Cultivation of Diverse Microorganisms from Hypersaline Lake and Impact of Delay in Sample Processing on Cell Viability

A Pipeline for the Isolation and Cultivation of Microalgae and Cyanobacteria from Hypersaline Environments

Microorganisms in high-salinity environments play a critical role in biogeochemical cycles, primary production, and the biotechnological exploitation of extremozymes and bioactive compounds. The main challenges in current research include isolating and cultivating these microorganisms under laboratory conditions and understanding their complex adaptive mechanisms to high salinity. Currently, universally recognized protocols for isolating microalgae and cyanobacteria from salt pans, salterns, and similar natural habitats are lacking. Establishing axenic laboratory cultures is essential for identifying new species thriving in high-salinity environments and for exploring the synthesis of high-value metabolites by these microorganisms ex situ. Our ongoing research primarily focuses on photosynthetic microorganisms with significant biotechnological potential, particularly for skincare applications. By integrating data from the existing literature with our empirical findings, we propose a standardized pipeline for the isolation and laboratory cultivation of microalgae and cyanobacteria originating from aqueous environments characterized by elevated salt concentrations, such as solar salterns. This approach will be particularly useful for researchers working with microorganisms adapted to hypersaline waters.

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.

Deciphering the salt induced morphogenesis and functional potentials of Hortaea werneckii; a black pigmented halotolerant yeast isolated from solar saltern

An intense black pigmented halotolerant yeast GUBPC1, was obtained from the solar salterns of Nerul, Goa-India. The isolate could tolerate 0 to 20 % NaCl. FE-SEM analysis revealed its polymorphic nature, exhibiting oval cells at higher salt concentrations and filamentous spindle like shapes at lower concentrations. Initially, the cells appear oval, yeast like in shape but gradually after 15 days of incubation, it becomes elongated and undergoes budding, exhibiting various budding patterns, from single polar bud to bipolar buds with annellidic ring, to lateral buds and eventually forming filamentous hyphae. The intracellular black pigment was identified as melanin based on ultraviolet-visible spectroscopy analysis. The molecular identification of the culture showed closest similarity with Hortaea werneckii. Plant polymer-degrading enzymatic activities such as cellulase, laccase, chitinase, xylanase, pectinase, amylase and protease were exhibited by the isolate GUBPC1. To further understand and explore its biotechnological potential, we performed whole-genome sequencing and analysis. The obtained genome size was 26.93 Mb with 686 contigs and a GC content of 53.24 %. We identified 9383 protein-coding genes, and their functional annotation revealed the presence of 435 CAZyme genes and 16 functional genes involved in secondary metabolite synthesis, thus providing a basis for its potential value in various biotechnological applications.

Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region

The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.

Microbial diversity in polyextreme salt flats and their potential applications

Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.

Lipingzhangella rawalii sp. nov., a novel halophile isolated from Sambhar Salt Lake, Rajasthan, India

A haloalkaliphilic actinobacterial strain LS1_29T, isolated from an inland hypersaline Sambhar Salt Lake, situated in Rajasthan, India, was subjected to taxonomic characterisation using the polyphasic approach. Cells of the strain were Gram stain positive and aerobic, having reticulate and aerial hyphae. The major fatty acids detected were iso C16:0 (38.23%), anteiso C17:0 (20.52%), iso C18:0 10 methyl (8.09%), iso C18:0 (7.74%) and iso C17:0 (7.48%). The major polar lipids identified were diphosphatidyl glycerol, phosphatidylglycerol, phosphatidylcholine and phospholipids. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain belonged to the genus Lipingzhangella with the highest similarity of 94.09% to Lipingzhangella halophila EGI 80537 T and formed a separate clade within the genus Lipingzhangella. The DNA G + C content of genomic DNA of strain LS1_29T was 67.99 mol%. The strain showed the highest orthologous average nucleotide identity (OrthoANI) value of 72.80% and digital DNA-DNA hybridization (dDDH) value of 20.3% with Lipingzhangella halophila EGI 80537 T. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, strain LS1_29T represents a novel species within the genus Lipingzhangella, for which the name Lipingzhangella rawalii sp. nov. is proposed. The type strain of the type species is LS1_29T (= KCTC 49199 T = JCM 32979 T = MCC 3420 T).

Elevated inorganic carbon and salinity enhances photosynthesis and ATP synthesis in picoalga Picocystis salinarum as revealed by label free quantitative proteomics

Saline soda lakes are of immense ecological value as they niche some of the most exclusive haloalkaliphilic communities dominated by bacterial and archaeal domains, with few eukaryotic algal representatives. A handful reports describe Picocystis as a key primary producer with great production rates in extremely saline alkaline habitats. An extremely haloalkaliphilic picoalgal strain, Picocystis salinarum SLJS6 isolated from hypersaline soda lake Sambhar, Rajasthan, India, grew robustly in an enriched soda lake medium containing mainly Na₂CO₃, 50 g/l; NaHCO_3, 50 g/l, NaCl, 50 g/l (salinity ≈150‰) at pH 10. To elucidate the molecular basis of such adaptation to high inorganic carbon and NaCl concentrations, a high-throughput label-free quantitation based quantitative proteomics approach was applied. Out of the total 383 proteins identified in treated samples, 225 were differentially abundant proteins (DAPs), of which 150 were statistically significant (p < 0.05) including 70 upregulated and 64 downregulated proteins after 3 days of growth in highly saline-alkaline medium. Most DAPs were involved in photosynthesis, oxidative phosphorylation, glucose metabolism and ribosomal structural components envisaging that photosynthesis and ATP synthesis were central to the salinity-alkalinity response. Key components of photosynthetic machinery like photosystem reaction centres, adenosine triphosphate (ATP) synthase ATP, Rubisco, Fructose-1,6-bisphosphatase, Fructose-bisphosphate aldolase were highly upregulated. Enzymes peptidylprolyl isomerases (PPIase), important for correct protein folding showed remarkable marked-up regulation along with other chaperon proteins indicating their role in osmotic adaptation. Enhanced photosynthetic activity exhibited by P. salinarum in highly saline-alkaline condition is noteworthy as photosynthesis is suppressed under hyperosmotic conditions in most photosynthetic organisms. The study provided the first insights into the proteome of extremophilic alga P. salinarum exhibiting extraordinary osmotic adaptation and proliferation in polyextreme conditions prevailing in saline sodic ecosystems, potentially unraveling the basis of resilience in this not so known organism and paves the way for a promising future candidate for biotechnological applications and model organism for deciphering the molecular mechanisms of osmotic adaptation. The mass spectrometry proteomics data is available at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD037170.

Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments

Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L-1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L-1 NaCl between pH values 2-10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.

Natronococcus pandeyae sp. nov., a Novel Haloarchaeon from Sambhar Salt Lake

A halophilic archaeon, designated strain LS1_42^T, was isolated from Sambhar Salt Lake, Rajasthan, India. Cells were non-motile, coccoid, Gram-stain-variable and present in irregular clusters with light pink pigmented colonies. The strain was strictly aerobic and able to grow without Mg²⁺. Growth of the strain LS1_42^T was observed at 25-45 °C, pH 7.0-11.0 and NaCl concentrations of 10-35% (w/v). The nearest phylogenetic neighbor of strain LS1_42^T was Natronococcus amylolyticus Ah-36^T based on 16S rRNA and rpoB' genes with similarity of 95.4% and 91.9%, respectively. Phylogenetic analysis based on 16S rRNA gene, rpoB' gene and whole-genome sequences indicate that the strain LS1_42^T belongs to the genus Natronococcus and is closely related to N. amylolyticus. The genome size was 5.38 Mb with 98.9% completeness. The DNA G + C content of the strain LS1_42^T was 63.0 mol%. The average nucleotide identity, average amino acid identity and DNA-DNA hybridization values between LS1_42^T and N. amylolyticus Ah-36^T were 81.3%, 77.7% and 24.8%, respectively. The major polar lipids detected were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. On the basis of phenotypic, chemotaxonomic and genome-based analysis, strain LS1_42^T represents a novel species within the genus Natronococcus, for which the name Natronococcus pandeyae sp. nov. is proposed. The type strain is LS1_42^T (MCC 3654^T = JCM 33003^T = KCTC 4280^T = CGMCC 1.16738^T).

Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils

Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.

Thalassobacillus, a genus of extreme to moderate environmental halophiles with biotechnological potential

Thalassobacillus is a moderately halophilic genus that has been isolated from several sites worldwide, such as hypersaline lakes, saline soils, salt flats, and volcanic mud. Halophilic bacteria have provided functional stable biomolecules in harsh conditions for industrial purposes. Despite its potential biotechnological applications, Thalassobacillus has not been fully characterized yet. This review describes the Thalassobacillus genus, with the few species reported, pointing out its possible applications in enzymes (amylases, cellulases, xylanases, and others), biosurfactants, bioactive compounds, biofuels production, bioremediation, and plant growth promotion. The Thalassobacillus genus represents a little-explored biological resource but with a high potential.

Halophilic Prokaryotes in Urmia Salt Lake, a Hypersaline Environment in Iran

In this study, fluorescence in situ hybridization (FISH) and PCR-amplified fragments of the 16SrDNA gene were used to determine prokaryotes diversity in Urmia Salt Lake. Prokaryote cell population in Urmia lake range from 3.1 ± 0.3 × 10⁶, 2 ± 0.2 × 10⁸, 4 ± 0.3 × 10⁸, and 1.8 ± 0.2 × 10⁸ cells ml^-1 for water, soil, sediment, and salt samples by DAPI (4́, 6-diamidino-2-phenylindole) direct count, respectively. The proportion of bacteria and archaea in the samples determinable by FISH ranged between 36.1 and 55% and 48.5 and 55.5%, respectively. According to the DGGE method, some bands were selected and separated from the gel, then amplified and sequenced. The results of sequences were related to two phyla Proteobacteria (16.6%) and Bacteroidetes (83.3%), which belonged to four genera Salinibacter, Mangroviflexus, Pseudomonas, and Cesiribacter, and the archaeal sequences were related to Euryarchaeota phyla and three genera Halonotius, Haloquadratum, and Halorubrum. According to our results, it seems that prokaryotic populations in this hypersaline environment are more diverse than expected, and bacteria are so abundant and diverse and form the metabolically active part of the microbial population inhabiting this extreme environment. Molecular dependent and independent approaches revealed a different aspect of this environment microbiota.