Abstract
It is critical to identify and evaluate efficient phosphate-solubilizing bacteria (PSB) that enable P uptake from unavailable forms, and therefore improve the phosphorus (P) uptake efficiency of crops. The Enterobacter cloacae strain NG-33, belonging to PSB, was isolated and identified from calcareous rhizosphere soils in Nonggang National Reserve, Guangxi, China. The stain NG-33 could reduce the pH of the medium to below 5.6, and had the ability to release soluble phosphorus (P; 180.7 μg ml-1) during the culture in the National Botanical Research Institute's Phosphate medium (NBRIP), and produced such organic acids as gluconic acid (4,881 mg L-1), acetic acid (346 mg L-1), and indole-3-acetic acid (20.4 μg ml-1). It could also convert inorganic P in AlPO4 (Al-P) and FePO4 (Fe-P) into soluble P, with conversion efficiencies of 19.2 μg ml-1 and 16.3 μg ml-1, respectively. Under pot experiments and when compared controls without inoculating NG-33, the shoot and root biomass of maize seedlings showed increases by 140% for shoot biomass and by 97% for root biomass in loamy soil (P sufficient) inoculated with NG-33. In sandy soil (P deficit) supplemented with tricalcium phosphate and inoculated with NG-33, the soluble P content was significantly higher, 58.6% in soil and 33.6% in roots, meanwhile, the biomass of shoots and roots increased by 14.9 and 24.9%, respectively. The growth-promoting effects coupled to the significant increase in leaf net photosynthetic rate and stomatal conductance of plants grown in NG-33-inoculated soil. Inoculating NG-33 could significantly improve the diversity and richness of bacterial population and altered the dominant bacterial population in soil.
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Affiliation(s)
- Xinxin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Guangxi, Nanning, China
| | - Caihe Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Guangxi, Nanning, China
| | - Jairo A. Palta
- UWA School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - Youzhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Guangxi, Nanning, China
| | - Xianwei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Guangxi, Nanning, China
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Lyautey E, Billard E, Tissot N, Jacquet S, Domaizon I. Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments. MICROBIAL ECOLOGY 2021; 82:559-571. [PMID: 33538855 DOI: 10.1007/s00248-021-01689-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.
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Affiliation(s)
- Emilie Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France.
| | - Elodie Billard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Nathalie Tissot
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Stéphan Jacquet
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Isabelle Domaizon
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
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Mącik M, Gryta A, Sas-Paszt L, Frąc M. The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. Int J Mol Sci 2020; 21:E8003. [PMID: 33121206 PMCID: PMC7663420 DOI: 10.3390/ijms21218003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.
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Affiliation(s)
- Mateusz Mącik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Lidia Sas-Paszt
- Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100 Skierniewice, Poland;
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
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Frąc M, Lipiec J, Usowicz B, Oszust K, Brzezińska M. Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 2020; 8:e9501. [PMID: 32953254 PMCID: PMC7474522 DOI: 10.7717/peerj.9501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Bogusław Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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Gryta A, Frąc M. Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi. SENSORS 2020; 20:s20113292. [PMID: 32527006 PMCID: PMC7309186 DOI: 10.3390/s20113292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 01/24/2023]
Abstract
The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
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Johnston‐Monje D, Lopez Mejia J. Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11334. [PMID: 32351795 PMCID: PMC7186905 DOI: 10.1002/aps3.11334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/28/2020] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.
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Affiliation(s)
- David Johnston‐Monje
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
- Max Planck Institute for Plant Breeding ResearchDepartment of Plant Microbe InteractionsCarl-von-Linne-Weg 10D-50829CologneGermany
| | - Jessica Lopez Mejia
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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Almendras K, García J, Carú M, Orlando J. Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens. Molecules 2018; 23:E3077. [PMID: 30477264 PMCID: PMC6320784 DOI: 10.3390/molecules23123077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.
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Affiliation(s)
- Katerin Almendras
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Jaime García
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Margarita Carú
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
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Walitang DI, Kim CG, Jeon S, Kang Y, Sa T. Conservation and transmission of seed bacterial endophytes across generations following crossbreeding and repeated inbreeding of rice at different geographic locations. Microbiologyopen 2018; 8:e00662. [PMID: 29888428 PMCID: PMC6436425 DOI: 10.1002/mbo3.662] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/01/2018] [Accepted: 04/30/2018] [Indexed: 01/08/2023] Open
Abstract
There are comparatively diverse bacterial communities inside seeds, which are vertically transmitted and conserved, becoming sources of endophytes in the next generation of host plants. We studied how rice seed endophyte composition changed over time following crossbreeding, repeated inbreeding, subsequent human selection and planting of different rice seeds in different ecogeographical locations. Using terminal-restriction fragment length polymorphism analysis to study bacterial communities, we observed that diversity between the original parents and their offspring may show significant differences in richness, evenness and diversity indices. Heat maps reveal substantial contributions of both or either parent in the shaping of the bacterial seed endophytes of the offspring. Most of the terminal restriction fragments (T-RFs) of the subsequent progeny could be traced to any or both of its parents while unique T-RFs of the offspring suggest external sources of colonization particularly when the seeds were cultivated in different locations. Many similar groups of endophytic bacteria persist in the seeds even after recultivation in different locations, indicating resilience to environmental changes and conservation of bacteria across generations. This study suggests that parent plants contributed to the shaping of seed bacterial endophytes of their offspring, although it is also possible that these soil grown rice plants recruit similar populations of endophytes from the soil generation after generation. This study also highlights some bacterial groups belonging to Herbaspirillum, Microbacterium, Curtobacterium, Stenotrophomonas, Xanthomonas and Enterobacter that may be part of a transmitted and conserved "core microbiota" that are ubiquitous and dominant members of the endophytic communities of the rice seeds.
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Affiliation(s)
- Denver I Walitang
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, South Korea
| | - Chan-Gi Kim
- Bio-Evaluation Center, KRIBB, Cheongju, South Korea
| | - Sunyoung Jeon
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, South Korea
| | - Yeongyeong Kang
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, South Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, South Korea
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Wang YF, Zhu HW, Wang Y, Zhang XL, Tam NFY. Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs. Front Microbiol 2018; 9:952. [PMID: 29867858 PMCID: PMC5962692 DOI: 10.3389/fmicb.2018.00952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/24/2018] [Indexed: 01/11/2023] Open
Abstract
Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.
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Affiliation(s)
- Ya Fen Wang
- Laboratory of Basin Hydrology and Wetland Eco-restoration, School of Environmental Studies, China University of Geosciences, Wuhan, China.,Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Hao Wen Zhu
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Ying Wang
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Xiang Ling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
| | - Nora Fung Yee Tam
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong
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13
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Walitang DI, Kim CG, Kim K, Kang Y, Kim YK, Sa T. The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars. BMC PLANT BIOLOGY 2018; 18:51. [PMID: 29587643 PMCID: PMC5870378 DOI: 10.1186/s12870-018-1261-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Inherent characteristics and changes in the physiology of rice as it attains salt tolerance affect the colonizing bacterial endophytic communities of the rice seeds. These transmissible endophytes also serve as a source of the plant's microbial community and concurrently respond to the host and environmental conditions. This study explores the influence of the rice host as well as the impact of soil salinity on the community structure and diversity of seed bacterial endophytes of rice with varying tolerance to salt stress. Endophytic bacterial diversity was studied through culture-dependent technique and Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. RESULTS Results revealed considerably diverse communities of bacterial endophytes in the interior of rice seeds. The overall endophytic bacterial communities of the indica rice seeds based on 16S rRNA analysis of clones and isolates are dominated by phylum Proteobacteria followed by Actinobacteria and Firmicutes. Community profiles show common ribotypes found in all cultivars of the indica subspecies representing potential core microbiota belonging to Curtobacterium, Flavobacterium, Enterobacter, Xanthomonas, Herbaspirillum, Microbacterium and Stenotrophomonas. Clustering analysis shows that the host genotype mainly influences the seed endophytic community of the different rice cultivars. Under salt stress conditions, endophytic communities of the salt-sensitive and salt-tolerant rice cultivars shift their dominance to bacterial groups belonging to Flavobacterium, Pantoea, Enterobacter, Microbacterium, Kosakonia and Curtobacterium. CONCLUSION The endophytic communities of rice indica seeds are shaped by the hosts' genotype, their physiological adaptation to salt stress and phylogenetic relatedness. Under salt stress conditions, a few groups of bacterial communities become prominent causing a shift in bacterial diversity and dominance.
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Affiliation(s)
- Denver I. Walitang
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
| | - Chang-Gi Kim
- Bio-Evaluation Center, KRIBB, Cheongju, 281-16 South Korea
| | - Kiyoon Kim
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
| | - Yeongyeong Kang
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
| | - Young Kee Kim
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
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14
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Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture. Biodegradation 2017; 29:23-39. [PMID: 29177812 PMCID: PMC5773621 DOI: 10.1007/s10532-017-9811-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/02/2017] [Indexed: 11/13/2022]
Abstract
An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)3 as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a 13C-carbon label from 13C10-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.
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15
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Colin Y, Goñi-Urriza M, Gassie C, Carlier E, Monperrus M, Guyoneaud R. Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters. MICROBIAL ECOLOGY 2017; 73:39-49. [PMID: 27581035 DOI: 10.1007/s00248-016-0842-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 103 cells l-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.
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Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France.
- INRA, UMR 1136 INRA/Université de Lorraine, Interactions Arbres Micro-organismes, Centre de Nancy, 54280, Champenoux, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Claire Gassie
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Elisabeth Carlier
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Mathilde Monperrus
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
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16
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Bornemann M, Bussmann I, Tichy L, Deutzmann J, Schink B, Pester M. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance. FEMS Microbiol Ecol 2016; 92:fiw123. [PMID: 27267930 DOI: 10.1093/femsec/fiw123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/14/2022] Open
Abstract
Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.
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Affiliation(s)
- Maren Bornemann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Meeresstation Helgoland, Kurpromenade 201, D-27498 Helgoland, Germany
| | - Lucas Tichy
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg Deutzmann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany Department of Civil and Environmental Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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17
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Molecular analysis of dominant species in Listeria monocytogenes-positive biofilms in the drains of food processing facilities. Appl Microbiol Biotechnol 2015; 100:3165-75. [PMID: 26658820 DOI: 10.1007/s00253-015-7203-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
Abstract
Listeria monocytogenes exhibits symbiotic codependence with the dominant commensal bacteria, which may help it avoid being removed or inactivated by disinfectants in local environments. In this study, we investigated L. monocytogenes-positive biofilms at food production facilities, and the dominant bacterial species of the biofilms were identified to determine the properties of the microbiological background. For this purpose, the ISO 11290 method was used for the detection and isolation of L. monocytogenes, and the species were further identified based on 16S rRNA and hly genes. 16S rRNA gene-based cloning, terminal restriction fragment length polymorphism, and denaturing gradient gel electrophoresis were combined to evaluate the dominant bacteria of the drain biofilms. Out of 100 drain samples, 8 were naturally contaminated with L. monocytogenes. Three molecular methods consistently showed that Pseudomonas psychrophila, Pseudomonas sp., and Klebsiella oxytoca were dominant species in 3Q, 5Q, and 6Q samples; Aeromonas hydrophila and Klebsiella sp. were significantly dominant in 1-2, 1-3, and 3-2 samples; A. hydrophila and K. oxytoca were dominant in the 2-3 sample; and A. hydrophila and Pseudomonas sp. were prominent in the 3-3 sample. Different biofilms from the same plant shared common bands, suggesting that similar bacteria can be found and can be dominant in different biofilms. This study provides a better understanding of the dominant compositions in these bacterial communities. Further studies to determine the mechanism of co-culture with L. monocytogenes will be of critical importance in predicting effective disinfection strategies.
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18
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Cho KC, Lee DG, Fuller ME, Hatzinger PB, Condee CW, Chu KH. Application of (13)C and (15)N stable isotope probing to characterize RDX degrading microbial communities under different electron-accepting conditions. JOURNAL OF HAZARDOUS MATERIALS 2015; 297:42-51. [PMID: 25935409 DOI: 10.1016/j.jhazmat.2015.04.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/04/2023]
Abstract
This study identified microorganisms capable of using the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or its metabolites as carbon and/or nitrogen sources under different electron-accepting conditions using (13)C and (15)N stable isotope probing (SIP). Mesocosms were constructed using groundwater and aquifer solids from an RDX-contaminated aquifer. The mesocosms received succinate as a carbon source and one of four electron acceptors (nitrate, manganese(IV), iron(III), or sulfate) or no additional electron acceptor (to stimulate methanogenesis). When RDX degradation was observed, subsamples from each mesocosm were removed and amended with (13)C3- or ring-(15)N3-, nitro-(15)N3-, or fully-labeled (15)N6-RDX, followed by additional incubation and isolation of labeled nucleic acids. A total of fifteen 16S rRNA sequences, clustering in α- and γ-Proteobacteria, Clostridia, and Actinobacteria, were detected in the (13)C-DNA fractions. A total of twenty seven sequences were derived from different (15)N-DNA fractions, with the sequences clustered in α- and γ-Proteobacteria, and Clostridia. Interestingly, sequences identified as Desulfosporosinus sp. (in the Clostridia) were not only observed to incorporate the labeled (13)C or (15)N from labeled RDX, but also were detected under each of the different electron-accepting conditions. The data suggest that (13)C- and (15)N-SIP can be used to characterize microbial communities involved in RDX biodegradation, and that the dominant pathway of RDX biodegradation may differ under different electron-accepting conditions.
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Affiliation(s)
- Kun-Ching Cho
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Do Gyun Lee
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | | | | | | | - Kung-Hui Chu
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA.
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19
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Wu L, Wang J, Huang W, Wu H, Chen J, Yang Y, Zhang Z, Lin W. Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture. Sci Rep 2015; 5:15871. [PMID: 26515244 PMCID: PMC4626807 DOI: 10.1038/srep15871] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/07/2015] [Indexed: 11/11/2022] Open
Abstract
Under consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
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Affiliation(s)
- Linkun Wu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Juanying Wang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Weimin Huang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Hongmiao Wu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Jun Chen
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Yanqiu Yang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Zhongyi Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
| | - Wenxiong Lin
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China.,Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P. R. China
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20
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Mühling M, Beier R, Müller P, Petzsch P, Drechsel A, Schlömann M, Labudde D. OEZY: Optimising
E
n
ZY
me selection for best performing terminal restriction fragment length polymorphism analysis using ARB. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Martin Mühling
- TU Bergakademie Freiberg Institute of Biological Sciences Leipziger Str. 29 09599 Freiberg Germany
| | - Rico Beier
- University of Applied Sciences Mittweida Technikumplatz 17 09648 Mittweida Germany
| | - Patricia Müller
- TU Bergakademie Freiberg Institute of Biological Sciences Leipziger Str. 29 09599 Freiberg Germany
| | - Patrick Petzsch
- TU Bergakademie Freiberg Institute of Biological Sciences Leipziger Str. 29 09599 Freiberg Germany
| | - Anna Drechsel
- TU Bergakademie Freiberg Institute of Biological Sciences Leipziger Str. 29 09599 Freiberg Germany
| | - Michael Schlömann
- TU Bergakademie Freiberg Institute of Biological Sciences Leipziger Str. 29 09599 Freiberg Germany
| | - Dirk Labudde
- University of Applied Sciences Mittweida Technikumplatz 17 09648 Mittweida Germany
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21
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Popp D, Schrader S, Kleinsteuber S, Harms H, Sträuber H. Biogas production from coumarin-rich plants—inhibition by coumarin and recovery by adaptation of the bacterial community. FEMS Microbiol Ecol 2015; 91:fiv103. [DOI: 10.1093/femsec/fiv103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 11/13/2022] Open
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22
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Liang Y, Meggo R, Hu D, Schnoor JL, Mattes TE. Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination. Appl Microbiol Biotechnol 2015; 99:6515-26. [PMID: 25820643 DOI: 10.1007/s00253-015-6545-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent, and bioaccumulative. In this study, we investigated bacterial communities in soil microcosms spiked with PCB 52, 77, and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal, and redox cycling (i.e., sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting, and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after 2 weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests that they play a role in PCB dechlorination therein.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
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23
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Aida AA, Kuroda K, Yamamoto M, Nakamura A, Hatamoto M, Yamaguchi T. Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage. Microbes Environ 2015; 30:157-63. [PMID: 25817585 PMCID: PMC4462926 DOI: 10.1264/jsme2.me14105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors.
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Affiliation(s)
- Azrina A Aida
- Department of Environmental Systems Engineering, Nagaoka University of Technology
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24
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Sakai K, Miyake S, Iwama K, Inoue D, Soda S, Ike M. Polyhydroxyalkanoate (PHA) accumulation potential and PHA-accumulating microbial communities in various activated sludge processes of municipal wastewater treatment plants. J Appl Microbiol 2014; 118:255-66. [DOI: 10.1111/jam.12683] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/26/2014] [Accepted: 10/26/2014] [Indexed: 11/27/2022]
Affiliation(s)
- K. Sakai
- Division of Sustainable Energy and Environmental Engineering; Osaka University; Suita Osaka Japan
| | - S. Miyake
- Division of Sustainable Energy and Environmental Engineering; Osaka University; Suita Osaka Japan
| | - K. Iwama
- Division of Sustainable Energy and Environmental Engineering; Osaka University; Suita Osaka Japan
| | - D. Inoue
- Department of Health Science; Kitasato University; Sagamihara-Minami Kanagawa Japan
| | - S. Soda
- Division of Sustainable Energy and Environmental Engineering; Osaka University; Suita Osaka Japan
| | - M. Ike
- Division of Sustainable Energy and Environmental Engineering; Osaka University; Suita Osaka Japan
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Aida AA, Hatamoto M, Yamamoto M, Ono S, Nakamura A, Takahashi M, Yamaguchi T. Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage. J Biosci Bioeng 2014; 118:540-5. [DOI: 10.1016/j.jbiosc.2014.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/01/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
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Pfeiffer S, Pastar M, Mitter B, Lippert K, Hackl E, Lojan P, Oswald A, Sessitsch A. Improved group-specific primers based on the full SILVA 16S rRNA gene reference database. Environ Microbiol 2014; 16:2389-407. [PMID: 25229098 DOI: 10.1111/1462-2920.12350] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.
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Johnston-Monje D, Mousa WK, Lazarovits G, Raizada MN. Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize. BMC PLANT BIOLOGY 2014; 14:233. [PMID: 25227492 PMCID: PMC4189167 DOI: 10.1186/s12870-014-0233-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Endophytes are microbes that live within plants such as maize (corn, Zea mays L.) without causing disease. It is generally assumed that most endophytes originate from soil. If this is true, then as humans collected, domesticated, bred and migrated maize globally from its native Mexico, they moved the species away from its native population of endophyte donors. The migration of maize persists today, as breeders collect wild and exotic seed (as sources of diverse alleles) from sites of high genetic diversity in Mexico for breeding programs on distant soils. When transported to new lands, it is unclear whether maize permits only selective colonization of microbes from the Mexican soils on which it co-evolved, tolerates shifts in soil-derived endophytes, or prevents colonization of soil-based microbes in favour of seed-transmitted microbes. To test these hypotheses, non-sterilized seeds of three types of maize (pre-domesticated-Mexican, ancient-Mexican, modern-temperate) were planted side-by-side on indigenous Mexican soil, Canadian temperate soil or sterilized sand. The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping. RESULTS Multivariate analysis showed that bacterial 16S-rDNA TRFLP profiles from young, surface-sterilized maize plants were more similar when the same host genotype was grown on the different soils than when different maize genotypes were grown on the same soil. There appeared to be two reasons for this result. First, the largest fraction of bacterial 16S-signals from soil-grown plants was shared with parental seeds and/or plants grown on sterilized sand, suggesting significant inheritance of candidate endophytes. The in vitro activities of soil-derived candidate endophytes could be provided by bacteria that were isolated from sterile sand grown plants. Second, many non-inherited 16S-signals from sibling plants grown on geographically-distant soils were shared with one another, suggesting maize can select microbes with similar TRFLP peak sizes from diverse soils. Wild, pre-domesticated maize did not possess more unique 16S-signals when grown on its native Mexican soil than on Canadian soil, pointing against long-term co-evolutionary selection. The modern hybrid did not reject more soil-derived 16S-signals than did ancestral maize, pointing against such rejection as a mechanism that contributes to yield stability across environments. A minor fraction of 16S-signals was uniquely associated with any one soil. CONCLUSION Within the limits of TRFLP profiling, the candidate bacterial endophyte populations of pre-domesticated, ancient and modern maize are partially buffered against the effects of geographic migration --- from a Mexican soil associated with ancestral maize, to a Canadian soil associated with modern hybrid agriculture. These results have implications for understanding the effects of domestication, migration, ex situ seed conservation and modern breeding, on the microbiome of one of the world's most important food crops.
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Affiliation(s)
- David Johnston-Monje
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
- />A&L Biologicals, Agroecology Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5 Canada
| | - Walaa Kamel Mousa
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
- />Department of Pharmacognosy, Mansoura University, Mansoura, 35516 Egypt
| | - George Lazarovits
- />A&L Biologicals, Agroecology Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5 Canada
| | - Manish N Raizada
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
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Volant A, Bruneel O, Desoeuvre A, Héry M, Casiot C, Bru N, Delpoux S, Fahy A, Javerliat F, Bouchez O, Duran R, Bertin PN, Elbaz-Poulichet F, Lauga B. Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage. FEMS Microbiol Ecol 2014; 90:247-63. [PMID: 25070063 DOI: 10.1111/1574-6941.12394] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/10/2014] [Accepted: 07/16/2014] [Indexed: 11/30/2022] Open
Abstract
Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community.
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Affiliation(s)
- Aurélie Volant
- Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
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Paver SF, Youngblut ND, Whitaker RJ, Kent AD. Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes. Environ Microbiol 2014; 17:816-28. [PMID: 24912130 DOI: 10.1111/1462-2920.12529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/03/2014] [Indexed: 11/27/2022]
Abstract
Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.
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Affiliation(s)
- Sara F Paver
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA
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Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. ISME JOURNAL 2014; 8:2029-44. [PMID: 24722631 DOI: 10.1038/ismej.2014.51] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/08/2022]
Abstract
Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with (13)C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills.
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Liang Y, Martinez A, Hornbuckle KC, Mattes TE. Potential for Polychlorinated Biphenyl Biodegradation in Sediments from Indiana Harbor and Ship Canal. INTERNATIONAL BIODETERIORATION & BIODEGRADATION 2014; 89:50-57. [PMID: 24764649 PMCID: PMC3993986 DOI: 10.1016/j.ibiod.2014.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Polychlorinated biphenyls (PCBs) are carcinogenic, persistent, and bioaccumulative contaminants that pose risks to human and environmental health. In this study, we evaluated the PCB biodegradation of sediments from Indiana Harbor and Ship Canal (IHSC), a PCB-contaminated site (average PCB concentration = 12,570 ng/g d.w.). PCB congener profiles and bacterial community structure in a core sediment sample (4.57 m long) were characterized. Analysis of vertical PCB congener profile patterns in sediment and pore water strongly suggest that in situ dechlorination occurred in sediments. However, 16S rRNA genes from putative PCB-dechlorinating Chloroflexi were relatively more abundant in upper 2 m sediments, as were genes indicative of aerobic biodegradation potential (i.e. biphenyl dioxygenase (bphA)). Characterization of the bacterial community by terminal restriction fragment length polymorphism and comparison of these with sediment and pore water PCB congener profiles with the Mantel test revealed a statistical correlation (p<0.001). Sequences classified as Acinetobacter and Acidovorax were highly abundant in deep sediments. Overall, our results suggest that PCB dechlorination has already occurred, and that IHSC sediments have the potential for further aerobic and anaerobic PCB biodegradation.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Andres Martinez
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Keri C. Hornbuckle
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Timothy E. Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
- Corresponding author: Tel.: +1 319 335 5065, Fax: +1 319 335 5660,
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van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC. Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 2014; 89:316-30. [DOI: 10.1111/1574-6941.12308] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 01/25/2023] Open
Affiliation(s)
- Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | | | - Anne S. Palmer
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mark Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Ian Snape
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Jonathan S. Stark
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Ben Raymond
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - John McKinlay
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Tristrom Winsley
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
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Prakash O, Pandey PK, Kulkarni GJ, Mahale KN, Shouche YS. Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP). Indian J Microbiol 2014; 54:255-61. [PMID: 24891731 DOI: 10.1007/s12088-014-0461-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/22/2014] [Indexed: 11/30/2022] Open
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) is a rapid, robust, inexpensive and simple tool for microbial community profiling. Methods used for DNA extraction, PCR amplification and digestion of amplified products have a considerable impact on the results of T-RFLP. Pitfalls of the method skew the similarity analysis and compromise its high throughput ability. Despite a high throughput method of data generation, data analysis is still in its infancy and needs more attention. Current article highlights the limitations of the methods used for data generation and analysis. It also provides an overview of the recent methodological developments in T-RFLP which will assist the readers in obtaining real and authentic profiles of the microbial communities under consideration while eluding the inherent biases and technical difficulties.
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Prashant K Pandey
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Girish J Kulkarni
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Kiran N Mahale
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, 411007 Maharashtra India
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Romi W, Keisam S, Ahmed G, Jeyaram K. Reliable differentiation of Meyerozyma guilliermondii from Meyerozyma caribbica by internal transcribed spacer restriction fingerprinting. BMC Microbiol 2014; 14:52. [PMID: 24575831 PMCID: PMC3946169 DOI: 10.1186/1471-2180-14-52] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/24/2014] [Indexed: 11/10/2022] Open
Abstract
Background Meyerozyma guilliermondii (anamorph Candida guilliermondii) and Meyerozyma caribbica (anamorph Candida fermentati) are closely related species of the genetically heterogenous M. guilliermondii complex. Conventional phenotypic methods frequently misidentify the species within this complex and also with other species of the Saccharomycotina CTG clade. Even the long-established sequencing of large subunit (LSU) rRNA gene remains ambiguous. We also faced similar problem during identification of yeast isolates of M. guilliermondii complex from indigenous bamboo shoot fermentation in North East India. There is a need for development of reliable and accurate identification methods for these closely related species because of their increasing importance as emerging infectious yeasts and associated biotechnological attributes. Results We targeted the highly variable internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and identified seven restriction enzymes through in silico analysis for differentiating M. guilliermondii from M. caribbica. Fifty five isolates of M. guilliermondii complex which could not be delineated into species-specific taxonomic ranks by API 20 C AUX and LSU rRNA gene D1/D2 sequencing were subjected to ITS-restriction fragment length polymorphism (ITS-RFLP) analysis. TaqI ITS-RFLP distinctly differentiated the isolates into M. guilliermondii (47 isolates) and M. caribbica (08 isolates) with reproducible species-specific patterns similar to the in silico prediction. The reliability of this method was validated by ITS1-5.8S-ITS2 sequencing, mitochondrial DNA RFLP and electrophoretic karyotyping. Conclusions We herein described a reliable ITS-RFLP method for distinct differentiation of frequently misidentified M. guilliermondii from M. caribbica. Even though in silico analysis differentiated other closely related species of M. guilliermondii complex from the above two species, it is yet to be confirmed by in vitro analysis using reference strains. This method can be used as a reliable tool for rapid and accurate identification of closely related species of M. guilliermondii complex and for differentiating emerging infectious yeasts of the Saccharomycotina CTG clade.
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Affiliation(s)
| | | | | | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India.
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35
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Osborne CA. Terminal restriction fragment length polymorphism (T-RFLP) profiling of bacterial 16S rRNA genes. Methods Mol Biol 2014; 1096:57-69. [PMID: 24515360 DOI: 10.1007/978-1-62703-712-9_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
T-RFLP profiling is a very effective method for comparing many samples in an environmental microbiology study, because fingerprints of microbial diversity can be generated in a sensitive, reproducible, and cost-effective manner. This protocol describes the steps required to generate T-RFLP profiles of the dominant members of a bacterial community, by PCR amplification of the bacterial 16S rRNA genes and three restriction endonuclease digests to generate three different profiles for each sample. The generation of multiple profiles per sample provides enough information to confidently differentiate rich environmental bacterial communities.
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Affiliation(s)
- Catherine A Osborne
- Department of Civil Engineering, Centre for Water Sensitive Cities, Monash University, Clayton, VIC, Australia
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Livermore JA, Jin YO, Arnseth RW, Lepuil M, Mattes TE. Microbial community dynamics during acetate biostimulation of RDX-contaminated groundwater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:7672-7678. [PMID: 23781876 DOI: 10.1021/es4012788] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biostimulation of groundwater microbial communities (e.g., with carbon sources) is a common approach to achieving in situ bioremediation of organic pollutants (e.g., explosives). We monitored a field-scale approach to remediate the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in an aquifer near the Iowa Army Ammunition Plant in Middletown, IA. The purpose of the study was to gain insight into the effect of biostimulation on the microbial community. Biostimulation with acetate led to the onset of RDX reduction at the site, which was most apparent in monitoring well MW309. Based on previous laboratory experiments, we hypothesized that RDX degradation and metabolite production would correspond to enrichment of one or more Fe(III)-reducing bacterial species. Community DNA from MW309 was analyzed with 454 pyrosequencing and terminal restriction fragment length polymorphism. Production of RDX metabolites corresponded to a microbial community shift from primarily Fe(III)-reducing Betaproteobacteria to a community dominated by Fe(III)-reducing Deltaproteobacteria (Geobacteraceae in particular) and Bacteroidetes taxa. This data provides a firsthand field-scale microbial ecology context to in situ RDX bioremediation using modern sequencing techniques that will inform future biostimulation applications.
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Affiliation(s)
- Joshua A Livermore
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa , Iowa City, Iowa 52242, USA
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Cho KC, Lee DG, Roh H, Fuller ME, Hatzinger PB, Chu KH. Application of (13)C-stable isotope probing to identify RDX-degrading microorganisms in groundwater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 178:350-360. [PMID: 23603473 DOI: 10.1016/j.envpol.2013.03.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/13/2013] [Accepted: 03/19/2013] [Indexed: 06/02/2023]
Abstract
We employed stable isotope probing (SIP) with (13)C-labeled hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) to identify active microorganisms responsible for RDX biodegradation in groundwater microcosms. Sixteen different 16S rRNA gene sequences were derived from microcosms receiving (13)C-labeled RDX, suggesting the presence of microorganisms able to incorporate carbon from RDX or its breakdown products. The clones, residing in Bacteroidia, Clostridia, α-, β- and δ-Proteobacteria, and Spirochaetes, were different from previously described RDX degraders. A parallel set of microcosms was amended with cheese whey and RDX to evaluate the influence of this co-substrate on the RDX-degrading microbial community. Cheese whey stimulated RDX biotransformation, altered the types of RDX-degrading bacteria, and decreased microbial community diversity. Results of this study suggest that RDX-degrading microorganisms in groundwater are more phylogenetically diverse than what has been inferred from studies with RDX-degrading isolates.
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Affiliation(s)
- Kun-Ching Cho
- Zachry Department of Civil Engineering, 3136 TAMU, 205G WERC, Texas A&M University, College Station, TX 77843-3136, USA
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Galand PE, Alonso-Sáez L, Bertilsson S, Lovejoy C, Casamayor EO. Contrasting activity patterns determined by BrdU incorporation in bacterial ribotypes from the Arctic Ocean in winter. Front Microbiol 2013; 4:118. [PMID: 23750155 PMCID: PMC3657686 DOI: 10.3389/fmicb.2013.00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/26/2013] [Indexed: 11/13/2022] Open
Abstract
The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low-energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analog bromodeoxyuridine (BrdU), followed by immunocapturing, terminal restriction fragment length polymorphism fingerprinting, cloning, and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, the Alphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly, Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity) that contributed in contrasting ways to the active communities in the incubations. Polaribacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU-labeled DNA. In contrast, SAR11 and two other Colwellia clusters were underrepresented in the BrdU-labeled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, including Polaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct metabolic features.
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Affiliation(s)
- Pierre E Galand
- Biogeodynamics and Biodiversity Group, Centre d'Estudis Avançats de Blanes, Centre d'Estudis Avançats de Blanes-Consejo Superior de Investigaciones Científicas Blanes, Spain ; UPMC Univ Paris 06 France ; CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls Banyuls sur Mer, France
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Bajerski F, Wagner D. Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica. FEMS Microbiol Ecol 2013; 85:128-42. [PMID: 23480659 DOI: 10.1111/1574-6941.12105] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/29/2022] Open
Abstract
Antarctic glacier forefields are extreme environments and pioneer sites for ecological succession. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats, and new terrain is becoming exposed to soil formation and microbial colonization. However, only little is known about the impact of environmental changes on microbial communities and how they develop in connection to shifting habitat characteristics. In this study, using a combination of molecular and geochemical analysis, we determine the structure and development of bacterial communities depending on soil parameters in two different glacier forefields on Larsemann Hills, East Antarctica. Our results demonstrate that deglaciation-dependent habitat formation, resulting in a gradient in soil moisture, pH and conductivity, leads to an orderly bacterial succession for some groups, for example Cyanobacteria, Bacteroidetes and Deltaproteobacteria in a transect representing 'classical' glacier forefields. A variable bacterial distribution and different composed communities were revealed according to soil heterogeneity in a slightly 'matured' glacier forefield transect, where Gemmatimonadetes, Flavobacteria, Gamma- and Deltaproteobacteria occur depending on water availability and soil depth. Actinobacteria are dominant in both sites with dominance connected to certain trace elements in the glacier forefields.
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Potsdam, Germany.
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Daebeler A, Gansen M, Frenzel P. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil. PLoS One 2013; 8:e53656. [PMID: 23341965 PMCID: PMC3544908 DOI: 10.1371/journal.pone.0053656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.
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Affiliation(s)
- Anne Daebeler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martina Gansen
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Peter Frenzel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Weissbrodt DG, Shani N, Sinclair L, Lefebvre G, Rossi P, Maillard J, Rougemont J, Holliger C. PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data. BMC Microbiol 2012; 12:306. [PMID: 23270314 PMCID: PMC3566925 DOI: 10.1186/1471-2180-12-306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/18/2012] [Indexed: 12/23/2022] Open
Abstract
Background In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems. Results PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes. Conclusions PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.
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Affiliation(s)
- David G Weissbrodt
- Ecole Polytechnique Fédérale de Lausanne, School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, Lausanne 1015, Switzerland
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Bhattarai S, Ross KA, Schmid M, Anselmetti FS, Bürgmann H. Local conditions structure unique archaeal communities in the anoxic sediments of meromictic Lake Kivu. MICROBIAL ECOLOGY 2012; 64:291-310. [PMID: 22430505 DOI: 10.1007/s00248-012-0034-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 02/26/2012] [Indexed: 05/31/2023]
Abstract
Meromictic Lake Kivu is renowned for its enormous quantity of methane dissolved in the hypolimnion. The methane is primarily of biological origin, and its concentration has been increasing in the past half-century. Insight into the origin of methane production in Lake Kivu has become relevant with the recent commercial extraction of methane from the hypolimnion. This study provides the first culture-independent approach to identifying the archaeal communities present in Lake Kivu sediments at the sediment-water interface. Terminal restriction fragment length polymorphism analysis suggests considerable heterogeneity in the archaeal community composition at varying sample locations. This diversity reflects changes in the geochemical conditions in the sediment and the overlying water, which are an effect of local groundwater inflows. A more in-depth look at the archaeal community composition by clone library analysis revealed diverse phylogenies of Euryarchaeota and Crenarachaeota. Many of the sequences in the clone libraries belonged to globally distributed archaeal clades such as the rice cluster V and Lake Dagow sediment environmental clusters. Several of the determined clades were previously thought to be rare among freshwater sediment Archaea (e.g., sequences related to the SAGMEG-1 clade). Surprisingly, there was no observed relation of clones to known hydrogentrophic methanogens and less than 2 % of clones were related to acetoclastic methanogens. The local variability, diversity, and novelty of the archaeal community structure in Lake Kivu should be considered when making assumptions on the biogeochemical functioning of its sediments.
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MESH Headings
- Anaerobiosis
- Archaea/classification
- Archaea/genetics
- Archaea/growth & development
- Archaea/metabolism
- Cloning, Molecular
- Crenarchaeota/classification
- Crenarchaeota/genetics
- Crenarchaeota/growth & development
- Crenarchaeota/metabolism
- DNA, Archaeal/analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Ribosomal/analysis
- Ecosystem
- Euryarchaeota/classification
- Euryarchaeota/genetics
- Euryarchaeota/growth & development
- Euryarchaeota/metabolism
- Gene Library
- Genes, rRNA
- Geologic Sediments/microbiology
- Lakes/microbiology
- Methane/metabolism
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Susma Bhattarai
- Department of Surface Waters-Research and Management, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Seestrasse 79, 6047, Kastanienbaum, Switzerland
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Maeda T, Hirose E, Chikaraishi Y, Kawato M, Takishita K, Yoshida T, Verbruggen H, Tanaka J, Shimamura S, Takaki Y, Tsuchiya M, Iwai K, Maruyama T. Algivore or phototroph? Plakobranchus ocellatus (Gastropoda) continuously acquires kleptoplasts and nutrition from multiple algal species in nature. PLoS One 2012; 7:e42024. [PMID: 22848693 PMCID: PMC3404988 DOI: 10.1371/journal.pone.0042024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/29/2012] [Indexed: 01/19/2023] Open
Abstract
The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts) in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1) adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2) it behaves as a mixotroph (photoautotroph and herbivorous consumer) and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae.
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Affiliation(s)
- Taro Maeda
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Euichi Hirose
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Yoshito Chikaraishi
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Masaru Kawato
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Kiyotaka Takishita
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Heroen Verbruggen
- Phycology Research Group, Ghent University, Ghent, Belgium
- School of Botany, The University of Melbourne, Victoria, Australia
| | - Jiro Tanaka
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, Japan
| | - Shigeru Shimamura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Masashi Tsuchiya
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Kenji Iwai
- Okinawa Prefectural Fisheries and Ocean Research Center, 1-3-1 Nishizaki, Itoman-shi, Okinawa, Japan
| | - Tadashi Maruyama
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
- * E-mail:
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Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS One 2012; 7:e40467. [PMID: 22808168 PMCID: PMC3395703 DOI: 10.1371/journal.pone.0040467] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/07/2012] [Indexed: 01/10/2023] Open
Abstract
The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ∼4% read abundance across biological, and ∼2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific ‘in vivo’ fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.
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Persistence and degrading activity of free and immobilised allochthonous bacteria during bioremediation of hydrocarbon-contaminated soils. Biodegradation 2012; 24:1-11. [PMID: 22555628 DOI: 10.1007/s10532-012-9553-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/23/2012] [Indexed: 11/27/2022]
Abstract
Rhodococcus sp. and Pseudomonas sp. bioremediation experiments were carried out using free and immobilized cells on natural carrier material (corncob powder) in order to evaluate the feasibility of its use in the bioremediation of hydrocarbon-contaminated soils. Terminal restriction fragment length polymorphism analysis was performed on the 16S rRNA gene as molecular fingerprinting method in order to assess the persistence of inoculated strains in the soil over time. Immobilized Pseudomonas cells degraded hydrocarbons more efficiently in the short term compared to the free ones. Immobilization seemed also to increase cell growth and stability in the soil. Free and immobilized Rhodococcus cells showed comparable degradation percentages, probably due to the peculiarity of Rhodococcus cells to aggregate into irregular clusters in the presence of hydrocarbons as sole carbon source. It is likely that the cells were not properly adsorbed on the porous matrix as a result of the small size of its pores. When Rhodococcus and Pseudomonas cells were co-immobilized on the matrix, a competition established between the two strains, that probably ended in the exclusion of Pseudomonas cells from the pores. The organic matrix might act as protective agent, but it also possibly limited cell density. Nevertheless, when the cells were properly adsorbed on the porous matrix, the immobilization became a suitable bioremediation strategy.
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Prischl M, Hackl E, Pastar M, Pfeiffer S, Sessitsch A. Genetically modified Bt maize lines containing cry3Bb1, cry1A105 or cry1Ab2 do not affect the structure and functioning of root-associated endophyte communities. APPLIED SOIL ECOLOGY 2012. [PMID: 0 DOI: 10.1016/j.apsoil.2011.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Roberts DM, Schofield PG, Donn S, Daniell TJ. Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal-restriction fragment length polymorphisms. Methods Ecol Evol 2011. [DOI: 10.1111/j.2041-210x.2011.00139.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fortuna AM, Marsh TL, Honeycutt CW, Halteman WA. Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism. Appl Microbiol Biotechnol 2011; 91:1193-202. [PMID: 21667276 DOI: 10.1007/s00253-011-3363-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 03/29/2011] [Accepted: 05/02/2011] [Indexed: 11/29/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments' relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.
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Affiliation(s)
- Ann-Marie Fortuna
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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Johnston-Monje D, Raizada MN. Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. PLoS One 2011; 6:e20396. [PMID: 21673982 PMCID: PMC3108599 DOI: 10.1371/journal.pone.0020396] [Citation(s) in RCA: 292] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 05/01/2011] [Indexed: 11/18/2022] Open
Abstract
Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.
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Affiliation(s)
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
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Szukics U, Hackl E, Zechmeister-Boltenstern S, Sessitsch A. Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils. Microbiol Res 2011; 167:103-9. [PMID: 21632226 DOI: 10.1016/j.micres.2011.04.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 11/26/2022]
Abstract
Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental factors are still poorly understood. The present study aims at comparing the capacity of AOA and AOB to momentarily respond to N input and increased soil moisture in two contrasting forest soils. Soils from the pristine Rothwald forest and the managed Schottenwald forest were amended with either NH(4)(+)-N or NO(3)(-)-N and were incubated at 40% and 70% water-filled pore space (WFPS) for four days. Nitrification rates were measured and AOA and AOB abundance and community composition were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP) analysis of bacterial and archaeal amoA genes. Our study reports rapid and distinct changes in AOA and AOB abundances in the two forest soils in response to N input and increased soil moisture but no significant effects on net nitrification rates. Functional microbial communities differed significantly in the two soils and responded specifically to the treatments during the short-term incubation. In the Rothwald soil the abundance and community composition of AOA were affected by the water content, whereas AOB communities responded to N amendment. In the Schottenwald soil, by contrast, AOA responded to N addition. These results suggest that AOA and AOB may be selectively influenced by soil and management factors.
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Affiliation(s)
- Ute Szukics
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-3430 Tulln an der Donau, Austria.
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