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Singh AK, Kumari M, Sharma N, Rai AK, Singh SP. Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. Curr Genet 2022; 68:565-579. [PMID: 35927361 DOI: 10.1007/s00294-022-01247-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 12/14/2022]
Abstract
Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.
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Affiliation(s)
- Ashutosh Kumar Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Megha Kumari
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India.
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Singh AK, Gupta RK, Purohit HJ, Khardenavis AA. Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil. World J Microbiol Biotechnol 2022; 38:140. [PMID: 35705700 DOI: 10.1007/s11274-022-03311-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/15/2022] [Indexed: 11/26/2022]
Abstract
Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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The first diagnostic test for specific detection of Mycobacterium simiae using an electrochemical label-free DNA nanobiosensor. Talanta 2022; 238:123049. [PMID: 34801906 DOI: 10.1016/j.talanta.2021.123049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/06/2021] [Accepted: 11/06/2021] [Indexed: 01/08/2023]
Abstract
Mycobacterium simiae has been reported to be the most prevalent species of Nontuberculous mycobacteria (NTM) in many countries. As both phenotypic and molecular detection of M. simiae and other NTMs have limitations, finding an accurate, fast, and low-cost diagnostic method is critical for the management of infections. Here, we report the development of a new type of label-free electrochemical biosensor using a gold electrode decorated with l-cysteine/PAMAM dendrimer for specific targeting of M. simiae ITS sequence. DNA hybridization was monitored by measuring changes in the free guanine electrical signal with changing ssDNA target concentrations by differential pulse voltammetry (DPV) method. Response surface methodology (RSM) was applied for the optimization of variables affecting biosensor response. Under optimal conditions, the biosensor revealed a wide linear range from 10-14 M to 10-6 M and a detection limit of 1.40 fM. The fabricated biosensor showed an excellent selectivity to M. simiae in the presence of other similar pathogenic bacteria. Moreover, experimental results confirmed that this biosensor exhibited great precision and high reproducibility, hence provides a low-cost, label-free, and faster detection analysis, representing a novel strategy in detecting other NTMs.
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Khasimov MK, Laurinavichene TV, Petushkova EP, Tsygankov AA. Relations between Hydrogen and Sulfur Metabolism in Purple Sulfur Bacteria. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Wang Q, Lu X, Chen X, Zhao L, Han M, Wang S, Zhang Y, Fan Y, Ye W. Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.). BMC PLANT BIOLOGY 2021; 21:386. [PMID: 34416873 PMCID: PMC8377987 DOI: 10.1186/s12870-021-03170-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium. RESULTS A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress. CONCLUSIONS Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.
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Affiliation(s)
- Qinqin Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
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Hao L, He Y, Shi C, Hao X. Performance and mechanisms for V(v) bio-reduction by straw: key influencing factors. RSC Adv 2021; 11:27246-27256. [PMID: 35480689 PMCID: PMC9037681 DOI: 10.1039/d1ra03201a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022] Open
Abstract
A high concentration of vanadium [V(v)] in groundwater is extremely harmful for humans. Weak movability and low toxicity after microbial V(v) reduction have attracted remarkable attention, especially for using solid carbon sources. However, the influencing factors remain unclear. In this study, the initial V(v) concentration, inocula amount and straw dosage were examined to ascertain the mechanisms behind them. Increasing the initial V(v) concentration led to the decrease of the V(v) removal efficiency, which was also positively correlated with the straw dosage within a certain range. The initial sludge amount was not a main factor affecting microbial V(v) removal in this study. With the initial amount of 10 mg L-1 V(v), 25 mL initial inocula and 5 g straw, 88.2% of V(v) was removed. According to the dissolved organic matter (DOM) analysis results, microbial activity prevailed in groups with higher V(v) removal efficiency, indicating that the V(v) bio-reduction was attributed to the microbial activity, which was considered a major factor. Functional species as unclassified_f_Enterobacteriaceae presumably contributed to the V(v) bioreduction, with upregulated ABC transporter genes and enzymes.
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Affiliation(s)
- Liting Hao
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies, Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture Beijing 100044 China
| | - Yuanyuan He
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies, Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture Beijing 100044 China
| | - Chen Shi
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies, Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture Beijing 100044 China
| | - Xiaodi Hao
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies, Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture Beijing 100044 China
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Draft Genome Sequence of Mycobacterium simiae, a Potential Pathogen Isolated from the Normal Human Oral Cavity. Microbiol Resour Announc 2020; 9:9/46/e01185-20. [PMID: 33184164 PMCID: PMC7661003 DOI: 10.1128/mra.01185-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We report the draft genome sequence of Mycobacterium simiae, a slowly growing nontuberculous mycobacterium (NTM) isolated from a mouthwash sample of a healthy person. This genome of 6,603,693 bp exhibited a 66.13% GC content and 6,391 genes with 6,257 coding sequences, 3 rRNAs, and 78 tRNAs. We report the draft genome sequence of Mycobacterium simiae, a slowly growing nontuberculous mycobacterium (NTM) isolated from a mouthwash sample of a healthy person. This genome of 6,603,693 bp exhibited a 66.13% GC content and 6,391 genes with 6,257 coding sequences, 3 rRNAs, and 78 tRNAs.
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Affiliation(s)
- Jean-Francois Jabbour
- Division of Infectious Diseases, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Amal Hamieh
- Division of Infectious Diseases, Department of Internal Medicine, Al Rassoul Al Azam Hospital, Beirut, Lebanon
| | - Sima L. Sharara
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Souha S. Kanj
- Division of Infectious Diseases, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- * E-mail:
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Karl JP, Barbato RA, Doherty LA, Gautam A, Glaven SM, Kokoska RJ, Leary D, Mickol RL, Perisin MA, Hoisington AJ, Van Opstal EJ, Varaljay V, Kelley-Loughnane N, Mauzy CA, Goodson MS, Soares JW. Meeting report of the third annual Tri-Service Microbiome Consortium symposium. ENVIRONMENTAL MICROBIOME 2020; 15:12. [PMID: 32835172 PMCID: PMC7356122 DOI: 10.1186/s40793-020-00359-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 05/05/2023]
Abstract
The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations and to facilitate resource, material and information sharing among consortium members. The 2019 annual symposium was held 22-24 October 2019 at Wright-Patterson Air Force Base in Dayton, OH. Presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) human microbiomes; 2) transitioning products into Warfighter solutions; 3) environmental microbiomes; 4) engineering microbiomes; and 5) microbiome simulation and characterization. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 3rd annual TSMC symposium.
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Affiliation(s)
- J. Philip Karl
- Military Nutrition Division, United States Army Research Institute of Environmental Medicine, Natick, MA USA
| | - Robyn A. Barbato
- United States Army Cold Regions Research and Engineering Laboratory, Hanover, NH USA
| | - Laurel A. Doherty
- Soldier Performance Optimization Directorate, United States Army Combat Capabilities Development Command Soldier Center, Natick, MA USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC USA
| | - Robert J. Kokoska
- Physical Sciences Directorate, United States Army Research Laboratory – United States Army Research Office, Research Triangle Park, Durham, NC USA
| | - Dagmar Leary
- Center for Biomolecular Science & Engineering, United States Naval Research Laboratory, Washington, DC USA
| | | | - Matthew A. Perisin
- Biotechnology Branch, United States Army Combat Capabilities Development Command-Army Research Laboratory, Adelphi, MD USA
| | - Andrew J. Hoisington
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, Dayton, OH USA
- Military and Veteran Microbiome: Consortium for Research and Education, Aurora, CO USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO USA
- Department of Physical Medicine & Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Edward J. Van Opstal
- Human Systems Directorate, Office of the Underscretary of Defense for Research & Engineering, Washington, DC USA
| | - Vanessa Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Camilla A. Mauzy
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Michael S. Goodson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH USA
| | - Jason W. Soares
- Soldier Performance Optimization Directorate, United States Army Combat Capabilities Development Command Soldier Center, Natick, MA USA
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De Vico G, Carella F. Nocardiosis and mycobacteriosis of bivalves: “Yet‐to‐emerge” zoonoses of public concern? Zoonoses Public Health 2019; 66:559-561. [DOI: 10.1111/zph.12614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gionata De Vico
- Department of Biology University of Naples Federico II, Complesso Universitario di Monte S. Angelo Naples Italy
| | - Francesca Carella
- Department of Biology University of Naples Federico II, Complesso Universitario di Monte S. Angelo Naples Italy
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A mycobacterial disease is associated with the silent mass mortality of the pen shell Pinna nobilis along the Tyrrhenian coastline of Italy. Sci Rep 2019; 9:2725. [PMID: 30804364 PMCID: PMC6389904 DOI: 10.1038/s41598-018-37217-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/04/2018] [Indexed: 11/28/2022] Open
Abstract
Disease is an increasing threat for marine bivalves worldwide. Recently, a mass mortality event (MME) impacting the bivalve Pinna nobilis was detected across a wide geographical area of the Spanish Mediterranean Sea and linked to a haplosporidian parasite. In 2017–2018, mass mortality events affecting the pen shell Pinna nobilis were recorded in two different regions of Italy, Campania and Sicily, in the Tyrrhenian Sea (Mediterranean Sea). Histopathological and molecular examinations of specimens showed the presence of Haplosporidium sp. in only one specimen in one area. Conversely, in all of the surveyed moribund animals, strong inflammatory lesions at the level of connective tissue surrounding the digestive system and gonads and linked to the presence of intracellular Zhiel-Neelsen-positive bacteria were observed. Molecular analysis of all of the diseased specimens (13) confirmed the presence of a Mycobacterium. Blast analysis of the sequences from all of the areas revealed that they were grouped together with the human mycobacterium M. sherrisii close to the group including M. shigaense, M. lentiflavum and M. simiae. Based on pathological and molecular findings, it is proposed that a mycobacterial disease is associated with the mortality episodes of Pinna nobilis, indicating that, at this time, Haplosporidium sp. is not responsible for these events in Campanian and Sicilian waters.
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Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field. Antonie van Leeuwenhoek 2018; 111:2473-2484. [DOI: 10.1007/s10482-018-1136-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/26/2018] [Indexed: 11/25/2022]
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