Natronorubrum sulfidifaciens sp. nov., an extremely haloalkaliphilic archaeon isolated from Aiding salt lake in Xin-Jiang, China

Proposed minimal standards for description of new taxa of the class Halobacteria

Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.

Archaeal lipids

The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.

Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena

The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either Natrinema or Haloterrigena, mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently rpoB’ gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of Natrinema and Haloterrigena and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species Haloterrigena hispanica, Haloterrigena limicola, Haloterrigena longa, Haloterrigena mahii, Haloterrigena saccharevitans, Haloterrigena thermotolerans, and Halopiger salifodinae should be transferred to the genus Natrinema, as Natrinema hispanicum, Natrinema limicola, Natrinema longum, Natrinema mahii, Natrinema saccharevitans, Natrinema thermotolerans, and Natrinema salifodinae, respectively. On the contrary, the species Haloterrigena turkmenica, Haloterrigena salifodinae, and Haloterrigena salina will remain as the only representative species of the genus Haloterrigena. Besides, the species Haloterrigena daqingensis should be reclassified as a member of the genus Natronorubrum, as Natronorubrum daqingense. At the species level, Haloterrigena jeotgali and Natrinema ejinorense should be considered as a later heterotypic synonyms of the species Haloterrigena (Natrinema) thermotolerans and Haloterrigena (Natrinema) longa, respectively. Synteny analysis and phenotypic features also supported those proposals.

Natronorubrum halalkaliphilum sp. nov., a haloalkaliphilic archaeon isolated from soda lake in Inner Mongolia Autonomous Region, China

A haloalkaliphilic strain JWXQ-INN-674^T was isolated from the water sample of a soda lake in Inner Mongolia Autonomous Region, China. Cells of the strain were coccoid, motile, and strictly aerobic. The strain was able to grow in presence of 2.6-5.4 M NaCl (optimum concentration is 3.4 M) at 30-50 °C (optimum temperature is 42 °C) and pH 7-9.5 (optimum pH is 9.0). The 16S rRNA gene sequence of strain JWXQ-INN-674^T showed 95.3-96.6% similarity to members of the genus Natronorubrum of the family Natrialbaceae. The whole genome sequencing of strain JWXQ-INN-674^T revealed a genome size of 4.56 M bp and a DNA G + C content of 62.5 mol%. Genome relatedness of strain JWXQ-INN-674^T and other species in the genus Natronorubrum was analyzed by average nucleotide identity and digital DNA-DNA hybridization with the values of 76.8-90.6 and 23.1-39.3%, respectively. The strain possessed the polar lipids phosphatidylglycerol and methylated phosphatidylglycerol phosphate lipid. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of genus Natronorubrum, Natronorubrum halalkaliphilum sp. nov. (type strain JWXQ-INN-674^T = CGMCC 1.17283^T = JCM 34245^T).

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes

Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.

Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith

Carbon monoxide occurs at relatively high concentrations (≥800 parts per million) in Mars' atmosphere, where it represents a potentially significant energy source that could fuel metabolism by a localized putative surface or near-surface microbiota. However, the plausibility of CO oxidation under conditions relevant for Mars in its past or at present has not been evaluated. Results from diverse terrestrial brines and saline soils provide the first documentation, to our knowledge, of active CO uptake at water potentials (-41 MPa to -117 MPa) that might occur in putative brines at recurrent slope lineae (RSL) on Mars. Results from two extremely halophilic isolates complement the field observations. Halorubrum str. BV1, isolated from the Bonneville Salt Flats, Utah (to our knowledge, the first documented extremely halophilic CO-oxidizing member of the Euryarchaeota), consumed CO in a salt-saturated medium with a water potential of -39.6 MPa; activity was reduced by only 28% relative to activity at its optimum water potential of -11 MPa. A proteobacterial isolate from hypersaline Mono Lake, California, Alkalilimnicola ehrlichii MLHE-1, also oxidized CO at low water potentials (-19 MPa), at temperatures within ranges reported for RSL, and under oxic, suboxic (0.2% oxygen), and anoxic conditions (oxygen-free with nitrate). MLHE-1 was unaffected by magnesium perchlorate or low atmospheric pressure (10 mbar). These results collectively establish the potential for microbial CO oxidation under conditions that might obtain at local scales (e.g., RSL) on contemporary Mars and at larger spatial scales earlier in Mars' history.

Halobellus rarus sp. nov., a halophilic archaeon from an inland salt lake of China

Two halophilic archaeal strains, YC21(T) and YC77, were isolated from an inland salt lake of China. Both have pleomorphic rod-shaped cells that lyse in distilled water, stain Gram-negative and form red-pigmented colonies. They are neutrophilic, require at least 2.1 M NaCl for growth under the optimum growth temperature of 37 °C. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), two major glycolipids (GL1 and GL2) chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Trace amounts of two unidentified lipids (GL0-1 and GL0-2) were also detected. The 16S rRNA gene sequences of the two strains are 99.9 % identical, show 94.0-98.9 % similarity to the closest relative members of Halobellus of the family Halobacteriaceae. The rpoB' gene similarity between strains YC21(T) and YC77 is 99.8 % and show 90.3-95.3 % similarity to the closest relative members of Halobellus. The DNA G+C content of strains YC21(T) and YC77 were 66.1 and 66.2 mol%, respectively. The DNA-DNA hybridization value between strain YC20(T) and strain YC77 was 89 %, and the two strains showed low DNA-DNA relatedness with Halobellus limi TBN53(T), the most related member of Halobellus. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC21(T) and YC77 represent a novel species of the genus Halobellus, for which the name Halobellus rarus sp. nov. is proposed. The type strain is YC21(T) (=CGMCC 1.12121(T) = JCM 18362(T)).

Natronorubrum texcoconense sp. nov., a haloalkaliphilic archaeon isolated from soil of the former lake Texcoco (Mexico)

A new haloalkaliphilic archaeon, strain B4(T), was isolated from the former lake Texcoco in Mexico. The cells were Gram-negative, pleomorphic-shaped, pink to red pigmented and aerobic. Strain B4(T) required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. It was able to grow over a pH range of 7.5-10.0 and temperature of 25-50 °C, with optimal growth at pH 9 and 37 °C. Cells are lysed in hypotonic treatment with less than 1.3 M NaCl. The major polar lipids of strain B4(T) were phosphatidylglycerol and methyl-phosphatidylglycerophosphate. Phospholipids were detected, but not glycolipids. The nucleotide sequence of the 16S rRNA gene revealed that the strain B4(T) was phylogenetically related to members of the genus Natronorubrum. Sequence similarity with Natronorubrum tibetense was 96.28 %, with Natronorubrum sulfidifaciens 95.06 % and Natronorubrum sediminis 94.98 %. The G+C content of the DNA was 63.3 mol%. The name of Natronorubrum texcoconense sp. nov. is proposed. The type strain is B4(T) (=CECT 8067(T) = JCM 17497(T)).

Natronorubrum sediminis sp. nov., an archaeon isolated from a saline lake

Two novel haloalkaliphilic archaea, strains CG-6T and CG-4, were isolated from sediment of the hypersaline Lake Chagannor in Inner Mongolia, China. Cells of the two strains were pleomorphic, non-motile and strictly aerobic. They required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. They grew at pH 8.0-11.0, with optimum growth at pH 9.0. Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. The two strains had similar polar lipid compositions, possessing C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Comparison of 16S rRNA gene sequences and morphological features placed them in the genus Natronorubrum. 16S rRNA gene sequence similarities to strains of recognized species of the genus Natronorubrum were 96.2-93.8%. Detailed phenotypic characterization and DNA-DNA hybridization studies revealed that the two strains belong to a novel species in the genus Natronorubrum, for which the name Natronorubrum sediminis sp. nov. is proposed; the type strain is CG-6T (=CECT 7487T =CGMCC 1.8981T =JCM 15982T).