Biology subjects

Rahi, P.

Publications and source records attributed to Rahi, P..

4 recordsLinked to original sources

bioRxiv2023

Neisseria leonis sp. nov. isolated from rabbits, reclassification of Uruburuella suis, Uruburuella testudinis, Kingella potus, Bergeriella denitrificans and Morococcus cerebrosus into Neisseria genus and reclassification of Neisseria shayeganii into Eikenella genus

Genome sequence-based identification of two strains (3986T and 51.81) isolated from rabbits in France in 1972 and 1981 and deposited in the Collection of Institut Pasteur (CIP) has led to the description of a novel species in the genus Neisseria. The cells of both strains were non-motile, Gram-stain-negative and diplococcobacilli. Optimal growth on trypticase soy agar was recorded at 37{degrees}C and pH 8.5 in aerobic conditions. Phylogeny based on 16S rRNA gene placed the strains close to Neisseria bacilliformis ATCC BAA-1200T (96.38%) nesting with the members of Neisseriaceae family. Furthermore, the phylogenetic analysis based on bac120 gene set from the Genome Taxonomy Database (GTDB) placed both strains within the monophyletic Neisseria clade, which also included type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis and Uruburuella testudinis. However, Neisseria shayeganii strain 871T was placed outside Neisseria clade and close to the members of Eikenella genus. Strains 3986T and 51.81 were placed in a branch distinct from all species of the genus Neisseria and exhibited the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the species demarcation values. In contrast, ANI value within the two strains was 96.9% confirming that they represent same species. The genomic DNA G+C content of strain 3986T was 56.92%. Based on the phylogenetic and phenotypic data, the strains 3986T and 51.81 represent a novel species of the genus Neisseria, for which the name Neisseria leonis sp. nov. is proposed (type strain 3986T = CIP 109994T = LMG 32907T). Additionally, based on phylogenetic analysis, DUS dialect and average amino acid identity (AAI) values, we also proposed the reclassification of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis and Uruburuella testudinis into Neisseria genus and Neisseria shayeganii into Eikenella genus. Author NotesThe GenBank accession numbers for the 16S rRNA gene sequence of strains 3986T and 51.81 are respectively OQ121838.1 and OQ428162.1. The draft genome sequences have been deposited in GenBank under the accession numbers JAPQFK000000000 (strain 3986T) and JAPQFL000000000 (strain 51.81). Further explanations mentioned in the article as well as 7 supplementary tables and 7 supplementary figures are available with the online version of this article.

evolutionary biology↗

bioRxiv2020

Rhizobium desertarenae sp. nov., isolated from the Saline Desert Soil from the Rann of Kachchh, India.

A novel bacterial strain designated ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78T grows best at 28{degrees}C and pH 7.0 and can tolerate up to 2% (w/v) NaCl. Based on 16S rRNA gene phylogeny, the strain ADMK78T belongs to the genus Rhizobium, with the highest similarity to Rhizobium wuzhouense W44T (98.7%) and Rhizobium ipomoeae shin9-1T (97.9%). Core-genes based phylogenetic analysis revealed that the strain ADMK78T forms a distinct branch in between Rhizobium ipomoeae shin9-1T and Rhizobium selenitireducens BAA-1503T. The average nucleotide identity of ADMK78T was less than 82%, to members of the family Rhizobiaceae. The genomic DNA G+C content of strain ADMK78T is 58.6 mol%. The major fatty acids of strain ADMK78T were C18:0 and C18:1 {omega}7c. 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 could be distinguished from the recognized species of the genus Rhizobium. It is suggested to represent a novel species of this genus, for which the name Rhizobium desertarenae sp. nov. is proposed. The type strain is ADMK78T (=MCC 3400T; KACC 21383T; JCM 33657T).

microbiology↗

bioRxiv2019

Description of Klebsiella indica sp. nov., isolated from the surface of tomato.

A novel bacterial strain designated TOUT106T was isolated from the surface of a tomato collected from the local vegetable market in Pune, India. The cells were rod shaped, Gram-stain-negative, encapsulated and non-motile. The strain TOUT106T grows as mucoid and translucent colonies on blood agar medium and the best growth was observed at 28{degrees}C and at pH 7.0, and could tolerate up to 2% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain TOUT106T was placed under Salmonella clade, with close similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.42%). Genome-based phylogenetic analysis revealed that the strain forms a distinct branch within the Klebsiella clade and K. michiganensis DSM25444T and K. oxytoca NBRC105695T were the closest neighbor. The genomic DNA G+C content of strain TOUT106T was 53.53 mol%. The average nucleotide identity of TOUT106T was less 86.4% with closely related members of the family Enterobacteriaceae. The major fatty acids of strain TOUT106T were C16:0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14:0, C19:0 cyclo w8c, C18:1 w6c/C18:1 w7c, C12:0 and C16:1 w7c/C16:1 w6c. The strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS to its closest relatives. Based on the phenotypic including chemotaxonomic properties and phylogenetic analysis the strain TOUT106T could be distinguished from the recognized species of the genus Klebsiella, was suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T).

microbiology↗

bioRxiv2019

Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Conservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

microbiology↗