Description of a novel genus and novel species isolated from the Rann of Kachchh.

Members of Rhizobiaceae are found in diverse ecosystems, including aquatic and marine ecosystems. Microbes belonging to genera Georhizobium, Hoefea, Lentilitoribacter, Martelella, Rhizobium, and Pseudorhizobium have been mainly reported from marine or aquatic environments. Rhizobium is one of the major genera in the family Rhizobiaceae. Currently, genus Rhizobium consists of 91 validly published species. The majority of Rhizobium species play key role in symbiotic fixation of nitrogen within the root nodules of leguminous plants. However, non-symbiotic and free living members of Rhizobium are found in various niches like soils, including the rhizosphere, bioreactor, lake water, arsenic-rich groundwater, and beach sand. Recently, different new genus names such as Allorhizobium, Pararhizobium, Neorhizobium, and Pseudorhizobium have been proposed in genus Rhizobium.

Rann of Kachchh (Google images)

Rann of Kachchh is the largest desert in the world and is a transitional area between marine and terrestrial ecosystems. This region experiences fluctuation in temperature. Due to the hot and hypersaline environment, there is a high probability of finding novel halophilic and halotolerant microorganisms with high economic and industrial potential in this region. The strain ADMK78T was isolated from the saline desert soil of Rann of Kachchh, it showed less than 98.7% 16S rRNA sequence similarity. The collaborative study conducted by the researchers at NCMR-NCCS Pune and UGC-Centre of Advanced Study, Sardar Patel University, Gujarat demonstrated the taxonomic position of strain ADMK78T through a polyphasic and genomic analysis.

The strain was isolated on Zobell Marine Agar following the serial dilution of the saline desert soil collected from the Rann of Kachchh, Gujarat. 16S rRNA phylogeny, whole genome sequencing and core-genes based phylogeny was studied. Physiology and chemotaxonomic analysis was also done.  The strain showed highest similarity to Rhizobium wuzhouense followed by Rhizobium ipomoeae. The sequence search resulted in more than 99% sequence similarity for two sequences. The first one was from an alpha-proteobacterium associated with Microcystis aeruginosa culture, and the second one was from Ciceribacter sp. isolated from low salinity lakes on the Tibetan plateau. Several species of Rhizobium were distantly placed from the core clade that contained the type species of the genus making it a non-monophyletic group. The genome size of this strain is 4,342,374 bp, which is smaller than the genome size of symbiotic members of Rhizobium and in the range of the sizes of the non-symbiotic strains of Rhizobium.

Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity revealed that the strain ADMK78T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. The study proposed re-classifcation 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 ADMK78T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. 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 represents a novel species, Peteryoungia desertarenae sp. nov. The strain is deposited at NCMR with accession number MCC 3400T. The study 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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