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

Transformative strategies for saline soil restoration: Harnessing halotolerant microorganisms and advanced technologies

Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotolerant microorganisms and their synergistic interactions with plants. Halotolerant microorganisms enhance plant resilience through diverse mechanisms under salinity, including exopolysaccharide production, sodium sequestration, and phytohormone regulation. It improves ionic balance, nutrient uptake, and root development, facilitated by osmoregulatory and genetic adaptations. In this discussion, we explored emerging technologies, including genome editing (e.g., CRISPR-Cas9), synthetic biology, and advanced omics-based tools such as metagenomics and metatranscriptomics. These cutting-edge approaches offer profound insights into microbial diversity and their functional adaptations to saline environments. By leveraging these technologies, it is possible to design targeted bioremediation strategies through the customization of microbial functionalities to address specific environmental challenges effectively. Advanced methodologies, such as microbial volatile organic compounds (mVOCs), nanotechnology, and stress-tolerant microbial consortia, significantly enhance plant stress tolerance and facilitate soil restoration. Moreover, integrating digital technologies, including machine learning and artificial intelligence (AI), optimizes bioremediation processes by providing precise, scalable, and adaptable solutions tailored to diverse agricultural ecosystems. The synergistic application of halotolerant microbe-mediated approaches with advanced biotechnological and digital innovations presents a transformative strategy for saline soil restoration. Future research should focus on harmonizing these technologies and methodologies to maximize plant-microbe interactions and establish resilient, sustainable agricultural systems.

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.

Response of microbial diversity and function to the degradation of Barkol Saline Lake

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

Phylogeny and functional diversity of halophilic microbial communities from a thalasso environment

The El-Rawda solar saltern, located in North Sinai, Egypt, is formed through the process of water evaporation from the Bradawil lagoon. This evaporation leads to the precipitation of gypsum, halite minerals, and salt flats, which subsequently cover the southern and eastern areas of the lagoon. This study employed the shotgun metagenomic approach, the illumine platform, and bioinformatic tools to investigate the taxonomic composition and functional diversity of halophilic microbial communities in solar saltern. The metagenomic reads obtained from the brine sample exhibited a greater count compared to those from the sediment sample. Notably, the brine sample was primarily characterized by an abundance of archaea, while the sediment sample displayed a dominant abundance of bacteria. Both samples exhibited a relatively low abundance of eukaryotes, while viruses were only found in the brine sample. Furthermore, the comparative analysis of functional pathways showed many important processes related to central metabolism and protein processing in brine and sediment samples. In brief, this research makes a valuable contribution to the understanding of very halophilic ecosystems in Egypt, providing insights into their microbial biodiversity and functional processes.

Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat

The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO₄^2-, Na⁺, CO₃^2-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded saline lakes under environmental change.

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.

Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World

The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133^T exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.

Diversity of prokaryotic microorganisms in alkaline saline soil of the Qarhan Salt Lake area in the Qinghai-Tibet Plateau

The composition of microbial communities varies considerably across ecological environments, particularly in extreme environments, where unique microorganisms are typically used as the indicators of environmental conditions. However, the ecological reasons for the differences in microbial communities remain largely unknown. Herein, we analyzed taxonomic and functional community profiles via high-throughput sequencing to determine the alkaline saline soil bacterial and archaeal communities in the Qarhan Salt Lake area in the Qinghai-Tibet Plateau. The results showed that Betaproteobacteria (Proteobacteria) and Halobacteria (Euryarchaeota) were the most abundant in the soils of this area, which are common in high salinity environments. Accordingly, microbes that can adapt to local extremes typically have unique metabolic pathways and functions, such as chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, ureolysis, nitrate reduction, fermentation, dark hydrogen oxidation, and methanogenesis. Methanogenesis pathways include hydrogenotrophic methanogenesis, CO2 reduction with H2, and formate methanogenesis. Thus, prokaryotic microorganisms in high salinity environments are indispensable in nitrogen and carbon cycling via particular metabolic pathways.

Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing

Microorganisms thrive nearly everywhere including extreme environments where few other forms of life can exist. Geochemistry of extreme sites plays a major role in shaping these microbial communities and microbes thriving in such harsh conditions are untapped sources of novel biomolecules. To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. Barcoded amplicon sequencing technique was used to study the microbial communities. Physicochemical analysis of these sites was also conducted to study the dynamics of microbial communities under stressed conditions. Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. Proteobacteria were predominant in saline soil while Firmicutes were most abundant in hot spring sediment. The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. OTUs from genus Alkalibacillus were most abundant in hot spring sediments, whereas Haloarcula were more prevalent in saline soil. Some unidentified sequences were also present at each taxonomic level. Multivariate analysis indicated that electrical conductivity and pH are the major environmental factors involved in modelling microbial communities. This study revealed a poly-extremophilic microbial community in the Murtazaabad hot spring and characterised the unexplored halophilic microbial diversity of saline soil of Pakistan.