DEOP: a database on osmoprotectants and associated pathways

Microscopy and spatial-metabolomics identify tissue-specific metabolic pathways uncovering salinity and drought tolerance mechanisms in Avicennia marina and Phoenix dactylifera roots

In arid and semi-arid climates, native plants have developed unique strategies to survive challenging conditions. These adaptations often rely on molecular pathways that shape plant architecture to enhance their resilience. Date palms (Phoenix dactylifera) and mangroves (Avicennia marina) endure extreme heat and high salinity, yet the metabolic pathways underlying this resilience remain underexplored. Here, we integrate tissue imaging with spatial metabolomics to uncover shared and distinct adaptive features in these species. We found that mangrove roots accumulate suberin and lignin in meristematic tissues, this is unlike other plant species, where only the differentiation zones contain these compounds. Our metabolomic analysis shows that date palm roots are enriched in metabolites involved in amino acid biosynthesis, whereas compounds involved in lignin and suberin production were more abundant in mangrove roots. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed tissue- and species-specific metabolite distributions in root tissues. We identified common osmoprotectants accumulating in the exodermis/epidermis of date palm and mangrove root meristems, along with a unique metabolite highly abundant in the inner cortex of date palm roots. These findings provide valuable insights into stress adaptation pathways and highlight key tissue types involved in root stress response.

Intracellular and Extracellular Metabolic Response of the Lactic Acid Bacterium Weissella confusa Under Salt Stress

BACKGROUND

Weissella confusa is a member of the lactic acid bacterium group commonly found in many salt-fermented foods. Strains of W. confusa isolated from high-salinity environments have been shown to tolerate salt stress to some extent. However, the specific responses and mechanisms of W. confusa under salt stress are not fully understood.

METHODS

To study the effect of NaCl stress on W. confusa, growth performance and metabolite profiles of the strains were compared between a NaCl-free group and a 35% NaCl-treated group. Growth performance was assessed by measuring viable cell counts and examining the cells using scanning electron microscopy (SEM). Intracellular and extracellular metabolites were analyzed by non-targeted metabolomics based on liquid chromatography-mass spectrometry (LC-MS).

RESULTS

It was found that the viable cell count of W. confusa decreased with increasing salinity, and cells could survive even in saturated saline (35%) medium for 24 h. When exposed to 35% NaCl, W. confusa cells exhibited surface pores and protein leakage. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, 42 different metabolites were identified in the cells and 18 different metabolites in the culture medium. These different metabolites were mainly involved in amino acid metabolism, carbohydrate metabolism, and nucleotide metabolism. In addition, salt-exposed cells exhibited higher levels of intracellular ectoine and lactose, whose precursors, such as aspartate, L-2,4-diaminobutanoate, and galactinol, were reduced in the culture medium.

CONCLUSIONS

This study provides insight into the metabolic responses of W. confusa under salt stress, revealing its ability to maintain viability and alter metabolism in response to high NaCl concentrations. Key metabolites such as ectoine and lactose, as well as changes in amino acid and nucleotide metabolism, may contribute to its tolerance to salt. These findings may improve our understanding of the bacterium's survival mechanisms and have potential applications in food fermentation and biotechnology.

Unveiling the role of emerging metagenomics for the examination of hypersaline environments

Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE

The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome

Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.

Roles of Bacterial Mechanosensitive Channels in Infection and Antibiotic Susceptibility

Bacteria accumulate osmolytes to prevent cell dehydration during hyperosmotic stress. A sudden change to a hypotonic environment leads to a rapid water influx, causing swelling of the protoplast. To prevent cell lysis through osmotic bursting, mechanosensitive channels detect changes in turgor pressure and act as emergency-release valves for the ions and osmolytes, restoring the osmotic balance. This adaptation mechanism is well-characterized with respect to the osmotic challenges bacteria face in environments such as soil or an aquatic habitat. However, mechanosensitive channels also play a role during infection, e.g., during host colonization or release into environmental reservoirs. Moreover, recent studies have proposed roles for mechanosensitive channels as determinants of antibiotic susceptibility. Interestingly, some studies suggest that they serve as entry gates for antimicrobials into cells, enhancing antibiotic efficiency, while others propose that they play a role in antibiotic-stress adaptation, reducing susceptibility to certain antimicrobials. These findings suggest different facets regarding the relevance of mechanosensitive channels during infection and antibiotic exposure as well as illustrate that they may be interesting targets for antibacterial chemotherapy. Here, we summarize the recent findings on the relevance of mechanosensitive channels for bacterial infections, including transitioning between host and environment, virulence, and susceptibility to antimicrobials, and discuss their potential as antibacterial drug targets.

Contribution of Exogenous Proline to Abiotic Stresses Tolerance in Plants: A Review

Abiotic stresses are the major environmental factors that play a significant role in decreasing plant yield and production potential by influencing physiological, biochemical, and molecular processes. Abiotic stresses and global population growth have prompted scientists to use beneficial strategies to ensure food security. The use of organic compounds to improve tolerance to abiotic stresses has been considered for many years. For example, the application of potential external osmotic protective compounds such as proline is one of the approaches to counteract the adverse effects of abiotic stresses on plants. Proline level increases in plants in response to environmental stress. Proline accumulation is not just a signal of tension. Rather, according to research discussed in this article, this biomolecule improves plant resistance to abiotic stress by rising photosynthesis, enzymatic and non-enzymatic antioxidant activity, regulating osmolyte concentration, and sodium and potassium homeostasis. In this review, we discuss the biosynthesis, sensing, signaling, and transport of proline and its role in the development of various plant tissues, including seeds, floral components, and vegetative tissues. Further, the impacts of exogenous proline utilization under various non-living stresses such as drought, salinity, high and low temperatures, and heavy metals have been extensively studied. Numerous various studies have shown that exogenous proline can improve plant growth, yield, and stress tolerance under adverse environmental factors.

Chemical Profiling, Bioactivity Evaluation and the Discovery of a Novel Biopigment Produced by Penicillium purpurogenum CBS 113139

Biobased pigments are environmentally friendly alternatives to synthetic variants with an increased market demand. Production of pigments via fermentation is a promising process, yet optimization of the production yield and rate is crucial. Herein, we evaluated the potential of Penicillium purpurogenum to produce biobased pigments. Optimum sugar concentration was 30 g/L and optimum C:N ratio was 36:1 resulting in the production of 4.1–4.5 AU (namely Pigment Complex A). Supplementation with ammonium nitrate resulted in the production of 4.1–4.9 AU (namely Pigment Complex B). Pigments showed excellent pH stability. The major biopigments in Pigment Complex A were N-threonyl-rubropunctamin or the acid form of PP-R (red pigment), N-GABA-PP-V (violet pigment), PP-O (orange pigment) and monascorubrin. In Pigment Complex B, a novel biopigment annotated as N-GLA-PP-V was identified. Its basic structure contains a polyketide azaphilone with the same carboxyl-monascorubramine base structure as PP-V (violet pigment) and γ-carboxyglutamic acid (GLA). The pigments were not cytotoxic up to 250 μg/mL.

Niche breadth affects bacterial transcription patterns along a salinity gradient

Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum habitat, generalists with broad NB adapt to multiple environments. The main objective of this study was to identify general transcriptional patterns that would distinguish bacterial strains characterized by contrasted NBs along a salinity gradient. More specifically, we hypothesized that genes encoding fitness-related traits, such as biomass production, have a higher degree of transcriptional regulation in specialists than in generalists, because the fitness of specialists is more variable under environmental change. By contrast, we expected that generalists would exhibit enhanced transcriptional regulation of genes encoding traits that protect them against cellular damage. To test these hypotheses, we assessed the transcriptional regulation of fitness-related and adaptation-related genes of 11 bacterial strains in relation to their NB and stress exposure under changing salinity conditions. The results suggested that transcriptional regulation levels of fitness- and adaptation-related genes correlated with the NB and/or the stress exposure of the inspected strains. We further identified a shortlist of candidate stress marker genes that could be used in future studies to monitor the susceptibility of bacterial populations or communities to environmental changes.

Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity

The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.

Physiological and metabolic adjustments in the xero-halophyte Haloxylon salicornicum conferring drought tolerance

Drought is one of the most catastrophic abiotic stresses that affects global food production severely. The present work investigates the metabolic and physiological adaptation mechanisms in the xero-halophyte Haloxylon salicornicum to counter the effects of drought. This xero-halophyte can withstand a prolonged drought period of 14 days and recovered within 7 days of irrigation with minimal effects of drought on growth and physiological parameters. Photosynthetic parameters such as P_N , g_s , and E decreased significantly, whereas WUE increased under drought condition. Drought induces a significant decline in the Fv/Fm ratio. However, the value of Fv/Fm ratio successfully recovered within 7 days of the recovery period. Differential regulations of various antioxidative enzymes increase the drought tolerance potential of H. salicornicum. The metabolomic analysis of H. salicornicum shoot identified 63 metabolites: 43 significantly increased and 20 significantly decreased under drought conditions. These metabolites mainly include amino acids, organic acids, amines, sugar alcohols, sugars, fatty acids, alkaloids, and phytohormones. The metabolites that have a significant contribution towards drought tolerance include citric acid, malic acid, tartaric acid, d-erythrose, glyceric acid, sucrose, pentanoic acid, d-mannitol, ABA, and palmitic acid. KEGG pathway enrichment analysis showed that the vital drought-responsive metabolic pathways mainly include galactose metabolism, aminoacyl-tRNA biosynthesis, glyoxylate and dicarboxylate metabolism, citrate cycle (TCA cycle), alanine, aspartate, and glutamate metabolism. This study offers comprehensive information on physiological, antioxidative and metabolic adaptations and overall drought tolerance mechanisms in H. salicornicum. The information gained from this study will provide guidance to plant breeders and molecular biologists to develop drought-tolerant crop varieties.

Secondary Metabolites From Halotolerant Plant Growth Promoting Rhizobacteria for Ameliorating Salinity Stress in Plants

Soil salinization has emerged as one of the prime environmental constraints endangering soil quality and agricultural productivity. Anthropogenic activities coupled with rapid pace of climate change are the key drivers of soil salinity resulting in degradation of agricultural lands. Increasing levels of salt not only impair structure of soil and its microbial activity but also restrict plant growth by causing harmful imbalance and metabolic disorders. Potential of secondary metabolites synthesized by halotolerant plant growth promoting rhizobacteria (HT-PGPR) in the management of salinity stress in crops is gaining importance. A wide array of secondary metabolites such as osmoprotectants/compatible solutes, exopolysaccharides (EPS) and volatile organic compounds (VOCs) from HT-PGPR have been reported to play crucial roles in ameliorating salinity stress in plants and their symbiotic partners. In addition, HT-PGPR and their metabolites also help in prompt buffering of the salt stress and act as biological engineers enhancing the quality and productivity of saline soils. The review documents prominent secondary metabolites from HT-PGPR and their role in modulating responses of plants to salinity stress. The review also highlights the mechanisms involved in the production of secondary metabolites by HT-PGPR in saline conditions. Utilizing the HT-PGPR and their secondary metabolites for the development of novel bioinoculants for the management of saline agro-ecosystems can be an important strategy in the future.

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

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

Untargeted metabolomics as a hypothesis-generation tool in plant protection product discovery: Highlighting the potential of trehalose and glycerol metabolism of fungal conidiospores as novel targets

INTRODUCTION

The production of high quality and safe food represents a main priority for the agri-food sector in the effort to sustain the exponentially growing human population. Nonetheless, there are major challenges that require the discovery of new, alternative, and improved plant protection products (PPPs). Focusing on fungal plant pathogens, the dissection of mechanisms that are essential for their survival provides insights that could be exploited towards the achievement of the aforementioned aim. In this context, the germination of fungal spores, which are essential structures for their dispersal, survival, and pathogenesis, represents a target of high potential for PPPs. To the best of our knowledge, no PPPs that target the germination of fungal spores currently exist.

OBJECTIVES

Within this context, we have mined for changes in the metabolite profiles of the model fungus Aspergillus nidulans FGSC A4 conidiospores during germination, in an effort to discover key metabolites and reactions that could potentially become targets of PPPs.

METHODS

Untargeted GC/EI-TOF/MS metabolomics and multivariate analyses were employed to monitor time-resolved changes in the metabolomes of germinating A. nidulans conidiospores.

RESULTS

Analyses revealed that trehalose hydrolysis plays a pivotal role in conidiospore germination and highlighted the osmoregulating role of the sugar alcohols, glycerol, and mannitol.

CONCLUSION

The ineffectiveness to introduce active ingredients that exhibit new mode(s)-of-action as fungicides, dictates the urge for the discovery of PPPs, which could be exploited to combat major plant protection issues. Based on the crucial role of trehalose hydrolysis in conidiospore dormancy breakage, and the subsequent involvement of glycerol in their germination, it is plausible to suggest their biosynthesis pathways as potential novel targets for the next-generation antifungal PPPs. Our study confirmed the applicability of untargeted metabolomics as a hypothesis-generation tool in PPPs' research and discovery.

Metabolomic study reveals key metabolic adjustments in the xerohalophyte Salvadora persica L. during adaptation to water deficit and subsequent recovery conditions

Water deficit severely limits productivity of plants, and pose a major threat to modern agriculture system. Therefore, understanding drought adaptive mechanisms in drought-tolerant plants is imperative to formulate strategies for development of desiccation tolerance in crop plants. In present investigation, metabolic profiling employing GC-QTOF-MS/MS and HPLC-DAD was carried out to evaluate metabolic adjustments under drought stress in the xero-halophyte Salvadora persica. The metabolite profiling identified a total of 68 metabolites in S. persica leaf, including organic acids, amino acids, sugars, sugar alcohols, hormones, and polyphenols. The results showed that higher cellular osmolality under drought stress was accompanied by accumulations of several osmoprotectants like sugars and polyols (sucrose, glucose, mannose, galactose, erythrose, sorbose, glycerol, and myoinositol), organic acids (galactaric acid, tartaric acid, malic acid, oxalic acid, and citric acid), and amino acids (alanine, phenylalanine, tyrosine). Upregulation of ABA and JA support to achieve early drought tolerance in S. persica. Moreover, accumulation of coumarin, gallic acid, and chlorogenic acid provide antioxidative defense to S. persica. KEGG pathway enrichment analysis showed that altered metabolites were associated with starch and sucrose metabolism, galactose metabolism, inositol phosphate metabolism, and phenylalanine metabolism. While during recovery, metabolites associated with lysine biosynthesis and alanine, aspartate and glutamate metabolism were significantly altered. The results of the present study imply that coordinated regulations between various metabolites, metabolic processes, and pathways empower the xerohalophyte S. persica to adapt under drought environment. The knowledge from this study will enable the development of drought tolerance in crops using genetic engineering and breeding approaches.

Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors

The study of pathogenic agents in their natural niches allows for a better understanding of disease persistence and dissemination. Bacteria belonging to the Agrobacterium genus are soil-borne and can colonize the rhizosphere. These bacteria are also well known as phytopathogens as they can cause tumors (crown gall disease) by transferring a DNA region (T-DNA) into a wide range of plants. Most reviews on Agrobacterium are focused on virulence determinants, T-DNA integration, bacterial and plant factors influencing the efficiency of genetic transformation. Recent research papers have focused on the plant tumor environment on the one hand, and genetic traits potentially involved in bacterium-plant interactions on the other hand. The present review gathers current knowledge about the special conditions encountered in the tumor environment along with the Agrobacterium genetic determinants putatively involved in bacterial persistence inside a tumor. By integrating recent metabolomic and transcriptomic studies, we describe how tumors develop and how Agrobacterium can maintain itself in this nutrient-rich but stressful and competitive environment.

Osmoprotectants in Hybrid Liposome/HPMC Systems as Potential Glaucoma Treatment

The combination of acetazolamide-loaded nano-liposomes and Hydroxypropyl methylcellulose (HPMC) with similar components to the preocular tear film in an osmoprotectant media (trehalose and erythritol) is proposed as a novel strategy to increase the ocular bioavailability of poorly soluble drugs. Ophthalmic formulations based on acetazolamide-loaded liposomes, dispersed in the osmoprotectant solution (ACZ-LP) or in combination with HPMC (ACZ-LP-P) were characterized and in vivo evaluated. The pH and tonicity of both formulations resulted in physiological ranges. The inclusion of HPMC produced an increment in viscosity (from 0.9 to 4.7 mPa·s. 64.9 ± 2.6% of acetazolamide initially included in the formulation was retained in vesicles. In both formulations, a similar onset time (1 h) and effective time periods were observed (7 h) after a single instillation (25 μL) in normotensive rabbits' eyes. The AUC_0-8h of the ACZ-LP-P was 1.5-fold higher than of ACZ-LP (p < 0.001) and the maximum hypotensive effect resulted in 1.4-fold higher (p < 0.001). In addition, the formulation of ACZ in the hybrid liposome/HPMC system produced a 30.25-folds total increment in ocular bioavailability, compared with the drug solution. Excellent tolerance in rabbits' eyes was confirmed during the study.

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium 'LA0480.' Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The 'LA0480' genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the 'LA0480' protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in 'LA0480.' Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

Homeostasis of Second Messenger Cyclic-di-AMP Is Critical for Cyanobacterial Fitness and Acclimation to Abiotic Stress

Second messengers are intracellular molecules regulated by external stimuli known as first messengers that are used for rapid organismal responses to dynamic environmental changes. Cyclic di-AMP (c-di-AMP) is a relatively newly discovered second messenger implicated in cell wall homeostasis in many pathogenic bacteria. C-di-AMP is synthesized from ATP by diadenylyl cyclases (DAC) and degraded by specific c-di-AMP phosphodiesterases (PDE). C-di-AMP DACs and PDEs are present in all sequenced cyanobacteria, suggesting roles for c-di-AMP in the physiology and/or development of these organisms. Despite conservation of these genes across numerous cyanobacteria, the functional roles of c-di-AMP in cyanobacteria have not been well-investigated. In a unique feature of cyanobacteria, phylogenetic analysis indicated that the broadly conserved DAC, related to CdaA/DacA, is always co-associated in an operon with genes critical for controlling cell wall synthesis. To investigate phenotypes regulated by c-di-AMP in cyanobacteria, we overexpressed native DAC (sll0505) and c-di-AMP PDE (slr0104) genes in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis) to increase and decrease intracellular c-di-AMP levels, respectively. DAC- and PDE-overexpression strains, showed abnormal aggregation phenotypes, suggesting functional roles for regulating c-di-AMP homeostasis in vivo. As c-di-AMP may be implicated in osmotic responses in cyanobacteria, we tested whether sorbitol and NaCl stresses impacted expression of sll0505 and slr0104 or intracellular c-di-AMP levels in Synechocystis. Additionally, to determine the range of cyanobacteria in which c-di-AMP may function, we assessed c-di-AMP levels in two unicellular cyanobacteria, i.e., Synechocystis and Synechococcus elongatus PCC 7942, and two filamentous cyanobacteria, i.e., Fremyella diplosiphon and Anabaena sp. PCC 7120. C-di-AMP levels responded differently to abiotic stress signals in distinct cyanobacteria strains, whereas salt stress uniformly impacted another second messenger cyclic di-GMP in cyanobacteria. Together, these results suggest regulation of c-di-AMP homeostasis in cyanobacteria and implicate a role for the second messenger in maintaining cellular fitness in response to abiotic stress.

Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO4 at Identical Water Activity

Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such as the accumulation of certain organic solutes (known as either compatible solutes or osmolytes). Less well studied are responses to ionic environments such as sulfate-rich brines which are prevalent on Earth but can also be found on Mars. In this paper, we investigated the global metabolic response of the anaerobic bacterium Yersinia intermedia MASE-LG-1 to osmotic salt stress induced by either magnesium sulfate (MgSO4) or NaCl at the same water activity (0.975). Using a non-targeted mass spectrometry approach, the intensity of hundreds of metabolites was measured. The compatible solutes L-asparagine and sucrose were found to be increased in both MgSO4 and NaCl compared to the control sample, suggesting a similar osmotic response to different ionic environments. We were able to demonstrate that Yersinia intermedia MASE-LG-1 accumulated a range of other compatible solutes. However, we also found the global metabolic responses, especially with regard to amino acid metabolism and carbohydrate metabolism, to be salt-specific, thus, suggesting ion-specific regulation of specific metabolic pathways.

Growth arrest and a persister state enable resistance to osmotic shock and facilitate dissemination of Vibrio cholerae

Vibrio cholerae is a water-borne bacterial pathogen and causative agent of cholera. Although V. cholerae is a halophile, it can survive in fresh water, and this has a major role in cholera epidemics through consumption of contaminated water and subsequent fecal-oral spread. After dissemination from humans back into fresh water, V. cholerae encounters limited nutrient availability and an abrupt drop in conductivity but little is known about how V. cholerae adapts to, and survives in this environment. In this work, by abolishing or altering the expression of V. cholerae genes in a high-throughput manner, we observed that many osmotic shock tolerant mutants exhibited slowed or arrested growth, and/or generated a higher proportion of persister cells. In addition, we show that growth-arrested V. cholerae, including a persister subpopulation, are generated during infection of the intestinal tract and together allow for the successful dissemination to fresh water. Our results suggest that growth-arrested and persister subpopulations enable survival of V. cholerae upon shedding to the aquatic environment.

Global Metabolic Responses to Salt Stress in Fifteen Species

Cells constantly adapt to unpredictably changing extracellular solute concentrations. A cornerstone of the cellular osmotic stress response is the metabolic supply of energy and building blocks to mount appropriate defenses. Yet, the extent to which osmotic stress impinges on the metabolic network remains largely unknown. Moreover, it is mostly unclear which, if any, of the metabolic responses to osmotic stress are conserved among diverse organisms or confined to particular groups of species. Here we investigate the global metabolic responses of twelve bacteria, two yeasts and two human cell lines exposed to sustained hyperosmotic salt stress by measuring semiquantitative levels of hundreds of cellular metabolites using nontargeted metabolomics. Beyond the accumulation of osmoprotectants, we observed significant changes of numerous metabolites in all species. Global metabolic responses were predominantly species-specific, yet individual metabolites were characteristically affected depending on species’ taxonomy, natural habitat, envelope structure or salt tolerance. Exploiting the breadth of our dataset, the correlation of individual metabolite response magnitudes across all species implicated lower glycolysis, tricarboxylic acid cycle, branched-chain amino acid metabolism and heme biosynthesis to be generally important for salt tolerance. Thus, our findings place the global metabolic salt stress response into a phylogenetic context and provide insights into the cellular phenotype associated with salt tolerance.

DESM: portal for microbial knowledge exploration systems

Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.

Databases for Microbiologists

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.