Complete genome sequence of a Salimicrobium sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Salimicrobium sp. PL1-032A was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a single chromosome (2,705,688 bp) with a GC content of 47.2%. The isolation of Salimicrobium sp. PL1-032A contributes to the collection of culturable extremophiles and offers potential insight into the Pearse Lakes biome.

Sugar beet molasses: a sweet solution for ectoine production by Nesterenkonia sp.

Ectoine, a biologically significant compound, was successfully produced by a strain of bacteria capable of utilizing sucrose. In a ground-breaking approach, we harnessed the potential of sugar beet molasses, a by-product rich in sucrose, amino acid, and vitamins, as a growth medium for this purpose. Through meticulous investigation, we identified the ideal conditions for maximizing ectoine synthesis. This remarkable milestone was reached by introducing only 1 g of (NH4)2SO4 and 5 mL of molasses per liter, maintaining a pH level of 8.0, upholding a 7.5% NaCl concentration, employing agitation at 120 rpm, and sustaining a temperature of 30 °C. This study marks a pioneering endeavour as it represents the first instance where molasses has been effectively employed to produce ectoine through the cultivation of Nesterenkonia sp. We showcased the production of 75.56 g of the valuable compound ectoine utilizing 1 L of waste molasses with this specific bacterial strain. These findings hold tremendous promise, not only in terms of resource utilization but also for the potential applications of ectoine in various biological contexts.

Potential of halophiles and alkaliphiles in bioremediation of azo dyes-laden textile wastewater: a review.

Azo dye-laden textile wastewater must be treated before release due to various health and environmental concerns. Bioremediation of textile wastewater, however, is a challenge owing to its alkaline and saline nature as mesophilic microbes, in general, are either not able to thrive or show less efficiency under such hostile environment. Thus, pre-treatment for neutralization or salinity removal becomes a prerequisite before applying microbes for treatment, causing extra economical and technical burden. Extremophilic bacteria can be the promising bioremediating tool because of their inherent ability to survive and show toxicants removal capability under such extreme conditions without need of pre-treatment. Among extremophiles, halophilic and alkaliphilic bacteria which are naturally adapted to high salt and pH are of special interest for the decolorization of saline-alkaline-rich textile wastewater. The current review article is an attempt to provide an overview of the bioremediation of azo dyes and azo dye-laden textile wastewater using these two classes of extremophilic bacteria. The harmful effects of azo dyes on human health and environment have been discussed herein. Halo-alkaliphilic bacteria circumvent the extreme conditions by various adaptations, e.g., production of certain enzymes, adjustment at the protein level, pH homeostasis, and other structural adaptations that have been highlighted in this review. The unique properties of alkaliphiles and halophiles, to not only sustain but also harboring high dye removal competence at high pH and salt concentration, make them a good candidate for designing future bioremediation strategies for the management of alkaline, salt, and azo dye-laden industrial wastewaters.

'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics.

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like ß-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

Extremozymes and compatible solute production potential of halophilic and halotolerant bacteria isolated from crop rhizospheric soils of Southwest Saurashtra Gujarat.

Halophiles are one of the classes of extremophilic microorganisms that can flourish in environments with very high salt concentrations. In this study, fifteen bacterial strains isolated from various crop rhizospheric soils of agricultural fields along the Southwest coastline of Saurashtra, Gujarat, and identified by 16S rRNA gene sequencing as Halomonas pacifica, H. stenophila, H. salifodinae, H. binhaiensis, Oceanobacillus oncorhynchi, and Bacillus paralicheniformis were investigated for their potentiality to produce extremozymes and compatible solute. The isolates showed the production of halophilic protease, cellulase, and chitinase enzymes ranging from 6.90 to 35.38, 0.004-0.042, and 0.097-0.550 U ml-1, respectively. The production of ectoine-compatible solute ranged from 0.01 to 3.17 mg l-1. Furthermore, the investigation of the ectoine-compatible solute production at the molecular level by PCR showed the presence of the ectoine synthase gene responsible for its biosynthesis in the isolates. Besides, it also showed the presence of glycine betaine biosynthetic gene betaine aldehyde dehydrogenase in the isolates. The compatible solute production by these isolates may be linked to their ability to produce extremozymes under saline conditions, which could protect them from salt-induced denaturation, potentially enhancing their stability and activity. This correlation warrants further investigation.

Complete genome sequence of a Marinococcus sp. PL1-022 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Marinococcus sp. PL1-022 was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a chromosome (3,140,198 bp; 48.2% GC) and two plasmids (58,083 bp and 19,399 bp; 41.4 and 50.7% GC-content, respectively). Isolation of Marinococcus sp. PL1-022 adds to the increasing repertoire of culturable extremophiles.

Complete genome sequence of Idiomarina sp. PL1-037 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Idiomarina sp. PL1-037 was isolated from Pearse Lakes, Rottnest Island, Western Australia. The sequenced completed genome for PL1-037 is composed of a single chromosome (2,804,934 bp) with a GC content of 47.1%. Isolation of Idiomarina sp. PL1-037 provides insights about culturable extremophiles from the Pearse lakes microbiome.

Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes.

Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].

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.

A systematic analysis of affinity tags in the haloarchaeal expression system, Haloferax volcanii for protein purification.

Extremophilic proteins are valuable in various fields, but their expression can be challenging in traditional hosts like Escherichia coli due to misfolding and aggregation. Haloferax volcanii (H. volcanii), a halophilic expression system, offers a solution. This study examined cleavable and non-cleavable purification tags at both the N- and C-termini when fused with the superfolder green fluorescent protein (sfGFP) in H. volcanii. Our findings reveal that an N-terminal 8xHis-tag or Strep-tag®II significantly enhances protein production, purity, and yield in H. volcanii. Further experiments with mCherry and halophilic alcohol dehydrogenase (ADH) showed improved expression and purification yields when the 8xHis-tag or Strep-tag®II was positioned at the C-terminus for mCherry and at the N-terminus for ADH. Co-positioning 8xHis-tag and Twin-Strep-tag® at the N-terminus of sfGFP, mCherry, and ADH yielded significantly enhanced results. These findings highlight the importance of thoughtful purification tag design and selection in H. volcanii, providing valuable insights for improving protein production and purification with the potential to advance biotechnological applications.

Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration.

Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.

Genomic analysis of a halophilic bacterium Nesterenkonia sp. CL21 with ability to produce a diverse group of lignocellulolytic enzymes.

Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.

Taxonomic diversity of extremophilic prokaryotes adapted to special environmental parameters in Hungary: a review.

The taxonomic and metabolic diversity of prokaryotes and their adaptability to extreme environmental parameters have allowed extremophiles to find their optimal living conditions under extreme conditions for one or more environmental parameters. Natural habitats abundant in extremophilic microorganisms are relatively rare in Hungary. Nevertheless, alkaliphiles and halophiles can flourish in shallow alkaline lakes (soda pans) and saline (solonetz) soils, where extreme weather conditions favor the development of unique bacterial communities. In addition, the hot springs and thermal wells that supply spas and thermal baths and provide water for energy use are suitable colonization sites for thermophiles and hyperthermophiles. Polyextremophiles, adapted to multiple extreme circumstances, can be found in the aphotic, nutrient-poor and radioactive hypogenic caves of the Buda Thermal Karst, among others. The present article reviews the organization, taxonomic composition, and potential role of different extremophilic bacterial communities in local biogeochemical cycles, based on the most recent studies on extremophiles in Hungary.

Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins.

Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.

Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea.

Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx104 g-1 after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.

Effect of salinity on biological nitrogen removal from wastewater and its mechanism.

The nitrogen discharge from saline wastewater will cause significant pollution to the environment. As a high-efficiency and low-cost treatment method, biological treatment has a promising application prospect in the removal of nitrogen from high-salt wastewater. However, the inhibitory effect of high salt on microorganisms increases the difficulty of its treatment. This review discusses the influence of salinity on the nitrogen removal process, considering both traditional and novel biological techniques. Common methods to enhance the effectiveness of biological nitrogen removal processes and their mechanisms of action in engineering practice and research, including sludge acclimation and inoculation of halophilic bacteria, are also introduced. An outlook on the future development of biological nitrogen removal processes for high-salt wastewater is provided to achieve environmentally friendly discharge of high-salt wastewater.

Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment.

Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.

Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping.

Quickly identifying and characterizing isolates from extreme environments is currently challenging while very important to explore the Earth's biodiversity. As these isolates may, in principle, be distantly related to known species, techniques are needed to reliably identify the branch of life to which they belong. Proteotyping these environmental isolates by tandem mass spectrometry offers a rapid and cost-effective option for their identification using their peptide profiles. In this study, we document the first high-throughput proteotyping approach for environmental extremophilic and halophilic isolates. Microorganisms were isolated from samples originating from high-altitude Andean lakes (3700-4300 m a.s.l.) in the Chilean Altiplano, which represent environments on Earth that resemble conditions on other planets. A total of 66 microorganisms were cultivated and identified by proteotyping and 16S rRNA gene amplicon sequencing. Both the approaches revealed the same genus identification for all isolates except for three isolates possibly representing not yet taxonomically characterized organisms based on their peptidomes. Proteotyping was able to indicate the presence of two potentially new genera from the families of Paracoccaceae and Chromatiaceae/Alteromonadaceae, which have been overlooked by 16S rRNA amplicon sequencing approach only. The paper highlights that proteotyping has the potential to discover undescribed microorganisms from extreme environments.

Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia.

Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9 M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further.

Assessing the metabolism, phylogenomic, and taxonomic classification of the halophilic genus Halarchaeum.

In this study, a genomic approach was employed to evaluate the metabolic potentials and taxonomic classification of the halophilic genus Halarchaeum. Genomic analysis revealed that Halarchaeum members exhibit a predilection for amino acids as their primary energy source in high-salinity environments over carbohydrates. Genome analysis unveiled the presence of crucial genes associated with metabolic pathways, including the Embden-Meyerhof pathway, semi-phosphorylative Entner-Doudoroff pathway, and the urea cycle. Furthermore, the genomic analysis indicated that Halarchaeum members employ diverse mechanisms for osmotic regulation (encompassing both salt-in and salt-out strategies). Halarchaeum members also encode genes to alleviate acid and heat stress. The average nucleotide identity value between Halarchaeum solikamskense and Halarchaeum nitratireducens exceeded the established threshold (95%-96%) for defining distinct species. This high similarity suggests a close relationship between these two species, prompting the proposal to reclassify Halarchaeum solikamskense as a heterotypic synonym of Halarchaeum nitratireducens. The results of this study contribute to our knowledge of taxonomic classification and shed light on the adaptive strategies employed by Halarchaeum species in their specific ecological niches.