Molecular Mechanisms of Adaptation of the Moderately Halophilic Bacterium Halobacillis halophilus to Its Environment

Mitigating NaCl stress in Vigna radiata L. cultivars using Bacillus pseudomycoides

Salt stress is one of the significant abiotic stress factors that exert harmful effects on plant growth and yield. In this study, five cultivars of mung bean (Vigna radiata L.) were treated with different concentrations of NaCl and also inoculated with a salt-tolerant bacterial strain to assess their growth and yield. The bacterial strain was isolated from the saline soil of Sahiwal District, Punjab, Pakistan and identified as Bacillus pseudomycoides. Plant growth was monitored at 15-days interval and finally harvested after 120 days at seed set. Both sodium and potassium uptake in above and below-ground parts were assessed using a flame photometer. Fresh and dry mass, number of pods, seeds per plant, weight of seeds per plant and weight of 100 seeds reduced significantly as the concentration of NaCl increased from 3 to 15 dSm-1. There was a significant reduction in the growth and yield of plants exposed to NaCl stress without bacterial inoculum compared to the plants with bacterial inoculum. The latter plants showed a significant increase in the studied parameters. It was found that the cultivar Inqelab mung showed the least reduction in growth and yield traits among the studied cultivars, while Ramzan mung showed the maximum reduction. Among all the cultivars, maximum Na+ uptake occurred in roots, while the least uptake was observed in seeds. The study concludes that NaCl stress significantly reduces the growth and yield of mung bean cultivars, but Bacillus pseudomycoides inoculum alleviates salt stress. These findings will be helpful to cultivate the selected cultivars in soils with varying concentrations of NaCl.

The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K. Appl Environ Microbiol 2024;90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.

A review of microbial nitrogen transformations and microbiome engineering for biological nitrogen removal under salinity stress

The osmotic stress caused by salinity exerts severe inhibition on the process of biological nitrogen removal (BNR), leading to the deterioration of biosystems and the discharge of nitrogen with saline wastewater. Feasible strategies to solve the bottleneck in saline wastewater treatment have attracted great attention, but relevant studies to improve nitrogen transformations and enhance the salt-tolerance of biosystems in terms of microbiome engineering have not been systematically reviewed and discussed. This work attempted to provide a more comprehensive explanation of both BNR and microbiome engineering approaches for saline wastewater treatment. The effect of salinity on conventional BNR pathways, nitrification-denitrification and anammox, was summarized at cellular and metabolic levels, including the nitrogen metabolic pathways, the functional microorganisms, and the inhibition threshold of salinity. Promising nitrogen transformations, such as heterotrophic nitrification-aerobic denitrification, ammonium assimilation and the coupling of conventional pathways, were introduced and compared based on advantages and challenges in detail. Strategies to improve the salt tolerance of biosystems were proposed and evaluated from the perspective of microbiome engineering. Finally, prospects of future investigation and applications on halophilic microbiomes in saline wastewater treatment were discussed.

Tandem mass tag-based quantitative proteomics reveals osmotic adaptation mechanisms in Alkalicoccus halolimnae BZ-SZ-XJ29T , a halophilic bacterium with a broad salinity range for optimal growth

The moderate halophilic bacterium Alkalicoccus halolimnae BZ-SZ-XJ29T exhibits optimum growth over a wide range of NaCl concentrations (8.3-12.3%, w/v; 1.42-2.1 mol L-1 ). However, its adaptive mechanisms to cope with high salt-induced osmotic stress remain unclear. Using TMT-based quantitative proteomics, the cellular proteome was assessed under low (4% NaCl, 0.68 mol L-1 NaCl, control (CK) group), moderate (8% NaCl, 1.37 mol L-1 NaCl), high (12% NaCl, 2.05 mol L-1 NaCl), and extremely high (16% NaCl, 2.74 mol L-1 NaCl) salinity conditions. Digital droplet PCR confirmed the transcription of candidate genes related to salinity. A. halolimnae utilized distinct adaptation strategies to cope with different salinity conditions. Mechanisms such as accumulating different amounts and types of compatible solutes (i.e., ectoine, glycine betaine, glutamate, and glutamine) and the uptake of glycine betaine and glutamate were employed to cope with osmotic stress. Ectoine synthesis and accumulation were critical to the salt adaptation of A. halolimnae. The expression of EctA, EctB, and EctC, as well as the intracellular accumulation of ectoine, significantly and consistently increased with increasing salinity. Glycine betaine and glutamate concentrations remained constant under the four NaCl concentrations. The total content of glutamine and glutamate maintained a dynamic balance and, when exposed to different salinities, may play a role in low salinity-induced osmoadaptation. Moreover, cellular metabolism was severely affected at high salt concentrations, but the synthesis of amino acids, carbohydrate metabolism, and membrane transport related to haloadptation was preserved to maintain cytoplasmic concentration at high salinity. These findings provide insights into the osmoadaptation mechanisms of moderate halophiles and can serve as a theoretical underpinning for industrial production and application of compatible solutes.

Molecular evolution steered structural adaptations in the DNA polymerase III α subunit of halophilic bacterium Salinibacter ruber

A significant portion of the earth has a salty environment, and the literature on bacterial survival mechanisms in salty environments is limited. During molecular evolution, halophiles increase acidic amino acid residues on their protein surfaces which leads to a negatively charged surface potential that helps them to maintain the protein integrity and protect them from denaturation by competing with salt ions. Through protein family analysis, we have investigated the molecular-level adaptive features of DNA polymerase III's catalytic subunit (alpha) and its structure-function relationship. This study throws light on the novel understanding of halophilic bacterial replication and the molecular basis of salt adaptation. Comparisons of the amino acid contents and electronegativity of halophilic and mesophilic bacterial proteins revealed adaptations that allow halophilic bacteria to thrive in high salt concentrations. A significantly lower isoelectric point of halophilic bacterial proteins indicates the acidic nature. Also, an abundance of disordered regions in halophiles suggests the requirement of the salt ions that play a crucial role in their stable protein folding. Despite having similar topology, mesophilic and halophilic proteins, a set of very prominent molecular modifications was observed in the alpha subunit of halophiles.

Plant growth-promoting rhizobacteria: Salt stress alleviators to improve crop productivity for sustainable agriculture development

Soil salinity, a growing issue worldwide, is a detrimental consequence of the ever-changing climate, which has highlighted and worsened the conditions associated with damaged soil quality, reduced agricultural production, and decreasing land areas, thus resulting in an unsteady national economy. In this review, halo-tolerant plant growth-promoting rhizo-microbiomes (PGPRs) are evaluated in the salinity-affected agriculture as they serve as excellent agents in controlling various biotic-abiotic stresses and help in the augmentation of crop productivity. Integrated efforts of these effective microbes lighten the load of agro-chemicals on the environment while managing nutrient availability. PGPR-assisted modern agriculture practices have emerged as a green strategy to benefit sustainable farming without compromising the crop yield under salinity as well as salinity-affected supplementary stresses including increased temperature, drought, salinity, and potential invasive plant pathogenicity. PGPRs as bio-inoculants impart induced systemic tolerance (IST) to plants by the production of volatile organic compounds (VOCs), antioxidants, osmolytes, extracellular polymeric substances (EPS), phytohormones, and ACC-deaminase and recuperation of nutritional status and ionic homeostasis. Regulation of PGPR-induced signaling pathways such as MAPK and CDPK assists in salinity stress alleviation. The "Next Gen Agriculture" consists of the application of designer crop microbiomes through gene editing tools, for instance, CRISPR, and engineering of the metabolic pathways of the microbes so as to gain maximum plant resistance. The utilization of omics technologies over the traditional approaches can fulfill the criteria required to increase crop yields in a sustainable manner for feeding the burgeoning population and augment plant adaptability under climate change conditions, ultimately leading to improved vitality. Furthermore, constraints such as the crop specificity issue of PGPR, lack of acceptance by farmers, and legal regulatory aspects have been acknowledged while also discussing the future trends for product commercialization with the view of the changing climate.

The effect of salinity on ammonium-assimilating biosystems in hypersaline wastewater treatment

The ammonium-assimilating biosystem is a promising solution to improve the susceptible biological nitrogen removal (BNR) and to achieve nitrogen recovery in saline wastewater treatment. However, the treatment performance and functional stability of ammonium-assimilating biosystems have not been fully illuminated in hypersaline wastewater. In this study, although the dramatic decrease of removal efficiency of NH₄⁺-N and PO₄^3--P was observed in ammonium-assimilating biosystems under the salinity from 3% to 7%, the direction of nitrogen conversions through assimilation was insusceptible to high salinity. The extremely low concentrations of nitrite and nitrate accumulation and abundances of nitrification functional genes confirmed that the process of nitrification was negligible in all biosystems. Ammonium-assimilating biosystems maintained robustness and functional stability in hypersaline wastewater. The increase of salinity stimulated the production of EPS and changed the microbial community by enriching Proteobacteria and halophilic genera. We anticipate that the ammonium-assimilating biosystem could be a promising strategy for hypersaline wastewater treatment and future practical applications.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Ammonium-assimilating microbiome: A halophilic biosystem rationally optimized by carbon to nitrogen ratios with stable nitrogen conversion and microbial structure

The contradiction between theoretical metabolism of ammonium assimilation and experiential understanding of conventional biosystems makes the rational optimization of the ammonium-assimilating microbiome through carbon to nitrogen (C/N) ratios perplexing. The effect of different C/N ratios on ammonium-assimilating biosystems was investigated in saline wastewater treatment. C/N ratios significantly hindered the nutrient removal efficiency, but ammonium-assimilating biosystems maintained functional stability in nitrogen conversions and microbial communities. With sufficient biomass, higher than 86% ammonium and 73% phosphorus were removed when C/N ratios were higher than 25. Ammonium assimilation dominated the nitrogen metabolism in all biosystems even under relatively low C/N ratios, evidenced by the extremely low abundances of nitrification functional genes. Different C/N ratios did not significantly change the bacterial community structure of ammonium-assimilating biosystems. It is anticipated that the ammonium-assimilating biosystem with advantages of clear metabolic pathway and easy optimization can be applied to nutrient removal and recovery in saline environments.

Recent Trends in Microbial Approaches for Soil Desalination

Soil salinization has become a major problem for agriculture worldwide, especially because this phenomenon is continuously expanding in different regions of the world. Salinity is a complex mechanism, and in the soil ecosystem, it affects both microorganisms and plants, some of which have developed efficient strategies to alleviate salt stress conditions. Currently, various methods can be used to reduce the negative effects of this problem. However, the use of biological methods, such as plant-growth-promoting bacteria (PGPB), phytoremediation, and amendment, seems to be very advantageous and promising as a remedy for sustainable and ecological agriculture. Other approaches aim to combine different techniques, as well as the utilization of genetic engineering methods. These techniques alone or combined can effectively contribute to the development of sustainable and eco-friendly agriculture.

Antibiotic resistance genes alternation in soils modified with neutral and alkaline salts: interplay of salinity stress and response strategies of microbes

Growing evidence points to the pivotal roles of salt accumulation in mediating antibiotic resistance genes (ARGs) spread in soil, whereas how salt mediates ARGs dissemination remains unknown. Herein, the effects of neutral or alkaline (Ne/Al) salt at low, moderate and high levels (Ne/Al-L, Ne/Al-M, Ne/Al-H) on the dissemination of ten typical ARGs in soils were explored, by simultaneously considering the roles of salinity stress and response strategies of microbes. In the soils amended with Ne/Al-L and Al-M salt, the dissemination of ARGs was negligible and the relative abundances of ARGs and mobile genetic elements (MGEs) were decreased. However, Ne-M and Al-H salt contributed to the dissemination of ARGs in soils, with the significantly increased absolute and relative abundances of ARGs and MGEs. In Ne-H soil, although the absolute abundance of ARGs declined drastically due to serious oxidative damage, their relative abundances were promoted. The facilitated ARGs transfer was potentially related to the excessive generation of intracellular reactive oxygen species and increased activities of DNA repair enzymes involved in SOS system. In addition, the activated intracellular protective response including quorum sensing and energy metabolism largely provided essential factors for ARGs dissemination. The co-occurrence of ARGs and over-expressed salt-tolerant genes in specific halotolerant bacteria further suggested the selection of salt stress on ARGs. Moreover, less disturbance of alkaline salt than neutral salt on ARGs evolution was observed, due to the lower abiotic stress and selective pressure on microbes. This study highlights that soil salinity-sodicity could dose-dependently reshape the dissemination of ARGs and community structure of microbes, which may increase the ecological risks of ARGs in agricultural environment.

Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems

Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.

Salt Tolerance Mechanism of the Rhizosphere Bacterium JZ-GX1 and Its Effects on Tomato Seed Germination and Seedling Growth

Salinity is one of the strongest abiotic factors in nature and has harmful effects on plants and microorganisms. In recent years, the degree of soil salinization has become an increasingly serious problem, and the use of plant growth-promoting rhizobacteria has become an option to improve the stress resistance of plants. In the present study, the salt tolerance mechanism of the rhizosphere bacterium Rahnella aquatilis JZ-GX1 was investigated through scanning electron microscopy observations and analysis of growth characteristics, compatible solutes, ion distribution and gene expression. In addition, the effect of JZ-GX1 on plant germination and seedling growth was preliminarily assessed through germination experiments. R. aquatilis JZ-GX1 was tolerant to 0-9% NaCl and grew well at 3%. Strain JZ-GX1 promotes salt tolerance by stimulating the production of exopolysaccharides, and can secrete 60.6983 mg/L of exopolysaccharides under the high salt concentration of 9%. Furthermore, the accumulation of the compatible solute trehalose in cells as the NaCl concentration increased was shown to be the primary mechanism of resistance to high salt concentrations in JZ-GX1. Strain JZ-GX1 could still produce indole-3-acetic acid (IAA) and siderophores and dissolve inorganic phosphorus under salt stress, characteristics that promote the ability of plants to resist salt stress. When the salt concentration was 100 mmol/L, strain JZ-GX1 significantly improved the germination rate, germination potential, fresh weight, primary root length and stem length of tomato seeds by 10.52, 125.56, 50.00, 218.18, and 144.64%, respectively. Therefore, R. aquatilis JZ-GX1 is a moderately halophilic bacterium with good growth-promoting function that has potential for future development as a microbial agent and use in saline-alkali land resources.

Salt tolerance mechanism of a hydrocarbon-degrading strain: Salt tolerance mediated by accumulated betaine in cells

Rhodococcus sp. HX-2 could degrade diesel oil in the presence of 1%-10 % NaCl. The compatible solute betaine accumulated in cells with increasing NaCl concentration, and this was found to be the main mechanism of resistance of HX-2 to high salt concentration. Exogenously added betaine can be transported into cells, which improved cell growth and the percentage degradation of diesel oil in the presence of high [NaCl] in solution and in soil. Scanning electron microscopy data suggested that addition of exogenous betaine facilitated salt tolerance by stimulating exopolysaccharide production. Fourier-transform infrared analysis suggested that surface hydroxyl, amide and phosphate groups may be related to tolerance of high-salt environments. Four betaine transporter-encoding genes (H0, H1, H3, H5) and the betaine producer gene betB were induced in Rhodococcus sp. HX-2 by NaCl stress. The maximal induction of H0, H1, H3 and H5 transcription depended on high salinity plus the presence of betaine. These results demonstrate that salt tolerance is mediated by accumulated betaine in Rhodococcus sp. HX-2 cells, and the potential of this strain for application in bioremediation of hydrocarbon pollution in saline environments.

Census of halide-binding sites in protein structures

Motivation

Halides are negatively charged ions of halogens, forming fluorides (F⁻), chlorides (Cl⁻), bromides (Br⁻) and iodides (I⁻). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide–protein interactions, based on the entries in the Protein Data Bank.

Results

We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide–protein interactions and assist phasing experiments relying on halides as anomalous scatters.

Availability and implementation

All data described in this article can be reproduced via complied pipeline published at https://github.com/rostkick/Halide_sites/blob/master/README.md.

Supplementary information

Supplementary data are available at Bioinformatics online.

Distinct Osmoadaptation Strategies in the Strict Halophilic and Halotolerant Bacteria Isolated from Lunsu Salt Water Body of North West Himalayas

Two strict halophilic bacterial strains, Halobacillus trueperi SS1, and Halobacillus trueperi SS3, and three halotolerant bacterial strains, Shewanella algae SS2, Halomonas venusta SS5, and Marinomonas sp. SS8 of Lunsu salt water body, Himachal Pradesh, India, were selected to study the mechanism of salt tolerance and the role of osmolytes therein. A combination of flame photometry, chromatographic and colorimetric assays was used to study the mechanism of salt tolerance in the selected strict halophilic and halotolerant bacterial strains. The strict halophiles and, one of the halotolerants, Marinomonas sp. SS8 were found to utilize both "salt-in strategy" and "accumulation of compatible solutes strategy" for osmoregulation in hypersaline conditions. On the contrary, the remaining two halotolerants used "accumulation of compatible solutes strategy" under saline stress and not the "salt-in strategy". The present study suggests towards distinct mechanisms of salt tolerance in the two classes, wherein strict halophiles accumulate compatible solutes as well as adopt salt-in strategy, while the halotolerant bacteria accumulate a range of compatible solutes, except Marinomonas sp. SS8, which utilizes both the strategies to combat salt stress.

Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus

Halobacillus halophilus, a moderately halophilic bacterium, accumulates a variety of compatible solutes including glycine betaine, glutamate, glutamine, proline, and ectoine to cope with osmotic stress. Non-targeted analysis of intracellular organic compounds using 1H-NMR showed that a large amount of trans-4-hydroxy-L-proline (Hyp), which has not been reported as a compatible solute in H. halophilus, was accumulated in response to high NaCl salinity, suggesting that Hyp may be an important compatible solute in H. halophilus. Candidate genes encoding proline 4-hydroxylase (PH-4), which hydroxylates L-proline to generate Hyp, were retrieved from the genome of H. halophilus through domain searches based on the sequences of known PH-4 proteins. A gene, HBHAL_RS11735, which was annotated as a multidrug DMT transporter permease in GenBank, was identified as the PH-4 gene through protein expression analysis in Escherichia coli. The PH-4 gene constituted a transcriptional unit with a promoter and a rho-independent terminator, and it was distantly located from the proline biosynthetic gene cluster (pro operon). Transcriptional analysis showed that PH-4 gene expression was NaCl concentration-dependent, and was specifically induced by chloride anion, similar to the pro operon. Accumulation of intracellular Hyp was also observed in other bacteria, suggesting that Hyp may be a widespread compatible solute in halophilic and halotolerant bacteria.

Biodesalination-On harnessing the potential of nature's desalination processes

Water scarcity is now one of the major global crises, which has affected many aspects of human health, industrial development and ecosystem stability. To overcome this issue, water desalination has been employed. It is a process to remove salt and other minerals from saline water, and it covers a variety of approaches from traditional distillation to the well-established reverse osmosis. Although current water desalination methods can effectively provide fresh water, they are becoming increasingly controversial due to their adverse environmental impacts including high energy intensity and highly concentrated brine waste. For millions of years, microorganisms, the masters of adaptation, have survived on Earth without the excessive use of energy and resources or compromising their ambient environment. This has encouraged scientists to study the possibility of using biological processes for seawater desalination and the field has been exponentially growing ever since. Here, the term biodesalination is offered to cover all of the techniques which have their roots in biology for producing fresh water from saline solution. In addition to reviewing and categorizing biodesalination processes for the first time, this review also reveals unexplored research areas in biodesalination having potential to be used in water treatment.

A diverse group of halophilic bacteria exist in Lunsu, a natural salt water body of Himachal Pradesh, India

Five halophilic bacterial isolates namely SS1, SS2, SS3, SS5 and SS8 were isolated from soil sediments of Lunsu, a salty water body. All the bacterial isolates showed growth in LB medium containing up to 8.7% NaCl, pH 7-8 and at temperature range of 30-37°C. The bacterial isolates SS1 and SS3 require at least 3.8% NaCl for their growth, indicating their strict halophilic nature. Interestingly, bacterial isolates SS2, SS5 and SS8 but not SS1 and SS3 exhibited growth in medium supplemented with KCl. Accordingly, Na(+) and K(+) ions were detected at 1.39 and 0.0035%, respectively in Lunsu water. All the bacterial isolates were analyzed by random amplification of polymorphic DNA (RAPD) using four different random primers and produced PCR fragments ranging from 0.1 to 5 kb in size. Phylogenetic tree based on RAPD finger prints showed that SS1 and SS3 formed one group, while SS2 and SS5 formed the second group, whereas SS8 was out group. Sequence analysis of 16S rDNA identified SS1 and SS3 as Halobacillus trueperi, SS2 as Shewanella algae, SS5 as Halomonas venusta, and SS8 as Marinomonas sp. were deposited in GenBank with accession numbers of KM260166, KF751761, KF751760, KF751762 and KF751763, respectively. This is the first report on the presence of diverse halophilic bacteria in the foot hills of Himalayas.

Adaptive strategies in the double-extremophilic prokaryotes inhabiting soda lakes

Haloalkaliphiles are double extremophilic organisms thriving both at high salinity and alkaline pH. Although numerous haloalkaliphilic representatives have been identified among Archaea and Bacteria over the past 15 years, the adaptations underlying their prosperity at haloalkaline conditions are scarcely known. A multi-level adaptive strategy was proposed to occur in haloalkaliphilic organisms isolated from saline alkaline and soda environments including adjustments in the cell wall structure, plasma membrane lipid composition, membrane transport systems, bioenergetics, and osmoregulation. Isolation of chemolithoautotrophic sulfur-oxidizing γ-Proteobacteria from soda lakes allowed the elucidation of the structural and physiological differences between haloalkaliphilic (prefer NaCl) and natronophilic (prefer NaHCO3/Na2CO3, i.e. soda) microbes.

Comparison of bacterial biodiversity and enzyme production in three hypersaline lakes; urmia, howz-soltan and aran-bidgol

This research is a comparative study on the diversity of halophilic bacteria with hydrolytic activities in three significant hypersaline lakes; Urmia in the northwest and Howz-Soltan and Aran-Bidgol in the central desert in Iran. Isolated strains from these saline lakes were found to be halotolerant, moderately and extremely halophilic bacteria. The bacteria in each saline lake were able to produce different hydrolytic enzymes including amylase, protease, lipase, DNase, inulinase, xylanase, carboxy methyl cellulase, pectinase and pullulanase. 188, 302, 91 halophilic strains were isolated from Urmia Lake, Howz-Soltan and Aran-Bidgol playa, respectively. The numbers of Gram-positive strains were more than Gram-negatives, and among Gram-positive bacteria; spore-forming bacilli were most abundant. Due to the unique physico-chemical conditions of the lake environments, the hydrolytic activities of isolated strains were significantly different. For instance, isolated strains from Howz-Soltan playa did not produce pectinase, DNase, amylase, lipase and inulinase, while the isolates from Aran-Bidgol playa had a great ability to produce pectinase and DNase. The strains from Urmia Lake were also good producers of DNase but failed to show any chitinase activity. The diversity of halophilic bacteria from the mentioned three saline lakes was also determined using PCR-amplified 16S rRNA followed by phylogenetic analysis of the partial 16S rRNA sequences.

Glutamine synthetase 2 is not essential for biosynthesis of compatible solutes in Halobacillus halophilus

Halobacillus halophilus, a moderately halophilic bacterium isolated from salt marshes, produces various compatible solutes to cope with osmotic stress. Glutamate and glutamine are dominant compatible solutes at mild salinities. Glutamine synthetase activity in cell suspensions of Halobacillus halophilus wild type was shown to be salt dependent and chloride modulated. A possible candidate to catalyze glutamine synthesis is glutamine synthetase A2, whose transcription is stimulated by chloride. To address the role of GlnA2 in the biosynthesis of the osmolytes glutamate and glutamine, a deletion mutant (ΔglnA2) was generated and characterized in detail. We compared the pool of compatible solutes and performed transcriptional analyses of the principal genes controlling the solute production in the wild type strain and the deletion mutant. These measurements did not confirm the hypothesized role of GlnA2 in the osmolyte production. Most likely the presence of another, yet to be identified enzyme has the main contribution in the measured activity in crude extracts and probably determines the total chloride-modulated profile. The role of GlnA2 remains to be elucidated.