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Barcelo LAF, Lantican NB, Ventura RLG, Ventura JRS. Genetic characterization of biohydrogen-producing purple non-sulfur bacteria Rhodobacter johrii MAY2 isolate via whole genome analysis. Gene 2024; 924:148597. [PMID: 38782220 DOI: 10.1016/j.gene.2024.148597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Purple non-sulfur bacteria (PNSB) are a diverse group of bacteria studied for various possible applications. They are commonly surveyed in bioenergy research as they produce biohydrogen, a candidate for clean alternative energy. This study aimed to assess the biohydrogen production ability and genetically characterize a high biohydrogen-producing PNSB (MAY2) isolated from Los Baños, Laguna, Philippines via whole genome sequencing (WGS). MAY2, when grown in mixed volatile fatty acids, produced biogas with 38% hydrogen. WGS results revealed that the isolate is positively classified under the genus Rhodobacter johrii. Also, 82 genetic hallmarks for biohydrogen production were found in the isolated genome which are involved in the production of key enzymes and proteins relevant to the photofermentative and hydrogen regulation pathways. Its nitrogenase gene cluster is stringently regulated by two genes, nifA and rofN, whose function and expression are easily affected by several environmental factors.
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Affiliation(s)
- Leo Agustin F Barcelo
- Biomaterials and Environmental Engineering Laboratory, Department of Engineering Science, College of Engineering and Agro-Industrial Technology, University of the Philippines Los Baños, College, Laguna 4031 Philippines
| | - Nacita B Lantican
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna 4031 Philippines
| | - Ruby Lynn G Ventura
- University of the Philippines Rural High School, College of Arts and Sciences, University of the Philippines Los Baños, Paciano Rizal, Bay, Laguna, 4033, Philippines
| | - Jey-R S Ventura
- Biomaterials and Environmental Engineering Laboratory, Department of Engineering Science, College of Engineering and Agro-Industrial Technology, University of the Philippines Los Baños, College, Laguna 4031 Philippines.
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2
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, Ehrenreich A, Liebl W, García-Martínez T, Mauricio JC. Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS. Front Microbiol 2022; 13:1055010. [PMID: 36569054 PMCID: PMC9767973 DOI: 10.3389/fmicb.2022.1055010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different "omics" tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities' role in the vinegar-making industry.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, Córdoba, Spain,*Correspondence: Isidoro García-García,
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, Córdoba, Spain
| | - Armin Ehrenreich
- Department of Microbiology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
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Xiong Y, Du Y, Deng Y, Ma T, Wang Y. Feammox in alluvial-lacustrine aquifer system: Nitrogen/iron isotopic and biogeochemical evidences. WATER RESEARCH 2022; 222:118867. [PMID: 35870391 DOI: 10.1016/j.watres.2022.118867] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Groundwater nitrogen contamination is becoming increasingly serious worldwide, and natural nitrogen attenuation processes such as anaerobic ammonium oxidation coupled to iron reduction ("Feammox") play an important role in mitigating contamination. Although there has been intensive study of Feammox in soils and sediments, still lacks research on this process in groundwater. This study makes effort to demonstrate the occurrence of Feammox in groundwater by combining information from Fe/N isotope composition, the quantitative polymerase chain reaction (qPCR) assay, and 16S rRNA gene sequencing. Poyang Lake Plain of Yangtze River in central China was selected as the case study area. The critical evidences that indicate Feammox in groundwater include favorable hydrogeochemical conditions of the alluvia-lacustrine aquifer systems, the simultaneous enrichment of 15N in ammonium and 56Fe, the relative high abundance of Acidimicrobiaceae bacterium A6, and the joint elevation of the abundance of the Feammox bacteria and the concentration of Fe(III). Redundancy analysis (RDA) indicated that Geothrix and Rhodobacter may participate directly or cooperatively in the Feammox process. Ammonium-oxidizing archaea (AOA) involved in ammonium-oxidizing or Feammox process may be stimulated by Fe(III) under a low oxygen concentration and weakly acidic condition. Anammox may be indirectly enhanced by products of the nitrogen transformation processes involving Feammox bacteria and AOA. Fe(III) concentration is an important environmental factor affecting the abundance of functional microorganisms related to nitrogen cycling and the composition of ammonium-oxidizing and iron-reducing microbes. Specific geological background (such as the widespread red soils) and anthropogenic input of ammonium, iron, and acidic substances may jointly promote Feammox in groundwater.
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Affiliation(s)
- Yaojin Xiong
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, PR China; School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, PR China
| | - Yao Du
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, PR China; School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, PR China.
| | - Yamin Deng
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, PR China; School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, PR China
| | - Teng Ma
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, PR China; School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, PR China
| | - Yanxin Wang
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution & Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, PR China; School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, PR China
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Xiu W, Wu M, Nixon SL, Lloyd JR, Bassil NM, Gai R, Zhang T, Su Z, Guo H. Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10105-10119. [PMID: 35763428 DOI: 10.1021/acs.est.2c02623] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-arsenic (As) groundwaters, a worldwide issue, are critically controlled by multiple interconnected biogeochemical processes. However, there is limited information on the complex biogeochemical interaction networks that cause groundwater As enrichment in aquifer systems. The western Hetao basin was selected as a study area to address this knowledge gap, offering an aquifer system where groundwater flows from an oxidizing proximal fan (low dissolved As) to a reducing flat plain (high dissolved As). The key microbial interaction networks underpinning the biogeochemical pathways responsible for As mobilization along the groundwater flow path were characterized by genome-resolved metagenomic analysis. Genes associated with microbial Fe(II) oxidation and dissimilatory nitrate reduction were noted in the proximal fan, suggesting the importance of nitrate-dependent Fe(II) oxidation in immobilizing As. However, genes catalyzing microbial Fe(III) reduction (omcS) and As(V) detoxification (arsC) were highlighted in groundwater samples downgradient flow path, inferring that reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides mobilized As(V), followed by enzymatic reduction to As(III). Genes associated with ammonium oxidation (hzsABC and hdh) were also positively correlated with Fe(III) reduction (omcS), suggesting a role for the Feammox process in driving As mobilization. The current study illustrates how genomic sequencing tools can help dissect complex biogeochemical systems, and strengthen biogeochemical models that capture key aspects of groundwater As enrichment.
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Affiliation(s)
- Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, P. R. China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, P. R. China
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, P. R. China
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Min Wu
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Sophie L Nixon
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Ruixuan Gai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, P. R. China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, P. R. China
| | - Tianjing Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, P. R. China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, P. R. China
| | - Zhan Su
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, P. R. China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, P. R. China
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, P. R. China
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, P. R. China
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Demtröder L, Pfänder Y, Schäkermann S, Bandow JE, Masepohl B. NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus. Microbiologyopen 2019; 8:e921. [PMID: 31441241 PMCID: PMC6925177 DOI: 10.1002/mbo3.921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/09/2023] Open
Abstract
Rhodobacter capsulatus fixes atmospheric nitrogen (N2) by a molybdenum (Mo)‐nitrogenase and a Mo‐free iron (Fe)‐nitrogenase, whose production is induced or repressed by Mo, respectively. At low nanomolar Mo concentrations, both isoenzymes are synthesized and contribute to nitrogen fixation. Here we examined the regulatory interplay of the central transcriptional activators NifA and AnfA by proteome profiling. As expected from earlier studies, synthesis of the structural proteins of Mo‐nitrogenase (NifHDK) and Fe‐nitrogenase (AnfHDGK) required NifA and AnfA, respectively, both of which depend on the alternative sigma factor RpoN to activate expression of their target genes. Unexpectedly, NifA was found to be essential for the synthesis of Fe‐nitrogenase, electron supply to both nitrogenases, biosynthesis of their cofactors, and production of RpoN. Apparently, RpoN is the only NifA‐dependent factor required for target gene activation by AnfA, since plasmid‐borne rpoN restored anfH transcription in a NifA‐deficient strain. However, plasmid‐borne rpoN did not restore Fe‐nitrogenase activity in this strain. Taken together, NifA requirement for synthesis and activity of both nitrogenases suggests that Fe‐nitrogenase functions as a complementary nitrogenase rather than an alternative isoenzyme in R. capsulatus.
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Affiliation(s)
- Lisa Demtröder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yvonne Pfänder
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bernd Masepohl
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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