1
|
Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp. Catalysts 2022. [DOI: 10.3390/catal12111422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is challenging due to the harsh environmental conditions. To date, there is little information available concerning the capability for phenol biodegradation by indigenous Antarctic bacteria. In this study, enzyme activities and genes encoding phenol degradative enzymes identified using whole genome sequencing (WGS) were investigated to determine the pathway(s) of phenol degradation of Arthrobacter sp. strains AQ5-05 and AQ5-06, originally isolated from Antarctica. Complete phenol degradative genes involved only in the ortho-cleavage were detected in both strains. This was validated using assays of the enzymes catechol 1,2-dioxygenase and catechol 2,3-dioxygenase, which indicated the activity of only catechol 1,2-dioxygenase in both strains, in agreement with the results from the WGS. Both strains were psychrotolerant with the optimum temperature for phenol degradation, being between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.
Collapse
|
2
|
Przemieniecki SW, Oćwieja M, Ciesielski S, Halecki W, Matras E, Gorczyca A. Chemical Structure of Stabilizing Layers of Negatively Charged Silver Nanoparticles as an Effector of Shifts in Soil Bacterial Microbiome under Short-Term Exposure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14438. [PMID: 36361318 PMCID: PMC9658158 DOI: 10.3390/ijerph192114438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In this work, we have assessed the exposure of soil bacteria from potato monoculture to three types of silver nanoparticles (AgNPs) as well as silver ions (Ag+ ions) delivered in the form of silver nitrate and a commercially available fungicide. The diversity of the soil microbial community, enzymatic activity, and carbon source utilization were evaluated. It was found that only the fungicide significantly limited the abundance and activity of soil bacteria. Silver ions significantly reduced bacterial metabolic activity. In turn, one type of AgNPs prepared with the use of tannic acid (TA) increased bacterial load and activity. There was found in all AgNPs treated soils (1) a greater proportion of all types of persistent bacteria, i.e., Bacillus, Paenibacillus, and Clostridium; (2) a visible decrease in the proportion of Nocardioides, Arthrobacter, and Candidatus Solibacter; (3) almost complete depletion of Pseudomonas; (4) increase in the number of low-frequency taxa and decrease in dominant taxa compared to the control soil. Despite the general trend of qualitative changes in the bacterial community, it was found that the differences in the chemical structure of the AgNP stabilizing layers had a significant impact on the specific metabolic activity resulting from qualitative changes in the microbiome.
Collapse
Affiliation(s)
- Sebastian Wojciech Przemieniecki
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, PL-10721 Olsztyn, Poland
| | - Magdalena Oćwieja
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, PL-10719 Olsztyn, Poland
| | - Wiktor Halecki
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, PL-31120 Kraków, Poland
| | - Ewelina Matras
- Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, PL-31120 Krakow, Poland
| | - Anna Gorczyca
- Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, PL-31120 Krakow, Poland
| |
Collapse
|
3
|
Gushgari-Doyle S, Lui LM, Nielsen TN, Wu X, Malana RG, Hendrickson AJ, Carion H, Poole FL, Adams MWW, Arkin AP, Chakraborty R. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions. ISME COMMUNICATIONS 2022; 2:32. [PMID: 37938300 PMCID: PMC9723602 DOI: 10.1038/s43705-022-00113-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 07/04/2023]
Abstract
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
Collapse
Affiliation(s)
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ria G Malana
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Heloise Carion
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | |
Collapse
|
4
|
Chi BB, Lu YN, Yin PC, Liu HY, Chen HY, Shan Y. Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance. Front Microbiol 2021; 12:663217. [PMID: 34149650 PMCID: PMC8212970 DOI: 10.3389/fmicb.2021.663217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Heavy metal pollution is a global knotty problem and fungi hold promising potential for the remediation of wastewater containing heavy metals. Here, a new highly chromium-tolerance species, Penicillium janthinellum P1, is investigated. The genome of P1 was sequenced and assembled into 30 Mb genome size containing 10,955 predicted protein-coding genes with a GC content of 46.16% through an integrated method of Illumina short-read sequencing and single-molecule real-time Pacific Biosciences sequencing platforms. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of Penicillium janthinellum P1 and Penicillium oxalicum 114-2 was estimated to be 74 MYA. 33 secondary metabolism gene clusters were identified via antiSMASH software, mainly including non-ribosomal peptide synthase genes and T1 polyketide synthase genes. 525 genes were annotated to encode enzymes that act on carbohydrates, involving 101 glucose-degrading enzymes and 24 polysaccharide synthase. By whole-genome sequence analysis, large numbers of metal resistance genes were found in strain P1. Especially ABC transporter and Superoxide dismutase ensure that the P1 fungus can survive in a chromium-polluted environment. ChrA and ChrR were also identified as key genes for chromium resistance. Analysis of their genetic loci revealed that the specific coding-gene arrangement may account for the fungus’s chromium resistance. Genetic information and comparative analysis of Penicillium janthinellum are valuable for further understanding the mechanism of high resistance to heavy metal chromium, and gene loci analysis provides a new perspective for identifying chromium-resistant strains.
Collapse
Affiliation(s)
- Bin-Bin Chi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China.,Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Ya-Nan Lu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China.,Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Ping-Chuan Yin
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China.,Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Hong-Yan Liu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China.,Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Hui-Ying Chen
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China.,Guangxi Key Laboratory of Electrochemical and Magneto-Chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Yang Shan
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| |
Collapse
|
5
|
Han SR, Kim B, Jang JH, Park H, Oh TJ. Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. BMC Genomics 2021; 22:403. [PMID: 34078272 PMCID: PMC8171050 DOI: 10.1186/s12864-021-07734-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. RESULTS Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. CONCLUSIONS We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.
Collapse
Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Jong Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, 119 Dandae-ro, Dongnam-gu, 31116, Cheonan-si, Chungnam, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, 02841, Seoul, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea.
| |
Collapse
|
6
|
Madoroba E, Magwedere K, Chaora NS, Matle I, Muchadeyi F, Mathole MA, Pierneef R. Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa. Microorganisms 2021; 9:507. [PMID: 33673660 PMCID: PMC7997435 DOI: 10.3390/microorganisms9030507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.
Collapse
Affiliation(s)
- Evelyn Madoroba
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Nyaradzo Stella Chaora
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida 1710, South Africa;
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Farai Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Masenyabu Aletta Mathole
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| |
Collapse
|
7
|
Gu R, Gao J, Dong L, Liu Y, Li X, Bai Q, Jia Y, Xiao H. Chromium metabolism characteristics of coexpression of ChrA and ChrT gene. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111060. [PMID: 32768747 DOI: 10.1016/j.ecoenv.2020.111060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Serratia sp. S2 is a wild strain with chromium resistance and reduction ability. Chromium(VI) metabolic-protein-coding gene ChrA and ChrT were cloned from Serratia sp. S2, and ligated with prokaryotic expression vectors pET-28a (+) and transformed into E. coli BL21 to construct ChrA, ChrT and ChrAT engineered bacteria. By studying the characteristics of Cr(VI) metabolism in engineered bacteria, the function and mechanism of the sole expression and coexpression of ChrA and ChrT genes were studied. METHODS Using Serratia sp. S2 genome as template, ChrA and ChrT genes were amplified by PCR, and prokaryotic expression vectors was ligated to form the recombinant plasmid pET-28a (+)-ChrA, pET-28a (+)-ChrT and pET-28a (+)-ChrAT, and transformed into E. coli BL21 to construct ChrA, ChrT, ChrAT engineered bacteria. The growth curve, tolerance, and reduction of Cr(VI), the distribution of intracellular and extracellular Cr, activity of chromium reductase and intracellular oxidative stress in engineered bacteria were measured to explore the metabolic characteristics of Cr(VI) in ChrA, ChrT, ChrAT engineered bacteria. RESULTS ChrA, ChrT and ChrAT engineered bacteria were successfully constructed by gene recombination technology. The tolerance to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrA > ChrT > Control (P < 0.05), and the reduction ability to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrT > ChrA (P < 0.05). The chromium distribution experiments confirmed that Cr(VI) and Cr(III) were the main valence states. Effect of electron donors on chromium reductase activity was NADPH > NADH > non-NAD(P)H (P < 0.05). The activity of chromium reductase increased significantly with NAD(P)H (P < 0.05). The Glutathione and NPSH (Non-protein Sulfhydryl) levels of ChrA, ChrAT engineered bacteria increased significantly (P < 0.05) under the condition of Cr(VI), but there was no significant difference in the indexes of ChrT engineered bacteria (P > 0.05). CONCLUSION ChrAT engineered bacteria possesses resistance and reduction abilities of Cr(VI). ChrA protein endows the strain with the ability to resist Cr(VI). ChrT protein reduces Cr(VI) to Cr(III) by using NAD(P)H as electronic donor. The reduction process promotes the production of GSH, GSSG and NPSH to maintain the intracellular reduction state, which further improves the Cr(VI) tolerance and reduction ability of ChrAT engineered bacteria.
Collapse
Affiliation(s)
- Ruijia Gu
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China; Center for Disease Control and Prevention of Fucheng District, No.116 north section of Changhong Avenue, Fucheng District, Mianyang City, 621000, China
| | - Jieying Gao
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China
| | - Lanlan Dong
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China; Food and Drugs Authority of Nanchong, No.535 Jinyuling Road, Shunqing District, Nanchong City, 637000, China
| | - Yuan Liu
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China
| | - Xinglong Li
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China
| | - Qunhua Bai
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China
| | - Yan Jia
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China
| | - Hong Xiao
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China.
| |
Collapse
|
8
|
Guo X, Xie C, Wang L, Li Q, Wang Y. Biodegradation of persistent environmental pollutants by Arthrobacter sp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:8429-8443. [PMID: 30706270 DOI: 10.1007/s11356-019-04358-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 01/23/2019] [Indexed: 05/17/2023]
Abstract
Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.
Collapse
Affiliation(s)
- Xiaohong Guo
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Chengyun Xie
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Lijuan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Qinfan Li
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Yan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
9
|
Draft Genome Sequence of Arthrobacter oryzae TNBS02, a Bacterium Containing Heavy Metal Resistance Genes, Isolated from Soil of Antarctica. Microbiol Resour Announc 2019; 8:MRA01501-18. [PMID: 30701242 PMCID: PMC6346191 DOI: 10.1128/mra.01501-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/19/2018] [Indexed: 11/20/2022] Open
Abstract
Arthrobacter oryzae TNBS02 was isolated from soil at Terra Nova Bay of Victoria Land, Antarctica. The genome consists of a chromosome with 4,248,670 bp which contains a total of 3,994 genes. Arthrobacter oryzae TNBS02 was isolated from soil at Terra Nova Bay of Victoria Land, Antarctica. The genome consists of a chromosome with 4,248,670 bp which contains a total of 3,994 genes. It was identified that this strain has many heavy metal resistance genes similar to other Arthrobacter strains isolated from contaminated environments.
Collapse
|
10
|
Sugiura M, Nakahara M, Yamada C, Arakawa T, Kitaoka M, Fushinobu S. Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase. J Biol Chem 2018; 293:17375-17386. [PMID: 30224354 PMCID: PMC6231136 DOI: 10.1074/jbc.ra118.004963] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/14/2018] [Indexed: 01/30/2023] Open
Abstract
Levoglucosan is the 1,6-anhydrosugar of d-glucose formed by pyrolysis of glucans and is found in the environment and industrial waste. Two types of microbial levoglucosan metabolic pathways are known. Although the eukaryotic pathway involving levoglucosan kinase has been well-studied, the bacterial pathway involving levoglucosan dehydrogenase (LGDH) has not been well-investigated. Here, we identified and cloned the lgdh gene from the bacterium Pseudarthrobacter phenanthrenivorans and characterized the recombinant protein. The enzyme exhibited high substrate specificity toward levoglucosan and NAD+ for the oxidative reaction and was confirmed to be LGDH. LGDH also showed weak activities (∼4%) toward l-sorbose and 1,5-anhydro-d-glucitol. The reverse (reductive) reaction using 3-keto-levoglucosan and NADH exhibited significantly lower Km and higher kcat values than those of the forward reaction. The crystal structures of LGDH in the apo and complex forms with NADH, NADH + levoglucosan, and NADH + l-sorbose revealed that LGDH has a typical fold of Gfo/Idh/MocA family proteins, similar to those of scyllo-inositol dehydrogenase, aldose-aldose oxidoreductase, 1,5-anhydro-d-fructose reductase, and glucose-fructose oxidoreductase. The crystal structures also disclosed that the active site of LGDH is distinct from those of these enzymes. The LGDH active site extensively recognized the levoglucosan molecule with six hydrogen bonds, and the C3 atom of levoglucosan was closely located to the C4 atom of NADH nicotinamide. Our study is the first molecular characterization of LGDH, providing evidence for C3-specific oxidation and representing a starting point for future biotechnological use of LGDH and levoglucosan-metabolizing bacteria.
Collapse
Affiliation(s)
| | | | - Chihaya Yamada
- From the Department of Biotechnology and
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 and
| | - Takatoshi Arakawa
- From the Department of Biotechnology and
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 and
| | - Motomitsu Kitaoka
- the Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Shinya Fushinobu
- From the Department of Biotechnology and
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 and
| |
Collapse
|
11
|
Zhao X, Wang L, Ma F, Yang J. Characterisation of an efficient atrazine-degrading bacterium, Arthrobacter sp. ZXY-2: an attempt to lay the foundation for potential bioaugmentation applications. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:113. [PMID: 29692866 PMCID: PMC5905105 DOI: 10.1186/s13068-018-1113-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 04/10/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The isolation of atrazine-degrading microorganisms with specific characteristics is fundamental for bioaugmenting the treatment of wastewater containing atrazine. However, studies describing the specific features of such microorganisms are limited, and further investigation is needed to improve our understanding of bioaugmentation. RESULTS AND CONCLUSIONS In this study, strain Arthrobacter sp. ZXY-2, which displayed a strong capacity to degrade atrazine, was isolated and shown to be a potential candidate for bioaugmentation. The factors associated with the biodegrading capacity of strain ZXY-2 were investigated, and how these factors likely govern the metabolic characteristics that control bioaugmentation functionality was determined. The growth pattern of Arthrobacter sp. ZXY-2 followed the Haldane-Andrews model with an inhibition constant (Ki) of 52.76 mg L-1, indicating the possible augmentation of wastewater treatment with relatively high atrazine concentrations (> 50 ppm). Real-time quantitative PCR (RT-qPCR) results showed a positive correlation between the atrazine degradation rate and the expression levels of three functional genes (trzN, atzB, and atzC), which helped elucidate the role of strain ZXY-2 in bioaugmentation. In addition, multiple copies of the atzB gene were putatively identified, explaining the higher expression levels of this gene than those of the other functional genes. Multiple copies of the atzB gene may represent a compensatory mechanism that ensures the biodegradation of atrazine, a feature that should be exploited in future bioaugmentation applications.
Collapse
Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Li Wang
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090 China
| |
Collapse
|
12
|
New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens. GENOME ANNOUNCEMENTS 2017. [PMID: 28642378 PMCID: PMC5481584 DOI: 10.1128/genomea.00565-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from the stem and leaves of the medicinal plant Echinacea purpurea and able to inhibit human-pathogenic bacterial strains. The genome sequencing of this strain may lead to the identification of genes involved in the production of antimicrobial molecules.
Collapse
|
13
|
Zhao X, Ma F, Feng C, Bai S, Yang J, Wang L. Complete genome sequence of Arthrobacter sp. ZXY-2 associated with effective atrazine degradation and salt adaptation. J Biotechnol 2017; 248:43-47. [PMID: 28315371 DOI: 10.1016/j.jbiotec.2017.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 10/20/2022]
Abstract
An atrazine-degrading strain Arthrobacter sp. ZXY-2 was originally isolated from Jilin Pesticide Plant (China). Strain ZXY-2 demonstrated excellent atrazine degradation performance and saline tolerance. Here we report the complete genome sequence of strain ZXY-2 contained a circular chromosome and five circular plasmids encoding for the mechanism of salt adaptation and pollutant degradation.
Collapse
Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China; Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628CN, Delft, The Netherlands
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China
| | - Cuijie Feng
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628CN, Delft, The Netherlands
| | - Shunwen Bai
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China.
| | - Li Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China.
| |
Collapse
|
14
|
Xu L, Shi W, Zeng XC, Yang Y, Zhou L, Mu Y, Liu Y. Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China. Stand Genomic Sci 2017; 12:11. [PMID: 28138355 PMCID: PMC5259909 DOI: 10.1186/s40793-017-0231-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/12/2017] [Indexed: 11/26/2022] Open
Abstract
Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated from the arsenic-contaminated aquifer sediment in the Datong basin, China. This strain displays high resistance to arsenic, and can dynamically transform arsenic under aerobic condition. Here, we described the high quality draft genome sequence, annotations and the features of Arthrobacter sp. B6. The G + C content of the genome is 64.67%. This strain has a genome size of 4,663,437 bp; the genome is arranged in 8 scaffolds that contain 25 contigs. From the sequences, 3956 protein-coding genes, 264 pseudo genes and 89 tRNA/rRNA-encoding genes were identified. The genome analysis of this strain helps to better understand the mechanism by which the microbe efficiently tolerates arsenic in the arsenic-contaminated environment.
Collapse
Affiliation(s)
- Linghua Xu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China.,School of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi, China
| | - Wanxia Shi
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Ye Yang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Lingli Zhou
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Yichen Liu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| |
Collapse
|
15
|
Comparative genome analysis reveals the molecular basis of nicotine degradation and survival capacities of Arthrobacter. Sci Rep 2015; 5:8642. [PMID: 25721465 PMCID: PMC4342571 DOI: 10.1038/srep08642] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/23/2015] [Indexed: 01/06/2023] Open
Abstract
Arthrobacter is one of the most prevalent genera of nicotine-degrading bacteria; however, studies of nicotine degradation in Arthrobacter species remain at the plasmid level (plasmid pAO1). Here, we report the bioinformatic analysis of a nicotine-degrading Arthrobacter aurescens M2012083, and show that the moeB and mogA genes that are essential for nicotine degradation in Arthrobacter are absent from plasmid pAO1. Homologues of all the nicotine degradation-related genes of plasmid pAO1 were found to be located on a 68,622-bp DNA segment (nic segment-1) in the M2012083 genome, showing 98.1% nucleotide acid sequence identity to the 69,252-bp nic segment of plasmid pAO1. However, the rest sequence of plasmid pAO1 other than the nic segment shows no significant similarity to the genome sequence of strain M2012083. Taken together, our data suggest that the nicotine degradation-related genes of strain M2012083 are located on the chromosome or a plasmid other than pAO1. Based on the genomic sequence comparison of strain M2012083 and six other Arthrobacter strains, we have identified 17 σ(70) transcription factors reported to be involved in stress responses and 109 genes involved in environmental adaptability of strain M2012083. These results reveal the molecular basis of nicotine degradation and survival capacities of Arthrobacter species.
Collapse
|
16
|
Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics 2015; 16:36. [PMID: 25649291 PMCID: PMC4326396 DOI: 10.1186/s12864-015-1220-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/02/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. RESULTS Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. Notwithstanding genome incompleteness, these differences together with the decreased metabolic versatility are indicative of genome content scaling. CONCLUSIONS The genomes of the seven Antarctic Arthrobacter isolates contained several features that may be beneficial for growth and survival in the Antarctic soil environment, although these features were not unique to the Antarctic isolates. These genome sequences allow further investigations into the expression of physiological traits that enable survival under extreme conditions and, more importantly, into the ability of these bacteria to respond to future perturbations including climate change and human impacts.
Collapse
Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Susan J Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand.
| | | |
Collapse
|