Phylogeny, novel bacterial lineage and enzymatic potential of haloalkaliphilic bacteria from the saline coastal desert of Little Rann of Kutch, Gujarat, India

Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation

The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.

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.

Efficacy of the Fruit and Vegetable Peels as Substrates for the Growth and Production of α-Amylases in Marine Actinobacteria

Enzymes from haloalkaliphilic microorganisms have recently focused attention on their potential and suitability in various applications. In this study, the growth and production of extracellular amylases in the marine actinomycetes, using kitchen waste as the raw starch source, have been investigated. Actinobacteria were isolated from the seawater of the Kachhighadi Coast near Dwarika, Gujarat. Seven Actinobacterial isolates of pre-monsoon, monsoon, and post-monsoon seasons belonging to different strains of Nocardiopsis genera were screened and selected for amylase production. The amylase production was initially assessed on the solid media supplemented with the extracts of different fruits and vegetable peels as a substrate by agar plate assay. The strains Kh-2(13), Kh-2(1), and Kh-3(12) produced maximum amylase with potato peel as a substrate, while no significant differences were found with the media containing other peels. Nevertheless, all strains produced amylases at a significant level with other raw substrates as well. For the optimization of the growth and enzyme production, the selected two isolates Kh-2(13) and Kh-3(12) of the monsoon and winter seasons were cultivated in a liquid medium under the submerged fermentation conditions, with potato peel as a substrate. In both organisms, the optimum amylase production was observed in the stationary phase of growth. For amylase production, the effect of different physical and chemical parameters was evaluated. The optimum growth and amylase production was achieved in 2% inoculum size, at pH 8.0, 28℃, and 5% salt concentration. On the basis of the amylase production index (API) (a ratio of the amylase units and cell growth), both isolates produced significant amylase with the only extract of potato peels, without any other supplements. The trends further indicated that while additional complex sources, such as yeast extract and peptone can enhance the cell growth of the actinobacteria, the amylase production remained unaltered. The study projects the significance of waste raw materials for the production of enzymes in extremophilic microorganisms.

Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Molecule N-3-Oxododecanoyl Homoserine Lactone

Quorum sensing (QS) in bacteria has been well studied as a cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in nontraditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and their signaling intermediates. Considering this relationship and considering the recent demonstration of the species Lactobacillus plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. We used an approach combining techniques from both systems and synthetic biology to identify a number of native QS-response genes and to alter associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified lactic acid bacteria (LAB) for use in human-health-promoting applications and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.

Long-term impacts of climate change on coastal and transitional eco-systems in India: an overview of its current status, future projections, solutions, and policies

Urbanization and industrial development are increasing rapidly. These are accompanied by problems of population explosion, encroachment of agricultural, and construction lands, increased waste generation, effluent release, and escalated concentrations of several greenhouse gases (GHGs) and pollutants in the atmosphere. This has led to wide-scale adverse impacts. Visible effects are fluctuations in temperatures and precipitation, rising sea levels, unpredictable floods, storms and cyclones, and disruption to coastal and transitional ecosystems. In a country like India with a massive population of nearly 1.4 billion and around 420 million people dwelling on or near the coasts, this effect is pre-dominant. India has extensive coastlines on both sides that are subject to greater contact and high impact from the water bodies. The factors impacting climate change, its consequences, and future predictions must be analyzed immediately for implementing precautionary measures to ameliorate the detrimental effects. Several endemic species have been endangered as these changes have resulted in the loss of habitat and interfered with the food webs. Climatic impacts on transitional ecosystems also need to be considered to preserve the diversity of each. The cooperation of governmental, independent organizations and policymakers throughout the world is essential to control and mediate the impacts on health, agriculture, and other related sectors, the details of which have been elaborated in this review. The review analyses the trends in climatic variation with time and discusses a few extremities which have left permanent effects on the population primarily concerning the coastal - Indian scenario and its eco-systems.

Characterization of thermo/halo stable cellulase produced from halophilic Virgibacillus salarius BM-02 using non-pretreated biomass

The production of extremozymes from halophilic bacteria has increased significantly due to their stability and efficiency in catalyzing a reaction, as well as their capacity to display optimum activity at various salt concentrations. In the current study, the halophilic bacterium Virgibacillus salarius strain BM-02 could utilize many non-pretreated substrates including cellulose, corn stover, sugarcane bagasse and wheat bran as a sole carbon source. However, wheat bran was the best substrate for achieving optimum saccharification yield (90.1%). The partially purified cellulase was active and stable at a wide range of pH (5-8) with residual activities > 58%. Moreover, it was stable at 5-12% of NaCl. Metal ions have a variable impact on the activity of partially purified cellulase however, Fe⁺³ exhibited the highest increase in the cellulase activity. The enzyme exhibited a thermal stability at 40, 50 and 60 °C with half-lives of 1049.50, 168.14 and 163.5 min, respectively. The value of V_max was 22.27 U/mL while Km was 2.1 mM. The activation energy of denaturation E_d 69.81 kJ/mol, the enthalpy values (ΔH_d) were positive, and the entropy values (ΔS) were negative. Therefore, V. Salarius is recommended as a novel promising halophilic extremozyme producer and agricultural waste remover in the bio-industrial applications.

Diversity and bioprospecting for industrial hydrolytic enzymes of microbial communities isolated from deserted areas of south-east Morocco

The current study aimed to analyze bacterial communities' diversity and abundance in three different deserted areas (Merzouga, Mhamid Elghizlane, and Erg lihoud) located in Moroccan Sahara, as well as to investigate osmotolerant microorganisms producing hydrolytic enzymes. The isolates were taxonomically affiliated using 16S rRNA gene sequencing. Four different hydrolase activities (amylase, lipase, cellulase, and protease) and osmotic stress tolerance were evaluated. The phylogenetic analysis of 364 screened isolates belonged to three phyla (Firmicutes 73%, Proteobacteria 26% and Actinobacteria 1%) and 18 different genera, from Bacillus, Ornithinibacillus, Paenibacillus, Geobacillus, Pseudomonas, Acinetobacter, Agrobacterium, Arthrobacter, Paenarthrobacter, Enterobacter, Staphylococcus, Erwinia, Herbasprillum, Ocuria, Massilia, Planomicrobium, Hodococcus, and Stenotrophomonas. The results detected a high proportion of osmotolerant and enzymes producing bacteria, many isolates can tolerate up to 55 °C (40%, 28%, and 30% in Merzouga, Mhamid Elghizlane, and Erg lihoudi, respectively). Meanwhile, the salinity tolerance reached 12% in some isolates with different proportions in each site, 29% in Merzouga, 24% in Mhamid Elghizlane, and 9% in Erg lihoudi. Furthermore, the enzymatic tests showed the presence of an amylolytic, lipolytic, cellulolytic, proteolytic activities in 20%, 31%, 63% and 72% of total strains, respectively. As a result, the present study is thus a preliminary yet critical step towards identifying the best bacterial candidates for further biotechnological applications.

Genetic and Phenotypic Heterogeneity of the Nocardiopsis alba Strains of Seawater

This study deals with the genetic and phenotypic heterogeneity of the marine Nocardiopsis alba strains isolated during pre-monsoon, monsoon and post-monsoon seasons. The isolates were characterized for their morphological and biochemical attributes, growth media preferences, antibiotic susceptibility and extracellular enzyme secretion. Nocardiopsis alba strains were assessed against 12 different antibiotics, and the responses were expressed in terms of the multiple antibiotic resistance (MAR) number. The majority of the strains produced multiple extracellular enzymes: proteases, amylases and lipases. Further, the strains were characterized on the basis of 16S rRNA gene sequencing and the majority were identified as Nocardiopsis alba along with few strains of Streptomyces lopnurensis, Nocardiopsis synnemataformans and Nocardiopsis dassonvillei. Neighbor-joining (NJ) phylogenetic tree suggested variation among the genetically similar Nocardiopsis alba species. The study establishes significant heterogeneity with respect to genetic and phenotypic characteristics of the strains of Nocardiopsis alba. Phylogenetic tree and phenogram-based comparison reflect the heterogeneity in terms of different clustering patterns of the strains. Further, the whole genome sequence data available in the literature also confirm the observed heterogeneity. Nocardiopsis alba strains displayed a relatively regressive pattern of dependence on the environmental factors based on the canonical correspondence analysis plot. The study represents cultivation, characterization, phylogenetic analysis and enzymatic potential of the Nocardiopsis alba species of seawater origin.

Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic Bacillus lehensis JO-26

An alkaline protease gene of Bacillus lehensis JO-26 from saline desert, Little Rann of Kutch, was cloned and expressed in Escherichia coli BL21 (DE3). A 1,014-bp ORF encoded 337 amino acids. The recombinant protease (APrBL) with Asp 97, His 127, and Ser 280 forming catalytic triad belongs to the subtilase S8 protease family. The gene was optimally expressed in soluble fraction with 0.2 mM isopropyl β-D-thiogalactopyranoside (IPTG), 2% (w/v) NaCl at 28°C. APrBL, a monomer with a molecular mass of 34.6 kDa was active over pH 8–11 and 30°C−70°C, optimally at pH 10 and 50°C. The enzyme was highly thermostable and retained 73% of the residual activity at 80°C up to 3 h. It was significantly stimulated by sodium dodecyl sulfate (SDS), Ca²⁺, chloroform, toluene, n-butanol, and benzene while completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and Hg²⁺. The serine nature of the protease was confirmed by its strong inhibition by PMSF. The APrBL gene was phylogenetically close to alkaline elastase YaB (P20724) and was distinct from the well-known commercial proteases subtilisin Carlsberg (CAB56500) and subtilisin BPN′ (P00782). The structural elucidation revealed 31.75% α-helices, 22.55% β-strands, and 45.70% coils. Although high glycine and fewer proline residues are a characteristic feature of the cold-adapted enzymes, the similar observation in thermally active APrBL suggests that this feature cannot be solely responsible for thermo/cold adaptation. The APrBL protease was highly effective as a detergent additive and in whey protein hydrolysis.

Salinity profile in coastal non-agricultural land in Gaza

The objectives of this study were to characterize the electric conductivity (EC), total dissolved salts (TDS), highly soluble salts (HSS), less soluble salts (LSS), cations (Na⁺, K⁺, Ca⁺⁺ and Mg⁺⁺) and anions (Cl^-, NO^-₃, SO^--₄, PO^---₄) profiles in non-agricultural coastal land in Gaza Strip and to evaluate the effect of trees in salinity. Six locations were selected randomly in coastal zone in Gaza Strip and used for soil profile digging. Soil samples were collected from different layers between 0 and 150 cm depth, air dried and kept in plastic bags at lab temperature. Ten grams of soil were mixed with 25 mL distilled water and kept under shaking for 24 h, then EC, pH and TDS were determined. Then additional 25 ml distilled water was added to each bottle and kept for additional 24 h of shaking. EC and TDS were determined again. Then the soil filtrates were collected by centrifugation and used to determine cations and anions. Results showed that concentrations of TDS, HSS and LSS were higher at the top soil layer than at deeper soil layers. Concentrations of cations and anions have similar trends to TDS, HSS and LSS. Behavior of cations and anions in the soil profiles under trees were different from those in open field. Comparing between the data of soil profiles under trees (site 2 and 5) and those in the open field (sites 1, 3, 4 and 6) showed slight effects on availability of cations and anions. Strong correlations were found between cations and anions in soil profiles under trees, and week correlations were found in soil profile in open field. In conclusion the coastal soil profiles are characterized with elevated levels of TDS, HSS and LSS in the top soil layers. Accumulations of salts were more pronounced in top soil layers. These properties suggest high potential damage to the ecosystem.

Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase

The obligately anaerobic haloalkaliphilic bacterium Alkalitalea saponilacus can use xylan as the sole carbon source and produce propionate as the main fermentation product. Using mixed carbon sources of 0.4% (w/v) sucrose and 0.1% (w/v) birch xylan, xylanase production from A. saponilacus was 3.2-fold greater than that of individual carbon sources of 0.5% (w/v) sucrose or 0.5% (w/v) birch xylan. The xylanse is halostable and exhibits optimal activity over a broad salt concentration (2–6% NaCl). Its activity increased approximately 1.16-fold by adding 0.2% (v/v) Tween 20. To understand the potential genetic mechanisms of xylan degradation and molecular adaptation to saline-alkali extremes, the complete genome sequence of A. saponilacus was performed with the pacBio single-molecule real-time (SMRT) and Illumina Misseq platforms. The genome contained one chromosome with a total size of 4,775,573 bps, and a G+C genomic content of 39.27%. Ten genes relating to the pathway for complete xylan degradation were systematically identified. Furthermore, various genes were predicted to be involved in isosmotic cytoplasm via the “compatible-solutes strategy” and cytoplasmic pH homeostasis though the “influx of hydrogen ions”. The halostable xylanase from A. saponilacus and its genomic sequence information provide some insight for potential applications in industry under double extreme conditions.