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Avellaneda H, Arbeli Z, Teran W, Roldan F. Transformation of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109 and exploration of the associated enzymes. World J Microbiol Biotechnol 2020; 36:190. [PMID: 33247357 DOI: 10.1007/s11274-020-02962-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
The nitrated compounds 2,4-dinitrotoluene (2,4-DNT), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN) are toxic xenobiotics widely used in various industries. They often coexist as environmental contaminants. The aims of this study were to evaluate the transformation of 100 mg L-1 of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109c and identify enzymes that may participate in the transformation. These strains were selected from 34 TNT transforming bacteria. Cupriavidus metallidurans DNT was used as a reference strain for comparison purposes. Strains DNT, M30b and M109c transformed 2,4-DNT (100%), TNT (100, 94.7 and 63.6%, respectively), and PETN (72.7, 69.3 and 90.7%, respectively). However, the presence of TNT negatively affects 2,4-DNT and PETN transformation (inhibition > 40%) in strains DNT and M109c and fully inhibited (100% inhibition) 2,4-DNT transformation in R. planticola M30b.Genomes of R. planticola M30b and R. radiobacter M109c were sequenced to identify genes related with 2,4-DNT, TNT or PETN transformation. None of the tested strains presented DNT oxygenase, which has been previously reported in the transformation of 2,4-DNT. Thus, unidentified novel enzymes in these strains are involved in 2,4-DNT transformation. Genes encoding enzymes homologous to the previously reported TNT and PETN-transforming enzymes were identified in both genomes. R. planticola M30b have homologous genes of PETN reductase and xenobiotic reductase B, while R. radiobacter M109c have homologous genes to GTN reductase and PnrA nitroreductase. The ability of these strains to transform explosive mixtures has a potentially biotechnological application in the bioremediation of contaminated environments.
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Affiliation(s)
- Hernán Avellaneda
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Ziv Arbeli
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Wilson Teran
- Facultad de Ciencias, Departamento de Biología, Biología de Plantas y Sistemas Productivos, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fabio Roldan
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia.
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2
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Kong X, Han Z, Tai X, Jin D, Ai S, Zheng X, Bai Z. Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere. FEMS Microbiol Ecol 2020; 96:5722120. [PMID: 32016365 DOI: 10.1093/femsec/fiaa020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 02/03/2020] [Indexed: 11/14/2022] Open
Abstract
The plant-microbe interaction can affect ecosystem function, and many studies have demonstrated that plant species influence relevant microorganisms. In this study, microbial communities in bulk soil, rhizosphere soil and phyllosphere from different maize varieties were investigated using high-throughput sequencing method. Results demonstrated that cultivar Gaoneng 1 (G1) showed higher bacterial diversity in soil (both bulk and rhizosphere soils) and lower bacterial diversity in the phyllosphere, while cultivar Gaoneng 2 (G2) had lower fungal diversity in both the soil and phyllosphere compare to the other cultivars. The bacterial community structure of soils among the three varieties was significantly different; however, no significant differences were found in the soil fungal community and phyllosphere bacterial and fungal community. The soil networks from cultivar G1 and phyllosphere networks from cultivar Zhengdan (ZD) have the highest complexity in contrast to the other two cultivars. In conclusion, the bacterial community structure in bulk soil of different cultivars was significantly different, so do the co-occurrence ecological networks of phyllosphere bacterial community. This study comprehensively analyzed the microbial community among different maize cultivars and could be useful for guiding practices, such as evaluation of new plant cultivars and quality predictions of these varieties at the microbial level.
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Affiliation(s)
- Xiao Kong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.,School of Health and Public, Qingdao University, Qingdao 266071, China
| | - Zhenfei Han
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Xin Tai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Decai Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Ai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xiaoxu Zheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Higdon SM, Pozzo T, Tibbett EJ, Chiu C, Jeannotte R, Weimer BC, Bennett AB. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts. PLoS One 2020; 15:e0239081. [PMID: 32925972 PMCID: PMC7489573 DOI: 10.1371/journal.pone.0239081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N2-fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate's potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one diazotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms.
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Affiliation(s)
- Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Tania Pozzo
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Emily J. Tibbett
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Colleen Chiu
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Bart C. Weimer
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, California, United States of America
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Abstract
Raoultella genus consists of Gram-negative, aerobic, encapsulated and non-motile rods. The name of the genus derives from the name of the French bacteriologist Raoul. Currently, four species belong to the genus: R. planticola, R. ornithinolytica, R. terrigena and R. electrica. The standard biochemical test used to identify Raoultella genus should be supplemented with additional tests, because of the close relationship between the genera Raoultella and Klebsiella. In 2001 Klebsiella planticola, K. ornithinolytica and K. terrigena were re-classified to new genus Raoultella. Re-classification was based on 16S rRNA sequence and rpoB, gyrA and gyrB genes. An alternative to phenotypic identification may be mass spectrometry or genetic methods (16s rRNA). These bacteria are commonly associated with natural environments (plants, water, soil). Raoultella spp. rods are not a highly virulent pathogen. Their virulence factors include polysaccharide capsule, fimbriae, siderophores, toxins and ability to form a biofilm. It has been shown that Raoultella spp. may colonize the gastrointestinal and upper respiratory tract in humans and cause cholangitis and lung infections. The literature also includes works on the antimicrobial activity of Raoultella rods and the possibility of using them in the environment protection. This review summarizes the current knowledge of Raoultella species identification, virulence and the possibility of using them in the protection of the environment.
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Affiliation(s)
- Alicja Sękowska
- Department of Microbiology, Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland
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Complete Genome Sequence of Raoultella electrica 1GB (DSM 102253 T), Isolated from Anodic Biofilms of a Glucose-Fed Microbial Fuel Cell. Microbiol Resour Announc 2019; 8:8/43/e00800-19. [PMID: 31649093 PMCID: PMC6813382 DOI: 10.1128/mra.00800-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type strain Raoultella electrica 1GB (DSM 102253T) was isolated from anodic biofilms of glucose-fed microbial fuel cells. The fully assembled, closed, circular 5.27-Mb genome and corresponding 0.52-Mb plasmid DNA sequences were elucidated. Potential electron transfer and pathogenicity mechanisms were deduced. The type strain Raoultella electrica 1GB (DSM 102253T) was isolated from anodic biofilms of glucose-fed microbial fuel cells. The fully assembled, closed, circular 5.27-Mb genome and corresponding 0.52-Mb plasmid DNA sequences were elucidated. Potential electron transfer and pathogenicity mechanisms were deduced.
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Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai R. Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source. Front Microbiol 2018; 9:2097. [PMID: 30233558 PMCID: PMC6131576 DOI: 10.3389/fmicb.2018.02097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 08/16/2018] [Indexed: 02/02/2023] Open
Abstract
In a search for life-supporting, not life-assisting, D-amino acid metabolism, an environmental strain that grows better with D-glutamate as the sole carbon source was isolated from an ordinary river. The strain, designated as A25, exhibited a faster growth rate and greater cell yield with D-glutamate than with L-glutamate. Conversely, the D/L ratio of total cellular glutamate was as low as 4/96, which suggests that D-glutamate is more likely catabolized than anabolized. Strain A25 was phylogenetically most closely related to the gamma-proteobacterial species Raoultella ornithinolytica, with a 16S rRNA gene sequence similarity of 100%. A standard strain, R. ornithinolytica JCM 6096T, also showed similarly enhanced growth with D-glutamate, which was proven for the first time. Gene expression of the enzymes involved in D-amino acid metabolism was assayed by reverse-transcription quantitative PCR (RT-qPCR) using specifically designed primers. The targets were the genes encoding D-amino acid dehydrogenase (DAD; EC 1.4.99.1), glutamate racemase (EC 5.1.1.3), D-glutamate oxidase (EC 1.4.3.7 or EC 1.4.3.15), and UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate ligase (EC 6.3.2.9). As a result, the growth of strains A25 and R. ornithinolytica JCM 6096T on D-glutamate was conspicuously associated with the enhanced expression of the DAD gene (dadA) in the exponential phase compared with the other enzyme genes. Pseudomonas aeruginosa is also known to grow on D-glutamate as the sole carbon source but to a lesser degree than with L-glutamate. A standard strain of P. aeruginosa, JCM 5962T, was tested for gene expression of the relevant enzymes by RT-qPCR and also showed enhanced dadA expression, but in the stationary phase. Reduction of ferricyanide with D-glutamate was detected in cell extracts of the tested strains, implying probable involvement of DAD in the D-glutamate catabolizing activity. DAD-mediated catalysis may have advantages in the one-step production of α-keto acids and non-production of H2O2 over other enzymes such as racemase and D-amino acid oxidase. The physiological and biochemical importance of DAD in D-amino acid metabolism is discussed.
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Affiliation(s)
- Takeshi Naganuma
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan.,School of Biological Science, Hiroshima University, Higashihiroshima, Japan.,Astrobiology Center, National Institutes of Natural Sciences, Tokyo, Japan
| | - Yoshiakira Iinuma
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Hitomi Nishiwaki
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Ryota Murase
- School of Biological Science, Hiroshima University, Higashihiroshima, Japan
| | - Kazuo Masaki
- National Research Institute of Brewing, Higashihiroshima, Japan
| | - Ryosuke Nakai
- Microbial and Genetic Resources Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Applied Molecular Microbiology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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7
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Thijs S, Sillen W, Truyens S, Beckers B, van Hamme J, van Dillewijn P, Samyn P, Carleer R, Weyens N, Vangronsveld J. The Sycamore Maple Bacterial Culture Collection From a TNT Polluted Site Shows Novel Plant-Growth Promoting and Explosives Degrading Bacteria. FRONTIERS IN PLANT SCIENCE 2018; 9:1134. [PMID: 30123233 PMCID: PMC6085565 DOI: 10.3389/fpls.2018.01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/13/2018] [Indexed: 05/23/2023]
Abstract
Military activities have worldwide introduced toxic explosives into the environment with considerable effects on soil and plant-associated microbiota. Fortunately, these microorganisms, and their collective metabolic activities, can be harnessed for site restoration via in situ phytoremediation. We characterized the bacterial communities inhabiting the bulk soil and rhizosphere of sycamore maple (Acer pseudoplatanus) in two chronically 2,4,6-trinitrotoluene (TNT) polluted soils. Three hundred strains were isolated, purified and characterized, a majority of which showed multiple plant growth promoting (PGP) traits. Several isolates showed high nitroreductase enzyme activity and concurrent TNT-transformation. A 12-member bacterial consortium, comprising selected TNT-detoxifying and rhizobacterial strains, significantly enhanced TNT removal from soil compared to non-inoculated plants, increased root and shoot weight, and the plants were less stressed than the un-inoculated plants as estimated by the responses of antioxidative enzymes. The sycamore maple tree (SYCAM) culture collection is a significant resource of plant-associated strains with multiple PGP and catalytic properties, available for further genetic and phenotypic discovery and use in field applications.
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Affiliation(s)
- Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sascha Truyens
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Bram Beckers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jonathan van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Pieter van Dillewijn
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Pieter Samyn
- Applied and Analytical Chemistry, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Robert Carleer
- Applied and Analytical Chemistry, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Nele Weyens
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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8
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Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. Front Microbiol 2018; 9:1132. [PMID: 29915565 PMCID: PMC5994547 DOI: 10.3389/fmicb.2018.01132] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/24/2022] Open
Abstract
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.
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Affiliation(s)
- Muneer A Malla
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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9
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Thijs S, Op De Beeck M, Beckers B, Truyens S, Stevens V, Van Hamme JD, Weyens N, Vangronsveld J. Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys. Front Microbiol 2017; 8:494. [PMID: 28400755 PMCID: PMC5368227 DOI: 10.3389/fmicb.2017.00494] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies.
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Affiliation(s)
- Sofie Thijs
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | | | - Bram Beckers
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Sascha Truyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Vincent Stevens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University Kamloops, BC, Canada
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
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Metabolic Engineering of Raoultella ornithinolytica BF60 for Production of 2,5-Furandicarboxylic Acid from 5-Hydroxymethylfurfural. Appl Environ Microbiol 2016; 83:AEM.02312-16. [PMID: 27795308 DOI: 10.1128/aem.02312-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/17/2016] [Indexed: 01/15/2023] Open
Abstract
2,5-Furandicarboxylic acid (FDCA) is an important renewable biotechnological building block because it serves as an environmentally friendly substitute for terephthalic acid in the production of polyesters. Currently, FDCA is produced mainly via chemical oxidation, which can cause severe environmental pollution. In this study, we developed an environmentally friendly process for the production of FDCA from 5-hydroxymethyl furfural (5-HMF) using a newly isolated strain, Raoultella ornithinolytica BF60. First, R. ornithinolytica BF60 was identified by screening and was isolated. Its maximal FDCA titer was 7.9 g/liter, and the maximal molar conversion ratio of 5-HMF to FDCA was 51.0% (mol/mol) under optimal conditions (100 mM 5-HMF, 45 g/liter whole-cell biocatalyst, 30°C, and 50 mM phosphate buffer [pH 8.0]). Next, dcaD, encoding dicarboxylic acid decarboxylase, was mutated to block FDCA degradation to furoic acid, thus increasing FDCA production to 9.2 g/liter. Subsequently, aldR, encoding aldehyde reductase, was mutated to prevent the catabolism of 5-HMF to HMF alcohol, further increasing the FDCA titer, to 11.3 g/liter. Finally, the gene encoding aldehyde dehydrogenase 1 was overexpressed. The FDCA titer increased to 13.9 g/liter, 1.7 times that of the wild-type strain, and the molar conversion ratio increased to 89.0%. IMPORTANCE In this work, we developed an ecofriendly bioprocess for green production of FDCA in engineered R. ornithinolytica This report provides a starting point for further metabolic engineering aimed at a process for industrial production of FDCA using R. ornithinolytica.
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Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00608-16. [PMID: 27340073 PMCID: PMC4919412 DOI: 10.1128/genomea.00608-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations.
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12
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Draft Genome Sequence of Mesorhizobium sp. UFLA 01-765, a Multitolerant, Efficient Symbiont and Plant Growth-Promoting Strain Isolated from Zn-Mining Soil Using Leucaena leucocephala as a Trap Plant. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00050-16. [PMID: 26966214 PMCID: PMC4786649 DOI: 10.1128/genomea.00050-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the 7.4-Mb draft genome sequence of Mesorhizobium sp. strain UFLA 01-765, a Gram-negative bacterium of the Phyllobacteriaceae isolated from Zn-mining soil in Minas Gerais, Brazil. This strain promotes plant growth, efficiently fixes N2 in symbiosis with Leucaena leucocephala on multicontaminated soil, and has potential for application in bioremediation of marginal lands.
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Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus. GENOME ANNOUNCEMENTS 2016; 4:4/1/e00028-16. [PMID: 26950324 PMCID: PMC4767914 DOI: 10.1128/genomea.00028-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report the 4.76-Mb draft genome of Pantoea ananatis GB1, a Gram-negative bacterium of the family Enterobacteriaceae, isolated from the roots of poplars planted for phytoremediation of a diesel-contaminated plume at the Ford Motor Company site in Genk, Belgium. Strain GB1 promotes plant growth in various hosts and metabolizes hydrocarbons.
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14
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Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01517-15. [PMID: 26701084 PMCID: PMC4691658 DOI: 10.1128/genomea.01517-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the Actinobacteria, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations.
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Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00607-15. [PMID: 26067957 PMCID: PMC4463521 DOI: 10.1128/genomea.00607-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Raoultella terrigena R1Gly is a diazotrophic endophyte isolated from surface-sterilized roots of Nicotiana tabacum. The whole-genome sequence was obtained to investigate the endophytic characteristics of this organism at the genetic level, as well as to compare this strain with its close relatives. To our knowledge, this is the first genome obtained from the Raoultella terrigena species and only the third genome from the Raoultella genus, after Raoultella ornitholytic and Raoultella planticola. This genome will provide a foundation for further comparative genomic, metagenomic, and functional studies of this genus.
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