Natrialba swarupiae sp. nov., a halophilic archaeon isolated from a hypersaline lake in India

A haloarchaeal strain (ESP3B_9T) was isolated from the salt pan of Sambhar salt lake, Rajasthan, India. Cells were coccoid, non-motile, Gram-stain-negative and formed reddish-pink pigmented colonies. The strain was aerobic, able to grow at 35–55 °C (optimum, 40 °C), in 20–35 % (25 %) NaCl and pH 8–10 (pH 9). Mg2+ not required for growth. The cells were lysed in distilled water and the minimum NaCl concentration that prevented cell lysis was 5 % w/v. The 16S rRNA gene sequence similarities between strain ESP3B_9T and Natrialba hulunbeirensis JCM 10989T and Natrialba magadii ATCC 43099T were 96.53 and 96.25 % respectively. The similarities of the RNA polymerase subunit B gene between strain ESP3B_9T and N. hulunbeirensis JCM 10989T and N. magadii ATCC 43099T were 84.47 and 84.9 % respectively. Genome sequencing revealed a genome size of 4.20 Mbp with DNA G+C content of 62.5 mol%. The major polar lipids were phosphotidylglycerol and phosphatidylglycerol phosphate methyl esters with minor amounts of unidentified lipids. The results of polyphasic analysis determined that strain ESP3B_9T represents a novel species of the genus Natrialba , for which the name Natrialba swarupiae sp. nov. is proposed. The type strain is ESP3B_9T (MCC 3419T=JCM 33002T=KCTC 4279T=CGMCC 1.16737T).

Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1

The unexpected lysis of a large culture of Halobacterium salinarum strain S9 was found to be caused by a novel myovirus, designated ChaoS9. Virus purification from the culture lysate revealed a homogeneous population of caudovirus-like particles. The viral genome is linear, dsDNA that is partially redundant and circularly permuted, has a unit length of 55,145 nt, a G + C% of 65.3, and has 85 predicted coding sequences (CDS) and one tRNA (Arg) gene. The left arm of the genome (0–28 kbp) encodes proteins similar in sequence to those from known caudoviruses and was most similar to myohaloviruses phiCh1 (host: Natrialba magadii) and phiH1 (host: Hbt. salinarum). It carries a tail-fiber gene module similar to the invertible modules present in phiH1 and phiCh1. However, while the tail genes of ChaoS9 were similar to those of phiCh1 and phiH1, the Mcp of ChaoS9 was most similar (36% aa identity) to that of Haloarcula hispanica tailed virus 1 (HHTV-1). Provirus elements related to ChaoS9 showed most similarity to tail/assembly proteins but varied in their similarity with head/assembly proteins. The right arm (29–55 kbp) of ChaoS9 encoded proteins involved in DNA replication (ParA, RepH, and Orc1) but the other proteins showed little similarity to those from phiH1, phiCh1, or provirus elements, and most of them could not be assigned a function. ChaoS9 is probably best classified within the genus Myohalovirus, as it shares many characteristics with phiH1 (and phiCh1), including many similar proteins. However, the head/assembly gene region appears to have undergone a recombination event, and the inferred proteins are different to those of phiH1 and phiCh1, including the major capsid protein. This makes the taxonomic classification of ChaoS9 more ambiguous. We also report a revised genome sequence and annotation of Natrialba virus phiCh1.

Utilization of Virus ϕCh1 Elements To Establish a Shuttle Vector System for Halo(alkali)philic Archaea via Transformation of Natrialba magadii

ABSTRACTIn the study described here, we successfully developed a transformation system for halo(alkali)philic members of theArchaea. This transformation system comprises a series ofNatrialba magadii/Escherichia colishuttle vectors based on a modified method to transform halophilic members of theArchaeaand genomic elements of theN. magadiivirus ϕCh1. The shuttle vector pRo-5, based on therepH-containing region of ϕCh1, stably replicated inE. coliandN. magadiiand in several halophilic and haloalkaliphilic members of theArchaeanot transformable so far. The ϕCh1 operon ORF53/ORF54 (repH) was essential for pRo-5 replication and was thus identified as the minimal replication origin. The plasmid allowed homologous and heterologous gene expression, as exemplified by the expression of ϕCh1 ORF3452, which encodes a structural protein, and the reporter genebgaHofHaloferax lucentenseinN. magadii. The new transformation/vector system will facilitate genetic studies withinN. magadiiand other haloalkaliphilic archaea and will allow the detailed characterization of the gene functions ofN. magadiivirus ϕCh1 in their extreme environments.