Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit

Abstract

A halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).

Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov

“…The family ‘ Haladaptataceae ’ has been proposed previously, only including the single genus Haladaptatus [9, 27] and the family name has not been validly published to date. In this study, the genera Halomicrococcus [28] and Halorussus [29] were found to be two relatives of the genus Haladaptatus and should be assigned to the family ‘ Haladaptataceae ’. The Natrialbaceae cluster contains 19 genera, Halobiforma [30], Halopiger [31], Halosolutus [20], Halostagnicola [32], Haloterrigena [33], Halovivax [34], Natrarchaeobaculum [35], Natrarchaeobius [36], Natrialba [37], Natribaculum [38], Natrinema [39], Natronobacterium [40], Natronobiforma [41], Natronococcus [40], Natronolimnohabitans [35], Natronorubrum [42], Natronolimnobius [43], Salinadaptatus [44] and Saliphagus [45].…”

Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern

“…They were unable to utilize d-fructose, l-sorbose, d-ribose, d-xylose, maltose, lactose, glycine, l-alanine or l-lysine. These two strains were sensitive to the following antimicrobial compounds (µg per disc, unless otherwise indicated): novobiocin (30) and nitrofurantoin (300); but resistant to trimethoprim (5), penicillin G (10 IU per disc), ampicillin (10), chloramphenicol (30), neomycin (30), norfloxacin (10), ciprofloxacin (5), streptomycin (10), kanamycin (30), vancomycin (30), gentamicin (10) and nalidixic acid (30). More detailed features of strains GSLN9 T and XZYJT29 T are given in the species descriptions.…”

Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

“…Most halophilic archaea harbour more divergent 16S rRNA gene copies with similarities lower than the recommended threshold (98.7 %) to separate two prokaryotic species [2]. These include species of the Haloarcula–Halomicrobium–Halomicroarcula groups [3, 4], Haloarchaeobius [5], Halobaculum [6], Halomicrococcus [7], Halorientalis [8], Halorubellus [9], Halorussus [10], Halosimplex [11], Halostella [12], Halovenus [13] and Natronoarchaeum [14]. The intragenomic heterogeneity of 16S rRNA genes might be an ancient and stable characteristic in most lineages of the class Halobacteria [15].…”

“…Strain HD8-45 T possessed two copies of 16S rRNA genes, rrn1 (1474 nt, KT261638) and rrn2 (1473 nt, KT261640), which differed in sequence by 8.7 %. The degree of intragenomic variability observed in the 16S rRNA genes is far greater than the average between-species divergence (~1.3 %) [2] and is higher than the most divergence found in Haloarcula (5.6 %) [24], Halomicroarcula (5.1 %) [4], Haloarchaeobius (5.6 %) [5], Halobaculum (4.0 %) [6], Halomicrococcus (3.7 %) [7], Halorientalis (6.9 %) [8], Halorubellus (3.8 %) [9], Halorussus (4.4 %) [10], Halosimplex (7.8 %) [25], Halostella (2.2 %) [12], Halovenus (6.8 %) [13] and Natronoarchaeum (2.2 %) [14]; lower than that in Halomicrobium (9.0 %) [3] which contained the highest 16S rRNA gene divergence in the class Halobacteria . The rrn1 of strain HD8-45 T showed 95.1 % similarity to that of Salinirussus salinus YGH44 T while the rrn2 showed 91.2 % similarity to that of Halovenus aranensis EB27 T ().…”