Population and genomic analysis of the genus Halorubrum

Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species

The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12T and S3CR25-11T, that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB' gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12T (= CECT 30620T = CCM 9252T) and S3CR25-11T (= CECT 30621T = CCM 9254T) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12T and S3CR25-11T, respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera.

Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium

Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.

Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach

An extremely halophilic archaeon, strain S1AR25-5AT, was isolated from a hypersaline soil sampled in Odiel Saltmarshes Natural Area (Huelva, Spain). The cells were Gram-stain-negative, motile, pleomorphic rods. Cell growth was observed in the presence of 15-30 % (w/v) NaCl [optimum, 25 % (w/v) NaCl], at pH 6.0-9.0 (optimum, pH 6.5-7.5) and at 25-50 °C (optimum, 37 °C). Based on the 16S rRNA and rpoB' gene sequence comparisons, strain S1AR25-5AT was affiliated to the genus Haloarcula. Taxogenomic analysis, including comparison of the genomes and the phylogenomic tree based on the core-orthologous proteins, together with the genomic indices, i.e., orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that strain S1AR25-5AT (=CCM 9249T=CECT 30619T) represents a new species of the genus Haloarcula, for which we propose the name Haloarcula terrestris sp. nov. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and an unidentified glycolipid, which correlated with the lipid profile of species of the genus Haloarcula. In addition, based on the modern approach in description of species in taxonomy of prokaryotes, the above mentioned genomic indexes indicated that the species Haloarcula tradensis should be considered as a heterotypic synonym of Haloarcula argentinensis.

Natrinema salsiterrestre sp. nov., an extremely halophilic archaeon isolated from a hypersaline soil

An extremely halophilic archaeal strain, designated S1CR25-10T, was isolated from hypersaline soil sampled in the Odiel Saltmarshes Natural Area in Southwestern Spain (Huelva) and subjected to a polyphasic taxonomic characterization. The cells were Gram-stain-negative, motile and their colonies were pink-pigmented. It was a strictly aerobic haloarchaeon that could grow at 25-55 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 12-30 % (w/v) total salts (optimum, 20-25 %, w/v). The phylogenetic analysis based on the comparison of the 16S rRNA gene sequences revealed that strain S1CR25-10T belongs to the genus Natrinema, with 98.9 % similarity to Natrinema salinisoli SLN56T. In addition, the values of orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity were below the threshold limits accepted for prokaryotic species delineation, with N. salinisoli SLN56T showing the highest relatedness values (92.6 % and 48.4 %, respectively). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content of the isolate was 63.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characterization and the whole genome results, strain S1CR25-10T represents a new species within the genus Natrinema, for which the name Natrinema salsiterrestre sp. nov., with type strain S1CR25-10T (=CECT 30623T=CCM 9251T), is proposed.

Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern

A novel extremely halophilic archaeon, strain RHB-CT, was isolated from a saturated brine pond of a solar saltern in Bolinao, Pangasinan, Philippines. Colonies were orange-red-pigmented, smooth, convex and round on a solid modified growth medium containing 25 % (w/v) of total salts. Cells of strain RHB-CT on the solid modified growth medium were ovoid-shaped (0.89–2.66 µm long), while the cells in a liquid modified growth medium were rod-shaped (1.53–5.65 µm long and 0.45–1.03 µm wide). The strain was Gram-stain-negative, motile and strictly aerobic. Strain RHB-CT grew with NaCl concentrations ranging from 10 to 30 % (w/v; optimum, 20–25 %), at pH 6.5–8.5 (optimum, pH 7.0–7.5) and at 20–55 °C (optimum, 40–45 °C). Furthermore, the strain grew even in the absence of Mg2+; however, when supplemented with Mg2+, growth was observed optimally at 0.2–0.4 M Mg2+. The 16S rRNA gene phylogeny inferred that the strain is a member of the genus Halorubrum and was related to Halorubrum xinjiangense CGMCC 1.3527T (99.0 %), Halorubrum sodomense DSM 3755T (98.8 %), Halorubrum coriense Ch2T (98.8 %), Halorubrum trapanicum NRC 34021T (98.4 %) and Halorubrum distributum JCM 9100T (98.1 %). The rpoB′ gene sequences also showed that strain RHB-CT is related to Hrr. xinjiangense JCM 12388T (97.1 %), Hrr. distributum JCM 9100T (97.1 %), Hrr. coriense JCM 9275T (96.5 %), Hrr. californiense JCM 14715T (96.5 %), Hrr. trapanicum JCM 10477T (96.3%), Hrr. sodomense JCM 8880T (96.2%) and Hrr. tebenquichense DSM 14210T (95.6 %). The DNA G+C content of strain RHB-CT was 68.7 mol% (genome). Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RHB-CT and the closely related species of Halorubrum were below 40 and 90 %, respectively, which are far below the thresholds to delineate a new species. The polar lipids of strain RHB-CT were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and sulfated mannosyl glycosyl diether. Based on dDDH and ANI values, and the significant morphological and physiological differences from known taxa, it is hereby suggested that strain RHB-CT represents a novel species of the genus Halorubrum , for which the name Halorubrum salinarum sp. nov. is proposed. The type strain is RHB-CT (=KCTC 4274T=CMS 2103T).

Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea

Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24A^T, F28, F27^T, and F13^T, phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537^T, Halomicroarcula salina JCM 18369^T and Halomicroarcula limicola JCM 18640^T, that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24A^T and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13^T), Halomicroarcula nitratireducens sp. nov. (type strain F27^T) and Halomicroarcula salinisoli sp. nov. (type strain F24A^T). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.

Beyond Archaea: The Table Salt Bacteriome

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon

Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.

Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis

The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

A halophilic archaeon, strain F20-122^T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w/v) total salts (optimum 25% salts). The phylogenetic analyses based on the 16S rRNA and rpoB’ genes showed its affiliation with the genus Natronomonas and suggested its placement as a new species within this genus. The in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) analyses of this strain against closely related species supported its placement in a new taxon. The DNA G + C content of this isolate was 63.0 mol%. The polar lipids of strain F20-122^T were phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol (PG), and phosphatidylglycerol sulfate (PGS). Traces of biphosphatidylglycerol (BPG) and other minor phospholipids and unidentified glycolipids were also present. Based on the phylogenetic, genomic, phenotypic, and chemotaxonomic characterization, we propose strain F20-122^T (= CCM 8891^T = CECT 9564^T = JCM 33320^T) as the type strain of a new species within the genus Natronomonas, with the name Natronomonas salsuginis sp. nov. Rhodopsin-like sequence analysis of strain F20-122^T revealed the presence of haloarchaeal proton pumps, suggesting a light-mediated ATP synthesis for this strain and a maximum wavelength absorption in the green spectrum.

Haloglomus irregulare gen. nov., sp. nov., a New Halophilic Archaeon Isolated from a Marine Saltern

A halophilic archaeal strain, designated F16-60^T, was isolated from Isla Cristina marine saltern in Huelva, Spain. Cells were pleomorphic, irregular, non-motile, and Gram-stain-negative. It produced red-pigmented colonies on agar plates. Strain F16-60^T was extremely halophilic (optimum at 30% (w/v) NaCl) and neutrophilic (optimum pH 7.5). Phylogenetic tree reconstructions based on 16S rRNA and rpoB´ gene sequences revealed that strain F16-60^T was distinct from species of the related genera Natronomonas, Halomarina, and Halomicrobium, of the order Halobacteriales. The polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and one glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). The DNA G+C content is 68.0 mol%. The taxonomic study, based on a combination of phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, suggest that strain F16-60^T (= CECT 9635^T = JCM 33318^T), represents a novel species of a new genus within the family Haloarculaceae and the order Halobacteriales, for which the name Haloglomus irregulare gen. nov., sp. nov. is proposed. Metagenomic fragment recruitment analysis revealed the worldwide distribution of members of this genus and suggested the existence of other closely related species to be isolated.

Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern

An extremely halophilic archaeon, strain F13-25^T, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. The novel strain had pink-pigmented, non-motile, coccoid cells. Optimal growth was achieved at 25 % (w/v) NaCl, pH 7.5 and 37 °C. Strain F13-25^T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) most closely related to Halorientalis persicus D108^T (97.6-99.2 % sequence similarity) and Halorientalis regularis TNN28^T (95.9-98.8 %). On the basis of the results of rpoB' gene sequence analysis, strain F13-25^T was also closely related to Halorientalis persicus IBRC-M 10043^T (89.9 %) and Halorientalis regularis TNN28^T (92.3 %). Relatedness values, computed using the Genome-to-Genome Distance Calculator, between strain F13-25^T and Halorientalis persicus IBRC-M 10043^T and Halorientalis regularis IBRC-M 10760^T were 34.6 and 36.2 %, respectively. Average nucleotide identity values based on orthoANI, ANIb and ANIm of strain F13-25^T and Halorientalis persicus IBRC-M 10043^T and Halorientalisregularis IBRC-M 10760^T were 88.0 and 88.8, 87.1 and 87.6 %, and 89.2 and 89.6 %, respectively. All values were far below the threshold accepted for prokaryotic species delineation. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and one glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content was 65.7 mol% (genome). The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain F13-25^T represents a novel species of the genus Halorientalis, for which the name Halorientalis pallida sp. nov., with type strain F13-25^T (=CECT 9384^T=IBRC-M 11176^T), is proposed.

New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea

Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15B^T and F9-27^T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525^T, Halonotius aquaticus F13-13^T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15B^T = CECT 9688^T = CCM 8954^T) and Halonotius roseus sp. nov. (type strain F9-27^T = CECT 9745^T = CCM 8956^T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B₁₂) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B₁₂) to the halophilic microbial communities at large.

Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine

A pleomorphic and non-motile halophilic archaeon forming light-red pigmented colonies, strain ZC67^T, was isolated from the Yuanyongjing Salt Mine, Yunnan, China. Based on similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain ZC67^T belongs to the genus Halorubrum and is closely related to the species of Halorubrum (Hrr.) saccharovorum JCM 8865^T, Hrr. persicum C49^T, Hrr. halophilum B8^T, Hrr. lipolyticum 9-3^T, Hrr. salsamenti Y69^T and Hrr. depositum Y78^T with 16S rRNA gene sequence similarities of 99.0%, 98.7%, 98.5%, 98.4%, 98.1% and 97.7%, respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain ZC67^T and its close relatives were less than 90.5% and 89.3%, respectively. In silico DNA-DNA hybridization (DDH) analysis showed that DNA-DNA relatedness between strain ZC67^T and its relatives is less than 45%. Values of ANI, AAI and in silico DDH were clearly below the thresholds used for the delineation of a new species. The major polar lipids of strain ZC67^T were similar to other neutrophilic members in the genus Halorubrum containing phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl-glucosyl-glycerol diether-1. The DNA G+C content was determined to be 66.3 mol% (based on the draft genome). Combined with other diagnostic characteristics, e.g. phenotypic and chemotaxonomic differences, strain ZC67^T is concluded to represent a novel species in the genus Halorubrum, for which the name Halorubrum amylolyticum sp. nov. is proposed. The type strain is ZC67^T (=CGMCC 1.15718^T = JCM 31850^T).

The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

Restriction⁻modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.

The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers

Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis.

Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006

A polyphasic comparative taxonomic study of Halorubrum ezzemoulense Kharroub et al. 2006, Halorubrum chaoviator Mancinelli et al. 2009 and eight new Halorubrum strains related to these haloarchaeal species was carried out. Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr. ezzemoulense DSM 17463^T, Hrr. chaoviator Halo-G*^T (=DSM 19316^T) and the eight Halorubrum strains formed a robust cluster, clearly separated from the remaining species of the genus Halorubrum. The orthoANI value and digital DNA-DNA hybridization value, calculated by the Genome-to-Genome Distance Calculator (GGDC), showed percentages among Hrr. ezzemoulense DSM 17463^T, Hrr. chaoviator DSM 19316^T and the eight Halorubrum strains ranging from 99.4 to 97.9 %, and from 95.0 to 74.2 %, respectively, while these values for those strains and the type strains of the most closely related species of Halorubrum were 88.7-77.4 % and 36.1-22.3 %, respectively. Although some differences were observed, the phenotypic and polar lipid profiles were quite similar for all the strains studied. Overall, these data show that Hrr. ezzemoulense, Hrr. chaoviator and the eight new Halorubrum isolates constitute a single species. Thus, Hrr. chaoviator should be considered as a later, heterotypic synonym of Hrr. ezzemoulense. We propose an emended description of Hrr. ezzemoulense, including the features of Hrr. chaoviator and those of the eight new isolates.

Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure

To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.

Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains

Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato. We also collected a total of 31 cold-adapted Arthrobacter sensu lato strains from two cold glaciers located in northwest China and two temperate glaciers in southwest China, and evaluated their diversity and population structure by MLSA. The glacier strains displayed high diversity, but rates of recombination among the four glacier groups were quite low, indicating that barriers to homologous recombination formed in the past among the populations on different glaciers. Our findings indicate that historical glaciation events shaped the contemporary distributions, taxonomic relationships, and phylogeographic patterns of Arthrobacter sensu lato species on glaciers.

Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia

The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The genome comprised 3,325,770 bp, with the G + C content of 68.0%. The strain has many genes which are responsible for secondary metabolites biosynthesis, transport and catabolism as compared to other Halorubrum archaea members. Abundant genes responsible for numerous transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The first genomic analysis encourages further research on comparative genomics, and biotechnological applications. The NCBI accession number for this genome is SAMN04278861 and ID: 4278861 and strain deposited with accession number KCTC 43215.

Impact of a homing intein on recombination frequency and organismal fitness

Inteins are parasitic genetic elements that excise themselves at the protein level by self-splicing, allowing the formation of functional, nondisrupted proteins. Many inteins contain a homing endonuclease (HEN) domain and rely on its activity for horizontal propagation. However, successful invasion of an entire population will make this activity redundant, and the HEN domain is expected to degenerate quickly under these conditions. Several theories have been proposed for the continued existence of the both active HEN and noninvaded alleles within a population. However, to date, these models were not directly tested experimentally. Using the natural cell fusion ability of the halophilic archaeon Haloferax volcanii we were able to examine this question in vivo, by mating polB intein-positive [insertion site c in the gene encoding DNA polymerase B (polB-c)] and intein-negative cells and examining the dispersal efficiency of this intein in a natural, polyploid population. Through competition between otherwise isogenic intein-positive and intein-negative strains we determined a surprisingly high fitness cost of over 7% for the polB-c intein. Our laboratory culture experiments and samples taken from Israel's Mediterranean coastline show that the polB-c inteins do not efficiently take over an inteinless population through mating, even under ideal conditions. The presence of the HEN/intein promoted recombination when intein-positive and intein-negative cells were mated. Increased recombination due to HEN activity contributes not only to intein dissemination but also to variation at the population level because recombination tracts during repair extend substantially from the homing site.

Intein Clustering Suggests Functional Importance in Different Domains of Life

Inteins, also called protein introns, are self-splicing mobile elements found in all domains of life. A bioinformatic survey of genomic data highlights a biased distribution of inteins among functional categories of proteins in both bacteria and archaea, with a strong preference for a single network of functions containing replisome proteins. Many nonorthologous, functionally equivalent replicative proteins in bacteria and archaea carry inteins, suggesting a selective retention of inteins in proteins of particular functions across domains of life. Inteins cluster not only in proteins with related roles but also in specific functional units of those proteins, like ATPase domains. This peculiar bias does not fully fit the models describing inteins exclusively as parasitic elements. In such models, evolutionary dynamics of inteins is viewed primarily through their mobility with the intein homing endonuclease (HEN) as the major factor of intein acquisition and loss. Although the HEN is essential for intein invasion and spread in populations, HEN dynamics does not explain the observed biased distribution of inteins among proteins in specific functional categories. We propose that the protein splicing domain of the intein can act as an environmental sensor that adapts to a particular niche and could increase the chance of the intein becoming fixed in a population. We argue that selective retention of some inteins might be beneficial under certain environmental stresses, to act as panic buttons that reversibly inhibit specific networks, consistent with the observed intein distribution.

Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake

Two extremely halophilic archaea, strains Cb34T and C170, belonging to the genus Halorubrum, were isolated from the brine of the hypersaline lake Aran-Bidgol in Iran. Cells of the two strains were motile, pleomorphic rods, stained Gram-variable and produced red-pigmented colonies. Strains Cb34T and C170 required 25 % (w/v) salts, pH 7.0 and 37 °C for optimal growth under aerobic conditions; 0.3 M Mg2+ was required. Cells of both isolates were lysed in distilled water and hypotonic treatment with < 10 % NaCl provoked cell lysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that these two strains were closely related to Halorubrum cibi B31T (98.8 %) and other members of the genus Halorubrum. In addition, studies based on the rpoB' gene revealed that strains Cb34T and C170 are placed among the species of Halorubrum and are closely related to Halorubrum cibi B31T, with rpoB' gene sequence similarity less than or equal to 95.7 %. The polar lipid patterns of both strains consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 62.1-62.4 mol%. DNA-DNA hybridization studies confirmed that strains Cb34T and C170 constitute a distinct species. Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp. nov. is proposed. The type strain is Cb34T ( = CECT 8745T = IBRC-M 10233T).

Microbial diversity of hypersaline environments: a metagenomic approach

Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadratum waslbyi, the bacteroidete Salinibacter ruber and nanohaloarchaea are predominant members at higher salt concentrations, while more diverse archaeal and bacterial taxa are observed in habitats with intermediate salinities. Additionally, metagenomic studies may provide insight into the isolation and characterization of the principal microbes in these habitats, such as the recently described gammaproteobacterium Spiribacter salinus.

Halovenus salina sp. nov., an extremely halophilic archaeon isolated from a saltern

An extremely halophilic archaeon was isolated from a water sample of Isla Bacuta saltern in Huelva, Spain. Strain ASP54(T) is a novel red-pigmented, motile, rod-shaped, Gram-stain-negative and strictly aerobic haloarchaeon. Strain ASP54(T) grew in media containing 15-30% (w/v) salts and optimally with 25% (w/v) salts. It grew between pH 5.0 and 9.0 (optimally at pH 7.5) and at 20-40 °C (optimally at 37 °C). Phylogenetic analysis based on multi-locus sequence analysis (MLSA) and the comparison of 16S rRNA gene sequences revealed that strain ASP54(T) is most closely related to the genus Halovenus. The closest relatives were Halovenus aranensis EB27(T) (92.1% 16S rRNA gene sequence similarity), Halorientalis regularis TNN28(T) (92.1%), and Halorientalis persicus D108(T) (92.0%). The polar lipid pattern of strain ASP54(T) consisted of biphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and a minor-phospholipid. The predominant respiratory quinone was menaquinone-8 (MK-8) (83%), and a minor amount of MK-8(VIII-H2) (17%) was also detected. The G+C content of the genomic DNA of this strain was 63.1 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain ASP54(T) represents a novel species of the genus Halovenus, for which the name Halovenus salina sp. nov. is proposed. The type strain is ASP54(T) ( = CEC(T) 8749(T) = IBRC-M 10946(T) = JCM 30072(T)).

Horizontal gene transfer, dispersal and haloarchaeal speciation

The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.

Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake

An extremely halophilic archaeon belonging to the genus Halorubrum, strain C49T, was isolated from sediment of the hypersaline lake Aran-Bidgol in Iran. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain C49T was closely related to Halorubrum saccharovorum JCM 8865T (99.5 %) and other species of the genus Halorubrum. Studies based on multilocus sequence analysis revealed that strain C49T is placed among the species of Halorubrum; the strain constituted a defined branch in comparison with the type strains of species of Halorubrum, while the 16S rRNA gene sequence divergence could not define the status of the newly isolated strain. For optimum growth, strain C49T required 20 % (w/v) salts at pH 7.0 and 37 °C under aerobic conditions. Mg2+ was not required. The cells were pleomorphic rods, motile and stained Gram-variable. Colonies of the strain were pink. Hypotonic treatment with <12 % NaCl provoked cell lysis. The polar lipid pattern of strain C49T consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester derived from both C20C20 and C20C25 archaeol, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 64.2 mol%. DNA-DNA hybridization studies and average nucleotide identity confirmed that strain C49T constitutes a distinct genospecies. Data obtained in this study show that strain C49T represents a novel species, for which the name Halorubrum persicum sp. nov. is proposed. The type strain is C49T ( = IBRC-M 10232T = JCM 30541T).

Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes

The accessory nidamental gland (ANG) of the female Hawaiian bobtail squid, Euprymna scolopes, houses a consortium of bacteria including members of the Flavobacteriales, Rhizobiales, and Verrucomicrobia but is dominated by members of the Roseobacter clade (Rhodobacterales) within the Alphaproteobacteria. These bacteria are deposited into the jelly coat of the squid’s eggs, however, the function of the ANG and its bacterial symbionts has yet to be elucidated. In order to gain insight into this consortium and its potential role in host reproduction, we cultured 12 Rhodobacterales isolates from ANGs of sexually mature female squid and sequenced their genomes with Illumina sequencing technology. For taxonomic analyses, the ribosomal proteins of 79 genomes representing both roseobacters and non-roseobacters along with a separate MLSA analysis of 33 housekeeping genes from Roseobacter organisms placed all 12 isolates from the ANG within two groups of a single Roseobacter clade. Average nucelotide identity analysis suggests the ANG isolates represent three genera (Leisingera, Ruegeria, and Tateyamaria) comprised of seven putative species groups. All but one of the isolates contains a predicted Type VI secretion system, which has been shown to be important in secreting signaling and/or effector molecules in host–microbe associations and in bacteria–bacteria interactions. All sequenced genomes also show potential for secondary metabolite production, and are predicted to be involved with the production of acyl homoserine lactones (AHLs) and/or siderophores. An AHL bioassay confirmed AHL production in three tested isolates and from whole ANG homogenates. The dominant symbiont, Leisingera sp. ANG1, showed greater viability in iron-limiting conditions compared to other roseobacters, possibly due to higher levels of siderophore production. Future comparisons will try to elucidate novel metabolic pathways of the ANG symbionts to understand their putative role in host development.

Viruses of haloarchaea

In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing Myoviridae, Siphoviridae, Podoviridae, Pleolipoviridae, Sphaerolipoviridae and Fuselloviridae families. This review overviews current knowledge of haloarchaeoviruses, providing information about classification, morphotypes, macromolecules, life cycles, genetic manipulation and gene regulation, and host-virus responses. In so doing, the review incorporates knowledge from laboratory studies of isolated viruses, field-based studies of environmental samples, and both genomic and metagenomic analyses of haloarchaeoviruses. What emerges is that some haloarchaeoviruses possess unique morphological and life cycle properties, while others share features with other viruses (e.g., bacteriophages). Their interactions with hosts influence community structure and evolution of populations that exist in hypersaline environments as diverse as seawater evaporation ponds, to hot desert or Antarctic lakes. The discoveries of their wide-ranging and important roles in the ecology and evolution of hypersaline communities serves as a strong motivator for future investigations of both laboratory-model and environmental systems.

Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer

BACKGROUND

Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2.

RESULTS

Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method.

CONCLUSIONS

The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.

Inteins as indicators of gene flow in the halobacteria

This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein's life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group.

Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations

Halobacteria require high NaCl concentrations for growth and are the dominant inhabitants of hypersaline environments above 15% NaCl. They are well-documented to be highly recombinogenic, both in frequency and in the range of exchange partners. In this study, we examine the genetic and genomic variation of cultured, naturally co-occurring environmental populations of Halobacteria. Sequence data from multiple loci (~2500 bp) identified many closely and more distantly related strains belonging to the genera Halorubrum and Haloarcula. Genome fingerprinting using a random priming PCR amplification method to analyze these isolates revealed diverse banding patterns across each of the genera and surprisingly even for isolates that are identical at the nucleotide level for five protein coding sequenced loci. This variance in genome structure even between identical multilocus sequence analysis (MLSA) haplotypes indicates that accumulation of genomic variation is rapid: faster than the rate of third codon substitutions.