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Hypersaline environments with salt concentrations up to NaCl saturation are inhabited by a great diversity of microorganisms belonging to the three domains of life. They all must cope with the low water activity of their environment, but different strategies exist to provide osmotic balance of the cells' cytoplasm with the salinity of the medium. One option used by many halophilic Archaea and a few representatives of the Bacteria is to accumulate salts, mainly KCl and to adapt the entire intracellular machinery to function in the presence of molar concentrations of salts. A more widespread option is the synthesis or accumulation of organic osmotic, so-called compatible solutes. Here, we review the mechanisms of osmotic adaptation in a number of model organisms, including the KCl accumulating Halobacterium salinarum (Archaea) and Salinibacter ruber (Bacteria), Halomonas elongata as a representative of the Bacteria that synthesize organic osmotic solutes, eukaryotic microorganisms including the unicellular green alga Dunaliella salina and the black yeasts Hortaea werneckii and the basidiomycetous Wallemia ichthyophaga, which use glycerol and other compatible solutes. The strategies used by these model organisms and by additional halophilic microorganisms presented are then compared to obtain an integrative picture of the adaptations to life at high salt concentrations in the microbial world.

Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes, such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales, and Natrialbales orders since the LCAHa MalDH. We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.

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 CBA1133 T , the sole species of Salella , formed a single tight cluster with Halosegnis longus F12-1 T , then with Halosegnis rubeus F17-44 T . The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133 T and Halosegnis longus F12-1 T 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 DT72 T , DT80 T , DT85 T , and DT116 T , 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 DT72 T (= CGMCC 1.18925 T  = JCM 35418 T ), DT80 T (= CGMCC 1.18926 T  = JCM 35419 T ), DT85 T (= CGMCC 1.19049 T  = JCM 35605 T ), and DT116 T (= CGMCC 1.19045 T  = JCM 35606 T ) 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.

The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63T, AD-5T, CG52T, and KLK7T, isolated from three saline lakes and a saline-alkaline land in China, were simultaneously subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses indicated that strain CCL63T (= CGMCC 1.18663T = JCM 35096T) represents a novel genus of the family Natrialbaceae, strains AD-5T (= CGMCC 1.13783T = JCM 33734T) and CG52T (= CGMCC 1.17139T = JCM 34160T) represent two novel species of the genus Natronococcus, and strain KLK7T (= MCCC 4K00128T = KCTC 4307T) represents a novel species of Haloterrigena. Halovalidus salilacus gen. nov., sp. nov., Natronococcus wangiae sp. nov., Natronococcus zhouii sp. nov., and Haloterrigena salinisoli sp. nov. are further proposed based on these type strains accordingly.

Soil salinity is a major constraint adversely affecting agricultural crops including wheat worldwide. The use of plant growth promoting rhizobacteria (PGPR) to alleviate salt stress in crops has attracted the focus of many researchers due to its safe and eco-friendly nature. The current study aimed to study the genetic potential of high halophilic Bacillus strains, isolated from the rhizosphere in the extreme environment of the Qinghai–Tibetan plateau region of China, to reduce salt stress in wheat plants. The genetic analysis of high halophilic strains, NMCN1, LLCG23, and moderate halophilic stain, FZB42, revealed their key genetic features that play an important role in salt stress, osmotic regulation, signal transduction and membrane transport. Consequently, the expression of predicted salt stress-related genes were upregulated in the halophilic strains upon NaCl treatments 10, 16 and 18%, as compared with control. The halophilic strains also induced a stress response in wheat plants through the regulation of lipid peroxidation, abscisic acid and proline in a very efficient manner. Furthermore, NMCN1 and LLCG23 significantly enhanced wheat growth parameters in terms of physiological traits, i.e., fresh weight 31.2% and 29.7%, dry weight 28.6% and 27.3%, shoot length 34.2% and 31.3% and root length 32.4% and 30.2%, respectively, as compared to control plants under high NaCl concentration (200 mmol). The Bacillus strains NMCN1 and LLCG23 efficiently modulated phytohormones, leading to the substantial enhancement of plant tolerance towards salt stress. Therefore, we concluded that NMCN1 and LLCG23 contain a plethora of genetic features enabling them to combat with salt stress, which could be widely used in different bio-formulations to obtain high crop production in saline conditions.

Intensive exploitation, poor recycling, low repeatable use, and unusual resistance of plastics to environmental and microbiological action result in accumulation of huge waste amounts in terrestrial and marine environments, causing enormous hazard for human and animal life. In the last decades, much scientific interest has been focused on plastic biodegradation. Due to the comparatively short evolutionary period of their appearance in nature, sufficiently effective enzymes for their biodegradation are not available. Plastics are designed for use in conditions typical for human activity, and their physicochemical properties roughly change at extreme environmental parameters like low temperatures, salt, or low or high pH that are typical for the life of extremophilic microorganisms and the activity of their enzymes. This review represents a first attempt to summarize the extraordinarily limited information on biodegradation of conventional synthetic plastics by thermophilic, alkaliphilic, halophilic, and psychrophilic bacteria in natural environments and laboratory conditions. Most of the available data was reported in the last several years and concerns moderate extremophiles. Two main questions are highlighted in it: which extremophilic bacteria and their enzymes are reported to be involved in the degradation of different synthetic plastics, and what could be the impact of extremophiles in future technologies for resolving of pollution problems.

This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1–0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named ‘Nanohaloarchaea’. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.

Halophilic extracellular proteases offer promising application in various fields. Information on these prominent proteins including the synthesizing organisms, biochemical properties, domain organisation, purification, and application challenges has never been covered in recent reviews. Although extracellular proteases from bacteria pioneered the study of proteases in halophiles, progress is being made in proteases from halophilic archaea. Recent advances in extracellular proteases from archaea revealed that archaeal proteases are more robust and applicable. Extracellular proteases are composed of domains that determine their mechanisms of action. The intriguing domain structure of halophilic extracellular proteases consists of N-terminal domain, catalytic domain, and C-terminal extension. The role of C-terminal domains varies among different organisms. A high diversity of C-terminal domains would endow the proteases with diverse functions. With the development of genomics, culture-independent methods involving heterologous expression, affinity chromatography, and in vitro refolding are deployed with few challenges on purification and presenting novel research opportunities. Halophilic extracellular proteases have demonstrated remarkable potentials in industries such as detergent, leather, peptide synthesis, and biodegradation, with desirable properties and ability to withstand harsh industrial processes.Key points• Halophilic extracellular proteases have robust properties suitable for applications.• A high diversity of C-terminal domains may endow proteases with diverse properties.• Novel protease extraction methods present novel application opportunities.

Background Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. Results The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation ( ect ABC and bet ABC), nitrogen intake through nitrate and nitrite transporters ( nas A, and nar GI), and phosphorus uptake ( pst ABCS) were shared among the Halomonas isolates. Conclusions The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis .

Copper pollution in hypersaline environments poses a significant challenge due to the inefficiency of conventional bioremediation strategies under high salinity and metal stress. Halophilic archaea represent a promising solution for heavy metal removal in saline environments due to their biocompatibility and cost-effectiveness. Here, we investigated the copper removal potential of a Halalkalicoccus sp. Dap5, a halophilic archaeon isolated from the Urmia Lake in Iran. This strain exhibited copper tolerance (MIC: 80 mg/L Cu²⁺) and tolerance to several other toxic metals, including cadmium (Cd²⁺), cobalt (Co²⁺), lead (Pb²⁺), zinc (Zn²⁺), and arsenite (As³⁺) under 15% (w/v) salinity. A Central Composite Design (CCD) was employed within the Response Surface Methodology (RSM) to optimize three key parameters: pH, initial copper concentration, and inoculum percentage, to maximize copper removal. The resulting model was statistically significant (R² = 0.9972, p  < 0.0001) and attained a maximum copper removal efficacy of 90.8% at pH 8.1, 28.8 mg/L Cu²⁺, and 4.8% (v/v) inoculum. Microscopic and spectroscopic analyses revealed that copper removal occurred through both biosorption and bioaccumulation mechanisms, supported by increased extracellular polymeric substance (EPS) production and specific functional group interactions identified via FTIR. The results demonstrate that Halalkalicoccus sp. Dap5 exhibits marked tolerance to copper and efficiently removes copper ions from saline environments, making it a valuable candidate for sustainable bioremediation under extreme conditions. This is the first report on optimization of copper bioremoval in a Halalkalicoccus strain using RSM, underscoring its biotechnological significance for green environmental management.