Choline–betaine pathway contributes to hyperosmotic stress and subsequent lethal stress resistance in Pseudomonas protegens SN15-2

Comparative genomic analysis of two putative novel Idiomarina species from hypersaline miocene deposits

BACKGROUND

Hypersaline habitats, as extreme environments, are a great source of well-adapted organisms with unique properties as they have evolved various strategies to cope with these extreme conditions. Bioinformatics and genomic mining may shed light on evolutionary relationships among them. Therefore, the aim of this study was to assess the biodiversity and especially the strategies evolved within the Idiomarina genus, with the primary focus on the taxonomy and genomic adaptations of two novel strains affiliated with Idiomarina genus isolated from unique environment - brines of two Early Miocene salt deposits.

RESULTS

Both analyzed species belonged to the Idiomarina loihiensis cluster with similarity levels of 16S rRNA gene sequences as high as 99.5% and showed a significant genome size reduction, known characteristic of Idiomarina genomes, though within the genome of Sol25 strain the lowest extent of the carbohydrate utilization genes reduction was observed t among the Idiomarina species. Moreover, the comparative genome analyses indicated that despite both strains being isolated from geographically and geologically similar environments (brines from at least 12 Ma), the species showed higher relatedness to other Idiomarina species than to each other.

CONCLUSION

The present findings highlighted the importance of genomic data in resolving taxonomic uncertainties and understanding of adaptation strategies of extremophiles. Geographic isolation likely contributed to population divergence of the Idiomarina genus, and the recent study offered insights into biogeographic patterns and allopatric speciation of this bacterial group.

Thermal and salt stress effects on the survival of plant growth-promoting bacteria Azospirillum brasilense in inoculants for maize cultivation

BACKGROUND

The plant growth-promoting bacteria (PGPB) Azospirillum brasilense is widely used as an inoculant for important grass crops, providing numerous benefits to the plants. However, one limitation to develop viable commercial inoculants is the control of PGPB survival, requiring strategies that guarantee their survival during handling and field application. The application of sublethal stress appears to be a promising strategy to increase bacterial cells tolerance to adverse environmental conditions since previous stress induces the activation of physiological protection in bacterial cell. In this work, we evaluated the effects of thermal and salt stresses on the survival of inoculant containing A. brasilense Ab-V5 and Ab-V6 strains and we monitored A. brasilense viability in inoculated maize roots after stress treatment of inoculant.

RESULTS

Thermal stress application (> 35 °C) in isolated cultures for both strains, as well as salt stress [sodium chloride (NaCl) concentrations > 0.3 mol L-1], resulted in growth rate decline. The A. brasilense enumeration in maize roots obtained by propidium monoazide quantitative polymerase chain reaction (PMA-qPCR), for inoculated maize seedlings grown in vitro for 7 days, showed that there is an increased number of viable cells after the salt stress treatment, indicating that A. brasilense Ab-V5 and Ab-V6 strains are able to adapt to salt stress (0.3 mol L-1 NaCl) growth conditions.

CONCLUSION

Azospirillum brasilense Ab-V5 and Ab-V6 strains had potential for osmoadaptation and salt stress, resulting in increased cell survival after inoculation in maize plants. © 2024 Society of Chemical Industry.

Integrated Genomics and Transcriptomics Provide Insights into Salt Stress Response in Bacillus subtilis ACP81 from Moso Bamboo Shoot (Phyllostachys praecox) Processing Waste

Salt stress is detrimental to the survival of microorganisms, and only a few bacterial species produce hydrolytic enzymes. In this study, we investigated the expression of salt stress-related genes in the salt-tolerant bacterial strain Bacillus subtilis ACP81, isolated from bamboo shoot processing waste, at the transcription level. The results indicate that the strain could grow in 20% NaCl, and the sub-lethal concentration was 6% NaCl. Less neutral protease and higher cellulase and β-amylase activities were observed for B. subtilis ACP81 under sub-lethal concentrations than under the control concentration (0% NaCl). Transcriptome analysis showed that the strain adapted to high-salt conditions by upregulating the expression of genes involved in cellular processes (membrane synthesis) and defense systems (flagellar assembly, compatible solute transport, glucose metabolism, and the phosphotransferase system). Interestingly, genes encoding cellulase and β-amylase-related (malL, celB, and celC) were significantly upregulated and were involved in starch and sucrose metabolic pathways, and the accumulated glucose was effective in mitigating salt stress. RT-qPCR was performed to confirm the sequencing data. This study emphasizes that, under salt stress conditions, ACP81 exhibits enhanced cellulase and β-amylase activities, providing an important germplasm resource for saline soil reclamation and enzyme development.

Effects of sublethal stress application on the survival of bacterial inoculants: a systematic review

The use of commercial bacterial inoculants formulated with plant-growth promoting bacteria (PGPB) in agriculture has shown significant prominence in recent years due to growth-promotion benefits provided to plants through different mechanisms. However, the survival and viability of bacterial cells in inoculants are affected during use and may decrease their effectiveness. Physiological adaptation strategies have attracted attention to solve the viability problem. This review aims to provide an overview of research on selecting sublethal stress strategies to increase the effectiveness of bacterial inoculants. The searches were performed in November 2021 using Web of Science, Scopus, PubMed, and Proquest databases. The keywords "nitrogen-fixing bacteria", "plant growth-promoting rhizobacteria", "azospirillum", "pseudomonas", "rhizobium", "stress pre-conditioning", "adaptation", "metabolic physiological adaptation", "cellular adaptation", "increasing survival", "protective agent" and "protective strategy" were used in the searches. A total of 2573 publications were found, and 34 studies were selected for a deeper study of the subject. Based on the studies analysis, gaps and potential applications related to sublethal stress were identified. The most used strategies included osmotic, thermal, oxidative, and nutritional stress, and the primary cell response mechanism to stress was the accumulation of osmolytes, phytohormones, and exopolysaccharides (EPS). Under sublethal stress, the inoculant survival showed positive increments after lyophilization, desiccation, and long-term storage processes. The effectiveness of inoculant-plants interaction also had positive increments after sublethal stress, improving plant development, disease control, and tolerance to environmental stresses compared to unappealed inoculants.

Effects and molecular mechanism of flagellar gene flgK on the motility, adhesion/invasion, and desiccation resistance of Cronobacter sakazakii

Cronobacter sakazakii (C. sakazakii), a food-borne pathogen, can infect neonates, elderly and immunocompromised populations with a high infection and mortality rate. However, the specific molecular mechanism of its motility, biofilm formation, cell adhesion, and desiccation resistance remains unclear, and flagellum hook associated protein (FlgK), a main component of the flagellar complex, may be an important determinant of its virulence and desiccation resistance. In this study, the flgK mutant strain (ΔflgK) was constructed using the homologous recombination method, and the cpflgK complementary strain was obtained by gene complementation, followed by analysis of the difference between the wild type (WT), mutant, and complementary strains in mobility, biofilm formation, cell adhesion, and desiccation resistance. Results indicated that flgK gene played a positive role in motility and invasion, with no significant effect on biofilm formation. Interestingly, flagellar assembly gene deletion showed increased resistance of C. sakazakii to dehydration. The mechanism underlying the negative correlation of flgK gene with dehydration resistance was further investigated by using the high-throughput sequencing technology to compare the gene expression between WT and ΔflgK strains after drying. The results revealed up-regulation in the expression of 54 genes, including genes involved in osmosis and formate dehydrogenase, while down-regulation in the expression of 50 genes, including genes involved in flagellum hook and nitrate reductase. qRT-PCR analysis of the RNA-seq data further indicated that the flgK gene played an important role in the environmental stress resistance of C. sakazakii by up-regulating the formate dehydrogenase, betaine synthesis, and arginine deiminase pathways, due to dynamic proton imbalance caused by lack of flagella. This study facilitates our understanding of the roles of flgK in motion-related functions and the molecular mechanism of desiccation resistance in C. sakazakii.

Characterizing microbiota and metabolomics analysis to identify candidate biomarkers in lung cancer

Background

Lung cancer is the leading malignant disease and cause of cancer-related death worldwide. Most patients with lung cancer had insignificant early symptoms so that most of them were diagnosed at an advanced stage. In addition to factors such as smoking, pollution, lung microbiome and its metabolites play vital roles in the development of lung cancer. However, the interaction between lung microbiota and carcinogenesis is lack of systematically characterized and controversial. Therefore, the purpose of this study was to excavate the features of the lung microbiota and metabolites in patients and verify potential biomarkers for lung cancer diagnosis.

Methods

Lung tissue flushing solutions and bronchoalveolar lavage fluid samples came from patients with lung cancer and non-lung cancer. The composition and variations of the microbiota and metabolites in samples were explored using muti-omics technologies including 16S rRNA amplicon sequencing, metagenomics and metabolomics.

Results

The metabolomics analysis indicated that 40 different metabolites, such as 9,10-DHOME, sphingosine, and cysteinyl-valine, were statistically significant between two groups (VIP > 1 and P < 0.05). These metabolites were significantly enriched into 11 signal pathways including sphingolipid, autophagy and apoptosis signaling pathway (P < 0.05). The analysis of lung microbiota showed that significant changes reflected the decrease of microbial diversity, changes of distribution of microbial taxa, and variability of the correlation networks of lung microbiota in lung cancer patients. In particular, we found that oral commensal microbiota and multiple probiotics might be connected with the occurrence and progression of lung cancer. Moreover, our study found 3 metabolites and 9 species with significantly differences, which might be regarded as the potential clinical diagnostic markers associated with lung cancer.

Conclusions

Lung microbiota and metabolites might play important roles in the pathogenesis of lung cancer, and the altered metabolites and microbiota might have the potential to be clinical diagnostic markers and therapeutic targets associated with lung cancer.

Exogenous Regulators Enhance the Yield and Stress Resistance of Chlamydospores of the Biocontrol Agent Trichoderma harzianum T4

Trichoderma strains have been successfully used in plant disease control. However, the poor stress resistance of mycelia and conidia makes processing and storage difficult. Furthermore, they cannot produce chlamydospores in large quantities during fermentation, which limits the industrialization process of chlamydospore preparation. It is important to explore an efficient liquid fermentation strategy for ensuring chlamydospore production in Trichoderma harzianum. We found that the addition of mannitol, glycine betaine, and N-acetylglucosamine (N-A-G) during liquid fermentation effectively increases the yield of chlamydospores. Furthermore, we provided evidence that chlamydospores have stronger tolerance to high temperature, ultraviolet, and hypertonic stress after the addition of mannitol and trehalose. Lipids are an important component of microbial cells and impact the stress resistance of microorganisms. We studied the internal relationship between lipid metabolism and the stress resistance of chlamydospores by detecting changes in the lipid content and gene expression. Our results showed that mannitol and trehalose cause lipid accumulation in chlamydospores and increase the unsaturated fatty acid content. In conclusion, we verified that these exogenous regulators increase the production of chlamydospores and enhance their stress resistance by regulating lipid metabolism. In addition, we believe that lipid metabolism is an important part of the chlamydospore production process and impacts the stress resistance of chlamydospores. Our findings provide clues for studying the differentiation pathway of chlamydospores in filamentous fungi and a basis for the industrial production of chlamydospores.

Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139

For bacteria to thrive in an environment with competitors, phages and environmental cues, they use different strategies, including Type VI Secretion Systems (T6SSs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to compete for space. Bacteria often use quorum sensing (QS), to coordinate their behavior as the cell density increases. Like other aliivibrios, Aliivibrio wodanis 06/09/139 harbors two QS systems, the main LuxS/LuxPQ system and an N-acyl homoserine lactone (AHL)-mediated AinS/AinR system and a master QS regulator, LitR. To explore the QS and survival strategies, we performed genome analysis and gene expression profiling on A. wodanis and two QS mutants (ΔainS and ΔlitR) at two cell densities (OD600 2.0 and 6.0) and temperatures (6 and 12°C). Genome analysis of A. wodanis revealed two CRISPR systems, one without a cas loci (CRISPR system 1) and a type I-F CRISPR system (CRISPR system 2). Our analysis also identified three main T6SS clusters (T6SS1, T6SS2, and T6SS3) and four auxiliary clusters, as well about 80 potential Type VI secretion effectors (T6SEs). When comparing the wildtype transcriptome data at different cell densities and temperatures, 13-18% of the genes were differentially expressed. The CRISPR system 2 was cell density and temperature-independent, whereas the CRISPR system 1 was temperature-dependent and cell density-independent. The primary and auxiliary clusters of T6SSs were both cell density and temperature-dependent. In the ΔlitR and ΔainS mutants, several CRISPR and T6SS related genes were differentially expressed. Deletion of litR resulted in decreased expression of CRISPR system 1 and increased expression of CRISPR system 2. The T6SS1 and T6SS2 gene clusters were less expressed while the T6SS3 cluster was highly expressed in ΔlitR. Moreover, in ΔlitR, the hcp1 gene was strongly activated at 6°C compared to 12°C. AinS positively affected the csy genes in the CRISPR system 2 but did not affect the CRISPR arrays. Although AinS did not significantly affect the expression of T6SSs, the hallmark genes of T6SS (hcp and vgrG) were AinS-dependent. The work demonstrates that T6SSs and CRISPR systems in A. wodanis are QS dependent and may play an essential role in survival in its natural environment.

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant's rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO₃ (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity

Pine honey is a unique type of honeydew honey produced exclusively in Eastern Mediterranean countries like Greece and Turkey. Although the antioxidant and anti-inflammatory properties of pine honey are well documented, few studies have investigated so far its antibacterial activity. This study investigates the antibacterial effects of pine honey against P. aeruginosa PA14 at the molecular level using a global transcriptome approach via RNA-sequencing. Pine honey treatment was applied at sub-inhibitory concentration and short exposure time (0.5× of minimum inhibitory concentration –MIC- for 45 min). Pine honey induced the differential expression (>two-fold change and p ≤ 0.05) of 463 genes, with 274 of them being down-regulated and 189 being up-regulated. Gene ontology (GO) analysis revealed that pine honey affected a wide range of biological processes (BP). The most affected down-regulated BP GO terms were oxidation-reduction process, transmembrane transport, proteolysis, signal transduction, biosynthetic process, phenazine biosynthetic process, bacterial chemotaxis, and antibiotic biosynthetic process. The up-regulated BP terms, affected by pine honey treatment, were those related to the regulation of DNA-templated transcription, siderophore transport, and phosphorylation. Pathway analysis revealed that pine honey treatment significantly affected two-component regulatory systems, ABC transporter systems, quorum sensing, bacterial chemotaxis, biofilm formation and SOS response. These data collectively indicate that multiple mechanisms of action are implicated in antibacterial activity exerted by pine honey against P. aeruginosa.