Soil Bacteria and Bacteriophages

Isolation, characterization and genomic analysis of the novel Arthrobacter sp. phage SWEP2

A new virulent phage, SWEP2, infecting the Arthrobacter sp. 5B strain, was isolated from black soil samples in northeastern China. SWEP2 has a latent period of 80 min and a burst size of 45 PFU (evaluated at an MOI of 0.1). Genomic analysis revealed that the 43,398-bp dsDNA genome of phage SWEP2 contains 64 open reading frames (ORFs) and one tRNA gene. Phylogenetic analysis indicated a close relationship between SWEP2 and Arthrobacter phage Liebe, with 82.98% identity and a query coverage of 48%. Based on its distinct phenotypic and genetic characteristics, SWEP2 is identified as a novel Arthrobacter phage.

Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica

Between 2014 and 2016, 16 Gram-stain-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria were isolated from exposed soils from the Utsteinen region, Sør Rondane Mountains, East Antarctica. Analysis of their 16S rRNA gene sequences revealed that the strains form a separate cluster in the genus Spirosoma, with Spirosoma rigui KCTC 12531^T as its closest neighbour (97.8 % sequence similarity). Comparative genome analysis of two representative strains (i.e. R-68523^T and R-68079) of the new group with the type strains of Spirosoma rigui (its closest neighbour) and Spirosoma linguale (type species of the genus), yielded average nucleotide identity values of 73.9-78.7 %. Digital DNA-DNA reassociation values of the two strains and these type strains ranged from 20.3 to 22.0 %. The predominant cellular fatty acids of the two novel strains were summed feature 3 (i.e. C_16 : 1  ω7c and/or iso-C₁₅ 2-OH), C_16 : 1  ω5c, C_16 : 0 and iso-C_15 : 0. The new Spirosoma strains grew with 0-0.5 % (w/v) NaCl, at pH 6.5-8.0 and displayed optimum growth between 15 and 25 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the new strains represent a novel species of the genus Spirosoma for which the name Spirosoma utsteinense sp. nov. is proposed. The type strain is R-68523^T (=LMG 31447^T=CECT 9925^T).

The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert

Arid zones cover over 30 % of the Earth's continental surface. In order to better understand the role of microbes in this type of harsh environment, we isolated and characterized the bacteriophages from samples of the surface sand of the Mesquite Flats region via electron microscopy and DNA sequencing of a select number of cloned phage DNAs. An electron microscopic analysis of the recovered virus-like particles revealed at least 11 apparently different morphotypes sharing structural characteristics of the Caudoviridae family of tailed phages. We found that 36 % of the sequences contained no significant identity (e-value >10(-3)) with sequences in the databases. Pilot sequencing of cloned 16S rRNA genes identified Bacteroidetes and Proteobacteria as the major bacterial groups present in this severe environment. The majority of the 16S rDNA sequences from the total (uncultured) bacterial population displayed ≤96 % identity to 16S rRNA genes in the database, suggesting an unexplored bacterial population likely adapted to a desert environment. In addition, we also isolated and identified 38 cultivable bacterial strains, the majority of which belonged to the genus Bacillus. Mitomycin-C treatment of the cultivable bacteria demonstrated that the vast majority (84 %) contained at least one SOS-inducible prophage.