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Ottosen CF, Bjerg PL, Kümmel S, Richnow HH, Middeldorp P, Draborg H, Lemaire GG, Broholm MM. Natural attenuation of sulfonamides and metabolites in contaminated groundwater - Review, advantages and challenges of current documentation techniques. WATER RESEARCH 2024; 254:121416. [PMID: 38489851 DOI: 10.1016/j.watres.2024.121416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024]
Abstract
Sulfonamides are applied worldwide as antibiotics. They are emerging contaminants of concern, as their presence in the environment may lead to the spread of antibiotic resistance genes. Sulfonamides are present in groundwater systems, which suggest their persistence under certain conditions, highlighting the importance of understanding natural attenuation processes in groundwater. Biodegradation is an essential process, as degradation of sulfonamides reduces the risk of antibiotic resistance spreading. In this review, natural attenuation, and in particular assessment of biodegradation, is evaluated for sulfonamides in groundwater systems. The current knowledge level on biodegradation is reviewed, and a scientific foundation is built based on sulfonamide degradation processes, pathways, metabolites and toxicity. An overview of bacterial species and related metabolites is provided. The main research effort has focused on aerobic conditions while investigations under anaerobic conditions are lacking. The level of implementation in research is laboratory scale; here we strived to bridge towards field application and assessment, by assessing approaches commonly used in monitored natural attenuation. Methods to document contaminant mass loss are assessed to be applicable for sulfonamides, while the approach is limited by a lack of reference standards for metabolites. Furthermore, additional information is required on relevant metabolites in order to improve risk assessments. Based on the current knowledge on biodegradation, it is suggested to use the presence of substituent-containing metabolites from breakage of the sulfonamide bridge as specific indicators of degradation. Microbial approaches are currently available for assessment of microbial community's capacities, however, more knowledge is required on indigenous bacteria capable of degrading sulfonamides and on the impact of environmental conditions on biodegradation. Compound specific stable isotope analysis shows great potential as an additional in situ method, but further developments are required to analyse for sulfonamides at environmentally relevant levels. Finally, in a monitored natural attenuation scheme it is assessed that approaches are available that can uncover some processes related to the fate of sulfonamides in groundwater systems. Nevertheless, there are still unknowns related to relevant bacteria and metabolites for risk assessment as well as the effect of environmental settings such as redox conditions. Alongside, uncovering the fate of sulfonamides in future research, the applicability of the natural attenuation documentation approaches will advance, and provide a step towards in situ remedial concepts for the frequently detected sulfonamides.
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Affiliation(s)
- Cecilie F Ottosen
- Department of Environmental and Resource Engineering, Technical University of Denmark (DTU), Bygningstorvet, building 115, 2800 Kgs. Lyngby, Denmark.
| | - Poul L Bjerg
- Department of Environmental and Resource Engineering, Technical University of Denmark (DTU), Bygningstorvet, building 115, 2800 Kgs. Lyngby, Denmark
| | - Steffen Kümmel
- Department Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Hans H Richnow
- Department Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | | | | | - Gregory G Lemaire
- Department of Environmental and Resource Engineering, Technical University of Denmark (DTU), Bygningstorvet, building 115, 2800 Kgs. Lyngby, Denmark
| | - Mette M Broholm
- Department of Environmental and Resource Engineering, Technical University of Denmark (DTU), Bygningstorvet, building 115, 2800 Kgs. Lyngby, Denmark
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Belmok A, de Almeida FM, Rocha RT, Vizzotto CS, Tótola MR, Ramada MHS, Krüger RH, Kyaw CM, Pappas GJ. Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid. Braz J Microbiol 2023; 54:239-258. [PMID: 36701110 PMCID: PMC9944591 DOI: 10.1007/s42770-022-00900-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 10/02/2022] [Indexed: 01/27/2023] Open
Abstract
A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).
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Affiliation(s)
- Aline Belmok
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Felipe Marques de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Rodrigo Theodoro Rocha
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Carla Simone Vizzotto
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Faculdade de Tecnologia, Universidade de Brasília, Brasilia, DF, Brazil
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Cynthia Maria Kyaw
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
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Analysis of the Comparative Growth Kinetics of Paenarthrobacter ureafaciens YL1 in the Biodegradation of Sulfonamide Antibiotics Based on Substituent Structures and Substrate Toxicity. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The high consumption and emission of sulfonamide antibiotics (SAs) have a considerable threat to humans and ecosystems, so there is a need to develop safer and more effective methods than conventional strategies for the optimal removal of these compounds. In this study, four SAs with different substituents, sulfadiazine (SDZ), sulfamerazine (SMR), sulfamethoxazole (SMX), and sulfamethazine (SMZ) were removed by a pure culture of Paenarthrobacter ureafaciens YL1. The effect of the initial SAs concentration on the growth rate of strain YL1 was investigated. The results showed that the strain YL1 effectively removed various SAs in the concentration range of 0.05–2.4 mmol·L−1. The Haldane model was used to perform simulations of the experimental data, and the regression coefficient of the model indicated that the model had a good predictive ability. During SAs degradation, the maximum specific growth rate of strain YL1 was ranked as SMX > SDZ > SMR > SMZ with constants of 0.311, 0.304, 0.302, and 0.285 h−1, respectively. In addition, the biodegradation of sulfamethoxazole (SMX) with a five-membered substituent was the fastest, while the six-membered substituent of SMZ was the slowest based on the parameters of the kinetic equation. Also, density functional theory (DFT) calculations such as frontier molecular orbitals (FMOs), and molecular electrostatic potential map analysis were performed. It was evidenced that different substituents in SAs can affect the molecular orbital distribution and their stability, which led to the differences in the growth rate of strain YL1 and the degradation rate of SAs. Furthermore, the toxicity of P. ureafaciens is one of the crucial factors affecting the biodegradation rate: the more toxic the substrate and the degradation product are, the slower the microorganism grows. This study provides a theoretical basis for effective bioremediation using microorganisms in SAs-contaminated environments.
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Zhu D, Sethupathy S, Gao L, Nawaz MZ, Zhang W, Jiang J, Sun J. Microbial diversity and community structure in deep-sea sediments of South Indian Ocean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45793-45807. [PMID: 35152353 DOI: 10.1007/s11356-022-19157-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.
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Affiliation(s)
- Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lu Gao
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Zohaib Nawaz
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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Zeng L, Li W, Wang X, Zhang Y, Tai Y, Zhang X, Dai Y, Tao R, Yang Y. Bibliometric analysis of microbial sulfonamide degradation: Development, hotspots and trend directions. CHEMOSPHERE 2022; 293:133598. [PMID: 35033513 DOI: 10.1016/j.chemosphere.2022.133598] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Microbial sulfonamide degradation (MSD) is an efficient and safe treatment in both natural and engineered ecosystems. In order to systematically understand the research status and frontier trends of MSD, this study employed CiteSpace to conduct a bibliometric analysis of data from the Web of Science (WoS) and the China National Knowledge Infrastructure (CNKI) published from 2000 to 2021. During this time, China, Germany, Spain, the United States and Australia played leading roles by producing numerous high impact publications, while the Chinese Academy of Sciences was the leading research institution in this interdisciplinary research category. The Chemosphere was the top journal in terms of the number of citations. MSD research has gradually progressed from basic laboratory-based experiments to more complex environmental microbial communities and finally to deeper research on molecular mechanisms and engineering applications. Although multi-omics and synthetic community are the key techniques in the frontier research, they are also the current challenges in this field. A summary of published articles shows that Proteobacteria, Gammaproteobacteria, Burkholderiales and Alcaligenaceae are the most frequently observed MSD phylum, class, order and family, respectively, while Bacillus, Pseudomonas and Achromobacter are the top three MSD genera. To our knowledge, this study is the first to investigate the development and current challenges of MSD research, put forward future perspective, and form a relatively complete list of sulfonamide-degrading microorganisms for reference.
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Affiliation(s)
- Luping Zeng
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Wanxuan Li
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Xiaoyan Wang
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Yixin Zhang
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Yiping Tai
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Xiaomeng Zhang
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Yunv Dai
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China
| | - Ran Tao
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China.
| | - Yang Yang
- Research Center of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, 510632, China.
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Solliec M, Roy-Lachapelle A, Storck V, Callender K, Greer CW, Barbeau B. A data-independent acquisition approach based on HRMS to explore the biodegradation process of organic micropollutants involved in a biological ion-exchange drinking water filter. CHEMOSPHERE 2021; 277:130216. [PMID: 33780680 DOI: 10.1016/j.chemosphere.2021.130216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Drinking water producers continuously develop innovative treatment processes to effectively remove organic micropollutants from raw water. Biological ion-exchange (BIEX) water treatment is one of these new techniques under development and showing great potential. In order to investigate if biodegradation is highly involved in such a removal technique, cultures were prepared with microorganisms sampled on the resins of a BIEX filter. Then, organic micropollutants were spiked into these cultures and their (bio)degradation was followed over 30 days by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS). The purpose of this study was firstly to develop an analytical method using UHPLC-HRMS able to monitor the degradation of three spiked organic micropollutants in culture. Beyond quantification, this method allowed the simultaneous recording of fragmentation information via the use of a data-independent acquisition approach to perform a non-exhaustive search of transformation products related to the spiked micropollutants in culture aliquots. Secondly, a data treatment approach was developed to process raw spectral data generated by aliquots analysis by optimizing the precursor isolation mass windows, the accurate mass tolerance, peak intensity thresholds and choice of database. The use of this new method with a post-data acquisition treatment approach completed by the exhaustive study of fragmentation spectra allowed the tentative identification of 11 transformation products related to the spiked compounds. Finally, 16S rRNA gene amplicon sequencing revealed that bacterial genera known for their ability to degrade the spiked micropollutants were present in the microbial community of the BIEX drinking water filter.
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Affiliation(s)
- Morgan Solliec
- NSERC Industrial Chair on Drinking Water, Department of Civil Engineering, Polytechnique School of Montreal, Montreal, QC, Canada.
| | - Audrey Roy-Lachapelle
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Montreal, QC, Canada
| | - Veronika Storck
- NSERC Industrial Chair on Drinking Water, Department of Civil Engineering, Polytechnique School of Montreal, Montreal, QC, Canada
| | - Katrina Callender
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC, Canada
| | - Benoit Barbeau
- NSERC Industrial Chair on Drinking Water, Department of Civil Engineering, Polytechnique School of Montreal, Montreal, QC, Canada
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Hayase N, Kondou M, Higashiyama A, Kita A, Yano J, Nakagawa K. Enhanced degradation of 4-aminobenzenesulfonate by a co-culture of Afipia sp. 624S and Diaphorobacter sp. 624L. J Biosci Bioeng 2021; 132:287-292. [PMID: 34134931 DOI: 10.1016/j.jbiosc.2021.05.006] [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: 07/25/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022]
Abstract
Two strains, Afipia sp. 624S and Diaphorobacter sp. 624L, were isolated from an enrichment culture with 4-aminobenzenesulfonate (4-ABS) as the only carbon source. Strain 624S utilized 4-ABS as the only source of carbon and energy and degraded 3.8 mM 4-ABS in 2 weeks, releasing a small amount of sulfate ions. On the other hand, strain 624L did not utilize 4-ABS. Additionally, a co-culture of strains 624S and 624L resulted in the enhanced degradation of 4-ABS, and no sulfite was accumulated in the degradation of 4-ABS. When incubated in 50 mM Tris-HCl buffer (pH 8.0) containing 2.2 mM sodium sulfite, strain 624S exhibited no sulfite oxidation; however, strain 624L completely oxidized the sulfite after 2 days. Furthermore, when manganase, which has the ability to oxidize sulfite, was added to the medium, the degradation rate of 4-ABS was increased in comparison with the non-addition control. These results indicate that the sulfite oxidation might stimulate the degradation of 4-ABS by strain 624S, suggesting syntrophic interaction between strains 624S and 624L based on sulfite oxidation.
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Affiliation(s)
- Nobuki Hayase
- Department of Applied Chemistry and Biotechnology, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan.
| | - Misaki Kondou
- Department of Applied Chemistry and Biotechnology, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan
| | - Akihiro Higashiyama
- Department of Applied Chemistry and Biotechnology, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan
| | - Akihisa Kita
- Department of Applied Chemistry and Biotechnology, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan
| | - Jun Yano
- Department of Fundamental Science, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan
| | - Katsuhiko Nakagawa
- Department of Applied Chemistry and Biotechnology, National Institute of Technology (KOSEN), Niihama College, Yagumo-cho, Niihama, Ehime 792-8580, Japan
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Segura A, Udaondo Z, Molina L. PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres. Environ Microbiol 2021; 23:2969-2991. [PMID: 33817928 PMCID: PMC8360164 DOI: 10.1111/1462-2920.15509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 01/23/2023]
Abstract
Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.
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Affiliation(s)
- Ana Segura
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
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Nagata Y, Kato H, Ohtsubo Y, Tsuda M. Lessons from the genomes of lindane-degrading sphingomonads. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:630-644. [PMID: 31063253 DOI: 10.1111/1758-2229.12762] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 05/27/2023]
Abstract
Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.
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Affiliation(s)
- Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Yoshiyuki Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Masataka Tsuda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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11
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Kaminski MA, Sobczak A, Dziembowski A, Lipinski L. Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis. Genes (Basel) 2019; 10:E688. [PMID: 31500174 PMCID: PMC6771000 DOI: 10.3390/genes10090688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.
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Affiliation(s)
- Michal A Kaminski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
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12
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Gan HM, Eng WWH, Dhanoa A. First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia. J Glob Antimicrob Resist 2019; 20:153-159. [PMID: 31325618 DOI: 10.1016/j.jgar.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Despite the increasing reports of carbapenem-resistant Enterobacteriaceae in Malaysia, genomic resources for carbapenem-resistant clinical strains of Klebsiella pneumoniae (K. pneumoniae) remain unavailable. This study aimed to sequence the genomes of multiple carbapenem-resistant K. pneumoniae strains from Malaysia and to identify the genetic basis for their resistance. METHODS Illumina whole genome sequencing was performed on eight carbapenem-resistant K. pneumoniae isolated from a Malaysian hospital. Genetic diversity was inferred from the assembled genomes based on in silico multilocus sequence typing (MLST). In addition, plasmid-derived and chromosome-derived contigs were predicted using the machine learning approach. After genome annotation, genes associated with carbapenem resistance were identified based on similarity searched against the ResFinder database. RESULTS The eight K. pneumoniae isolates were grouped into six different sequence types, some of which were represented by a single isolate in the MLST database. Genomic potential for carbapenem-resistance was attributed to the presence of plasmid-localised blaNDM (blaNDM-1/blaNDM-5) or blaKPC (blaKPC-2/blaKPC-6) in these sequenced strains. The majority of these carbapenem resistance genes was flanked by repetitive (transposase or integrase) sequences, suggesting their potential mobility. This study also reported the first blaKPC-6-harbouring plasmid contig to be assembled for K. pneumoniae, and the second for the genus Klebsiella. CONCLUSION This study reported the first genomic resources for carbapenem-resistant K. pneumoniae from Malaysia. The high diversity of carbapenem resistance genes and sequence types uncovered from eight isolates from the same hospital is worrying and indicates an urgent need to improve the genomic surveillance of clinical K. pneumoniae in Malaysia.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia; Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Wilhelm Wei Han Eng
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Amreeta Dhanoa
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; Tropical Medicine and Biology Platform, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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13
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Wang J, Wang C, Li J, Bai P, Li Q, Shen M, Li R, Li T, Zhao J. Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. Front Microbiol 2018; 9:2238. [PMID: 30319567 PMCID: PMC6167471 DOI: 10.3389/fmicb.2018.02238] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.
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Affiliation(s)
- Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jionghui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renhui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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14
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Complete genome sequence of Planococcus faecalis AJ003 T, the type species of the genus Planococcus and a microbial C30 carotenoid producer. J Biotechnol 2018; 266:72-76. [PMID: 29237561 DOI: 10.1016/j.jbiotec.2017.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]
Abstract
A novel type strain, Planococcus faecalis AJ003T, isolated from the feces of Antarctic penguins, synthesizes a rare C30 carotenoid, glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid. The complete genome of P. faecalis AJ003T comprises a single circular chromosome (3,495,892 bp; 40.9% G + C content). Annotation analysis has revealed 3511 coding DNA sequences and 99 RNAs; seven genes associated with the MEP pathway and five genes involved in the carotenoid pathway have been identified. The functionality and complementation of 4,4'-diapophytoene synthase (CrtM) and two copies of heterologous 4,4'-diapophytoene desaturase (CrtN) involved in carotenoid biosynthesis were analyzed in Escherichia coli.
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15
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Hegedüs B, Kós PB, Bende G, Bounedjoum N, Maróti G, Laczi K, Szuhaj M, Perei K, Rákhely G. Starvation- and xenobiotic-related transcriptomic responses of the sulfanilic acid-degrading bacterium, Novosphingobium resinovorum SA1. Appl Microbiol Biotechnol 2017; 102:305-318. [PMID: 29051988 DOI: 10.1007/s00253-017-8553-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/19/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
Novosphingobium resinovorum SA1 was the first single isolate capable of degrading sulfanilic acid, a widely used representative of sulfonated aromatic compounds. The genome of the strain was recently sequenced, and here, we present whole-cell transcriptome analyses of cells exposed to sulfanilic acid as compared to cells grown on glucose. The comparison of the transcript profiles suggested that the primary impact of sulfanilic acid on the cell transcriptome was a starvation-like effect. The genes of the peripheral, central, and common pathways of sulfanilic acid biodegradation had distinct transcript profiles. The peripheral genes located on a plasmid had very high basal expressions which were hardly upregulated by sulfanilic acid. The genomic context and the codon usage preference of these genes suggested that they were acquired by horizontal gene transfer. The genes of the central pathways were remarkably inducible by sulfanilic acid indicating the presence of a substrate-specific regulatory system in the cells. Surprisingly, the genes of the common part of the metabolic pathway had low and sulfanilic acid-independent transcript levels. The approach applied resulted in the identification of the genes of proteins involved in auxiliary processes such as electron transfer, substrate and iron transports, sulfite oxidases, and sulfite transporters. The whole transcriptome analysis revealed that the cells exposed to xenobiotics had multiple responses including general starvation-like, substrate-specific, and substrate-related effects. From the results, we propose that the genes of the peripheral, central, and common parts of the pathway have been evolved independently.
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Affiliation(s)
- Botond Hegedüs
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Center, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Péter B Kós
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Plant Biology, Biological Research Center, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Gábor Bende
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Center, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Gergely Maróti
- Seqomics Ltd, Mórahalom, Vállalkozók útja 7, Mórahalom, 6782, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary. .,Institute of Biophysics, Biological Research Center, Temesvári krt. 62, Szeged, 6726, Hungary. .,Institute of Environmental and Technological Sciences, Közép fasor 52, Szeged, 6726, Hungary.
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16
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Gan HM, Lee YP, Austin CM. Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia, and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga. Front Microbiol 2017; 8:1880. [PMID: 29046667 PMCID: PMC5632844 DOI: 10.3389/fmicb.2017.01880] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/14/2017] [Indexed: 11/13/2022] Open
Abstract
We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in H. intermedia, the sad operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various Hydrogenophaga strains. The absence of pabB gene in the complete genome of H. intermedia PBC is consistent with its p-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 Hydrogenophaga genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several Hydrogenophaga strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of Hydrogenophaga as "hydrogen eating bacteria."
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Affiliation(s)
- Han M Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Malaysia.,School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Yin P Lee
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Malaysia.,School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Christopher M Austin
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Malaysia.,School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
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