Ram Nageena Singh

Deciphering Diversity of Salt-Tolerant Bacilli from Saline Soils of Eastern Indo-gangetic Plains of India

The intensive use of chemical fertilizers, monoculture and irrigation with surface saline water has resulted in the deterioration of soil health by enhancing the level of salinity in the Eastern Indo-Gangetic Plains of India. Therefore, diversity of halotolerant bacteria adapted to that environment and possessed the ability to produce plant growth hormones was explored, that could be used for salt stress amelioration. The 16S rRNA gene sequencing and fatty acid methyl ester (FAME) were used for diversity analysis of salt-tolerant bacilli. Among the 95 isolates, 55 strains showed plant growth promotion traits, production of industrially important enzymes (amylase, protease and cellulase) and tolerance to more than 4% NaCl. Using partial 16S rRNA sequences and FAME comparisons, 21 different species of Bacillus and Bacillus-derived genera were identified, viz. Bacillus megaterium, B. subtilis, B. licheniformis, B. firmus, B. horikoshii, B. pumilus, Bacillus sp., B. safensis, B. thuringiensis, B. simplex, B. agri, B. flexus, B. oceanisediminis, B. cereus, B. arsenicus, Paenibacillus dendritiformis, Lysinibacillus sp., L. sphaericus, B. marisflavi, Terribacillus sp., and B. mycoides. These isolates possess the ability to tolerate high salt, form endospores, withstand harsh environments, and also have the potential for plant growth promotion, which could be useful in formulation of new inoculants to enhance the availability of nutrients for crop growth under saline conditions.

Biochemical and molecular characterization of thermo-alkali tolerant xylanase producing bacteria from thermal springs of Manikaran

One hundred ten alkalo-tolerant thermophilic bacteria were isolated from 17 samples (water and sediment) collected from Manikaran. Of 110 isolates, 70 showed the production of xylanases and were further screened for growth and production of xylanases at different temperature ranging from 40 to 75°C. Eleven isolates that showed growth and xylanase production at temperatures ≥50°C were selected for quantitative estimation in modified Reese mineral liquid medium containing wheat bran. Maximum xylanase activity was produced by isolate H-7 followed by H-9 and R-9 and was statistically superior to other isolates. The microscopic observation showed that the isolates possessed the typical rod with endospore, characteristic of genus Bacillus. The isolates were found to be oxidase and catalase positive. Using BIOLOG Microlog 3 software, the isolates H7, H9 and R9 were identified as Paenibacillus ehemensis, Bacillus cereus/B. thuringiensis and B. subtilis respectively, based on utilization of 95 carbon sources. PCR-RFLP analysis of 16S rDNA indicated that the isolates were genetically different from each other. DNA sequencing of the three isolates and phylogenetic analysis revealed that all the isolates obtained from Manikaran thermal springs showed 97 to 100% similarity with the sequences within the GenBank. The closest phylogenetic neighbours according to the 16S rRNA gene sequence data for the three isolates H-7, H-9, and R-9 were Paenibacillus ehemensis, Bacillus cereus and Bacillus subtilis, respectively.

Deciphering the Mechanisms of Endophyte-Mediated Biofortification of Fe and Zn in Wheat

An investigation was carried out to understand the mechanism(s) underlying enhanced Fe or Zn uptake in low Fe–Zn accumulator wheat genotype 4HPYT-414, due to inoculation of siderophore-producing and zinc-solubilizing endophytes—Arthrobacter sulfonivorans DS-68 and Arthrobacter sp. DS-179. Root anatomical features, using transmission electron microscopy (TEM), qualitative and quantitative aspects of production of organic acids and sugars in root exudates, and expression of TaZIP genes were analysed to relate to endophyte-mediated higher concentrations of Fe and Zn in the roots and shoots of wheat plants. TEM studies revealed that the endodermis, cortical region, root hair extension, xylem and xylem vessels, pericycle and vascular bundles were more pronounced and thicker in inoculated treatments, as compared to control. The organic acid profile of root exudates revealed five types of organic acids, with citric acid being predominant. Inoculation of A. sulfonivorans and Arthrobacter sp. brought about 5- and eightfold increases in the amounts of acids, respectively, as compared to control, particularly citric acid, succinic acid and acetic acid. Among the four TaZIP genes targeted, expression was achieved only for TaZIP3 and TaZIP7 genes, which showed 1–2 fold increases in the inoculated treatments. The results clearly indicated that the endophyte-mediated overexpression of TaZIP3 and TaZIP7 genes in roots and shoots, and the observed anatomical and exudate changes were acting synergistically in facilitating higher Fe and Zn translocation in roots and shoots.

Bacterial communities in ancient permafrost profiles of Svalbard, Arctic

Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 103 to 2.22 × 105 CFU g−1, total bacterial numbers range from 1.14 × 105 to 5.52 × 105 cells g−1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny‐Ålesund (79°N), Arctic.

Draft Genome Sequence of Halolamina pelagica CDK2 Isolated from Natural Salterns from Rann of Kutch, Gujarat, India

ABSTRACT Halolamina pelagica strain CDK2, a halophilic archaeon (growth range 1.36 to 5.12 M NaCl), was isolated from rhizosphere of wild grasses of hypersaline soil of the Rann of Kutch, Gujarat, India. Its draft genome contains 2,972,542 bp and 3,485 coding sequences, depicting genes for halophilic serine proteases and trehalose synthesis.

Genome wide survey and analysis of microsatellites in Tombusviridae family

Abstract Microsatellites are small repetitive sequences found in all kingdoms of life including viruses. Members of the Tombusviridae family severely affect growth of wide range of plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 47 species of Tombusviridae family. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, dinucleotide repeats followed by mononucleotide repeats were found to be highly predominant. Mononucleotide repeats were found to be underrepresented in majority of Tombusviridae genomes. Poly G and Poly C repeats were more abundant as compared to poly A or poly T nucleotides. TG/GT and AG/CA was the most abundant dinucleotide repeat motif observed in Tombusviridae genomes. Repeats larger than trinucleotide were never found in these viral genomes. Comparative study of relative abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were lower than many RNA virus genomes. To our knowledge, this is the first analysis of microsatellites occurring in Tombusviridae genomes. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.