Molecular characterization of Nocardiopsis species from Didwana dry salt lake of Rajasthan, India

The genus Nocardiopsis is well known to produce secondary metabolites especially antibacterial bioactive compound. Isolation and characterization of bioactive compounds producing novel isolates from unusual habitats are crucial. The present study was aimed to explore Didwana dry salt lake of Rajasthan state in India for the isolation and characterization of actinomycetes. The isolated actinomycetes isolates were characterized based on culture characteristics, biochemical tests and 16S rRNA gene sequencing. The 16S rRNA gene sequence analysis revealed that all the five isolates inhabiting soil of the said dry salt lake of Didwana, Rajasthan belonged to four species of Nocardiopsis viz., N. synnemataformans, N. potens, N. prasina and N. dassonvillei subsp. albirubida. The molecular identification based on 16S rRNA gene sequences was found accurate and robust. The phylogram generated through multiple sequence alignment of all the test isolates of Nocardiopsis revealed that the isolates aroused from a single branch and validated monophyletic association. The present study is the first report of exploring Nocardiopsis isolates from the dry salt lake. These characterized Nocardiopsis isolates isolated from Didwana dry salt lake habitat are novel stains and can be of significance in the detection and utilization of novel bioactive compounds

Molecular characterization of microsymbionts associated with root nodules of <em>Crotalaria burhia</em> Buch.-Ham. ex Benth., a native keystone legume species from Thar Desert of India

373-384Establishment of legume-rhizobia symbiosis has ample agronomic and ecological significance. Characterization of native rhizobia could enhance our understanding of their natural distribution and co-evolution. The Great Indian Thar Desert is an ecologically significant unique habitat with its flora and fauna. Crotalaria spp. is an economically important legume widely distributed in the Thar Desert and can be considered its one of the bioresources, particularly for biological nitrogen fixation with their symbiotic rhizobia. Here, we examined the legume Crotalaria burhia Buch.-Ham. ex Benth. in search of potential novel rhizobial species. Out of 72 root nodule bacterial (RNB) strains isolated from C. burhia, 51 rhizobia-like strains were examined for genetic diversity based on ARDRA and RAPD patterns. BLASTn sequence similarity results based on 16S rRNA gene of selective thirteen strains representing four ARDRA types revealed that they were related to genera Ensifer, Rhizobium and Bradyrhizobium. In 16S rRNA gene phylogeny, five (CB5, CB17, CB36, CB44, CB56) strains were closer to Ensifer kostiensis, three (CB6, CB12, CB32) to E. terangae and CB11 showed similarity with E. kostiensis and E. saheli. Strain CB4 was similar to Bradyrhizobium yuanmingense and three (CB29, CB31, CB46) strains were closer to species of Rhizobium (R. etli, R. sullae and R. borbori respectively). Symbiotic (nodA and nifH) genes phylogeny of Ensifer sp. CB56 was incongruent and showed close similarity with E. fredii whereas sym gene phylogeny of Bradyrhizobium sp. CB4 was congruent with 16S rRNA gene phylogeny. In Rhizobium strains sym genes could not be amplified and they failed to nodulate host. Our study suggests that C.burhia is nodulated by diverse strains of Ensifer and Bradyrhizobium in alkaline soil of Thar Desert and these strains effectively cross-nodulated crop Vigna radiata

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Not AvailableIndian Thar desert mostly covering North–Western parts of Rajasthan is known for high temperature, high wind velocity, low rainfall and minimum relative humidity. The harsh climatic conditions of the region had wide fungal diversity along with several unreported species. Present study was aimed to explore the diversity of gastroid fungi from the Indian Thar desert. During survey a gastroid fungus was found growing in the rainy season under Prosopis juliflora tree. The fungal fruiting bodies were collected and identified based on microscopic examination, scanning electron microscopy (SEM) and ITS-5.8S rRNA gene sequences as gasteroid fungus Broomeia congregata Berk., belonging to family Broomeiaceae (Basidiomycota). The ITS-5.8S rRNA gene sequences of the fungus were compared with that of available sequences using BLAST programme and submitted to NCBI, USA. The nucleotide sequence was assigned GenBank accession number MK208821 which is now available in public domain. The morphological characterization and molecular identification validated B. congregata Berk. as a new record from great Indian Thar desert.Not Availabl

Actinomycetes isolates of arid zone of Indian Thar Desert and efficacy of their bioactive compounds against human pathogenic bacteria

Twenty-six morphotypes of actinomycetes bacteria were isolated from the soils of arid zone of Indian Thar desert, Rajasthan. A significant and positive correlation was found between density of actinomycetes isolates and availability of nitrogen in sandy soil of arid zone suggesting the influence of soil nitrogen on occurrence and propagation of actinomycetes in this region. Molecular identification based on 16S rRNA gene sequencing revealed that the bacterial isolates belong to four actinomycetes genera, viz. Streptomyces (22 species), Nocardiopsis (two species), Saccharomonospora (one species) and Actinoalloteichus (one species). The preliminary screening of 26 isolates against five human pathogenic bacteria, viz. Escherichia coli, Vibrio cholera, Salmonella enterica typhimurium, Staphylococcus aureus and Enterococcus faecalis, showed that only four isolates, viz. Streptomyces sp. (ITD-27), S. enissocaesilis (ITD-29), S. Malachitospinus (ITD-35) and Streptomyces sp. (ITD-47), had antibacterial activity. The secondary screening of these four isolates revealed that the isolate S. malachitospinus (ITD-35) showed the maximum growth inhibition zone and inhibited the growth of all tested gram-positive and gram-negative pathogenic bacteria. Gas chromatography–mass spectrometry analysis of S. malachitospinus (ITD-35) cultural filtrate in n-butanol solvent identified three antibacterial compounds of medicinal significance, viz. 3-octanone, neopentyl isothiocyanate and 2-methyl butyl isothiocyanate

Nodulation of legumes from the Thar desert of India and molecular characterization of their rhizobia

Aims: To survey the occurrence of nodulated legumes in the arid and semi-arid areas of Western Rajasthan and to characterize their associated symbiotic bacteria. Methods: Herbaceous annual species were excavated whole, while tree species were studied as seedlings in the field or as trap plants in pot experiments. Nodules were examined by microscopy to confirm their effectiveness and to determine their internal structure. Bacteria isolated from the nodules were authenticated on their original hosts and were identified on the basis of 16S rRNA sequencing. Phylogenetic trees were inferred using the neighbour-joining method. Results: We studied 35 of more than 50 species of native legume reported from these areas. Legumes are drought escaping (annual species), drought tolerant perennials or trees possessing deep root systems and other adaptations to arid conditions. Nodulation was recorded in all members of the Papilionoideae and Mimosoideae, but only one species of Caesalpinioideae. Internal structure of nodules varied within these groups, especially with respect to the presence or absence of uninfected cells in the infected region. Full 16S rRNA gene sequencing revealed that the nodules harboured a range of nodulating bacteria belonging to the genera Sinorhizobium, Rhizobium and Bradyrhizobium, within which they formed separate sub clades. Conclusions: This study extends the range of legumes known to grow and nodulate in semi-arid regions, and provides information about their endosymbiont

An invasive Mimosa in India does not adopt the symbionts of its native relatives

BACKGROUND AND AIMS: The large monophyletic genus Mimosa comprises approx. 500 species, most of which are native to the New World, with Central Brazil being the main centre of radiation. All Brazilian Mimosa spp. so far examined are nodulated by rhizobia in the betaproteobacterial genus Burkholderia. Approximately 10 Mya, transoceanic dispersal resulted in the Indian subcontinent hosting up to six endemic Mimosa spp. The nodulation ability and rhizobial symbionts of two of these, M. hamata and M. himalayana, both from north-west India, are here examined, and compared with those of M. pudica, an invasive species. METHODS: Nodules were collected from several locations, and examined by light and electron microscopy. Rhizobia isolated from them were characterized in terms of their abilities to nodulate the three Mimosa hosts. The molecular phylogenetic relationships of the rhizobia were determined by analysis of 16S rRNA, nifH and nodA gene sequences. KEY RESULTS: Both native Indian Mimosa spp. nodulated effectively in their respective rhizosphere soils. Based on 16S rRNA, nifH and nodA sequences, their symbionts were identified as belonging to the alphaproteobacterial genus Ensifer, and were closest to the ‘Old World’ Ensifer saheli, E. kostiensis and E. arboris. In contrast, the invasive M. pudica was predominantly nodulated by Betaproteobacteria in the genera Cupriavidus and Burkholderia. All rhizobial strains tested effectively nodulated their original hosts, but the symbionts of the native species could not nodulate M. pudica. CONCLUSIONS: The native Mimosa spp. in India are not nodulated by the Burkholderia symbionts of their South American relatives, but by a unique group of alpha-rhizobial microsymbionts that are closely related to the ‘local’ Old World Ensifer symbionts of other mimosoid legumes in north-west India. They appear not to share symbionts with the invasive M. pudica, symbionts of which are mostly beta-rhizobial