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Khan KA, Ganeshprasad DN, Sachin HR, Shouche YS, Ghramh HA, Sneharani AH. Gut microbial diversity in Apis cerana indica and Apis florea colonies: a comparative study. Front Vet Sci 2023; 10:1149876. [PMID: 37252382 PMCID: PMC10213700 DOI: 10.3389/fvets.2023.1149876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Honey bee gut microbiota have an important role in host health, nutrition, host-symbiont interaction, and interaction behavior with the surrounding environment. Recent discoveries of strain-level variation, characteristics of protective and nutritional capabilities, and reports of eco-physiological significance to the microbial community have emphasized the importance of honey bee gut microbiota. Many regions of Asia and Africa are inhabited by the dwarf honey bee, Apis florea. Studying its microflora and potential for pollination is therefore of foremost importance. Methods In the present investigation, we aimed to explore the gut bacteriobiome composition of two distinct honey bee species, Apis florea and Apis cerana indica using high throughput sequencing. Functional predictions of bee gut bacterial communities using PICRUSt2 was carried out. Results and discussion The phylum Proteobacteria dominated the bacterial community in both A. cerana indica (50.1%) and A. florea (86.7%), followed by Firmicutes (26.29 and 12.81%), Bacteroidetes (23.19 and 0.04%) and Actinobacteria (0.4 and 0.02%) respectively. The gut bacteria of A. cerana indica was more diverse than that of A. florea. The observed variations in bacterial genomic diversity among these critical pollinator species may have been influenced by the apiary management techniques, ecological adaptation factors or habitat size. These variations can have a significant effect in understanding host-symbiont interactions and functioning of gut microbiota highlighting the importance of metagenomic survey in understanding microbial community ecology and evolution. This is the first comparative study on variation in bacterial diversity between two Asian honey bees.
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Affiliation(s)
- Khalid Ali Khan
- Applied College, Mahala Campus, King Khalid University, Abha, Saudi Arabia
- Unit of Bee Research and Honey Production, King Khalid University, Abha, Saudi Arabia
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
| | - D. N. Ganeshprasad
- Department of Studies and Research in Biochemistry, Jnana Kaveri Post Graduate Centre, Mangalore University, Chikka Aluvara, Karnataka, India
| | - H. R. Sachin
- Department of Studies and Research in Biochemistry, Jnana Kaveri Post Graduate Centre, Mangalore University, Chikka Aluvara, Karnataka, India
| | - Yogesh S. Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Hamed A. Ghramh
- Unit of Bee Research and Honey Production, King Khalid University, Abha, Saudi Arabia
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
| | - A. H. Sneharani
- Department of Studies and Research in Biochemistry, Jnana Kaveri Post Graduate Centre, Mangalore University, Chikka Aluvara, Karnataka, India
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Oligotrophic Bacterial Community Structure Associated with Muscovite Mineral Is Rich in Proteobacterial Microbiomes Revealed through Next-Generation Sequencing. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13020018] [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
The microbial life indigenous to mineral deposits are generally regarded as extremophiles as they are tolerant to extreme conditions. The microorganisms that thrive in such environments survive by modifying their metabolic pathway or mechanisms. The microbiome associated with ore deposits remain poorly studied. The present study is the first attempt to explore the taxonomic composition of the bacterial community associated with the muscovite ore deposit from Southern India by using high throughput Illumina sequencing employing the V3 and V4 region of the16S rDNA and bioinformatics channel. A total of 20 bacterial phyla with 55 classes, 96 orders, 192 families, 382 genera and 462 species were recovered in the study. The alpha diversity index suggests that muscovite ore deposits harbored highly variable bacterial communities. Among the bacterial communities, Proteobacteria (33%), Actinobacteria (29.9%), Firmicutes (25.4%), Bacteroidetes (5.5%) and Chloroflexi (2.7%) were the dominate phyla. A total of 156 abundant species and 306 rare species were observed and is an indication of the presence of novel species. This study helps to understand the survival strategy of oligotrophs, which are an important aspect of microbial ecology.
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Sharma P, Singh SP. Identification and profiling of microbial community from industrial sludge. Arch Microbiol 2022; 204:234. [PMID: 35362813 DOI: 10.1007/s00203-022-02831-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/05/2022] [Accepted: 03/06/2022] [Indexed: 02/03/2023]
Abstract
The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, 226 025, Uttar Pradesh, India.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208 001, India.
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Ganeshprasad DN, Lone JK, Jani K, Shouche YS, Khan KA, Sayed S, Shukry M, Dar SA, Mushtaq M, Sneharani AH. Gut Bacterial Flora of Open Nested Honeybee, Apis florea. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.837381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Honeybees are eusocial insects with close interaction with their surrounding environment. Gut microbiota in honeybees play a significant role in host health, biology, and interaction behavior with the surrounding environment. Apis florea, a wild bee, is the most primitive among all honeybees and is indigenous to the Indian subcontinent. Previous reports on reared honeybee species provide information on the gut microbiome. No such studies are reported on the gut microbiota of the wild honeybee species. This study aimed at studying the gut microbiome of the wild honeybee species, A. florea. The study reports the analysis and the identification of gut bacteria in the wild honeybee species, A. florea, employing culture-based and culture-independent methods. Cultured bacteria were identified and characterized by MALDI-TOF MS and 16S rRNA sequencing. A comprehensive analysis and identification of non-culturable bacteria were performed by 16S rRNA amplicon next-generation sequencing. This approach splits gut bacteria into four bacterial phyla, four families, and 10 genera in major. The dominant taxa identified in A. florea belonged to the family Enterobacteriaceae (79.47%), Lactobacillaceae (12.75%), Oxalobacteraceae (7.45%), and Nocardiaceae (0.13%). The prevailing bacteria belonged to Enterobacter, Lactobacillus, Escherichia-Shigella, Massilia, Klebsiella, Citrobacter, Pantoea, Serratia, Rhodococcus, and Morganella genera, belonging to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. This study observed the occurrence of a few bacteria that are not previously reported for their occurrence in other species of the Apis genus, making this investigation highly relevant with regard to the bee microbiome.
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Devi SP, Jani K, Sharma A, Jha DK. Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:9. [PMID: 34874481 DOI: 10.1007/s10661-021-09669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.
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Affiliation(s)
- Sashi Prava Devi
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India
| | - Kunal Jani
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Sharma
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India.
| | - Dhruva Kumar Jha
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India.
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Zada S, Xie J, Yang M, Yang X, Sajjad W, Rafiq M, Hasan F, Hu Z, Wang H. Composition and functional profiles of microbial communities in two geochemically and mineralogically different caves. Appl Microbiol Biotechnol 2021; 105:8921-8936. [PMID: 34738169 DOI: 10.1007/s00253-021-11658-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Microbial communities in cave ecosystems have specific survival strategies, which is far from being well explicated. Here, we reported the genetic and functional diversity of bacteria and archaea in typical limestone (Kashmir Cave) and silicate-containing (Tiser Cave) caves. X-ray diffraction (XRD) and Fourier transform infrared spectroscopic (FTIR) analyses revealed the different geochemical and mineral compositions of the two caves. Amplicon barcode sequencing revealed the dominancy of Actinobacteria and Proteobacteria in Kashmir and Tiser Caves. Bacteroidetes and Firmicutes were the dominant phyla in Tiser Cave, and the abundance is relatively small in Kashmir Cave. Archaea was also abundant prokaryotes in Kashmir Cave, but it only accounted for 0.723% of the total prokaryote sequences in Tiser Cave. Functional analysis based on metagenomic sequencing data revealed that a large number of functional potential genes involved in nutrient metabolism and biosynthesis of bioactive compounds in Tiser and Kashmir Cave samples could significantly influence the biogeochemical cycle and secondary metabolite production in cave habitats. In addition, the two caves were also found to be rich in biosynthetic genes, encoding bioactive compounds, such as monobactam and prodigiosin, indicating that these caves could be potential habitats for the isolation of antibiotics. This study provides a comprehensive insight into the diversity of bacteria and archaea in cave ecosystems and helps to better understand the special survival strategies of microorganisms in cave ecosystems.Key points• Geochemically distinct caves possess unique microbial community structure.• Cavernicoles could be important candidates for antibiotic production.• Cavernicoles are important for biogeochemical cycling.
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Affiliation(s)
- Sahib Zada
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Jianmin Xie
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Min Yang
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Xiaoyu Yang
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Engineering and Management Sciences, Balochistan University of Information Technology, Quetta, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-I-Azam University, Islamabad, Pakistan
| | - Zhong Hu
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Hui Wang
- Department of Biology, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China.
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Sharma P, Tripathi S, Chandra R. Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater. BIORESOURCE TECHNOLOGY 2021; 324:124681. [PMID: 33454444 DOI: 10.1016/j.biortech.2021.124681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India.
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Metagenomics analysis of rhizospheric bacterial communities of Saccharum arundinaceum growing on organometallic sludge of sugarcane molasses-based distillery. 3 Biotech 2020; 10:316. [PMID: 32612900 DOI: 10.1007/s13205-020-02310-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/19/2020] [Indexed: 10/24/2022] Open
Abstract
The present paper aims to explore the rhizospheric bacterial communities associated with Saccharum arundinaceum grown on organometallic pollutants-rich hazardous distillery sludge. The sequence analysis of 16S rRNA V3-V4 hypervariable region with Illumina MiSeq platform showed 621,897 OTUs derived from rhizospheric and non-rhizospheric distillery sludge samples out of 1,191,014 and 901,757 sequences read, respectively. The major phyla detected in rhizospheric sludge sample were Proteobacteria (50%), Bacteriodetes (33%), Firmicutes (5%) Gemmatimonadetes (2%), Chloroflexi (2%), and Tenericutes (2%). The dominant three genera were detected as Rheinheimera (21%), Sphingobacterium (17%), and Idiomarina (8%). In addition, other minor genera such as uncultured Bacillus (4%), Acidothermus (4%), Bacillus (3%), Pseudomonas (2%), Flavobacterium (2%), uncultured bacterium (2%), Parapedobacter (2%), Alcanivorax (2%), Acholeplasma (2%), Hyphomonas (1%), and Aquamicrobium were also detected (1%) in rhizospheric sludge. Our results suggested that rhizospheric bacterial communities associated with S. arundinaceum were substantially different in richness, diversity, and relative abundance of taxa compared to non-rhizospheric sludge. Further, the comparative organic pollutant analysis from non-rhizospheric and rhizospheric sludge samples through GC-MS analysis revealed the disappearance of few compounds and generation of some compounds as new metabolic products by the activity of rhizospheric bacterial communities. The results of this study will be helpful in understanding the role of rhizospheric bacterial communities responsible for degradation and detoxification of complex organometallic waste and, thus, can help in designing appropriate phytoremediation studies for eco-restoration of polluted sites.
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Anupma A, Tamang JP. Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India. Front Microbiol 2020; 11:905. [PMID: 32547501 PMCID: PMC7272576 DOI: 10.3389/fmicb.2020.00905] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
Filamentous fungi are important organisms in traditionally prepared amylase and alcohol-producing dry starters in India. We collected 40 diverse types of amylase and alcohol-producing starters from eight states in North East India viz. marcha, thiat, humao, hamei, chowan, phut, dawdim, and khekhrii. The average fungal population was 4.9 × 105 cfu/g with an average of pH 5.3 and 10.7%, respectively. In the present study, 131 fungal isolates were isolated and characterized based on macroscopic and microscopic characteristics and were grouped into 44 representative fungal strains. Based on results of morphological characteristics and ITS gene sequencing, 44 fungal strains were grouped into three phyla represented by Ascomycota (48%), Mucoromycota (38%), and Basidiomycota (14%). Taxonomical keys to species level was illustrated on the basis of morphological characteristics and ITS gene sequencing, aligned to the fungal database of NCBI GenBank, which showed seven genera with 16 species represented by Mucor circinelloides (20%), Aspergillus sydowii (11%), Penicillium chrysogenum (11%), Bjerkandera adusta (11%), Penicillium citrinum (7%), Rhizopus oryzae (7%), Aspergillus niger (5%), Aspergillus flavus (5%), Mucor indicus (5%) Rhizopus microsporus (5%), Rhizopus delemar (2%), Aspergillus versicolor (2%), Penicillium oxalicum (2%), Penicillium polonicum (2%), Trametes hirsuta (2%), and Cladosporium parahalotolerans (2%). The highest Shannon diversity index H was recorded in marcha of Sikkim (H: 1.74) and the lowest in hamei of Manipur (H: 0.69). Fungal species present in these amylolytic starters are morphologically, ecologically and phylogenetically diverse and showed high diversity within the community.
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Affiliation(s)
- Anu Anupma
- Department of Microbiology, DAICENTRE (Department of Biotechnology-National Institute of Advance Industrial Science and Technology (DBT-AIST) International Centre for Translational and Environmental Research) and Bioinformatics Centre, School of Life Sciences, Sikkim University, Gangtok, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, DAICENTRE (Department of Biotechnology-National Institute of Advance Industrial Science and Technology (DBT-AIST) International Centre for Translational and Environmental Research) and Bioinformatics Centre, School of Life Sciences, Sikkim University, Gangtok, India
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Kajale S, Deshpande N, Shouche Y, Sharma A. Cultivation of Diverse Microorganisms from Hypersaline Lake and Impact of Delay in Sample Processing on Cell Viability. Curr Microbiol 2020; 77:716-721. [PMID: 31912221 DOI: 10.1007/s00284-019-01857-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/24/2019] [Indexed: 10/25/2022]
Abstract
The Sambhar Salt Lake is a halite rich athalassohaline basin, provides a unique opportunity for microbial ecologists to study halophiles. The lake has a high proportion of Na+ and Cl- ions making it a hypersaline ecosystem. In the current study, archaea and bacteria from Sambhar Lake were isolated using two cultivation approaches. A total of 449 isolates were obtained, out of which 13 represent archaeal while 12 represent bacterial genera. Natronococcus and Alkalibacillus were found predominant groups among archaea and bacteria, respectively. Apart from the common genera in both the approaches Alteribacillus, Halobacillus, Halorubrum, Lentibacillus, Natronorubrum, Piscibacillus and Thalassobacillus were found only in the samples processed onsite however only three genera Aliidiomarina, Natrinema and Natronolimnobius were isolated when samples were processed in the laboratory after transportation using the same growth conditions. Other than the isolation of diverse group of organisms 13 putative novel taxa with similarity less than 98% were identified using 16S rRNA gene sequencing.
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Affiliation(s)
- Swapnil Kajale
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India.,Abasaheb Garware College, Pune, Maharashtra, 411004, India
| | | | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India.
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Li AZ, Han XB, Zhang MX, Zhou Y, Chen M, Yao Q, Zhu HH. Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica. Front Microbiol 2019; 10:2523. [PMID: 31787942 PMCID: PMC6856632 DOI: 10.3389/fmicb.2019.02523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.
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Affiliation(s)
- An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xi-Bin Han
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Grass Science, Guangdong Engineering Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Pradhan P, Tamang JP. Phenotypic and Genotypic Identification of Bacteria Isolated From Traditionally Prepared Dry Starters of the Eastern Himalayas. Front Microbiol 2019; 10:2526. [PMID: 31749787 PMCID: PMC6848222 DOI: 10.3389/fmicb.2019.02526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
Preparation of dry starters for alcohol production is an age-old traditional technology in the Eastern Himalayan regions of east Nepal, the Darjeeling hills, Sikkim, and Arunachal Pradesh in India, and Bhutan. We studied the bacterial diversity in 35 samples of traditionally prepared dry starters, represented by marcha of Nepal, Sikkim, the Darjeeling hills, and Bhutan, phab of Bhutan, and paa, pee, and phut of Arunachal Pradesh, respectively. Populations of bacteria in these starters were 105 to 108 cfu/g. A total of 201 bacterial strains were isolated from starter samples, phenotypically characterized, and their identities confirmed by the 16S rRNA sanger sequencing method. The dominant phylum was Firmicutes (85%), followed by Proteobacteria (9%), and Actinobacteria (6%). Lactic acid bacteria (LAB) (59%) formed the most abundant group, followed by non-LAB (32%) and Gram-negative bacteria (9%). Based on the 16S rRNA gene sequencing result, we identified LAB: Enterococcus durans, E. faecium, E. fecalis, E. hirae, E. lactis, Pediococcus acidilactici, P. pentosaceus, Lactobacillus plantarum subsp. plantarum, Lb. pentosus, Leuconostoc mesenteroides, and Weissella cibaria; non-LAB: Bacillus subtilis subsp. inaquosorum, B. circulans, B. albus, B. cereus, B. nakamurai, B. nitratireducens, B. pseudomycoides, B. zhangzhouensis, Kocuria rosea, Staphylococcus hominis subsp. hominis, S. warneri, S. gallinarum, S. sciuri, Lysinibacillus boronitolerans, Brevibacterium frigoritolerans, and Micrococcus yunnanensis; Gram-negative bacteria: Pseudomonas putida, Klebsiella pneumoniae, Enterobacter hormaechei subsp. xiangfangensis, E. hormaechei subsp. steigerwaltii, and Stenotrophomonas maltophilia. We characterized diversity indexes of the bacterial community present in traditionally prepared dry starters. This is the first report on the bacterial diversity of traditionally dry starters of the Eastern Himalayas by sanger sequencing.
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Affiliation(s)
| | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Auti AM, Narwade NP, Deshpande NM, Dhotre DP. Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019; 44:114. [PMID: 31719223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.
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Affiliation(s)
- Asim M Auti
- Department of Microbiology, MES Abasaheb Garware College, Pune, India
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Jani K, Bandal J, Rale V, Shouche Y, Sharma A. Antimicrobial resistance pattern of microorganisms isolated and identified from Godavari River across the mass gathering event. J Biosci 2019; 44:121. [PMID: 31719230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Kumbh Mela is considered the world's largest mass gathering event (MGE). It represents a unique anthropogenic burden on the river ecosystem and may confer antimicrobial resistance among microbial communities. The present study explains the characterization of microbial isolates associated with Godavari River under the advent of the mass bathing event using culture dependent approach. The isolates were identified by sequencing of 16S rRNA gene and ITS region. Further, the isolates were screened for antibiotic susceptibility against 22 antibiotics using disc diffusion method. A total of 63 bacterial and 21 fungal isolates were isolated under the temporal variation of the event. Kocuria and Staphylococcus were the most prevalent bacterial genera in the samples collected before and during the event, while Meyerozyma and Candida predominate among fungal communities. A group of antibiotics impeding the bacterial protein synthesis were found to be most effective against greater than or equal to 67% of bacterial isolates. However, greater than or equal to 37-67% of isolates could escape the action of inhibitors of bacterial cell wall synthesis. Moreover, bacterial isolates belonging to genera Acinetobacter, Corynebacterium and Brevibacterium showed higher resistance towards the antibiotics. Observations from the current study suggest likely microbial taxa as targets to mitigate the waterborne infections during the MGE.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411 021, India
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Jani K, Bandal J, Rale V, Shouche Y, Sharma A. Antimicrobial resistance pattern of microorganisms isolated and identified from Godavari River across the mass gathering event. J Biosci 2019. [DOI: 10.1007/s12038-019-9941-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019. [DOI: 10.1007/s12038-019-9936-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Jani K, Dhotre D, Bandal J, Shouche Y, Suryavanshi M, Rale V, Sharma A. World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India. MICROBIAL ECOLOGY 2018. [PMID: 29536131 DOI: 10.1007/s00248-018-1169-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Jayashree Bandal
- Department of Microbiology, KTHM College, Nashik, Maharashtra, 422002, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Mangesh Suryavanshi
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India.
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Sha SP, Jani K, Sharma A, Anupma A, Pradhan P, Shouche Y, Tamang JP. Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India. Sci Rep 2017; 7:10967. [PMID: 28887544 PMCID: PMC5591290 DOI: 10.1038/s41598-017-11609-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022] Open
Abstract
Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.
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Affiliation(s)
- Shankar Prasad Sha
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India
| | - Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, 411021, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, 411021, India
| | - Anu Anupma
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India
| | - Pooja Pradhan
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, 411021, India
| | - Jyoti Prakash Tamang
- DAILAB (DBT-AIST International Laboratory for Advanced Biomedicine), Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, India.
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Jani K, Ghattargi V, Pawar S, Inamdar M, Shouche Y, Sharma A. Anthropogenic Activities Induce Depletion in Microbial Communities at Urban Sites of the River Ganges. Curr Microbiol 2017; 75:79-83. [PMID: 28884372 DOI: 10.1007/s00284-017-1352-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/28/2017] [Indexed: 11/25/2022]
Abstract
The Ganges is the largest river of India, worshiped by Hindus with a belief that bathing in the river causes the remission of sins and is considered very pure. It is heavily polluted by the unrestricted human usage including ritual practices, urbanization, and industrialization. Such perturbations may subsequently influence the bacterial community composition and ecosystem functioning. Here, we applied targeted amplicon sequencing to determine the impact of spatial variation on the microbial community assemblage of the Ganga River. The river bacterial community demonstrates taxonomic variability across the sites with accumulation of Firmicutes (20.9%) Verrucomicrobia (6.09%), Actinobacteria (4.51%), and Synergistetes (1.16%), at rural site while Proteobacteria (49.4%) and Bacteroidetes (12.7%) predominate at urban sites. Furthermore, sites under study establish the unique taxonomic signature which could represent the impact of spatial variation on the microbial community assemblage.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Vikas Ghattargi
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Shrikant Pawar
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Mitali Inamdar
- Center for Citizen Science, Pune, Maharashtra, 411033, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India.
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De Mandal S, Chatterjee R, Kumar NS. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiol 2017; 17:90. [PMID: 28399822 PMCID: PMC5387202 DOI: 10.1186/s12866-017-1002-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/06/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline. RESULTS Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study. CONCLUSION The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.
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Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
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Sharma A, Paul D, Dhotre D, Jani K, Pandey A, Shouche YS. Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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