Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments

A hyperstable, low-salt adapted protease from halophilic archaeon with potential applications in salt-fermented foods

Salt-tolerant proteases with remarkable stability are highly desirable biocatalysts in the salt-fermented food industry. In this study, the undigested autocleavage product of HlyA (halolysin A), a low-salt adapted halolysin from halophilic archaeon Halococcus salifodinae, was investigated. HlyA underwent autocleavage of its C-terminal extension (CTE) at temperatures over 40 °C or NaCl concentrations below 2 M to yield HlyAΔCTE. HlyAΔCTE demonstrated robust stability over a wide range of -20-60 °C, 0.5-4 M NaCl, and pH 6.0-10.0 for at least 72 h. Notably, HlyAΔCTE is the first reported halolysin with such exceptional stability. Compared with HlyA, HlyAΔCTE preferred high temperatures (50-75 °C), low salinities (0.5-2.5 M NaCl), and near-neutral (pH 6.5-8.0) conditions to achieve high activity, consistently with its production conditions. HlyAΔCTE displayed a higher Vmax value against azocasein than HlyA. During fish sauce fermentation, HlyAΔCTE significantly enhanced fish protein hydrolysis, indicating its potential as a robust biocatalyst in the salt-fermented food industry.

Microbial communities in the Dead Sea and their potential biotechnological applications

The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.

Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil

Four halophilic archaeal strains YCN1T, YCN58T, LT38T, and LT62T were isolated from Yuncheng Salt Lake (Shanxi, China) and Tarim Basin (Xinjiang, China), respectively. Phylogenetic and phylogenomic analyses showed that these four strains tightly cluster with related species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The AAI, ANI, and dDDH values between these four strains and their related species of respective genera were lower than the proposed threshold values for species delineation. Strains YCN1T, YCN58T, LT38T, and LT62T could be differentiated from the current species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively, based on the comparison of diverse phenotypic characteristics. The polar lipid profiles of these four strains were closely similar to those of respective relatives within the genera Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The phenotypic, phylogenetic, and genome-based analyses indicated that strains YCN1T, YCN58T, LT38T, and LT62T represent respective novel species within the genera Halobacterium, Natronomonas, Halorentalis, and Halobellus, for which the names Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., and Halobellus salinisoli sp. nov. are proposed, respectively.

Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil

Four halophilic archaeal strains, BCD28T, BND7T, PSR21T, and PSRA2T, were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28T, BND7T, PSR21T, and PSRA2T could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7T. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28T (= CGMCC 1.18776T = JCM 34908T), BND7T (= CGMCC 1.18778T = JCM 34910T), PSR21T (= CGMCC 1.17027T = JCM 34147T), and PSRA2T (= CGMCC 1.17214T = JCM 34148T) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.

Halocin H4 is activated through cleavage by halolysin HlyR4

Halocins are antimicrobial peptides secreted by haloarchaea capable of inhibiting the growth of other haloarchaea or bacteria. Halocin H4 (HalH4) is secreted by the model halophilic archaeon Haloferax mediterranei ATCC 33500. Despite attempts to express halH4 heterologously in Escherichia coli and subsequent careful renaturation procedures commonly employed for haloarchaeal proteins, no active halocin was obtained. However, it was discovered that the antihaloarchaeal activity of this halocin could be activated through cleavage by halolysin R4 (HlyR4), a serine protease also secreted by Hfx. mediterranei ATCC 33500. Replacement of the cysteine at the number 115 amino acid with glycine and deletion of the internal trans-membrane region (15 aa) markedly abolished HalH4's antihaloarchaeal activity. Compared to the N-terminus, the C-terminal amino acid sequence was found to be more crucial for HalH4 to exert its antihaloarchaeal activity. Mass spectrometry analysis revealed that the biologically active antihaloarchaeal peptide produced after hydrolytic cleavage by HlyR4 was the C-terminus of HalH4, suggesting a potential mechanism of action involving pore formation within competitor species' cell membranes. Taken together, this study offers novel insights into the interplay between halocins and secreted proteases, as well as their contribution to antagonistic interaction within haloarchaea.

IMPORTANCE

The antihaloarchaeal function of halocin H4 (HalH4) can be activated by extracellular proteases from haloarchaea, as demonstrated in this study. Notably, we report the first instance of halocin activation through proteolytic cleavage, highlighting its significance in the field. The C-terminus of HalH4 (CTH4) has been identified as the antihaloarchaeal peptide present in hydrolysates generated by HlyR4. The CTH4 exhibited inhibitory activity against a range of haloarchaeal species (Haloarchaeobius spp., Haloarcula spp., Haloferax spp., Halorubellus spp., and Halorubrum spp.), as well as selected bacterial species (Aliifodinibius spp. and Salicola spp.), indicating its broad-spectrum inhibitory potential across domains. The encoding gene of halocin HalH4, halH4, from the model halophilic archaeon Haloferax mediterranei ATCC 33500 can be expressed in Escherichia coli without codon optimization.

Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat

The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133T, the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1T, then with Halosegnis rubeus F17-44T. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133T and Halosegnis longus F12-1T were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72T, DT80T, DT85T, and DT116T, isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72T (= CGMCC 1.18925T = JCM 35418T), DT80T (= CGMCC 1.18926T = JCM 35419T), DT85T (= CGMCC 1.19049T = JCM 35605T), and DT116T (= CGMCC 1.19045T = JCM 35606T) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.

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.

Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient

Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.

Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil

Two halophilic archaeal strains, ZS-10T and GSL13T, were isolated from the Zhoushan marine saltern in Zhejiang, and an inland saline soil from the Tarim Basin, Xinjiang, PR China, respectively. The cells of strain ZS-10T were pleomorphic while those of strain GSL13T were rod-shaped. Both of them stained Gram-negative and formed red-pigmented colonies on agar plates and their cells lysed in distilled water. The optimum growth of strain ZS-10T was observed at 40 °C, 3.4 M NaCl, 0.03 M MgCl2 and pH 7.5, while that of strain GSL13T was at 37 °C, 3.1 M NaCl, 0.5 M MgCl2 and pH 7.5. Phylogenetic and phylogenomic analyses indicated that these two strains were related to Salinigranum and Halohasta, respectively. Strains ZS-10T and GSL13T could be differentiated from the current members of Salinigranum and Halohasta based on the comparison of diverse phenotypic characteristics. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values among strain ZS-10T and current species of Salinigranum were 75.8-78.6 %, 80.6-81.9 % and 24.3-26.1 %, respectively. These values between strain GSL13T and current species of Halohasta were 78.4-80.8 %, 79.8-82.8% and 22.7-25.7 %, respectively, clearly below the threshold values for species demarcation. The polar lipids of strain ZS-10T were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulphated mannosyl glucosyl diether (S-DGD-1), while those of strain GSL13T were phosphatidic acid, PG, PGP-Me, phosphatidylglycerol sulphate and S-DGD-1. The polar lipid profile of strain GSL13T was identical to those of Halohasta, whereas strain ZS-10T did not contain the minor glycolipids detected in the current Salinigranum species. The phenotypic, phylogenetic and genome-based results suggested that strains ZS-10T (=CGMCC 1.12868T=JCM 30241T) and GSL13T (=CGMCC 1.15214T=JCM 30841T) represent two novel species, for which the names Salinigranum marinum sp. nov. and Halohasta salina sp. nov. are proposed.

Recent advances in the production, properties and applications of haloextremozymes protease and lipase from haloarchaea

Proteases and lipases are significant groups of enzymes for commercialization at the global level. Earlier, the industries depended on mesophilic proteases and lipases, which remain nonfunctional under extreme conditions. The discovery of extremophilic microorganisms, especially those belonging to haloarchaea, paved a new reserve of industrially competent extremozymes. Haloarchaea or halophilic archaea are polyextremophiles of domain Archaea that grow at high salinity, elevated temperature, pH range (pH 6-12), and low aw. Interestingly, haloarchaeal proteolytic and lipolytic enzymes also perform their catalytic function in the presence of 4-5 M NaCl in vivo and in vitro. Also, they are of great interest to study due to their capacity to function and are active at elevated temperatures, tolerance to pH extremes, and in non-aqueous media. In recent years, advances have been achieved in various aspects of genomic/molecular expression methods involving homologous and heterologous processes for the overproduction of these extremozymes and their characterization from haloarchaea. A few protease and lipase extremozymes have been successfully expressed in prokaryotic systems, especially E.coli, and enzyme modification techniques have improved the catalytic properties of the recombinant enzymes. Further, in-silico methods are currently applied to elucidate the structural and functional features of salt-stable protease and lipase in haloarchaea. In this review, the production and purification methods, catalytic and biochemical properties and biotechnological applications of haloextremozymes proteases and lipases are summarized along with recent advancements in overproduction and characterization of these enzymes, concluding with the directions for further in-depth research on proteases and lipases from haloarchaea.

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

Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.

Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands

Four extremely halophilic archaeal strains, LYG-108T, LYG-24, DT1T and YSSS71, were isolated from salted Laminaria produced in Lianyungang and saline soil from the coastal beach at Jiangsu, PR China. The four strains were found to be related to the current species of Halomicroarcula (showing 88.1-98.5% and 89.3-93.6% similarities, respectively) as revealed by phylogenetic analysis based on 16S rRNA and rpoB' genes. These phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes (average nucleotide identity, DNA-DNA hybridization and average amino acid identity) among these four strains and the Halomicroarcula species were 77-84 %, 23-30 % and 71-83 %, respectively, clearly below the threshold values for species demarcation. Additionally, the phylogenomic and comparative genomic analyses revealed that Halomicroarcula salina YGH18T is related to the current species of Haloarcula rather than those of Halomicroarcula, Haloarcula salaria Namwong et al. 2011 is a later heterotypic synonym of Haloarcula argentinensis Ihara et al. 1997, and Haloarcula quadrata Oren et al. 1999 is a later heterotypic synonym of Haloarcula marismortui Oren et al. 1990. The major polar lipids of strains LYG-108T, LYG-24, DT1T and YSSS71 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate, sulphated mannosyl glucosyl diether and additional glycosyl-cardiolipins. All these results showed that strains LYG-108T (=CGMCC 1.13607T=JCM 32950T) and LYG-24 (=CGMCC 1.13605=JCM 32949) represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula laminariae sp. nov. is proposed; strains DT1T (=CGMCC 1.18928T=JCM 35414T) and YSSS71 (=CGMCC 1.18783=JCM 34915) also represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula marina sp. nov. is proposed.

Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea

BACKGROUND

Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya.

RESULTS

Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan α exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan α represents the first lantibiotic and the first anti-archaeal SM from the archaea domain.

CONCLUSIONS

Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.

Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine

Four extremely halophilic archaeal strains (ZJ2^T, BND6^T, DT87^T, and YPL30^T) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2^T, BND6^T, DT87^T, YPL30^T and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2^T, BND6^T, DT87^T, and YPL30^T cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2^T, BND6^T, DT87^T, and YPL30^T could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S₂-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2^T (= CGMCC 1.18786 ^T = JCM 34918 ^T), BND6^T (= CGMCC 1.18777 ^T = JCM 34909 ^T), DT87^T (= CGMCC 1.18921 ^T = JCM 35420 ^T), and YPL30^T (= CGMCC 1.15337 ^T = JCM 31113 ^T) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.

Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications

Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.

Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena

Three novel filamentous halophilic archaea, strains DFN5^T, RDMS1, and QDMS1, were isolated from the coastal saline soil samples of the intertidal zones located in different regions of Jiangsu Province, China. The colonies of these strains were pinkish-white due to the presence of white spores. These three strains are extremely halophilic and grew optimally at 35-37 °C and pH 7.0-7.5. Based on 16S rRNA and rpoB' gene analysis, strains DFN5^T, RDMS1, and QDMS1 gathered together in phylogenetic trees and then clustered with the current species of the genus Halocatena showing 96.9-97.4% and 82.2-82.5% similarities, respectively. Both the 16S rRNA gene-based and rpoB' gene-based phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes indicated that strains DFN5^T, RDMS1, and QDMS1 should be a novel species of the genus Halocatena. Genome mining revealed that there are considerable differences in the genes related to β-carotene synthesis among these three strains and the current species of Halocatena. The major polar lipids of strains DFN5^T, RDMS1, and QDMS1 are PA, PG, PGP-Me, S-TGD-1, TGD-1, and TGD-2. The minor polar lipids, S-DGD-1, DGD-1, S₂-DGD, and S-TeGD may be detected. According to the phenotypic characteristics, phylogenetic analysis, genomic and chemotaxonomic features, strains DFN5^T (= CGMCC 1.19401 ^T = JCM 35422 ^T), RDMS1 (= CGMCC 1.19411) and QDMS1 (= CGMCC 1.19410) were classified as a novel species of the genus Halocatena with the proposed name, Halocatena marina sp. nov. This is the first report of the description of a novel filamentous haloarchaeon isolated from marine intertidal zones.

Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake

A filamentous cell-shaped halophilic archaeon (strain AD-1^T) was isolated from Aiding Salt Lake, PR China. Its colonies on HCM7 agar plates were pinkish white, 1-4 mm (diameter), elevated and round. The optimum conditions for growth were observed at 42 °C, 4.3 M NaCl, 0.01 M MgCl₂ and pH 7. Strain AD-1^T could hydrolyse Tween 60, Tween 80, starch and gelatin. Phylogenetic analysis based on 16S rRNA gene, rpoB' and the concatenated 484 single-copy orthologous proteins revealed that strain AD-1^T formed a clade with Halocatena pleomorpha SPP-AMP-1^T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AD-1^T and Halocatena pleomorpha SPP-AMP-1^T were both below the species delineation thresholds (95~96 and 70 %, respectively). The major phospholipids of strain AD-1^T were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, while the major glycolipids were sulphated galactosyl mannosyl glucosyl diether, galactosyl mannosyl glucosyl diether and glucosyl mannosyl glucosyl diether. The phenotypic, phylogenetic and genome-based analyses suggested that strain AD-1^T (=CGMCC 1.13724^T=JCM 32960^T) represents a novel species, for which the name Halocatena salina sp. nov. is proposed.

Selective enrichment on a wide polysaccharide spectrum allowed isolation of novel metabolic and taxonomic groups of haloarchaea from hypersaline lakes

Extremely halophilic archaea (haloarchaea) of the class Halobacteria is a dominant group of aerobic heterotrophic prokaryotic communities in salt-saturated habitats, such as salt lakes and solar salterns. Most of the pure cultures of haloarchaea were enriched, isolated, and cultivated on rich soluble substrates such as amino acids, peptides or simple sugars. So far, the evidences on the capability of haloarchaea to use different polysaccharides as growth substrates remained scarce. However, it is becoming increasingly obvious that these archaea can also actively participate in mineralization of complex biopolymers, in particular cellulose and chitin-two dominant biomass polysaccharides on the planet. Here we used an array of commercially available homo- and heteropolysaccharides to enrich hydrolytic haloarchaea from hypersaline salt lakes with neutral pH and from alkaline soda lakes. This resulted in isolation of a range of halo- and natrono-archaea, respectively, belonging to already described taxa as well as several new genus-level lineages. In some cases, the isolates enriched with different polysaccharides happened to be closely related, thus representing generalistic ecotype, while the others were narrow specialists. In general, soda lakes yielded a broader range of polysaccharide-utilizing specialists in comparison to neutral salt lakes. The results demonstrated a significant diversity of halo(natrono)archaea with a previously unrecognized potential for utilization of a broad range of natural polysaccharides in hypersaline habitats.

The cell biology of archaea

The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.

Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius

Three extremely halophilic archaeal strains (LT55T, SQT-29-1T and WLHS5T) were isolated from Gobi saline soil and a salt lake, China. These strains were most related to the genera Natribaculum and Halovarius (92.6–95.1 % similarities), and showed low similarities with other genera within the family Natrialbaceae based on 16S rRNA genes. Phylogenomic analysis confirmed that the three strains formed a distinct clade separated from the related genera Halostagnicola and Natronococcus , which indicated that they may represent a novel genus of the family Natrialbaceae . The average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and average amino acid identity (AAI) values among the three strains were no more than 87, 34 and 85 %, respectively, much lower than the threshold values for species demarcation. The major phospholipids of the three strains were phosphatidic acid (PA), phosphatidylglycerol (PG) and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid profiles of the three strains were diverse; sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD) were found in strains LT55T and WLHS5T, while mannosyl glucosyl diether (DGD-1) and S-DGD-1 in strain SQT-29-1T. The combination of phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strains WLHS5T (=CGMCC 1.13781T = JCM 33558T), SQT-29-1T (=CGMCC 1.16065T = JCM 33554T) and LT55T (=CGMCC 1.15188T = JCM 30838T) represent three novel species of a new genus within the family Natrialbaceae , for which the names, Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus gelatinilyticus sp. nov. and Halosolutus halophilus sp. nov., are proposed. Genome-based classification of genera Natribaculum and Halovarius revealed that Halovarius luteus should be transferred to the genus Natribaculum as Natribaculum luteum comb. nov. and Natribaculum longum as a heterotypic synonym of Natribaculum breve Liu et al. 2015.

The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities

Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.

Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil

Two extremely halophilic archaeal strains, PSR5^T and PSR8^T, were isolated from a saline soil sample collected from the Tarim Basin, Xinjiang, PR China. Both strains had two copies of the 16S rRNA genes rrn1 and rrn2, showing 2.6 and 3.9% divergence, respectively. The rrn1 gene of PSR5^T showed 98.4 and 95.3% similarity to the rrn1 and rrn2 genes of strain PSR8^T; the rrn2 gene of PSR5^T displayed 97.4 and 96.7% similarity to those of strain PSR8^T, respectively. Phylogenetic analyses based on the 16S rRNA and rpoB' genes revealed that strains PSR5^T and PSR8^T formed a single cluster, and then tightly clustered with the current four Haladaptatus species (93.5-97.1% similarities for the 16S rRNA gene and 89.3-90.9% similarities for the rpoB' gene, respectively). Several phenotypic characteristics differentiate strains PSR5^T and PSR8^T from current Haladaptatus members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester phosphatidylglycerol sulphate and three glycolipids. One of the glycolipids is sulphated mannosyl glucosyl diether, and the remaining two glycolipids are unidentified. The average nucleotide identity, in silico DNA-DNA hybridization, amino acid identity and percentage of conserved proteins values between the two strains were 88.5, 39.1, 89.3 and 72.8 %, respectively, much lower than the threshold values proposed as a species boundary. These values among the two strains and Haladaptatus members were 77.9-79.2, 22.0-23.5, 75.1-78.2 and 56.8-69.9 %, respectively, much lower than the recommended threshold values for species delimitation. These results suggested that strains PSR5^T and PSR8^T represent two novel species of Haladaptatus. Based on phenotypic, chemotaxonomic, genomic and phylogenetic properties, strains PSR5^T (=CGMCC 1.16851^T=JCM 34141^T) and PSR8^T (=CGMCC 1.17025^T=JCM 34142^T) represent two novel species of the genus Haladaptatus, for which the names Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov. are proposed.

Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt

Three halophilic archaeal strains, NEN8^T, GDY88^T and ZY14^T, were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8^T, GDY88^T and ZY14^T could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S₂-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8^T and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14^T. These results revealed that strains NEN8^T (= CGMCC 1.17213^T = JCM 34155^T), GDY88^T (= CGMCC 1.18548^T = JCM 34481^T) and ZY14^T (= CGMCC 1.17178^T = JCM 34154^T) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.

Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting

Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.

Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake

Four halophilic archaeal strains, YPL8T, SLN56T, LT61T and KZCA68T, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB′ genes among strains YPL8T, SLN56T, LT61T and the current members of Natrinema were 94.1–98.2 % and 89.3–95.1 %, respectively, while these values among strain KZCA68T and the current members of Haloterrigena were 97.2–97.4 % and 91.7–91.9 %, respectively. The average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8T contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56T contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61T contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68T were PA, PG and PGP-Me. These results showed that strains YPL8T (=CGMCC 1.13883T=JCM 31181T), SLN56T (=CGMCC 1.14945T=JCM 30832T) and LT61T (=CGMCC 1.14942T=JCM 30668T) represent novel species of the genus Natrinema , for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68T (=CGMCC 1.17211T=JCM 34158T) represents a novel species of Haloterrigena , for which the name Haloterrigena alkaliphila sp. nov. is proposed.

Halorhabdus amylolytica sp. nov. and Halorhabdus salina sp. nov., isolated from hypersaline environments

Two novel extremely halophilic archaeal strains, designated H27T and FL145T, were isolated from a salt mine and a kelp salt sample, respectively. Cells of both strains were Gram-stain-negative, motile and pleomorphic. The 16S rRNA and rpoB′ gene sequence similarities between strains H27T and FL145T were 96.60 and 88.77%. Strains H27T and FL145T were both closely related to Halorhabdus rudnickae WSM-64T, Halorhabdus tiamatea SARL4BT and Halorhabdus utahensis AX-2T, with a 16S rRNA gene sequence similarities of 98.14, 96.34 and 96.27% for strain H27T and 96.42, 95.82 and 96.17% for strain FL145T. The genome-based average nucleotide identity (ANI) values between strains H27T and FL145T, and these three species were 83.93, 79.79 and 79.09% (for strain H27T), and 78.32, 77.95 and 77.05% (for strain FL145T), respectively. The ANI value between strains H27T and FL145T was 78.65 %. The digital DNA–DNA hybridization values between strains H27T and FL145T, and these three species were less than 27.40%, which were below the recommended threshold for membership of the same species. The major polar lipids of both strains were found to consist of sulfated diglycosyl diether, triglycosyl diether, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol. The DNA G+C content was determined from genome to be 62.10 mol% for strain H27T and 61.51 mol% for strain FL145T. Based on phylogenetic, phenotypic, chemotaxonomic and genomic analyses, these two new isolates should be classified as representing two novel species in the genus Halorhabdus , with strain H27T (=CGMCC 1.16342T=NBRC 113589T) as the type strain of a new species for which we propose the name Halorhabdus amylolytica sp. nov., and strain FL145T (=CGMCC 1.13888T=NBRC 114260T) as the type strain of another new species for which we propose the name Halorhabdus salina sp. nov.

Halorussus halobius sp. nov., Halorussus marinus sp. nov. and Halorussus pelagicus sp. nov., isolated from salted brown alga Laminaria

Four halophilic archaeal strains, designated HD8-83T, LYG-36T, DLLS-82 and RC-68T, were isolated from the salted brown alga Laminaria of three different origins (Dalian, Lianyungang, Dalian and Rongcheng) in PR China. All strains had pleomorphic rod cells that were motile, lysed in distilled water, stained Gram-negative, and formed red-pigmented colonies on agar plate (except for DLLS-82, which formed white colonies). Based on phylogenetic analyses of the 16S rRNA genes, strain HD8-83T was closely related to Halorussus litoreus HD8-51T (97.9 % similarity), strain LYG-36T and DLLS-82 to Halorussus rarus TBN4T (94.4 % and 94.7 % similarities, respectively), and strain RC-68T to Halorussus salinus YJ-37-HT (96.9 % similarity). Results of phylogenetic analyses based on rpoB' genes and 728 concatenated single-copy orthologous clusters also showed that these strains formed three different branches and clustered tightly with the Halorussus members. The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values between strains LYG-36T and DLLS-82 were 98.9, 98 and 92.4%, showing that they were different strains of the same species. While those values between the isolates and other Halorussus members were below 84.7, 82.9 and 28.9 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strains HD8-83T, LYG-36T, DLLS-82 and RC-68T represent three novel species of the genus Halorussus for which the names Halorussus halobius sp. nov. (type strain: HD8-83T=CGMCC 1.15334T=JCM 31110T), Halorussus marinus sp. nov. (type strain: LYG-36T=CGMCC 1.13606T=JCM 32952T; reference strain: DLLS-82=CGMCC 1.13604=JCM 32951) and Halorussus pelagicus sp. nov. (type strain: RC-68T=CGMCC 1.13609T=JCM 32953T) are proposed.

Halobaculum rubrum sp. nov., an extremely halophilic archaeon isolated from a salt lake

A halophilic archaeal strain, designated C46T, was isolated from an inland salt lake in Qinghai Province, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C46T belongs to the genus Halobaculum , and the closest phylogenetic relative is Halobaculum gomorrense DSM 9297T with 97.7 % similarity. Despite this, strain C46T was more related to Halobaculum saliterrae WSA2T than other members of the genus Halobaculum based on genome comparison and analysis, and the average nucleotide identity, in silico DNA–DNA hybridization, amino acid identity and percentage of conserved protein values between the two strains were 89.1, 53.3, 89.2 and 75.6 %, respectively, which are lower than the cutoff values proposed for species delimitation. The physiological, biochemical, genetic and genomic characteristics of strain C46T were different from those of its closest phylogenetic neighbours, which indicated that this strain represents a novel species of the genus Halobaculum , for which the name Halobaculum rubrum sp. nov. is proposed. The type strain is C46T (=CGMCC 1.13737T=JCM 32959T).

Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil

Three halophilic archaeal strains, Gai1-5^T, SEDH52^T and SQT7-1^T were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23^T (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9^T (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5 ^T, SEDH52^T and SQT7-1^T from Haloprofundus halophilus NK23^T and Haloprofundus marisrubri SB9^T. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5^T (= CGMCC 1.16079^T = JCM 33561^T), SQT7-1^T (= CGMCC 1.16063^T = JCM 33553 ^T) and SEDH52^T (= CGMCC 1.17434^T) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.

Haloarchaea, excellent candidates for removing pollutants from hypersaline wastewater

Hypersaline wastewater is difficult to treat due to the inhibition of salt stress on microbes' viability and metabolic capabilities. Haloarchaea, native microorganisms that thrive in hypersaline habitats, overcome this key obstacle naturally. This review provides a comprehensive overview of the metabolic versatility of Haloarchaea in hypersaline wastewater treatment, including carbon, nitrogen, phosphorus, sulfur, and heavy metal metabolism. It also analyzes factors affecting pollutant removal and addresses metabolic mechanisms. Additionally, haloarchaea microbial characteristics and strategies to cope with salt stress are highlighted. Finally, the biotechnological potential of biomolecules produced from haloarchaea is investigated. To get better insight into the potential of haloarchaea, a deeper investigation of basic metabolism and more in-depth studies of their genomics and applications in actual wastewater are also necessary.