@article {43478, title = {Draft genome sequence of lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture}, journal = {Standards in Genomic Sciences}, volume = {12}, year = {2017}, month = {JAN}, pages = {Article Number: 15}, abstract = {Probiotic Lactobacillus species offer various health benefits, thus have been employed in treatment and prevention of various diseases. Due to the differences in the isolation source and the site of action, most of the lactobacilli tested in-vitro for probiotics properties fail to extend similar effects in-vivo. Consequently, the search of autochthonous, efficacious and probably population specific probiotics is a high priority in the probiotics research. In this regards, whole genome sequencing of as many Lactobacillus as possible will help to deepen our understanding of biology and their health effects. Here, we provide the genomic insights of two coherent oxalic acid tolerant Lactobacillus species (E2C2 and E2C5) isolated from two different healthy human gut flora. These two isolates were found to have higher tolerance towards oxalic acid (300 mM sodium oxalate). The draft genome of strain E2C2 consists of 3,603,563 bp with 3289 protein-coding genes, 94 RNA genes, and 43.99\% GC content, while E2C5 contained 3,615,168 bp, 3293 coding genes (93.4\% of the total genes), 95 RNA genes and 43.97\% GC content. Based on 16S rRNA gene sequence analysis followed by in silico DNA-DNA hybridization studies, both the strains were identified as Lactobacillus plantarum belonging to family Lactobacillaceae within the phylum Firmicutes. Both the strains were genomically identical, sharing 99.99\% CDS that showed 112 SNPs. Both the strains also exhibited deconjugation activity for the bile salts while genome analysis revealed that the L. plantarum strains E2C2 and E2C5 also have the ability to produce vitamins, biotin, alpha-and beta-glucosidase suggesting potential probiotic activities of the isolates. The description presented here is based on the draft genomes of strains E2C2 and E2C5 which are submitted to GenBank under the accession numbers LSST00000000.1 and LTCD00000000.1, respectively.}, doi = {10.1186/s40793-017-0222-x}, author = {Suryavanshi, Mangesh V. and Paul, Dhiraj and Doijad, Swapnil P. and Bhute, Shrikant S. and Hingamire, Tejashri B. and Gune, Rahul P. and Shouche, Yogesh S.} } @article {46844, title = {Characterisation of hyper tolerant Bacillus firmus L-148 for arsenic oxidation}, journal = {Environmental Pollution}, volume = {261}, year = {2020}, month = {JUN}, pages = {114124}, type = {Article}, abstract = {

Groundwater arsenic pollution causes millions of deaths worldwide. Long term natural and anthropogenic activities have increased arsenic levels in groundwater causing higher threats of arsenic exposure. Arsenic hyper-tolerant Firmicute Bacillus firmus L-148 was isolated from arsenic limiting Lonar lake soil, which tolerated more than 3 M arsenic and could oxidize 75 mM arsenite [As(III)] in 14 days. It oxidized As(III) in presence of heavy metals and had unusual pH optima at 9.2. B. firmus L-148 was studied at the biochemical, protein, genomic and transcript level for understanding its arsenic oxidizing machinery. The proteomic and transcript analysis exhibited the presence of ars and aio operon and supported the inducible nature of ars operon. Robust, hyper-tolerant, fast As(III) oxidizing, least nutrient requiring and multi-metal resistance qualities of the strain were used in microcosm studies for bioremediation. Artificial groundwater mimicking microcosm with 75 mM As(III) was developed. Modulation of carbon source, iron and multi metals affected growth and As(III) oxidation rate. The As(III) oxidation was recorded to be 77\% in 15 days in presence of sodium acetate and Fe ions. This microcosm study can be explored for bioremediation of arsenic contaminated water and followed by precipitation using other methods. (C) 2020 Elsevier Ltd. All rights reserved.

}, keywords = {Arsenic hyper-tolerance, Lonar lake, Microcosm studies, Multi-metal resistance, Next generation sequencing}, issn = {0269-7491}, doi = {10.1016/j.envpol.2020.114124}, author = {Bagade, Aditi and Nandre, Vinod and Paul, Dhiraj and Patil, Yugendra and Sharma, Nisha and Giri, Ashok and Kodam, Kisan} } @article {48177, title = {Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach}, journal = {Microbiological Research}, volume = {263}, year = {2022}, month = {OCT}, pages = {127157}, type = {Article}, abstract = {

Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 \% of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bioinoculants for enhancing aroma, yield, and sustainable rice cultivation.

}, keywords = {Metagenome, Microbial community, Microbiome, Oryza sativa, Rhizosphere, rice}, issn = {0944-5013}, doi = {10.1016/j.micres.2022.127157}, author = {Dhondge, V. Harshal and Barvkar, Vitthal T. and Paul, Dhiraj and Dastager, Syed G. and Pable, Anupama A. and Nadaf, Altafhusain B.} } @article {48780, title = {Seasonal dynamics and tree foliar habit drive the rhizobacterial diversity in congeneric Ficus species from Northern Western Ghats, India}, journal = {Rhizosphere}, volume = {28}, year = {2023}, month = {DEC}, pages = {100790}, type = {Article}, abstract = {

Tree species, annual climatic cycle, and geochemical properties influence the tree rhizospheric microbiome. However, its understanding in the moist deciduous forest of Northern Western Ghats (NWG), India, is limited. Moreover, the effects of foliar habits of trees and seasonal variations on rhizobacterial communities across congeneric tree species are unexplored. Hence, we employed high throughput 16 S rRNA gene sequencing to examine the effects of foliar habits of congeneric tree species and seasonal influences on the rhizobacterial community. For this study, rhizospheric soil from Ficus arnottiana (deciduous) and Ficus talboti (evergreen) trees from NWG, India, was collected during three seasons (summer, monsoon, and winter) and subjected to high throughput sequencing. A total of 3031 amplicon sequence variants (ASV) were observed, of which 1257 and 1181 ASV were unique to F. arnottiana and F. talboti, respectively, and 593 ASV were common to both species. The phyla Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi were ubiquitous and contributed \>90\% to the rhizobacterial community. Some bacterial phyla were exclusively associated with either of the tree species and seasons. Different bacterial phyla performed similar functions in different seasons, indicating their functional redundancy and emphasizing their resilience and adaptability across seasons. It was observed that seasonal dynamics mainly drove the rhizobacterial diversity; however, it was also influenced by the foliar habits of the trees and geochemical properties. The study enhances the understanding of congeneric tree microbiomes and offers valuable insights into their potential applications through microbiome engineering.

}, keywords = {Amplicon variants, Bacterial diversity, Ficus arnottiana, Ficus talboti, Rhizosphere}, doi = {10.1016/j.rhisph.2023.100790}, author = {Salunkhe, Vaishnavi H. and Kunte, Pooja S. and Paul, Dhiraj and Kasodekar, Amol K. and Kadoo, Narendra Y.} }