Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach

Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern

The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.

Isolation optimization and screening of halophilic enzymes and antimicrobial activities of halophilic archaea from the high-altitude, hypersaline Da Qaidam Salt Lake, China

AIM

The aim of this study is to increase the diversity of culturable halophilic archaea by comparing various isolation conditions and to explore the application of halophilic archaea for enzyme-producing activities and antimicrobial properties.

METHODS AND RESULTS

We systematically compared the isolation performance of various archaeal and bacterial media by isolating halophilic archaea from the Da Qaidam Salt Lake, a magnesium sulfate subtype hypersaline lake on the Qinghai-Tibet Plateau, China, using multiple enrichment culture and gradient dilution conditions. A total of 490 strains of halophilic archaea were isolated, which belonged to five families and 11 genera within the order Halobacteriales of the class Halobacteria of the phylum Euryarchaeota. The 11 genera consisted of nine known genera and two potentially new genera, the former including Halorubrum, Natranaeroarchaeum, Haloplanus, Haloarcula, Halorhabdus, Halomicrobium, Halobacterium, Natrinema, and Haloterrigene. Halorubrum was the dominant genus with a relative abundance of 78.98%. By comparing different culture conditions, we found that bacterial media 2216E and R2A showed much better isolation performance than all archaeal media, and enrichment culture after 60 d and dilution gradients of 10-1 and 10-2 were best fitted for halophilic archaea cultivation. The screening of 40 halophilic archaeal strains of different species indicated that these halophilic archaea had great extracellular enzyme activities, including amylase (62.5%), esterase (50.0%), protease (27.5%), and cellulase (15.0%), and possessed great antimicrobial activities against human pathogens. A total of 34 strains exhibited antimicrobial activity against four or more pathogens, and 19 strains exhibited antimicrobial activity against all six pathogens.

CONCLUSIONS

The diversity of culturable halophilic archaea was significantly increased by enrichment culture and selection of bacterial media, and screening of representative strains showed that halophilic archaea have multiple extracellular enzyme activities and broad-spectrum antimicrobial activity against human pathogens.

Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils

Saline soils and their microbial communities have recently been studied in response to ongoing desertification of agricultural soils caused by anthropogenic impacts and climate change. Here we describe the prokaryotic microbiota of hypersaline soils in the Odiel Saltmarshes Natural Area of Southwest Spain. This region has been strongly affected by mining and industrial activity and feature high levels of certain heavy metals. We sequenced 18 shotgun metagenomes through Illumina NovaSeq from samples obtained from three different areas in 2020 and 2021. Taxogenomic analyses demonstrate that these soils harbored equal proportions of archaea and bacteria, with Methanobacteriota, Pseudomonadota, Bacteroidota, Gemmatimonadota, and Balneolota as most abundant phyla. Functions related to the transport of heavy metal outside the cytoplasm are among the most relevant features of the community (i.e., ZntA and CopA enzymes). They seem to be indispensable to avoid the increase of zinc and copper concentration inside the cell. Besides, the archaeal phylum Methanobacteriota is the main arsenic detoxifier within the microbiota although arsenic related genes are widely distributed in the community. Regarding the osmoregulation strategies, "salt-out" mechanism was identified in part of the bacterial population, whereas "salt-in" mechanism was present in both domains, Bacteria and Archaea. De novo biosynthesis of two of the most universal compatible solutes was detected, with predominance of glycine betaine biosynthesis (betAB genes) over ectoine (ectABC genes). Furthermore, doeABCD gene cluster related to the use of ectoine as carbon and energy source was solely identified in Pseudomonadota and Methanobacteriota.

'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 β-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.

Unique Features of Extremely Halophilic Microbiota Inhabiting Solar Saltworks Fields of Vietnam

The artificial solar saltworks fields of Hon Khoi are important industrial and biodiversity resources in southern Vietnam. Most hypersaline environments in this area are characterized by saturated salinity, nearly neutral pH, intense ultraviolet radiation, elevated temperatures and fast desiccation processes. However, the extremely halophilic prokaryotic communities associated with these stressful environments remain uninvestigated. To fill this gap, a metabarcoding approach was conducted to characterize these communities by comparing them with solar salterns in northern Vietnam as well as with the Italian salterns of Motya and Trapani. Sequencing analyses revealed that the multiple reuses of crystallization ponds apparently create significant perturbations and structural instability in prokaryotic consortia. However, some interesting features were noticed when we examined the diversity of ultra-small prokaryotes belonging to Patescibacteria and DPANN Archaea. Surprisingly, we found at least five deeply branched clades, two from Patescibacteria and three from DPANN Archaea, which seem to be quite specific to the Hon Khoi saltworks field ecosystem and can be considered as a part of biogeographical connotation. Further studies are needed to characterize these uncultivated taxa, to isolate and cultivate them, which will allow us to elucidate their ecological role in these hypersaline habitats and to explore their biotechnological and biomedical potential.

The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov

The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.

Seasonal dynamics of eukaryotic microbial diversity in hypersaline Tuz Lake characterized by 18S rDNA sequencing

Microbial diversity found in hypersaline ecosystems is structurally unique and essential in many microbiological and ecological processes. Tuz Lake, the second biggest lake in Türkiye, is a talassohaline (over 32% [w/v]) lake with near-neutral pH. The aim of study was to investigate the composition of the eukaryotic microbial community in Tuz Lake by 18S rDNA amplicon sequencing, as well as its relationship and change with environmental factors during 1-year period. Next-generation sequencing and bioinformatic analysis were applied to describe the eukaryotic microbial community in Tuz Lake. As a result of bioinformatics analysis, Archaeplastida (39%) and Stramenopiles, Alveolata, Rhizaria (SAR) (51%) were the most abundant taxa represented in the dataset. The Archaeplastida phylum showed a significant difference between winter and summer and higher abundance in summer in contrast to the SAR group, which represented higher abundance in winter. Genus level assessment showed that the most abundant genera were Navicula, Chlorophyta;unclassified_taxa, Dunaliella, Cladosporium, Paraphelidium, Scuticociliates;unclassified_taxa, and Chlamydomonadales;unclassified_taxa. Navicula abundance was significantly different and overwhelmingly dominant in winter. On the other hand, Cladosporium and Chlorophyta; unclassified_taxa represented a significant difference between seasons and high abundance in summer. Furthermore, Dunaliella populations were not detected in midsummer and early fall when the temperature increased and water volume in the lake decreased.

Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau

The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.

A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils

Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.

Assessment of diversity of archaeal communities in Algerian chott

Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 10³ CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.

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.

Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov

The genus Natronomonas is classified on the family Haloarculaceae, within the class Halobacteria and currently includes six species isolated from salterns, saline or soda lakes, and salt mines. All are extremely halophilic (optimal growth at 20-25% [w/v] NaCl) and neutrophilic, except Natronomonas pharaonis, the type species of the genus, that is haloalkaliphilic (showing optimal growth at pH 9.0) and possesses distinct phenotypic features, such as a different polar lipid profile than the rest of species of the genus. We have carried out a genome-based study in order to determine the phylogenetic structure of the genus Natronomonas and elucidate its current taxonomic status. Overall genomic relatedness indexes, i.e., OrthoANI (Average Nucleotide Identity), dDDH (digital DNA-DNA hybridization), and AAI (Average Amino acid Identity), were determined with respect to the species of Natronomonas and other representative taxa of the class Halobacteria. Our data show that the six species of Natronomonas constitute a coherent cluster at the genus level. Besides, we have characterized a new haloarchaeon, strain F2-12^T, isolated from the brine of a pond of a saltern in Isla Cristina, Huelva, Spain, and we determined that it constitutes a new species of Natronomonas, for which we propose the name Natronomonas aquatica sp. nov. Besides, the metabolic analysis revealed a heterotrophic lifestyle and a versatile nitrogen metabolism for members of this genus. Finally, metagenomic fragment recruitments from a subset of hypersaline habitats, indicated that the species of Natronomonas are widely distributed in saline lakes and salterns as well as on saline soils. Species of this haloarchaeal genus can be considered as ubiquitous in intermediate to high salinity habitats.

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

The adaptation mechanisms of microbial communities to natural perturbations remain unexplored, particularly in extreme environments. The extremophilic communities of halite (NaCl) nodules from the hyper-arid core of the Atacama Desert are self-sustained and represent a unique opportunity to study functional adaptations and community dynamics with changing environmental conditions. We transplanted halite nodules to different sites in the desert and investigated how their taxonomic, cellular, and biochemical changes correlated with water availability, using environmental data modeling and metagenomic analyses. Salt-in strategists, mainly represented by haloarchaea, significantly increased in relative abundance at sites characterized by extreme dryness, multiple wet/dry cycles, and colder conditions. The functional analysis of metagenome-assembled genomes (MAGs) revealed site-specific enrichments in archaeal MAGs encoding for the uptake of various compatible solutes and for glycerol utilization. These findings suggest that opportunistic salt-in strategists took over the halite communities at the driest sites. They most likely benefited from compounds newly released in the environment by the death of microorganisms least adapted to the new conditions. The observed changes were consistent with the need to maximize cellular bioenergetics when confronted with lower water availability and higher salinity, providing valuable information on microbial community adaptations and resilience to climate change.

Biotechnological impacts of Halomonas: a promising cell factory for industrially relevant biomolecules

Extremophiles are the most fascinating life forms for their special adaptations and ability to offer unique extremozymes or bioactive molecules. Halophiles, the natural inhabitants of hypersaline environments, are one among them. Halomonas are the common genus of halophilic bacteria. To support growth in unusual environments, Halomonas produces various hydrolytic enzymes, compatible solutes, biopolymers like extracellular polysaccharides (EPS) and polyhydroxy alkaloates (PHA), antibiotics, biosurfactants, pigments, etc. Many of such molecules are being produced in large-scale bioreactors for commercial use. However, the prospect of the remaining bioactive molecules with industrial relevance is far from their application. Furthermore, the genetic engineering of the respective gene clusters could open up a new path to bio-prospect these molecules by overproducing their products through heterologous expression. The present survey on Halomonas highlights their ecological diversity, application potential of the their various industrially relevant biomolecules and impact of these biomolecules on respective fields.

Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain

Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNA^Thr, tRNA^Arg, tRNA^Gly and tRNA^Asn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.

Microbial communities of halite deposits and other hypersaline environments

Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.

Hypersaline environments as natural sources of microbes with potential applications in biotechnology: The case of solar evaporation systems to produce salt in Alicante County (Spain)

Extremophilic microbes show a unique metabolism due to the adaptations they display to deal with extreme environmental parameters characterizing the extreme ecosystems that they inhabit (high salt concentration, high temperatures, and extreme pH values, high exposure to solar radiation etc.). Halophilic microorganisms characterised and isolated from saltmarshes, brines, salted ponds, salty lagoons etc. have recently attracted attention due to their potential biotechnological applications (as whole cells used for different purposes like wastewater treatments, or their biomolecules: enzymes, antibiotics, carotenoids, bioplastics). Alicante county (southeast of Spain) accounts for a significant number of salty environments like coastal or inland salty ponds from where sodium chloride (NaCl)is obtained, marshes, salty lagoons, etc. The best system characterised so far from a microbiological point of view is "Salinas de Santa Pola", also termed "Salinas Bras del Port". However, there are many other salty environments to be explored, like the natural park of Torrevieja and la Mata lagoons, salty lagoon located in Calpe city or inland salted ponds like those located in the northwest of the county. This review summarises the most relevant biotechnological applications of halophilic microbes described up to now. In addition, special attention is focused on ecosystems such as the lagoons of Torrevieja or inland salt marshes as natural environments whose microbial biodiversity is worthy of being studied in search of new strains and species with the aim to analyze their potential biotechnological applications (pharmaceutical, food industry, biomedicine, etc.).

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

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

Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing

Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.

Extremely halophilic archaeal communities are resilient to short-term entombment in halite

Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.

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

As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00087-3.

Onshore soil microbes and endophytes respond differently to geochemical and mineralogical changes in the Aral Sea

There is limited knowledge about how microbiome develops along the geochemical and mineralogical change in onshore soils derived from continuous desiccation of lakes. In this study, geochemistry and mineralogy were studied in the Aral Sea onshore soils exposed in different periods (from the 1970s to 2018), followed by microbial analyses on the studied soils and the aboveground organs of dominant plants. The soils exhibited an increasing gradient of total soluble salts (TSS: 0.4-0.5 g/L to 71.3 g/L) and evaporite minerals (e.g., gypsum, halite) from the farshore to the nearshore. In the studied soils, microbial diversity decreased with increasing TSS, and microbial community dissimilarities among samples was positively correlated with the contents of gypsum and calcite minerals. Among the measured environmental variables, minerals contributed most to the observed microbial variation. In contrast, the endophytic microbial communities in the aboveground organs of dominant plants were not related to any of the measured variables, indicating that they differed from their soil counterparts with respect to their responses to geochemical and mineralogical variations in soils. In summary, these results help us understand the response of onshore soil microbiome to the decline of lake water caused by continuous desiccation.

Environmental dissolved DNA harbours meaningful biological information on microbial community structure

Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High-speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.

Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights

Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.

The microbiology of red brines

The brines of natural salt lakes with total salt concentrations exceeding 30% are often colored red by dense communities of halophilic microorganisms. Such red brines are found in the north arm of Great Salt Lake, Utah, in the alkaline hypersaline lakes of the African Rift Valley, and in the crystallizer ponds of coastal and inland salterns where salt is produced by evaporation of seawater or some other source of saline water. Red blooms were also reported in the Dead Sea in the past. Different types of pigmented microorganisms may contribute to the coloration of the brines. The most important are the halophilic archaea of the class Halobacteria that contain bacterioruberin carotenoids as well as bacteriorhodopsin and other retinal pigments, β-carotene-rich species of the unicellular green algal genus Dunaliella and bacteria of the genus Salinibacter (class Rhodothermia) that contain the carotenoid salinixanthin and the retinal protein xanthorhodopsin. Densities of prokaryotes in red brines often exceed 2-3×10⁷ cells/mL. I here review the information on the biota of the red brines, the interactions between the organisms present, as well as the possible roles of the red halophilic microorganisms in the salt production process and some applied aspects of carotenoids and retinal proteins produced by the different types of halophiles inhabiting the red brines.

Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India

The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na⁺) and chloride (Cl^–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.

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

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

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

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

Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses

Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.

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

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

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups

During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation‐independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline‐adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Spatial distribution of prokaryotic communities in hypersaline soils

Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC_1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.

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

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

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)

Hypersaline environments encompass aquatic and terrestrial habitats. While only a limited number of studies on the microbial diversity of saline soils have been carried out, hypersaline lakes and marine salterns have been thoroughly investigated, resulting in an aquatic-biased knowledge about life in hypersaline environments. To improve our understanding of the assemblage of microbes thriving in saline soils, we assessed the phylogenetic diversity and metabolic potential of the prokaryotic community of two hypersaline soils (with electrical conductivities of ~24 and 55 dS/m) from the Odiel saltmarshes (Spain) by metagenomics. Comparative analysis of these soil databases with available datasets from salterns ponds allowed further identification of unique and shared traits of microbial communities dwelling in these habitats. Saline soils harbored a more diverse prokaryotic community and, in contrast to their aquatic counterparts, contained sequences related to both known halophiles and groups without known halophilic or halotolerant representatives, which reflects the physical heterogeneity of the soil matrix. Our results suggest that Haloquadratum and certain Balneolaeota members may preferentially thrive in aquatic or terrestrial habitats, respectively, while haloarchaea, nanohaloarchaea and Salinibacter may be similarly adapted to both environments. We reconstructed 4 draft genomes related to Bacteroidetes, Balneolaeota and Halobacteria and appraised their metabolism, osmoadaptation strategies and ecology. This study greatly improves the current understanding of saline soils microbiota.

Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics

Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments

Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to "species") using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms.

Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland)

This study evaluates the changes in bacterial and archaeal community structure during the gradual evaporation of water from the brine (extracted from subsurface Jurassic deposits) in the system of graduation towers located in Ciechocinek spa, Poland. The communities were assessed with 16S rRNA gene sequencing (MiSeq, Illumina) and microscopic methods. The microbial cell density determined by direct cell count was at the order of magnitude of 10⁷ cells/mL. It was found that increasing salt concentration was positively correlated with both the cell counts, and species-level diversity of bacterial and archaeal communities. The archaeal community was mostly constituted by members of the phylum Euryarchaeota, class Halobacteria and was dominated by Halorubrum-related sequences. The bacterial community was more diverse, with representatives of the phyla Proteobacteria and Bacteroidetes as the most abundant. The proportion of Proteobacteria decreased with increasing salt concentration, while the proportion of Bacteroidetes increased significantly in the more concentrated samples. Representatives of the genera Idiomarina, Psychroflexus, Roseovarius, and Marinobacter appeared to be tolerant to changes of salinity. During the brine concentration, the relative abundances of Sphingobium and Sphingomonas were significantly decreased and the raised contributions of genera Fabibacter and Fodinibius were observed. The high proportion of novel (not identified at 97% similarity level) bacterial reads (up to 42%) in the 16S rRNA gene sequences indicated that potentially new bacterial taxa inhabit this unique environment.

Microbial diversity in the hypersaline Lake Meyghan, Iran

Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg-1 salinity brine, a red ~180 g kg-1 salinity brine and a white ~300 g kg-1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.

Spiribacter aquaticus sp. nov., a novel member of the genus Spiribacter isolated from a saltern

A moderately halophilic bacterium, designated strain SP30T, was isolated from a solar saltern located in Santa Pola, Alicante, on the East coast of Spain. It was a Gram-stain-negative, strictly aerobic bacterium, able to grow in 7.5-25 % (w/v) NaCl and optimally in 12.5 % (w/v) NaCl. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that the novel isolate is a member of the genus Spiribacter, with the most closely related species being Spiribacter roseus SSL50T (99.9 % sequence similarity) and Spiribacter curvatus UAH-SP71T (99.4 % sequence similarity). The 16S rRNA gene sequence similarity with the type species Spiribacter salinus M19-40T was 96.6 %. The DNA-DNA relatedness value between strain SP30T and S. roseus SSL50T and S. curvatus UAH-SP71T was 40 and 55 %, respectively; these values are lower than the 70 % threshold accepted for species delineation. The major fatty acids were C16:0, C18 : 1ω7c, C19 : 0 cyclo ω8c and C12 : 0. Similarly to other species of the genus Spiribacter, strain SP30Twas observed as curved rods and spiral cells. Metabolic versatility was reduced to the utilization of a few organic compounds as the sole carbon and energy sources, as with other members of Spiribacter. However, it differed in terms of colony pigmentation (brownish-yellow instead of pink) and in having a higher growth rate. Based on these data and on the phenotypic, genotypic and chemotaxonomic characterization, we propose the classification of strain SP30T as a novel species within the genus Spiribacter, with the name Spiribacter aquaticus sp. nov. The type strain is SP30T (=CECT 9238T=LMG 30005T).

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns

Seasonal sampling was carried out at three Argentinian salterns, Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal component analysis of the environmental data grouped SN and CG samples separately from G samples owing to G's higher pH values and sulfate concentration. Differences in microbial assemblages were also found. Many archaeal sequences belonged to uncultured members of Haloquadratum and Haloquadratum-related genera, with different environmental optima. Notably, nearly half of the archaeal sequences were affiliated to the recently described 'Candidatus Haloredividus' (phylum Nanohaloarchaeota), not previously detected in salt-saturated environments. Most bacterial sequences belonged to Salinibacter representatives, while sequences affiliated to the recently described genus Spiribacter were also found. Seasonal analysis showed at least 40% of the microbiota from the three salterns was prevalent through the year, indicating they are well adapted to environmental fluctuations. On the other hand, a minority of archaeal and bacterial sequences were found to be seasonally distributed. Five viral morphotypes and also eukaryal predators were detected, suggesting different mechanisms for controlling prokaryotic numbers. Notably, Guatraché was the saltern that harbored the highest virus-to-cell ratios reported to date for hypersaline environments.

Spiribacter roseus sp. nov., a moderately halophilic species of the genus Spiribacter from salterns

Four pink-pigmented, non-motile, Gram-staining-negative and moderately halophilic curved rods, designated strains SSL50T, SSL25, SSL97 and SSL4, were isolated from a saltern located in Isla Cristina, Huelva, south-west Spain. Phylogenetic analyses based on 16S rRNA gene sequences showed that they were members of the genus Spiribacter, most closely related to Spiribacter curvatus UAH-SP71T (99.3-99.5 % sequence similarity) and Spiribacter salinus M19-40T (96.5-96.7 %). Other related strains were Alkalilimnicola ehrlichii MLHE-1T (95.1-95.3 %), Arhodomonas recens RS91T (95.1-95.2 %) and Arhodomonas aquaeolei ATCC 49307T (95.0-95.1 %), all members of the family Ectothiorhodospiraceae. The major fatty acids were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0 and C12 : 0. The DNA G+C range was 64.0-66.3 mol%. The DNA-DNA hybridization values between strains SSL50T, SSL25, SSL97, SSL4 and S. piribacter. curvatus UAH-SP71T were 37-49 %. The average nucleotide identity (ANIb) values between the genome of strain SSL50T and those of the two other representatives of the genus Spiribacter, S. curvatus UAH-SP71T and S. salinus M19-40T, were 82.4 % and 79.1 %, respectively, supporting the proposal of a novel species of the genus Spiribacter. On the basis of the polyphasic analysis, the four new isolates are considered to represent a novel species of the genus Spiribacter, for which the name Spiribacter roseus sp. nov. is proposed. The type strain is SSL50T (=CECT 9117T=IBRC-M 11076T).

Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel

Stability of microbial communities can impact the ability of dispersed cells to colonize a new habitat. Saturated brines and their halophile communities are presumed to be steady state systems due to limited environmental perturbations. In this study, the bacteriorhodopsin-containing fraction of the haloarchaeal community from Eilat salt crystallizer ponds was sampled five times over 3 years. Analyses revealed the existence of a constant core as several OTUs were found repeatedly over the length of the study: OTUs comprising 52 % of the total cloned and sequenced PCR amplicons were found in every sample, and OTUs comprising 89 % of the total sequences were found in more than one, and often more than two samples. LIBSHUFF and UNIFRAC analyses showed statistical similarity between samples and Spearman's coefficient denoted significant correlations between OTU pairs, indicating non-random patterns in abundance and co-occurrence of detected OTUs. Further, changes in the detected OTUs were statistically linked to deviations in salinity. We interpret these results as indicating the existence of an ever-present core bacteriorhodopsin-containing Eilat crystallizer community that fluctuates in population densities, which are controlled by salinity rather than the extinction of some OTUs and their replacement through immigration and colonization.

Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern

A novel pink-pigmented bacterial strain, UAH-SP71T, was isolated from a saltern located in Santa Pola, Alicante (Spain) and the complete genome sequence was analysed and compared with that of Spiribacter salinus M19-40T, suggesting that the two strains constituted two separate species, with a 77.3% ANI value. In this paper, strain UAH-SP71T was investigated in a taxonomic study using a polyphasic approach. Strain UAH-SP71T was a Gram-stain-negative, strictly aerobic, non-motile curved rod that grew in media containing 5-20% (w/v) NaCl (optimum 10% NaCl), at 5-40 °C (optimum 37 °C) and at pH 5-10 (optimum pH 8). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed thatstrain UAH-SP71T is a member of the genus Spiribacter, showing a sequence similarity of 96.5% with Spiribacter salinus M19-40T. Other related species are also members of the family Ectothiorhodospiraceae, including Arhodomonas recens RS91T (95.5% 16S rRNA gene sequence similarity), Arhodomonas aquaeolei ATCC 49307T (95.4 %) and Alkalilimnicola ehrlichii MLHE-1T (94.9 %). DNA-DNA hybridization between strain UAH-SP71T and Spiribacter salinus M19-40T was 39 %. The major cellular fatty acids of strain UAH-SP71T were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c, C10 : 0 3-OH and C12 : 0, a pattern similar to that of Spiribacter salinus M19-40T. Phylogenetic, phenotypic and genotypic differences between strain UAH-SP71T and Spiribacter salinus M19-40T indicate that strainUAH-SP71T represents a novel species of the genus Spiribacter, for which the name Spiribacter curvatus sp. nov. is proposed. The type strain is UAH-SP71T (5CECT8396T5DSM 28542T).