Publications by authors named "Praveen Rahi"

27 Publications

  • Page 1 of 1

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 Aug 9;203(6):3591-3604. Epub 2021 May 9.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India.

A novel bacterial strain designated as ADMK78 was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78 grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78 with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44 (98.7%) and Rhizobium ipomoeae shin9-1 (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78 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 ADMK78 were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78 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 ADMK78 represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78 (= MCC 3400; KACC 21383; JCM 33657). 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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http://dx.doi.org/10.1007/s00203-021-02349-9DOI Listing
August 2021

Defining the Species Complex.

Genes (Basel) 2021 01 18;12(1). Epub 2021 Jan 18.

State Key Laboratory of Agrobiotechnology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing 100193, China.

Bacteria currently included in are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is . We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: , and itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
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http://dx.doi.org/10.3390/genes12010111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7831135PMC
January 2021

Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau.

Curr Microbiol 2020 Dec 20;77(12):4072-4084. Epub 2020 Oct 20.

National Center for Microbial Resource-National Center for Cell Science, Pune, 411021, India.

Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.
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http://dx.doi.org/10.1007/s00284-020-02244-4DOI Listing
December 2020

RTE4: A Tea Rhizobacterium With Potential for Plant Growth Promotion and Biosurfactant Production.

Front Bioeng Biotechnol 2020 29;8:861. Epub 2020 Jul 29.

Department of Microbiology, Savitribai Phule Pune University, Pune, India.

Tea is an ancient non-alcoholic beverage plantation crop cultivated in the most part of Assam, India. Being a long-term monoculture, tea plants are prone to both biotic and abiotic stresses, and requires massive amounts of chemicals as fertilizers and pesticides to achieve worthy crop productivity. The rhizosphere bacteria with the abilities to produce phytohormone, secreting hydrolytic enzyme, biofilm formation, bio-control activity provides induced systemic resistance to plants against pathogens. Thus, plant growth promoting (PGP) rhizobacteria represents as an alternative candidate to chemical inputs for agriculture sector. Further, deciphering the secondary metabolites, including biosurfactant (BS) allow developing a better understanding of rhizobacterial strains. The acidic nature of tea rhizosphere is predominated by followed by that enhances crop biomass and yield through accelerating uptake of nutrients. In the present study, a strain RTE4 isolated from tea rhizosphere soil collected from Rosekandy Tea Garden, Cachar, Assam was evaluated for various plant-growth promoting attributes. The strain RTE4 produces indole acetic acid (74.54 μg/ml), hydrolytic enzymes, and solubilize tri-calcium phosphate (46 μg/ml). Bio-control activity of RTE4 was recorded against two foliar fungal pathogens of tea ( and ) and a bacterial plant pathogen (). The strain RTE4 was positive for BS production in the preliminary screening. Detailed analytical characterization through TLC, FTIR, NMR, and LCMS techniques revealed that the strain RTE4 grown in M9 medium with glucose (2% w/v) produce di-rhamnolipid BS. This BS reduced surface tension of phosphate buffer saline from 71 to 31 mN/m with a critical micelle concentration of 80 mg/L. Purified BS of RTE4 showed minimum inhibitory concentration of 5, 10, and 20 mg/ml against , and , respectively. Capability of RTE4 BS to be employed as a biofungicide as compared to Carbendazim - commercially available fungicide is also tested. The strain RTE4 exhibits multiple PGP attributes along with production of di-rhamnolipid BS. This gives a possibility to produce di-rhamnolipid BS from RTE4 in large scale and explore its applications in fields as a biological alternative to chemical fertilizer.
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http://dx.doi.org/10.3389/fbioe.2020.00861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403194PMC
July 2020

Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas.

Syst Appl Microbiol 2020 Sep 30;43(5):126127. Epub 2020 Jul 30.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India.

Three strains of rhizobia isolated from effective root nodules of pea (Pisum sativum L.) collected from the Indian trans-Himalayas were characterized using 16S rRNA, atpD and recA genes. Phylogeny of the 16S rRNA genes revealed that the newly isolated strains were members of the genus Rhizobium with ≥99.9% sequence similarity to the members within the "Rhizobium leguminosarum" group. Phylogenetic analyses based on the concatenated sequences of atpD and recA gene, and 92 core genes extracted from the genome sequences indicated that strains JKLM 12A2 and JKLM 13E are grouped as a separate clade closely related to R. laguerreae FB206. In contrast, the strain JKLM 19E was placed with "R. hidalgonense" FH14. Whole-genome average nucleotide identity (ANI) values were 97.6% within strains JKLM 12A2 and JKLM 13E, and less than 94% with closely related species. The digital DNA-DNA hybridization (dDDH) values were 81.45 within the two strains and less than 54.8% to closely related species. The major cellular fatty acids were C in summed feature 8, C/C in summed feature 2, and C. The DNA G+C content of JKLM 12A2 and JKLM 13E was 60.8mol%. The data on genomic, chemotaxonomic, and phenotypic characteristics indicates that the strains JKLM 12A2 and JKLM 13E represent a novel species, Rhizobium indicum sp. nov. The type strain is JKLM 12A2 (= MCC 3961=KACC 21380=JCM 33658). However, the strain JKLM 19E represents a member of "R. hidalgonense" and the symbiovar viciae.
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http://dx.doi.org/10.1016/j.syapm.2020.126127DOI Listing
September 2020

MALDI-TOF-MS and 16S rRNA characterization of lead tolerant metallophile bacteria isolated from saffron soils of Kashmir for their sequestration potential.

Saudi J Biol Sci 2020 Aug 20;27(8):2047-2053. Epub 2020 Apr 20.

Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia.

Toxic metal contamination in soils due industrialization is nowadays a concern to the scientists worldwide. The current study deals with the evaluation of response and tolerance by isolated metallophilic bacteria in different lead concentrations (100 ppm to 1000 ppm). By taking optical densities of the isolates, the minimum inhibitory concentration (MIC) of Pb were determined.16S rRNA and MALDI-TOF MS were used for the identification of the bacteria. Total of 37 isolates were observed, among them 04 (, and ), isolated were detected having efficacy of Pbtolerance and sequestration at varying MIC. Furthermore, was observed to have highest (900 ppm) tolerance for lead and lowest (500 ppm) for Moreover, the highest (65.3%) sequestration potential has been observed for and least (52.8%) for The tolerance and sequestration potential properties of these isolated species can be utilised to exterminate heavy metals and reduce their toxicity from the contaminated environment.
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http://dx.doi.org/10.1016/j.sjbs.2020.04.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376117PMC
August 2020

Pea ( l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India.

Front Microbiol 2020 3;11:968. Epub 2020 Jun 3.

National Center for Microbial Resource, National Center for Cell Science, Pune, India.

Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of , , , , , and were significantly higher in the rhizosphere. At the same time, , , and were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.
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http://dx.doi.org/10.3389/fmicb.2020.00968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7283456PMC
June 2020

sp. nov., isolated from the surface of a tomato.

Int J Syst Evol Microbiol 2020 May;70(5):3278-3286

National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.

A novel bacterial strain, designated TOUT106, was isolated from the surface of a tomato. The cells were rod-shaped, Gram-negative, encapsulated and non-motile. Strain TOUT106 grows best at 28 °C and pH 7.0 and can tolerate up to 2 % (w/v) NaCl. Based on 16S rRNA gene phylogeny, strain TOUT106 was placed close to the clade, with close similarity to subsp. strain NCTC 8297 (98.42 %). Results of genome-based phylogenetic analysis revealed that strain TOUT106 is placed well in the clade, by forming a distinct branch with DSM25444, NCTC132727, 06D021 and SB6412. The genomic DNA G+C content of strain TOUT106 is 53.53 mol%. The average nucleotide identity values of TOUT106 were less than 86.5 % with closely related members of the family . The major fatty acids of strain TOUT106 were C, C cyclo, C 3OH/C iso, C, C cyclo ω8, C ω6/C ω7, C and C ω7/C ω6. Strain TOUT106 showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS compared to its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain TOUT106 could be distinguished from the recognized species of the genus . It is suggested to represent a novel species of this genus, for which the name sp. nov. is proposed. The type strain is TOUT106 (=MCC 2901=KACC 21384=JCM 33718).
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http://dx.doi.org/10.1099/ijsem.0.004168DOI Listing
May 2020

Distribution of Pathogenic Yeasts in Different Clinical Samples: Their Identification, Antifungal Susceptibility Pattern, and Cell Invasion Assays.

Infect Drug Resist 2020 20;13:1133-1145. Epub 2020 Apr 20.

National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, S.P. Pune University, Pune 411 007, Maharashtra, India.

Introduction: Species of genus are part of the common microbiota of humans; however, some of the species are known opportunistic pathogens. Formation of biofilms, resistance to antifungal drugs, and increase in asymptomatic infections demands more studies on isolation, identification and characterization of from clinical samples.

Methods: The present manuscript deals with assessment of authentic yeast identification by three methods viz., DNA sequencing of gene, protein profiles using MALDI-TOF MS, and colony coloration on chromogenic media. Antifungal susceptibility and in vitro cell invasion assays were performed to further characterize these isolates.

Results: Comparison of three methods showed that DNA sequence analysis correctly identified more than 99.4% of the isolates up to species level as compared to 89% by MALDI-TOF MS. In this study, we isolated a total of 176 yeasts from clinical samples and preliminary morphological characters indicated that these yeast isolates belong to the genus . The species distribution of isolates was as follows: 75 isolates of (42.61%), 50 of (28.40%), 22 of (12.5%), 14 of (7.95%) and 4 of (2.27%). Other species like sp., and were less than 2%. Antifungal susceptibility assay performed with 157 isolates showed that most of the isolates were resistant to the four azoles viz., clotrimazole, fluconazole, itraconazole, and ketoconazole, and the frequency of resistance was more in non-albicans isolates. The susceptibility to azole drugs ranged from 7% to 48%, while 75% of the tested yeasts were susceptible to nystatin. Moreover, 88 isolates were also tested for their capacity to invade human cells using HeLa cells. In vitro invasion assay showed that most of the isolates showed epithelial cell invasion as compared to isolates belonging to and .

Discussion: The identification of yeasts of clinical origin by sequencing of gene performed better than MALDI-TOF MS. The present study reiterates the world scenario wherein there is a shift from strains to emerging opportunistic pathogens which were earlier regarded as environmental strains. The present study enlightens the current understanding of identification methods for clinical yeast isolates, increased antifungal drug resistance, epithelial cell invasion as a virulence factor, and diversity of yeasts in Indian clinical samples.
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http://dx.doi.org/10.2147/IDR.S238002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182453PMC
April 2020

Editorial: MALDI-TOF MS Application in Microbial Ecology Studies.

Front Microbiol 2019 10;10:2954. Epub 2020 Jan 10.

Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.

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http://dx.doi.org/10.3389/fmicb.2019.02954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966959PMC
January 2020

Cultivable Microbial Diversity Associated With Cellular Phones.

Front Microbiol 2018 7;9:1229. Epub 2018 Jun 7.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.

A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this study, we investigated the diversity of microorganisms associated with cellular phones of 27 individuals using cultivation-based methods. Cellular phones were sampled using cotton swabs and a total of 554 isolates representing different morphotypes were obtained on four growth media. Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry could generate protein profiles for 527 isolates and species-level identification was obtained for 415 isolates. A dendrogram was constructed based on the protein profiles of the remaining isolates, to group 112 isolates under 39 different proteotypes. The representative strains of each group were selected for 16S rRNA gene and ITS region sequencing based identification. , , , and were the most frequently encountered bacteria, and , , , and were in case of fungi. At species-level the prevalence of , , , , , and was observed, most of these species are commensal microorganisms of human skin. UPGMA dendrogram and PCoA biplot generated based on the microbial communities associated with all cellular phones exhibited build-up of specific communities on cellular phones and the prevalence of objectionable microorganisms in some of the cellular phones can be attributed to the poor hygiene and sanitary practices. The study also revealed the impact of MALDI-TOF MS spectral quality on the identification results. Overall MALDI-TOF appears a powerful tool for routine microbial identification and de-replication of microorganisms. Quality filtering of MALDI-TOF MS spectrum, development of better sample processing methods and enriching the spectral database will improve the role of MALDI-TOF MS in microbial identifications.
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http://dx.doi.org/10.3389/fmicb.2018.01229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6000418PMC
June 2018

Subsaxibacter sediminis sp. nov., isolated from Arctic glacial sediment and emended description of the genus Subsaxibacter.

Int J Syst Evol Microbiol 2018 May 21;68(5):1678-1682. Epub 2018 Mar 21.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411021, India.

A Gram-stain-negative, yellowish-orange pigmented, rod-shaped, motile bacterium, designated strain ARC111, was isolated from sediment of Arctic permafrost at Midtre Lovénbreen glacier, Svalbard. 16S rRNA gene based identification of strain ARC111 demonstrated highest sequence similarities to Subsaxibacter broadyi P7 (97.8 %) and Subsaxibacter arcticus JCM30334 (97.5 %) and ≤95.2 % with all other members of the family Flavobacteriaceae. Phylogenetic analysis revealed the distinct positioning of strain ARC111 within the genus Subsaxibacter. The G+C content of ARC111 was 37.8±0.5 mol% while DNA-DNA hybridization depicted 35.6 % relatedness with S. arcticus JCM30334. Strain ARC111 had C15 : 0iso, C16 : 0iso 3-OH, C15 : 1iso G, C15 : 0anteiso, C16 : 1iso H and C17 : 0iso 3-OH as major (>5 % of the total) cellular fatty acids and MK-6 was the predominant respiratory quinone. The polar lipid profile of strain ARC111 consisted of phosphatidylethanolamine, aminolipid and an unidentified lipid. Strain ARC111 harboured sym-homospermidine as the major polyamine. Characteristic differences obtained using polyphasic analysis of strain ARC111 and its closest relatives suggested that strain ARC111 is a novel species of genus Subsaxibacter, for which the name Subsaxibacter sediminis sp. nov. has been proposed. The type strain is ARC111 (=MCC 3191=KCTC 42965=LMG 29783=GDMCC 1.1201).
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http://dx.doi.org/10.1099/ijsem.0.002729DOI Listing
May 2018

Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone.

Int J Syst Evol Microbiol 2018 Apr 9;68(4):1052-1058. Epub 2018 Feb 9.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India.

A cultivation-based study of the microbial diversity of cellular phone screens led to the isolation of a Gram-stain-positive, aerobic, rod-shaped and non-endospore-forming bacterium, designated S2T63, exhibiting phenotypic and genotypic characteristics unique to the type strains of closely related species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a member of Microbacterium, and most closely related to Microbacterium aurantiacum IFO 15234 and Microbacterium kitamiense Kitami C2. The DNA-DNA relatedness values of the strain S2T63 to M. aurantiacum KACC 20510, M. kitamiense KACC 20514and Microbacterium laevaniformans KACC 14463 were 65 % (±4), 29.5 % (±3) and 55.9 % (±4), respectively. The genomic DNA G+C content was 71.8 mol%. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified polar lipids. The peptidoglycan contained the amino acids glycine, lysine, alanine and glutamic acid, with substantial amounts of hydroxy glutamic acid detected, which is characteristic of peptidoglycan type B1α. The predominant menaquinones were MK-12 and MK-13. Rhamnose, fucose and galactose were the whole-cell sugars detected. The strain also showed biofilm production, estimated by using crystal violet assay. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new strain represents a novel species of the genus Microbacterium, for which the name Microbacteriumtelephonicum is proposed, with S2T63T (=MCC 2967=KACC 18715=LMG 29293) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.002622DOI Listing
April 2018

Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola.

Int J Syst Evol Microbiol 2017 Aug;67(8):2766-2772

Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India.

The taxonomic positions of Microterricola viridarii JCM 15926T, Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T were re-examined. Phylogenetic analysis and 16S rRNA gene sequence similarities revealed that all three strains are closely related with each other and form a monophyletic cluster with high sequence similarity (99.2 -99.9 %). A dendrogram constructed based on the protein spectra generated by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy also displayed close clustering of these three strains. The fatty acid profiles of three strains were very similar to each other and contained branched fatty acids (anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0) as the predominant cellular fatty acids. The polar lipid profiles of the three stains were similar and consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as major polar lipids and an unknown lipid. Comparisons of morphological, chemotaxonomic and physiological data of Microterricola viridarii JCM 15926T, Leifsonia pindariensis JCM 15132T and Phycicola gilvus DSM 18319T are in agreement with the features of a common genus. DNA-DNA hybridization data generated during this study showed less than 70 % reassociation value with each other indicating that they are different at species level. Based on the present study, we conclude that Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T should be reclassified under the genus Microterricola, since this genus has the nomenclatural priority, and reclassified as Microterricolagilva comb. nov. (type strain SSWW-21T=DSM 18319T=KCTC 19185T=JCM 30550T) and Microterricolapindariensis comb. nov. (type strain PON10T=LMG 24222T=JCM 15132T=MTCC9128T). An emended description of the genus Microterricola is also presented.
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http://dx.doi.org/10.1099/ijsem.0.002019DOI Listing
August 2017

Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone.

Int J Syst Evol Microbiol 2017 Jul 12;67(7):2289-2295. Epub 2017 Jul 12.

Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India.

A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10-55 °C) and at pH 7.0 (5.0-9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA-DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).
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http://dx.doi.org/10.1099/ijsem.0.001943DOI Listing
July 2017

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists.

Front Microbiol 2016 30;7:1359. Epub 2016 Aug 30.

Microbial Culture Collection, National Centre for Cell Science Pune, India.

Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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http://dx.doi.org/10.3389/fmicb.2016.01359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003876PMC
September 2016

Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity.

Genome Announc 2015 Sep 3;3(5). Epub 2015 Sep 3.

CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.

The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-3-acetic acid (IAA) production, and stress response.
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http://dx.doi.org/10.1128/genomeA.00943-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559727PMC
September 2015

Statistical Optimization of Medium Components for Mass Production of Plant Growth-Promoting Microbial Inoculant Pseudomonas trivialis BIHB 745 (MTCC5336).

Indian J Microbiol 2014 Jun 10;54(2):239-41. Epub 2013 Aug 10.

Plant Pathology and Microbiology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, P.O. Box No. 6, Palampur, 176 061 Himachal Pradesh India.

Optimizing nutritional requirements for mass production of microbial inoculants in shortened time has relevance for their economical field application. Therefore, the present study aimed at selecting suitable growth medium, optimizing its components, and up-scaling inoculum production for plant growth-promoting Pseudomonas trivialis BIHB 745. Of the different media tested, the culture exhibited maximal viable colony count in trypticase soya broth with 17.6 % increased biomass on optimizing levels of carbon source, nitrogen source, and NaCl using response surface methodology. A twofold higher biomass with 9 h shorter incubation period was obtained in optimized medium in a bioreactor in comparison to shake flasks.
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http://dx.doi.org/10.1007/s12088-013-0425-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188497PMC
June 2014

A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas.

Mol Ecol 2012 Jan 18;21(1):145-59. Epub 2011 Nov 18.

Plant Pathology and Microbiology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, PO Box 6, Palampur-176061 (HP), India.

Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon-source utilization pattern, and whole-cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by three sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000 m) had a distinctive whole-cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.
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http://dx.doi.org/10.1111/j.1365-294X.2011.05368.xDOI Listing
January 2012

Composition and antimicrobial activity of the essential oil of Heracleum thomsonii (Clarke) from the cold desert of the western Himalayas.

Nat Prod Res 2011 Aug;25(13):1250-60

Natural Plants Product Division, Institute of Himalayan Bioresource Technology (CSIR), Palampur (HP) 176061, India.

Volatile oil composition of hydro-distilled (HD) and supercritical carbon dioxide (SC-CO(2)) essential oil of freshly collected aerial parts of Heracleum thomsonii (Umbeliferae) from the western Himalayas was studied by GC-FID and GC-MS. Results revealed qualitative and quantitative dissimilarity in the composition of hydro-distilled and SC-CO(2) extracted oils. Nineteen constituents, which accounted for 89.32% of total constituents in HD oil, represented by limonene (4.31%), (Z)-β-ocimene (3.69%), terpinolene (22.24%), neryl acetate (36.19%), nerol (9.51%) and p-cymene-8-ol (2.61%) were identified. In SC-CO(2) extracted oil, 24 constituents representing 89.95% of total constituents were identified. Terpinolene (5.08%), germacrene D (2.17%), neryl acetate (51.62%), nerol (9.78%), geranyl acetate (2.06%), α-bisabolol (2.48%) and 1-nonadecanol (4.96%) were the dominating constituents. In vitro antimicrobial activity of hydro-distilled oil was conducted against microrobial strains including two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and five Gram-negative (Burkholderia cepacia, Escherichia coli, Enterobacter cloacae, Klebseilla pneumoniae and Pseudomonas aeruginosa) bacteria as well as seven fungi (Candida albicans, Issatchenkia orientalis, Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Aspergillus sydowii and Trichophyton rubrum) using broth microdilution method. The results of bioassay showed that the oil exhibited moderate to high antimicrobial activity against fungi C. albicans (MIC 625 µg ml(-1)), A. parasiticus (MIC 312.5 µg ml(-1)), A. sydowii (MIC 312.5 µg ml(-1)), T. rubrum (MIC 625 µg ml(-1)), Gram-positive bacteria B. subtilis (MIC 625 µg ml(-1)) and Gram-negative bacteria P. aeruginosa (MIC 312.5 µg ml(-1)).
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http://dx.doi.org/10.1080/14786419.2011.557375DOI Listing
August 2011

Diversity analysis of diazotrophic bacteria associated with the roots of tea (Camellia sinensis (L.) O. Kuntze).

J Microbiol Biotechnol 2011 Jun;21(6):545-55

Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, P.O. Box 6, Palampur (H.P), India.

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included alpha-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; gamma-Proteobacteria genera Pseudomonas and Stenotrophomonas; and beta-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.
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June 2011

Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential.

J Microbiol Biotechnol 2010 Dec;20(12):1724-34

Plant Pathology and Microbiology Laboratory, Hill Area Tea Sciences, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, P.O. Box No. 6, Palampur-176 061, Himachal Pradesh, India.

A phosphate-solubilizing bacterial strain isolated from Hippophae rhamnoides rhizosphere was identified as Rahnella sp. based on its phenotypic features and 16S rRNA gene sequence. The bacterial strain showed the growth characteristics of a cold-adapted psychrotroph, with the multiple plant growth-promoting traits of inorganic and organic phosphate solubilization, 1-aminocyclopropane-1- carboxylate-deaminase activity, ammonia generation, and siderophore production. The strain also produced indole- 3-acetic acid, indole-3-acetaldehyde, indole-3-acetamide, indole-3-acetonitrile, indole-3-lactic acid, and indole-3- pyruvic acid in tryptophan-supplemented nutrient broth. Gluconic, citric and isocitric acids were the major organic acids detected during tricalcium phosphate solubilization. A rifampicin-resistant mutant of the strain exhibited high rhizosphere competence without disturbance to the resident microbial populations in pea rhizosphere. Seed bacterization with a charcoal-based inoculum significantly increased growth in barley, chickpea, pea, and maize under the controlled environment. Microplot testing of the inoculum at two different locations in pea also showed significant increase in growth and yield. The attributes of coldtolerance, high rhizosphere competence, and broad-spectrum plant growth-promoting activity exhibited the potential of Rahnella sp. BIHB 783 for increasing agriculture productivity.
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December 2010

Organic acid production and plant growth promotion as a function of phosphate solubilization by Acinetobacter rhizosphaerae strain BIHB 723 isolated from the cold deserts of the trans-Himalayas.

Arch Microbiol 2010 Nov 7;192(11):975-83. Epub 2010 Sep 7.

Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology (CSIR), Himachal Pradesh, 176 061, India.

An efficient phosphate-solubilizing plant growth-promoting Acinetobacter rhizosphaerae strain BIHB 723 exhibited significantly higher solubilization of tricalcium phosphate (TCP) than Udaipur rock phosphate (URP), Mussoorie rock phosphate (MRP) and North Carolina rock phosphate (NCRP). Qualitative and quantitative differences were discerned in the gluconic, oxalic, 2-keto gluconic, lactic, malic and formic acids during the solubilization of various inorganic phosphates by the strain. Gluconic acid was the main organic acid produced during phosphate solubilization. Formic acid production was restricted to TCP solubilization and oxalic acid production to the solubilization of MRP, URP and NCRP. A significant increase in plant height, shoot fresh weight, shoot dry weight, root length, root dry weight, and root, shoot and soil phosphorus (P) contents was recorded with the inoculated treatments over the uninoculated NP(0)K or NP(TCP)K treatments. Plant growth promotion as a function of phosphate solubilization suggested that the use of bacterial strain would be a beneficial addition to the agriculture practices in TCP-rich soils in reducing the application of phosphatic fertilizers.
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http://dx.doi.org/10.1007/s00203-010-0615-3DOI Listing
November 2010

Stress tolerance and genetic variability of phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas.

Microb Ecol 2009 Aug 26;58(2):425-34. Epub 2009 Mar 26.

Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Palampur, (H.P.) 176 061, India.

Nineteen efficient phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas were screened for stress tolerance against temperature, alkalinity, salinity, calcium salts, and desiccation. Phylogenetic analysis based on 16S rRNA gene sequencing placed these bacteria under three groups with fourteen strains in Group I including Pseudomonas trivialis and P. poae, two strains in Group II together with Pseudomonas kilonensis and P. corrugata, and three strains in Group III along with Pseudomonas jessenii and P. moraviensis. Genetic diversity assessed by ERIC and BOX-PCR revealed variability among strains belonging to the same phylogenetic groups. Cluster analysis based on the growth characteristics under regimes of different stress levels placed the strains into three distinct clusters displaying no correlation to their phylogenetic groups. Stress-tolerant strains differed in the level of decline in phosphate solubilization under increasing intensity of various stress parameters. The highest decrease occurred with 5% CaCO(3,) followed by 2.5% CaCO(3), pH 11, 5% NaCl, temperature of 37 degrees C, 40% PEG, 5% CaSO(4), 2.5% NaCl, 2.5% CaSO(4), pH 9 and temperature of 15 degrees C. Two strains belonging to Phylogenetic Group I exhibited higher phosphate solubilization at lower temperature. The results revealed that stress-tolerance ability was not limited to any particular phylogenetic group. Knowledge about the genetic variants of phosphate-solubilizing fluorescent Pseudomonas with potential for tolerance to desiccation, alkalinity, temperature, and salinity could be useful in understanding their ecological role under stressful environments of low phosphate availability.
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http://dx.doi.org/10.1007/s00248-009-9511-2DOI Listing
August 2009

Plant growth-promoting and rhizosphere-competent Acinetobacter rhizosphaerae strain BIHB 723 from the cold deserts of the Himalayas.

Curr Microbiol 2009 Apr 10;58(4):371-7. Epub 2009 Jan 10.

Plant Pathology and Microbiology Laboratory, Hill Area Tea Sciences, Institute of Himalayan Bioresource Technology, Palampur, India.

A phosphate-solubilizing bacterial strain BIHB 723 isolated from the rhizosphere of Hippophae rhamnoides was identified as Acinetobacter rhizosphaerae on the basis of phenotypic characteristics, carbon source utilization pattern, fatty acid methyl esters analysis, and 16S rRNA gene sequence. The strain exhibited the plant growth-promoting attributes of inorganic and organic phosphate solubilization, auxin production, 1-aminocyclopropane-1-carboxylate deaminase activity, ammonia generation, and siderophore production. A significant increase in the growth of pea, chickpea, maize, and barley was recorded for inoculations under controlled conditions. Field testing with the pea also showed a significant increment in plant growth and yield. The rifampicin mutant of the bacterial strain effectively colonized the pea rhizosphere without adversely affecting the resident microbial populations.
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http://dx.doi.org/10.1007/s00284-008-9339-xDOI Listing
April 2009

Characterization of phosphate-solubilizing fluorescent pseudomonads from the rhizosphere of seabuckthorn growing in the cold deserts of Himalayas.

Curr Microbiol 2008 Jan 2;56(1):73-9. Epub 2007 Oct 2.

Institute of Himalayan Bioresource Technology, P.O. Box No. 6, Palampur, HP 176 061, India.

Isolation and characterization of fluorescent pseudomonads with high phosphate-solubilizing ability is reported from the alkaline and calcium-rich soils with low P availability in the cold desert region of Lahaul and Spiti in the trans-Himalayas of India. Of 216 phosphate-solubilizing isolates, 12 exhibiting high solubilization of tricalcium phosphate (TCP) in NBRIP liquid culture were identified as Pseudomonas trivialis, P. poae, P. fluorescens, and Pseudomonas spp. on the basis of phenotypic features, whole-cell fatty acids methyl ester (FAME) profiles, and 16S rDNA sequencing. These isolates also showed relatively high solubilization of North Carolina rock phosphate (NCRP) in comparison to the solubilization of Mussoorie rock phosphate (MRP) and Udaipur rock phosphate (URP). The solubilization of phosphate substrates by P. trivialis and P. poae is reported for the first time.
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http://dx.doi.org/10.1007/s00284-007-9042-3DOI Listing
January 2008

Phosphate solubilization potential and stress tolerance of Eupenicillium parvum from tea soil.

Mycol Res 2007 Aug 29;111(Pt 8):931-8. Epub 2007 Jun 29.

Plant Pathology and Microbiology, Hill Area Tea Sciences, Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061, India.

Eupenicillium parvum was recorded for first time during isolation of phosphate-solubilizing microorganisms from the tea rhizosphere. The fungus developed a phosphate solubilization zone on modified Pikovskaya agar, supplemented with tricalcium phosphate. Quantitative estimation of phosphate solubilization in Pikovskaya broth showed high solubilization of tricalcium phosphate and aluminium phosphate. The fungus also solubilized North Carolina rock phosphate and Mussoorie rock phosphate, and exhibited high levels of tolerance against desiccation, acidity, salinity, aluminium, and iron. Solubilization of inorganic phosphates by the fungus was also observed under high stress levels of aluminium, iron, and desiccation, though the significant decline in phosphate solubilization was marked in the presence of aluminium than iron. The fungal isolate showed 100% identity with E. parvum strain NRRL 2095 ITS 1, 5.8S rRNA gene and ITS 2, complete sequence; and 28S rRNA gene, partial sequence.
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http://dx.doi.org/10.1016/j.mycres.2007.06.003DOI Listing
August 2007
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