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The present study describes the rapid and efficient indirect lysis method for environmental DNA extraction from athalassohaline soil by newly formulated cell extraction buffer. The available methods are mostly based on direct lysis which leads to DNA shearing and co-extraction of extra cellular DNA that influences the community and functional analysis. Moreover, during extraction of DNA by direct lysis from athalassohaline soil, it was observed that, upon addition of poly ethylene glycol (PEG), isopropanol or absolute ethanol for precipitation of DNA, salt precipitates out and affecting DNA yield significantly. Therefore, indirect lysis method was optimized for extraction of environmental DNA from such soil containing high salts and low microbial biomass (CFU 4.3 × 104 per gram soil) using newly formulated cell extraction buffer in combination with low and high speed centrifugation. The cell extraction buffer composition and its concentration were optimized and PEG 8000 (1 %; w/v) and 1 M NaCl gave maximum cell mass for DNA extraction. The cell extraction efficiency was assessed with acridine orange staining of soil samples before and after cell extraction. The efficiency, reproducibility and purity of extracted DNA by newly developed procedure were compared with previously recognized methods and kits having different protocols including indirect lysis. The extracted environmental DNA showed better yield (5.6 ± 0.7 μg g−1) along with high purity ratios. The purity of DNA was validated by assessing its usability in various molecular techniques like restriction enzyme digestion, amplification of 16S rRNA gene using PCR and UV–Visible spectroscopy analysis.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0383-0) contains supplementary material, which is available to authorized users.

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AbstractA 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°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 ω7c. 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).

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