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Nathani NM, Mootapally C, Sharma P, Solomon S, Kumar R, Fulke AB, Kumar M. Microbial machinery dealing diverse aromatic compounds: Decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea. ENVIRONMENTAL RESEARCH 2023; 225:115603. [PMID: 36863652 DOI: 10.1016/j.envres.2023.115603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 05/25/2023]
Abstract
Aromatic hydrocarbons are persistent pollutants in aquatic systems as endocrine disruptors, significantly impacting natural ecosystems and human health. Microbes perform as natural bioremediators to remove and regulate aromatic hydrocarbons in the marine ecosystem. The present study focuses upon the comparative diversity and abundance of various hydrocarbon-degrading enzymes and their pathways from deep sediments along the Gulf of Kathiawar Peninsula and Arabian Sea, India. The elucidation of large number of degradation pathways in the study area under the presence of a wide range of pollutants whose fate needs to be addressed. Sediment core samples were collected, and the whole microbiome was sequenced. Analysis of the predicted ORFs (open reading frames) against the AromaDeg database revealed 2946 aromatic hydrocarbon-degrading enzyme sequences. Statistical analysis portrayed that the Gulfs were more diverse in degradation pathways compared to the open sea, with the Gulf of Kutch being more prosperous and more diverse than the Gulf of Cambay. The vast majority of the annotated ORFs belonged to groups of dioxygenases that included catechol, gentisate, and benzene dioxygenases, along with Rieske (2Fe-2S) and vicinal oxygen chelate (VOC) family proteins. From the sampling sites, only 960 of the total predicted genes were given taxonomic annotations, which mention the presence of many under-explored marine microorganism-derived hydrocarbon degrading genes and pathways. Through the present study, we tried to unveil the array of catabolic pathways of aromatic hydrocarbon degradation and genes from a marine ecosystem that upholds economic and ecological significance in India. Thus, this study provides vast opportunities and strategies for microbial resource recovery in marine ecosystems, which can be investigated to explore aromatic hydrocarbon degradation and their potential mechanisms under various oxic or anoxic environments. Future studies should focus on aromatic hydrocarbon degradation by considering degradation pathways, biochemical analysis, enzymatic, metabolic, and genetic systems, and regulations.
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Affiliation(s)
- Neelam M Nathani
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Chandrashekar Mootapally
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Parth Sharma
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India
| | - Solly Solomon
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science & Technology, Kochi, 682022, Kerala, India; Cochin Base of Fishery Survey of India, Post Box 853 Kochangady, Cochin, 682005, Kerala, India
| | - Rakesh Kumar
- School of Ecology and Environment Studies, Nalanda University, Rajgir, 803116, Bihar, India
| | - Abhay B Fulke
- Microbiology Division, CSIR - National Institute of Oceanography (CSIR-NIO), Regional Centre, Andheri (West), Maharashtra, 400053, India
| | - Manish Kumar
- Sustainability Cluster, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India; Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico.
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Vijayan J, Nathan VK, Ammini P, Ammanamveetil AMH. Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28383-28406. [PMID: 36680718 PMCID: PMC9862233 DOI: 10.1007/s11356-023-25195-2] [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: 07/19/2022] [Accepted: 01/04/2023] [Indexed: 04/16/2023]
Abstract
Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.
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Affiliation(s)
- Jasna Vijayan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India.
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamilnadu, India
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, Kerala, India
| | - Abdulla Mohamed Hatha Ammanamveetil
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India
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Srivastava A, Verma D. Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:752-772. [PMID: 35904740 DOI: 10.1007/s11356-022-22198-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V3-V4). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025
| | - Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025.
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Liu H, Lin G, Gao D, Chen H, He M, Lu J. Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf. MICROBIAL ECOLOGY 2023; 85:121-136. [PMID: 35039906 DOI: 10.1007/s00248-021-01946-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Genmei Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Dong Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Hongyu Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Miao He
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
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Microbial Diversity in the Indian Ocean Sediments: An Insight into the Distribution and Associated Factors. Curr Microbiol 2022; 79:115. [PMID: 35195780 DOI: 10.1007/s00284-022-02801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/23/2021] [Indexed: 11/03/2022]
Abstract
Indian Ocean is the third largest oceanic division of the world and shelter to a huge microbial diversity. These microbes play an important role in the metabolism of carbon, sulfur, nitrogen, and phosphorus in the ocean water. They are also major contributors of carbon fixing and sequestration, as much as terrestrial plants to achieve CO2 emissions reduction. The prokaryotic community in the East Indian Ocean primarily comprises of heterotrophic bacteria like Alphaproteobacteria and Gammaproteobacteria, followed by Firmicutes and Actinobacteria. The Arabian Sea and the Bay of Bengal are typically characterized by presence of vast areas of oxygen minimum zones (OMZs) and have been witnessing a shift in the microbial diversity due to the changing conditions in the ocean water. Several canonical correspondence analyses reveal temperature, salinity, and phosphate levels as crucial environmental factors in propelling the distribution of diazotrophs. The viral consortia are dominated by the Caudovirales, an order of tailed bacteriophages. Due to the rapid change in the environmental factors such as topography, temperature, and sunlight contributing toward climate change, their role in sustaining the chemical composition of the ocean can be drastically affected especially with the evidence of several bacterial and fungal communities responding to latitudinal and temperature change. Therefore, we aim to critically review the status of microbial diversity in Indian Ocean to predict their response toward climate change as they are the sentinels of change in marine life and to understand the dynamics of microbial communities in the various locations of Indian Ocean.
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Vijayan J, Ammini P, Nathan VK. Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3967-3982. [PMID: 34398377 DOI: 10.1007/s11356-021-15772-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.
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Affiliation(s)
- Jasna Vijayan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
| | - Parvathi Ammini
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India.
- Department of Biotechnology, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
| | - Vinod Kumar Nathan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
- School of Chemical and Biotechnology, Sastra Deemed University Tirumalaisamudram, Thanjavur, Tamilnadu, 613401, India
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Parvathi A, Catena M, Jasna V, Phadke N, Gogate N. Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50579-50592. [PMID: 33963997 DOI: 10.1007/s11356-021-14263-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
In the present study, we analyzed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary [CE]), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Statistical analysis indicated significant variations in bacterial communities between freshwater and mesohaline and euryhaline regions, as well as between the monsoon (wet) and nonmonsoon (dry) periods. The abundance of Betaproteobacteria was higher in the freshwater regions, while Alphaproteobacteria and Epsilonproteobactera were more abundant in mesohaline and euryhaline regions of the estuary. Gammaproteobacteria was more abundant in regions with high nutrient concentrations. Various bacterial genera indicating the presence of fecal contamination and eutrophication were detected. Corrplot based on Pearson correlation analysis demonstrated the important physico-chemical variables (temperature, salinity, dissolved oxygen, and inorganic nutrients) that influence the distribution of dominant phyla, class, and genera. The observed spatio-temporal variations in bacterial community structure in the CE were governed by regional variations in anthropogenic inputs and seasonal variations in monsoonal rainfall and tidal influx.
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Affiliation(s)
- Ammini Parvathi
- CSIR-National Institute of Oceanography, Regional Centre , Dr. Salim Ali Road, Post Box No. 1913, Kochi, 682 018, India.
| | - Michela Catena
- CSIR-National Institute of Oceanography, Regional Centre , Dr. Salim Ali Road, Post Box No. 1913, Kochi, 682 018, India
| | - Vijayan Jasna
- CSIR-National Institute of Oceanography, Regional Centre , Dr. Salim Ali Road, Post Box No. 1913, Kochi, 682 018, India
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | - Nikhil Phadke
- GenePath Dx, Shivajinagar, Pune, Maharashtra, 411004, India
| | - Nikhita Gogate
- GenePath Dx, Shivajinagar, Pune, Maharashtra, 411004, India
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Mohammed Hadi WA, Edwin BT, Jayakumaran Nair A. Isolation and identification of marine Bacillus altitudinis KB1 from coastal Kerala: asparaginase producer. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF INDIA. MARINE BIOLOGICAL ASSOCIATION OF INDIA 2021; 63:43-48. [PMID: 35903758 PMCID: PMC9326817 DOI: 10.6024/jmbai.2021.63.2.2195-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
L-asparaginase is a target for many researchers as its properties against cancer, especially leukaemia, and protective agents reduce acrylamide in fried food. In this study, the water samples from Thumba Arattuvazhi Beach in Kerala were screened for l-asparaginase producing microorganisms. This was followed by colourimetric screening using modified M9 media with 0.009% Phenol red dye and using l-asparagine as a sole nitrogen source. Then, the Nessler assay was performed to quantify the enzyme. Molecular identification was made by 16SrRNA sequencing and aligned the sequence with GeneBank for phylogenetic tree construction using BLAST. Seawater was serially diluted for 10-1 to 10-6 using nutrient agar plates. A total of 19 bacterial colonies were isolated. The colonies were evaluated to produce l-asparaginase according to the pink zone around the colonies on the modified M9 medium using a red phenol indicator. The KB1 sample was selected for further studies according to plate colour assay. Nessler assay of L-asparaginase quantified as 2.537 IU/ml. Molecular characterisation showed the sequence association with Bacillus altitudinis the sequence submitted in Genebank as B. altitudinis KB1 strain. The l-asparaginase II gene (AnsB) was amplified based on the entire length of the hypothetical protein of annotated genome with accession number CP022319.2. The l-asparaginase activity in this study was 57% higher than the reference organism B. altitudinis BITHSP010. The l-asparaginase producing bacterium B. altitudinis KB1 from a marine source in Kerala can produce asparaginase, which can be utilised for biotechnology applications.
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Affiliation(s)
- Wael Ali Mohammed Hadi
- Inter University Center for Genomic and Gene Technology (IUCGGT), University of Kerala, Thiruvananthapuram-695 581, Kerala, India
| | - Boby T. Edwin
- CEPCI Laboratory and Research Institute, Kollam-691 001, Kerala, India
| | - Ananthakrishnan Jayakumaran Nair
- Inter University Center for Genomic and Gene Technology (IUCGGT), University of Kerala, Thiruvananthapuram-695 581, Kerala, India
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Hadi WAM, Edwin BT, Nair AJ. Whole genome sequence data of Bacillus australimaris strain B28A, isolated from Marine Water in India. Data Brief 2021; 37:107240. [PMID: 34235237 PMCID: PMC8250166 DOI: 10.1016/j.dib.2021.107240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
Bacillus genus members are dominant in the Eastern Arabian Sea and are known for producing many industrial enzymes. Bacillus australimaris B28A, isolated from seawater, had an enzymatic activity. Here, the whole genome sequence of Bacillus australimaris B28A is reported. The 3,766,107-bp genome, with a GC content of 41.6%, comprised 3936 protein-coding genes, seven ribosomal RNA, and 75 transfer RNA. Several bioactive secondary metabolite genes in the genome, including surfactin, lichenysin, bacillibactin, bacilysin, paenilamicin, fengycin, and carotenoid, were identified using antiSMASH. The 1396 proteins were predicted using RAST, including asparaginase enzyme: an anticancer enzyme. Sequence data have been deposited in the DDBJ/ENA/GenBank database under the accession number JAGQFH000000000. The version described in this paper is JAGQFH000000000.1. The BioProject ID in the GenBank database is PRJNA670955. The raw data is publicly available at "https://www.ncbi.nlm.nih.gov/sra/SRR14203888".
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Affiliation(s)
| | - Boby T Edwin
- CEPCI Laboratory & Research Institute, Kollam, Kerala, India
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