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Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
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Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
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Roy B, Maitra D, Biswas A, Chowdhury N, Ganguly S, Bera M, Dutta S, Golder S, Roy S, Ghosh J, Mitra AK. Efficacy of High-Altitude Biofilm-Forming Novel Bacillus subtilis Species as Plant Growth-Promoting Rhizobacteria on Zea mays L. Appl Biochem Biotechnol 2024; 196:643-666. [PMID: 37171757 DOI: 10.1007/s12010-023-04563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 05/13/2023]
Abstract
With the global population explosion, the need for increasing crop productivity is reaching its peak. The significance of organic means of cultivation including biofertilizers and biopesticides is undeniable in this context. Over the last few decades, the use of rhizobacteria to induce crop productivity has gained particular interest of researchers. Of these, several Bacillus spp. have been known for their potential plant growth-promoting and phyto-pathogenic actions. Keeping this background in mind, this study was formulated with an aim to unravel the PGPR and phyto-pathogenic potency of Bacillus sp. isolated from extreme environmental conditions, viz. high-altitude waters of Ganges at Gangotri (Basin Extent Longitude Latitude-73° 2' to 89° 5' E 21° 6' to 31° 21' N). Based on recent studies showing the impact of biofilm on bacterial PGPR potency, three novel strains of Bacillus subtilis were isolated on basis of their extremely high biofilm-producing abilities (BRAM_G1: Accession Number MW006633; BRAM_G2: Accession Numbers MT998278-MT998280; BRAM_G3: Accession Number MT998617), and were tested for their PGPR properties like nutrient sequestration, growth hormone production (IAA, GA3), stress-responsive enzyme production (ACC deaminase) and lignocellulolytic and agriculturally important enzyme productions. The strains were further tested for the plethora of metabolites (liquid and VOCs) exuded by them. Finally, the strains both in individually and in an association, i.e. consortium was tested on a test crop, viz. Zea mays L., and the data were collected at regular intervals and the results were statistically analysed. In the present study, the role of high-altitude novel Bacillus subtilis strains as potent PGPR has been analysed statistically.
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Affiliation(s)
- Bedaprana Roy
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India.
| | - Debapriya Maitra
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Abhik Biswas
- Department of Mathematics, St. Xavier's College (Autonomous), Kolkata, India
| | - Niti Chowdhury
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Saswata Ganguly
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Mainak Bera
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Shijini Dutta
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Samriddhi Golder
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Sucharita Roy
- Department of Mathematics, St. Xavier's College (Autonomous), Kolkata, India
| | - Jaydip Ghosh
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Arup Kumar Mitra
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
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Microbial community structure analysis of hypersaline niches and elucidation of their role in the biogeochemical cycling of nitrogen, sulphur and methane. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Prokaryotic communities adapted to microhabitats on the Indian lotus (Nelumbo nucifera) growing in the high-altitude urban Dal Lake. Int Microbiol 2022; 26:257-267. [PMID: 36378397 DOI: 10.1007/s10123-022-00297-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 08/18/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022]
Abstract
Indian lotus (Nelumbo nucifera) is one of the dominant aquatic plants cultivated in Dal Lake, situated at 1586 m above mean sea level (MSL) in the northeast of Srinagar, Kashmir. Despite their economic and ecological role, the microbial communities associated with the lotus plant are still unexplored. In this study, we investigated the prokaryotic communities on surfaces of different lotus microhabitats (roots, rhizome, leaves, flowers, and fruits), lake water, and sediments using 16S rRNA gene amplicon sequencing. Overall, prokaryotic diversity decreased significantly on the surface of lotus microhabitats in comparison to the lake water and sediments. Among the microhabitats of lotus, roots and leaves harbored more diverse communities in comparison to rhizomes, fruits, and flowers. A total of 98 genera were shared by lotus and the Dal Lake sediments and water. However, significant differences were found in their relative abundance; for example, Pseudomonas was the most dominant genus on the majority of lotus microhabitats. On the other hand, Flavobacterium was highly abundant in the lake water, while a higher abundance of Acinetobacter was recorded in sediments. Additionally, we also noted the presence of potential human pathogenic genera including Escherichia-Shigella, Enterobacter, Pantoea, Raoultella, Serratia, and Sphingomonas on the lotus microhabitats. Predicted functions of prokaryotic communities revealed a higher abundance of genes associated with nutrient uptake in the microhabitats of the lotus. This study offered first-hand information on the prokaryotic communities harbored by lotus plants and water and sediments of the Dal Lake and demonstrated the adaptation of diverse communities to microhabitats of lotus.
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Wang X, Ren Y, Yu Z, Shen G, Cheng H, Tao S. Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156148. [PMID: 35609688 DOI: 10.1016/j.scitotenv.2022.156148] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuxuan Ren
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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Rahi P, Khairnar M, Hagir A, Narayan A, Jain KR, Madamwar D, Pansare A, Shouche Y. Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae. Arch Microbiol 2021; 203:3591-3604. [PMID: 33966089 DOI: 10.1007/s00203-021-02349-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/27/2022]
Abstract
A novel bacterial strain designated as ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78T grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78T with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44T (98.7%) and Rhizobium ipomoeae shin9-1 T (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. We propose re-classification of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78T represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78T (= MCC 3400T; KACC 21383T; JCM 33657T). We also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.
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Affiliation(s)
- Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India.
| | - Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Ashwini Hagir
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Narayan
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Kunal R Jain
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Aabeejjeet Pansare
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
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Dixit K, Davray D, Chaudhari D, Kadam P, Kshirsagar R, Shouche Y, Dhotre D, Saroj SD. Benchmarking of 16S rRNA gene databases using known strain sequences. Bioinformation 2021; 17:377-391. [PMID: 34092959 PMCID: PMC8131573 DOI: 10.6026/97320630017377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at various taxonomic levels using various methods and databases.
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Affiliation(s)
- Kunal Dixit
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Dimple Davray
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Diptaraj Chaudhari
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Pratik Kadam
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Rudresh Kshirsagar
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Yogesh Shouche
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Dhiraj Dhotre
- Reliance Life Sciences Pvt Ltd, Rabale, Mumbai, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
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