Amino acids improve acid tolerance and internal pH maintenance in Bacillus cereus ATCC14579 strain

Genomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium

Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.

Effect of Goji Berry extract on cell viability of Lactiplantibacillus plantarum M5 microcapsules during in vitro gastrointestinal digestion

Lactiplantibacillus plantarum M5 and Goji Berry extract were co-microencapsulated to maintain the activity of cells during gastrointestinal digestion, and the mechanism by which they could maintain high activity was investigated. The results showed that the microcapsules with 3% Goji Berry extract(A-GE-3) had the largest encapsulation efficiency(EE) of 92.41 ± 0.58%. SEM showed that the structure of A-GE-3 microcapsules were smoother and denser. Cell viability in A-GE-3 microcapsules remained at 7.17 log10 CFU/g after gastrointestinal digestion. Meanwhile, during the gastrointestinal digestion with 3% Goji Berry extract, cell membrane damage detected by fluorescent probes propidium iodide(PI) and 1.1-N-phenylnaphthylamine(NPN) was significantly reduced; the contents of arginine, glutamic acid and oleic acid in cell membrane were increased, which helped to maintain the dynamic balance of intracellular pH and regulated cell membrane fluidity in response to gastrointestinal environment. This study demonstrated the potential of Goji Berry extract as a probiotic protector in gastrointestinal digestion.

Effect of the initial pH of the culture medium on the nutrient consumption pattern of Bifidobacterium animalis subsp. lactis Bb12 and the improvement of acid resistance by purine and pyrimidine compounds

AIMS

During fermentation, the accumulation of acidic products can induce media acidification, which restrains the growth of Bifidobacterium animalis subsp. lactis Bb12 (Bb12). This study investigated the nutrient consumption patterns of Bb12 under acid stress and effects of specific nutrients on the acid resistance of Bb12.

METHODS AND RESULTS

Bb12 was cultured in chemically defined medium (CDM) at different initial pH values. Nutrient consumption patterns were analyzed in CDM at pH 5.3, 5.7, and 6.7. The patterns varied with pH: Asp + Asn had the highest consumption rate at pH 5.3 and 5.7, while Ala was predominant at pH 6.7. Regardless of the pH levels (5.3, 5.7, or 6.7), ascorbic acid, adenine, and Fe2+ were vitamins, nucleobases, and metal ions with the highest consumption rates, respectively. Nutrients whose consumption rates exceeded 50% were added individually in CDM at pH 5.3, 5.7, and 6.7. It was demonstrated that only some of them could promote the growth of Bb12. Mixed nutrients that could promote the growth of Bb12 were added to three different CDM. In CDM at pH 5.3, 5.7, and 6.7, it was found that the viable cell count of Bb12 was the highest after adding mixed nutrients, which were 8.87, 9.02, and 9.10 log CFU ml-1, respectively.

CONCLUSIONS

The findings suggest that the initial pH of the culture medium affects the nutrient consumption patterns of Bb12. Specific nutrients can enhance the growth of Bb12 under acidic conditions and increase its acid resistance.

Acid tolerance of Lactobacillus spp. on root carious lesions: A complex and multifaceted response

Lactobacillus spp. are acidogenic and aciduric bacteria and are among the main cariogenic microorganisms associated with the carious process.

OBJECTIVE

This study aimed to identify genes involved in the acid-tolerance of Lactobacillus spp. and potential functions attributed to these genes within the metatranscriptome of sound root surfaces and carious root surfaces.

DESIGN

Genomic libraries were built from mRNA isolated from the biofilm samples (10 from sound root and 9 from carious root using Illumina HiSeq 2500). Reads generated by RNA-seq were mapped against 162 oral microbial genomes and genes potentially related to acid tolerance were manually extracted from the Lactobacillus spp. genomes using L. paracasei ATCC 344 as reference genome. The R package DESeq2 was used to calculate the level of differential gene expression between those two clinical conditions.

RESULTS

Fifteen Lactobacillus spp. genomes were identified and a total of 653 acid tolerance genes were overexpressed in carious root surfaces. Multiple functions, as translation, ribosomal structure and biogenesis, transport of nucleotides and amino acids, are involved in Lactobacillus spp. acid tolerance. Species-specific functions also seem to be related to the fitness of Lactobacillus spp. in acidified environments such as that of the cariogenic biofilm associated with carious root lesions.

CONCLUSIONS

The response of Lactobacillus spp. to an acidic environment is complex and multifaceted. This finding suggests several possible avenues for further research into the adaptive mechanisms of these bacteria.

Modification of the second PEP4-allele facilitates an industrial Saccharomyces cerevisiae to tolerate tartaric acid stress

The practical significance of constructing robust industrial production strains against organic acid stress lies not only in improving fermentation efficiency but also in reducing manufacturing costs. In a previous study, we constructed an industrial Saccharomyces cerevisiae strain by modifying another PEP4-allele of a mutant that already had one PEP4-allele disrupted. This modification enhanced cellular tolerance to citric acid stress during growth. Unlike citric acid, which S. cerevisiae can consume, tartaric acid is often added to grape must during winemaking to increase total acidity and is not metabolizable. The results of the present study indicate that the modification of the second PEP4-allele improves the cellular tolerance of the strain with one PEP4-allele disrupted against tartaric acid stress during growth and contributes to maintaining intracellular pH homeostasis in cells subjected to tartaric acid stress. Moreover, under tartaric acid stress, a significant improvement in glucose-ethanol conversion performance, conferred by the modification of the second PEP4-allele, was observed. This study not only broadens our understanding of the role of the PEP4-allele in cellular regulation but also provides a prospective approach to reducing the concentration of sulfur dioxide used in winemaking.

Metabolomic and physiological changes of acid-tolerant Graesiella sp. MA1 during long-term acid stress

Algae plays a significant role for the primary production in the oligotrophic ecosystems such as the acid mine pit lakes. Graesiella sp. MA1 was a new acid-tolerant photosynthetic protist isolated from an acid mine pit lake. To understand the acid responses of Graesiella sp. MA1, its physiological changes and metabolomics were studied during long-term acid stress. Photosynthetic pigments, soluble proteins, and antioxidant systems of Graesiella sp. MA1 cells displayed two phases, the adaptation phase and the growth phase. During the adaptation phase, both photosynthetic pigments and soluble proteins were inhibited, while antioxidant activity of SOD, APX, and GSH were promoted to response to the organism's damage. Metabolomics results revealed lipids and organic acids were abundant components in Graesiella sp. MA1 cells. In response to acid stress, the levels of acid-dependent resistant amino acids, including glutamate, aspartate, arginine, proline, lysine, and histidine, accumulated continuously to maintain orderly intracellular metabolic processes. In addition, fatty acids were mainly unsaturated, which could improve the fluidity of the cell membranes under acid stress. Metabolomic and physiological changes showed that Graesiella sp. MA1 had tolerance during long-term acid stress and the potential to be used as a bioremediation strain for the acidic wastewater.

Contribution of amino acids to Alicyclobacillus acidoterrestris DSM 3922T resistance towards acid stress

Spoilage of juice and beverages by a thermo-acidophilic bacterium, Alicyclobacillus acidoterrestris, has been considered to be a major and widespread concern for juice industry. Acid-resistant property of A. acidoterrestris supports its survival and multiplication in acidic juice and challenges the development of corresponding control measures. In this study, intracellular amino acid differences caused by acid stress (pH 3.0, 1 h) were determined by targeted metabolomics. The effect of exogenous amino acids on acid resistance of A. acidoterrestris and the related mechanisms were also investigated. The results showed that acid stress affected the amino acid metabolism of A. acidoterrestris, and the selected glutamate, arginine, and lysine contributed to its survival under acid stress. Exogenous glutamate, arginine, and lysine significantly increased the intracellular pH and ATP level, alleviated cell membrane damage, reduced surface roughness, and suppressed deformation caused by acid stress. Additionally, the up-regulated gadA and speA genes and the enhanced enzymatic activity confirmed that glutamate and arginine decarboxylase systems played a crucial role in maintaining pH homeostasis of A. acidoterrestris under acid stress. Our research reveals an important factor contributing to acid resistance of A. acidoterrestris, which provides an alternative target for effectively controlling this contaminant in fruit juices.

Journey of the Probiotic Bacteria: Survival of the Fittest

This review aims to bring a more general view of the technological and biological challenges regarding production and use of probiotic bacteria in promoting human health. After a brief description of the current concepts, the challenges for the production at an industrial level are presented from the physiology of the central metabolism to the ability to face the main forms of stress in the industrial process. Once produced, these cells are processed to be commercialized in suspension or dried forms or added to food matrices. At this stage, the maintenance of cell viability and vitality is of paramount for the quality of the product. Powder products requires the development of strategies that ensure the integrity of components and cellular functions that allow complete recovery of cells at the time of consumption. Finally, once consumed, probiotic cells must face a very powerful set of physicochemical mechanisms within the body, which include enzymes, antibacterial molecules and sudden changes in pH. Understanding the action of these agents and the induction of cellular tolerance mechanisms is fundamental for the selection of increasingly efficient strains in order to survive from production to colonization of the intestinal tract and to promote the desired health benefits.

The Arginine Biosynthesis Pathway of Candida albicans Regulates Its Cross-Kingdom Interaction with Actinomyces viscosus to Promote Root Caries

The cross-kingdom interactions between Candida albicans and Actinomyces viscosus play critical roles in root caries. However, the key pathway by which C. albicans regulates its interactions with A. viscosus is unclear. Here, we first employed 39 volunteers with root caries and 37 caries-free volunteers, and found that the abundances of C. albicans and A. viscosus were significantly increased in the individuals with root caries and showed a strong positive correlation. Their dual-species combination synergistically promoted biofilm formation and root caries in rats. The arginine biosynthesis pathway of C. albicans was significantly upregulated in dual-species biofilms and dental plaques from another 10 root caries volunteers compared with the 10 caries-free volunteers. The exogenous addition of arginine increased the cariogenicity of the dual-species biofilm. The C. albicansARG4, a key gene from the arginine biosynthesis pathway, null mutant failed to promote dual-species biofilm formation and root caries in rats; however, the addition of arginine restored its synergistic actions with A. viscosus. Our results identified the critical roles of the C. albicans arginine biosynthesis pathway in its cross-kingdom interactions with A. viscosus for the first time and indicated that targeting this pathway was a practical way to treat root caries caused by multiple species.

IMPORTANCE Root caries is a critical problem that threatens the oral health of the elderly population. Our results identified the essential roles of the C. albicans arginine biosynthesis pathway in its cross-kingdom interactions with A. viscosus in root caries for the first time and indicated that targeting this pathway was a practical way to treat root caries caused by multiple species.

Antibacterial efficacy and possible mechanism of action of 2-hydroxyisocaproic acid (HICA)

The exploitation of natural antimicrobial compounds that can be used in food preservation has been fast tracked by the development of antimicrobial resistance to existing antimicrobials and the increasing consumer demand for natural food preservatives. 2-hydroxyisocaproic acid (HICA) is a natural compound produced through the leucine degradation pathway and is produced in humans and by certain microorganisms such as lactic acid bacteria and Clostridium species. The present study investigated the antibacterial efficacy of HICA against some important bacteria associated with food quality and safety and provided some insights into its possible antimicrobial mechanisms against bacteria. The results revealed that HICA was effective in inhibiting the growth of tested Gram-positive and Gram-negative bacteria including a multi-drug resistant P. aeruginosa strain in this study. The underlying mechanism was investigated by measuring the cell membrane integrity, membrane permeability, membrane depolarisation, and morphological and ultrastructural changes after HICA treatment in bacterial cells. The evidence supports that HICA exerts its activity via penetration of the bacterial cell membranes, thereby causing depolarisation, rupture of membranes, subsequent leakage of cellular contents and cell death. The current study suggests that HICA has potential to be used as an antibacterial agent against food spoilage and food-borne pathogenic bacteria, targeting the bacterial cell envelope.

Acidic Neutralization by Indigenous Bacteria Isolated from Abandoned Mine Areas

Soil acidification has been a serious problem in abandoned mine areas, and could be exacerbated by acid deposition with the release of mine wastes. In this study, three different indigenous bacterial consortia were isolated from abandoned mines in South Korea, from which the potential for acid neutralization of microorganisms was evaluated. They were all able to neutralize acidity within 24 h in the liquid nutrient medium. Moreover, a strong positive correlation (R = +0.922, p < 0.05) was established between the ammonium ion (NH4+) production yield and the resulting pH, indicating that NH4+ served as an important metabolite for biological neutralization. Serratialiquefaciens, Citrobacter youngae, Pseudescherichia vulneris, and Serratia grimesii had higher acid neutralization ability to generate NH4+ by the metabolism of nitrogen compounds such as carboxylation and urea hydrolysis. Therefore, acidic soils can be expected to be ameliorated by indigenous microorganisms through in situ biostimulation with the adequate introduction of nitrogenous substances into the soil environments.

Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo

Streptococcus sanguinis is an oral commensal and an etiological agent of infective endocarditis. Previous studies have identified the SsaACB manganese transporter as essential for endocarditis virulence; however, the significance of SsaACB in the oral environment has never been examined. Here we report that a ΔssaACB deletion mutant of strain SK36 exhibits reduced growth and manganese uptake under acidic conditions. Further studies revealed that these deficits resulted from the decreased activity of TmpA, shown in the accompanying paper to function as a ZIP‐family manganese transporter. Transcriptomic analysis of fermentor‐grown cultures of SK36 WT and ΔssaACB strains identified pH‐dependent changes related to carbon catabolite repression in both strains, though their magnitude was generally greater in the mutant. In strain VMC66, which possesses a MntH transporter, loss of SsaACB did not significantly alter growth or cellular manganese levels under the same conditions. Interestingly, there were only modest differences between SK36 and its ΔssaACB mutant in competition with Streptococcus mutans in vitro and in a murine oral colonization model. Our results suggest that the heterogeneity of the oral environment may provide a rationale for the variety of manganese transporters found in S. sanguinis.

Profiles of Small Regulatory RNAs at Different Growth Phases of Streptococcus thermophilus During pH-Controlled Batch Fermentation

Small regulatory RNA (sRNA) has been shown to play an important role under various stress conditions in bacteria, and it plays a vital role in regulating growth, adaptation and survival through posttranscriptional control of gene expression in bacterial cells. Streptococcus thermophilus is widely used as a starter culture in the manufacture of fermented dairy products. However, the lack of reliable information on the expression profiles and potential physiological functions of sRNAs in this species hinders our understanding of the importance of sRNAs in S. thermophilus. The present study was conducted to assess the expression profiles of sRNAs in S. thermophilus and to identify sRNAs that exhibited significant changes. A total of 530 potential sRNAs were identified, including 198 asRNAs, 135 sRNAs from intergenic regions, and 197 sRNAs from untranslated regions (UTRs). Significant changes occurred in the expression of 238, 83, 194, and 139 sRNA genes during the lag, early exponential growth, late exponential growth, and stationary phases, respectively. The expression of 14 of the identified sRNAs was verified by qRT-PCR. Predictions of the target genes of these candidate sRNAs showed that the primary metabolic pathways targeted were involved in carbon metabolism, biosynthesis of amino acids, ABC transporters, the metabolism of amino and nucleotide sugars, purine metabolism, and the phosphotransferase system. The expression of the predicted target genes was further analyzed to better understand the roles of sRNAs during different growth stages. The results suggested that these sRNAs play crucial roles by regulating biological pathways during different growth phases of S. thermophilus. According to the results, sRNAs sts141, sts392, sts318, and sts014 are involved in the regulation of osmotic stress. sRNAs sts508, sts087, sts372, sts141, sts375, and sts119 are involved in the regulation of starvation stress. sRNAs sts129, sts226, sts166, sts231, sts204, sts145, and sts236 are involved in arginine synthesis. sRNAs sts033, sts341, sts492, sts140, sts230, sts172, and sts377 are involved in the ADI pathway. The present study provided valuable information for the functional study of sRNAs in S. thermophilus and indicated a future research direction for sRNA in S. thermophilus. Overall, our results provided new insights for understanding the complex regulatory network of sRNAs in S. thermophilus.

Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages

BACKGROUND

Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB.

METHOD

First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined.

RESULTS

A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time.

CONCLUSION

The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.

Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions

The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.

Morphological Features and Cold-Response Gene Expression in Mesophilic Bacillus cereus Group and Psychrotolerant Bacillus cereus Group under Low Temperature

At low temperatures, psychrotolerant B. cereus group strains exhibit a higher growth rate than mesophilic strains do. However, the different survival responses of the psychrotolerant strain (BCG³⁴) and the mesophilic strain (BCG^T) at low temperatures are unclear. We investigated the morphological and genomic features of BCG^T and BCG³⁴ to characterize their growth strategies at low temperatures. At low temperatures, morphological changes were observed only in BCG^T. These morphological changes included the elongation of rod-shaped cells, whereas the cell shape in BCG³⁴ was unchanged at the low temperature. A transcriptomic analysis revealed that both species exhibited different growth-related traits during low-temperature growth. The BCG^T strain induces fatty acid biosynthesis, sulfur assimilation, and methionine and cysteine biosynthesis as a survival mechanism in cold systems. Increases in energy metabolism and fatty acid biosynthesis in the mesophilic B. cereus group strain might explain its ability to grow at low temperatures. Several pathways involved in carbohydrate mechanisms were downregulated to conserve the energy required for growth. Peptidoglycan biosynthesis was upregulated, implying that a change of gene expression in both RNA-Seq and RT-qPCR contributed to sustaining its growth and rod shape at low temperatures. These results improve our understanding of the growth response of the B. cereus group, including psychrotolerant B. cereus group strains, at low temperatures and provide information for improving bacterial inhibition strategies in the food industry.

Sulphate-Reducing Bacteria’s Response to Extreme pH Environments and the Effect of Their Activities on Microbial Corrosion

Sulphate-reducing bacteria (SRB) are dominant species causing corrosion of various types of materials. However, they also play a beneficial role in bioremediation due to their tolerance of extreme pH conditions. The application of sulphate-reducing bacteria (SRB) in bioremediation and control methods for microbiologically influenced corrosion (MIC) in extreme pH environments requires an understanding of the microbial activities in these conditions. Recent studies have found that in order to survive and grow in high alkaline/acidic condition, SRB have developed several strategies to combat the environmental challenges. The strategies mainly include maintaining pH homeostasis in the cytoplasm and adjusting metabolic activities leading to changes in environmental pH. The change in pH of the environment and microbial activities in such conditions can have a significant impact on the microbial corrosion of materials. These bacteria strategies to combat extreme pH environments and their effect on microbial corrosion are presented and discussed.

The Bacillus cereus Food Infection as Multifactorial Process

The ubiquitous soil bacterium Bacillus cereus presents major challenges to food safety. It is responsible for two types of food poisoning, the emetic form due to food intoxication and the diarrheal form emerging from food infections with enteropathogenic strains, also known as toxico-infections, which are the subject of this review. The diarrheal type of food poisoning emerges after production of enterotoxins by viable bacteria in the human intestine. Basically, the manifestation of the disease is, however, the result of a multifactorial process, including B. cereus prevalence and survival in different foods, survival of the stomach passage, spore germination, motility, adhesion, and finally enterotoxin production in the intestine. Moreover, all of these processes are influenced by the consumed foodstuffs as well as the intestinal microbiota which have, therefore, to be considered for a reliable prediction of the hazardous potential of contaminated foods. Current knowledge regarding these single aspects is summarized in this review aiming for risk-oriented diagnostics for enteropathogenic B. cereus.

Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii

The non-conventional yeast Pichia kudriavzevii is considered to be a promising biotechnological host for the production of organic acids under low-pH conditions. However, little is known about the low-pH stress response in P. kudriavzevii, which significantly restricts its future development. In this study, P. kudriavzevii N-X showed great tolerance to low-pH stress, but the cell aggregation upon extremely acidic conditions might be unfavorable for low-pH fermentation. We therefore conducted RNA-Seq to compare global gene expression of P. kudriavzevii N-X in response to different pH stresses. Totally 434 genes were identified to be differentially expressed genes (DEGs), and annotation and enrichment analysis suggested that multiple genes associated with regulation of membrane lipid composition, filamentous growth and arginine metabolism were differentially expressed. The increased specific activity of arginase and intracellular ammonia concentration of P. kudriavzevii cultured at pH 2.0 further implied potential roles of arginine in response to extreme low-pH conditions. Extracellular supplementation of 5 mM arginine resulted in increased pHi and cell growth at pH 2.0, meanwhile the cell aggregation was partially suppressed. Additionally, overexpression of ARG J involving in arginine synthesis can also enhance the cell growth and reduce the aggregation effect. These results suggested that increasing arginine flux might be an alternative approach in the developing of P. kudriavzevii as a platform host for production of organic acids under low-pH conditions.

Physiological and Transcriptional Responses of Streptomyces albulus to Acid Stress in the Biosynthesis of ε-Poly-L-lysine

Streptomyces albulus has commercially been used for the production of ε-poly-L-lysine (ε-PL), a natural food preservative, where acid stress is inevitably encountered in the biosynthesis process. To elucidate the acid tolerance response (ATR), a comparative physiology and transcriptomic analysis of S. albulus M-Z18 at different environmental pH (5.0, 4.0, and 3.0) was carried out. In response to acid stress, cell envelope regulated the membrane fatty acid composition and chain length to reduce damage. Moreover, intracellular pH homeostasis was maintained by increasing H⁺-ATPase activity and intracellular ATP and amino acid (mainly arginine, glutamate, aspartate and lysine) concentrations. Transcriptional analysis based on RNA-sequencing indicated that acid stress aroused global changes and the differentially expressed genes involved in transcriptional regulation, stress-response protein, transporter, cell envelope, secondary metabolite biosynthesis, DNA and RNA metabolism and ribosome subunit. Consequently, the ATR of S. albulus was preliminarily proposed. Notably, it is indicated that the biosynthesis of ε-PL is also a response mechanism for S. albulus to combat acid stress. These results provide new insights into the ATR of S. albulus and will contribute to the production of ε-PL via adaptive evolution or metabolic engineering.

Microbial response to acid stress: mechanisms and applications

Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.

Recent advances of pH homeostasis mechanisms in Corynebacterium glutamicum

Corynebacterium glutamicum is generally regarded as a safe microorganism, and widely used in the large-scale production of various amino acids and organic acids, such as L-glutamate, L-lysine and succinic acid. During the process of industrial fermentation, C. glutamicum is usually exposed to varying environmental stresses, such as variations in pH, salinity, temperature, and osmolality. Among them, pH fluctuations are regarded as one of the most frequent environmental stresses in microbial fermentation. In this review, we summarize the current knowledge of pH homeostasis mechanisms adopted by C. glutamicum for coping with low acidic pH and high alkaline pH stresses. Facing with low pH environments, C. glutamicum develops a variety of strategies to maintain intracellular pH homeostasis, such as lowering intracellular reactive oxygen species, the improvement of potassium transport, the regulation of mycothiol-related pathways, as well as the repression of sulfur assimilation. While during alkaline pH stresses, the Mrp-type Na⁺/H⁺ antiporters are shown to play a dominant role in conferring C. glutamicum cells resistance to alkaline pH. Furthermore, we also discuss the general strategies and prospects on metabolic engineering of C. glutamicum to improve alkaline or acid resistance.

A method to increase the survival of probiotic bacteria Lactobacillus brevis at a lowered pH

Lactobacillus brevis PCM 2570 is a strain of lactic acid bacteria, i.e. probiotic bacteria whose major fermentation product is lactic acid. The efficiency of lactic acid production is limited by the value of ambient pH. This study aimed to increase the survival of this bacterial strain at a reduced pH (3.9), which would result in an increased yield of lactic acid fermentation. In our experiment the survival rate of probiotic bacteria L. brevis PCM 2570 was increased 1.2-fold to 6.96-fold due to the presence of Fe3O4 magnetic nanoparticles, as compared to the control. The minimum concentration of nanoparticles with a positive effect was 8 mg/ml, but the optimum concentration was 20 mg/ml.

Kinetics and Catabolic Pathways of the Insecticide Chlorpyrifos, Annotation of the Degradation Genes, and Characterization of Enzymes TcpA and Fre in Cupriavidus nantongensis X1T

Chlorpyrifos is one of the most used organophosphorus insecticides. It is commonly degraded to 3,5,6-trichloro-2-pyridinol (TCP), which is water-soluble and toxic. Bacteria can degrade chlorpyrifos and TCP, but the biodegradation mechanism has not been well-characterized. Recently isolated Cupriavidus nantongensis X1^T can completely degrade 100 mg/L chlorpyrifos and 20 mg/L TCP with half-lives of 6 and 8 h, respectively. We annotated a complete gene cluster responsible for TCP degradation in recently sequenced strain X1^T. Two key genes, tcpA and fre, were cloned from X1^T and transferred and expressed in Escherichia coli BL21(DE3). Degradation of TCP by X1^T whole cell was compared with that by the enzymes 2,4,6-trichlorophenol monooxygenase and NAD(P)H:flavin reductase expressed and purified from E. coli BL21(DE3). Novel metabolites of TCP were isolated and characterized, indicating stepwise dechlorination of TCP, which was confirmed by TCP disappearance, mass balance, and detection and formation kinetics of chloride ion from TCP.

Profiles of Streptococcus thermophilus MN-ZLW-002 nutrient requirements in controlled pH batch fermentations

This study aimed to evaluate the profiles of Streptococcus thermophilus nutrient requirements to guide the design of media for high cell density culturing. The growth kinetics, physiological state, and nutrient requirement profiles of S. thermophilus were analyzed in chemically defined media. The results showed that the intracellular ATP concentration, H⁺‐ATPase activity, NADH/NAD⁺, and NH₃ concentrations varied with intracellular pH. The nutrient components with the highest amounts required were Leu and Asp; ascorbic acid and p‐amino benzoic acid; K⁺ and PO₄³⁻; and guanine and uracil. The nutrient components with the largest required ratios were Arg, His, and Met; folic acid, cyanocobalamine, biotin, and nicotinic acid; Ca²⁺ and Mg²⁺; and guanine and uracil. In this study, different nutrient components were primarily used at different phase. Trp, Tyr, calcium pantothenate, thiamine, guanine, and Mg²⁺ were mainly used from late‐lag to midexponential phase. Met, Pro, Phe, Ala, Gly, nicotinic acid, and riboflavin were mainly used from midexponential to late‐exponential phase. The highest bioavailabilities of nutrient components were also found at diverse phase. Met, Leu, Ile, Asn, Glu, Lys, Pro, Gly, riboflavin, nicotinic acid, adenine, uracil, inosine, and Ca²⁺ had the highest bioavailability from late‐lag to midexponential phase. Lactose, Glu, Asp, His, Trp, Cys, Val, Arg, Phe, Ala, Ser, Thr, Tyr, folate and cobalamin, calcium pantothenate, ascorbic acid, thiamine, biotin, p‐amino benzoic acid, vitamin B₆, K⁺, Mg²⁺, guanine, xanthine, and PO₄³⁻ had the highest bioavailability from midexponential to late‐exponential phase. This study elucidated the nutrient requirement profiles with culture time and biomass at various average growth rates during the growth of S. thermophilus. The present results will help to formulate complex media for high cell density cultivation and provide the theoretical basis for S. thermophilus feeding strategies.

Effect of aspartic acid and glutamate on metabolism and acid stress resistance of Acetobacter pasteurianus

Background

Acetic acid bacteria (AAB) are widely applied in food, bioengineering and medicine fields. However, the acid stress at low pH conditions limits acetic acid fermentation efficiency and high concentration of vinegar production with AAB. Therefore, how to enhance resistance ability of the AAB remains as the major challenge. Amino acids play an important role in cell growth and cell survival under severe environment. However, until now the effects of amino acids on acetic fermentation and acid stress resistance of AAB have not been fully studied.

Results

In the present work the effects of amino acids on metabolism and acid stress resistance of Acetobacter pasteurianus were investigated. Cell growth, culturable cell counts, acetic acid production, acetic acid production rate and specific production rate of acetic acid of A. pasteurianus revealed an increase of 1.04, 5.43, 1.45, 3.30 and 0.79-folds by adding aspartic acid (Asp), and cell growth, culturable cell counts, acetic acid production and acetic acid production rate revealed an increase of 0.51, 0.72, 0.60 and 0.94-folds by adding glutamate (Glu), respectively. For a fully understanding of the biological mechanism, proteomic technology was carried out. The results showed that the strengthening mechanism mainly came from the following four aspects: (1) Enhancing the generation of pentose phosphates and NADPH for the synthesis of nucleic acid, fatty acids and glutathione (GSH) throughout pentose phosphate pathway. And GSH could protect bacteria from low pH, halide, oxidative stress and osmotic stress by maintaining the viability of cells through intracellular redox equilibrium; (2) Reinforcing deamination of amino acids to increase intracellular ammonia concentration to maintain stability of intracellular pH; (3) Enhancing nucleic acid synthesis and reparation of impaired DNA caused by acid stress damage; (4) Promoting unsaturated fatty acids synthesis and lipid transport, which resulted in the improvement of cytomembrane fluidity, stability and integrity.

Conclusions

The present work is the study to show the effectiveness of Asp and Glu on metabolism and acid stress resistance of A. pasteurianus as well as their working mechanism. The research results will be helpful for development of nutrient salts, the optimization and regulation of high concentration of cider vinegar production process.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0717-6) contains supplementary material, which is available to authorized users.

Short communication: Nutrient consumption patterns of Lactobacillus acidophilus KLDS 1.0738 in controlled pH batch fermentations

This work focused on elucidating the nutrient consumption patterns of Lactobacillus acidophilus to guide the design of media for high-cell-density culture. We investigated the nutrient consumption patterns of L. acidophilus KLDS 1.0738 in chemically defined media in controlled pH batch fermentations. The most abundantly consumed amino acids, vitamins, ions, and purines and pyrimidines were Glu and Gly, pyridoxine and nicotinamide, K⁺ and PO₄^3-, and guanine and uracil, respectively. The highest consumption rates for amino acids, vitamins, ions, and purines and pyrimidines were Asp and Arg, folic acid and pyridoxine, Fe²⁺ and Mn²⁺, and uracil and thymine, respectively. Furthermore, most of the amino acids, as well as guanine, thymine, pyridoxine, folic acid, nicotinamide, Mg²⁺, PO₄^3-, and K⁺ had the highest bioavailability from the end of the lag growth phase to the mid-exponential growth phase. The overall consumption of glucose, adenine nucleotides, 2'-deoxyguanosine monohydrate, calcium pantothenate, Fe²⁺ and Mn²⁺ decreased with increasing average growth rate, indicating more effective use of these nutritional components at a higher average growth rate, as biomass yield based on nutritional component consumption increased. Our findings help to formulate complex media for high-cell-density cultivation and provide a theoretical basis for L. acidophilus feeding strategies.

System-wide analysis of manganese starvation-induced metabolism in key elements of Lactobacillus plantarum

To analyze the response mechanisms of Lactobacillus plantarum against manganese starvation stress, different metabolisms from physiology, proteomics and transporters aspects in L. plantarum CCFM 436 were systematically investigated.

Enhanced succinic acid production under acidic conditions by introduction of glutamate decarboxylase system in E. coli AFP111

Biological synthesis of succinic acid at low pH values was favored since it not only decreased investment cost but also simplified downstream purification process. In this study, the feasibility of using glutamate decarboxylase system to improve succinic acid production of Escherichia coli AFP111, a succinate-producing candidate with mutations in pfl, ldhA, and ptsG, under acidic conditions was investigated. By overexpressing gadBC operon in AFP111, a recombinant named as BA201 (AFP111/pMD19T-gadBC) was constructed. Fermentation at pH 5.6 showed that 30 g L^-1 glucose was consumed and 26.58 g L^-1 succinic acid was produced by BA201, which was 1.22- and 1.32-fold higher than that by the control BA200 (AFP111/pMD19T) containing the empty vector. Analysis of intracellular enzymes activities and ATP concentrations revealed that the activities of key enzymes involved in glucose uptake and products synthesis and intracellular ATP levels were all increased after overexpression of gadBC which were benefit for cell metabolism under weak acidic conditions. To further improve the succinic acid titer by recombinant BA201 at pH 5.6, the extracellular glutamate concentration was optimized and the final succinic acid titer increased 20.4% to 32.01 g L^-1. Besides, the fermentation time was prolonged by repetitive fermentation and additional 15.78 g L^-1 succinic acid was produced by recovering cells into fresh medium. The results here demonstrated a potential strategy of overexpressing gadBC for increased succinic acid production of E. coli AFP111 under weak acidic conditions.

Adaptation in Bacillus cereus: From Stress to Disease

Bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. After ingestion, B. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic pH in the stomach and changing oxygen conditions in the human intestine. B. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and minimizing damage to cellular infrastructure. As reviewed in this article, B. cereus adapts to acidic pH and changing oxygen conditions through diverse regulatory mechanisms and then exploits its metabolic flexibility to grow and produce enterotoxins. We then focus on the intricate link between metabolism, redox homeostasis, and enterotoxins, which are recognized as important contributors of food-borne disease.

Influence of arginine on the growth, arginine metabolism and amino acid consumption profiles of Streptococcus thermophilus T1C2 in controlled pH batch fermentations

AIMS

The aim of this study was to elucidate the effect of arginine on the growth, arginine metabolism and amino acid consumption profiles of Streptococcus thermophilus T1C2.

METHODS AND RESULTS

The growth kinetics, intracellular pH, extracellular osmotic pressure, expression of key genes in the arginine metabolism pathway and amino acid consumption profiles were analysed in chemically defined medium with different initial arginine concentrations. The results showed that arginine stimulated the growth of Strep. thermophilus T1C2 under low intracellular pH and high extracellular osmotic pressure. The expression of key genes in the arginine degradation pathway indicated that arginine relieved the drop in the intracellular pH by consuming protons and generating NH3 . Additionally, the results showed that arginine degradation did not occur via the arginine deiminase pathway but through the arginine decarboxylase-urease pathway. Furthermore, the utilization efficiency of amino acids was improved in the presence of arginine.

CONCLUSIONS

Arginine improved the growth of Strep. thermophilus due to protecting Strep. thermophilus against intracellular acid stress, which was revealed at the transcriptional level of key genes. This study showed that the acid resistance of Strep. thermophilus was achieved through the arginine decarboxylase-urease pathway.

SIGNIFICANCE AND IMPACT OF THE STUDY

The arginine-stimulated growth of Strep. thermophilus improved the utilization efficiency of amino acids and reduced nitrogen waste, which could be useful for the optimization of cultivation media.

Systematic understanding of the potential manganese-adsorption components of a screened Lactobacillus plantarum CCFM436

Manganese (Mn) is a toxic heavy metal that has a variety of adverse effects on human health under excess exposure.

Metabolic engineering of acid resistance elements to improve acid resistance and propionic acid production of Propionibacterium jensenii

Propionic acid (PA) and its salts are widely used in the food, pharmaceutical, and chemical industries. Microbial production of PA by propionibacteria is a typical product-inhibited process, and acid resistance is crucial in the improvement of PA titers and productivity. We previously identified two key acid resistance elements-the arginine deaminase and glutamate decarboxylase systems-that protect propionibacteria against PA stress by maintaining intracellular pH homeostasis. In this study, we attempted to improve the acid resistance and PA production of Propionibacterium jensenii ATCC 4868 by engineering these elements. Specifically, five genes (arcA, arcC, gadB, gdh, and ybaS) encoding components of the arginine deaminase and glutamate decarboxylase systems were overexpressed in P. jensenii. The activities of the five enzymes in the engineered strains were 26.7-489.0% higher than those in wild-type P. jensenii. The growth rates of the engineered strains decreased, whereas specific PA production increased significantly compared with those of the wild-type strain. Among the overexpressed genes, gadB (encoding glutamate decarboxylase) increased PA resistance and yield most effectively; the PA resistance of P. jensenii-gadB was more than 10-fold higher than that of the wild-type strain, and the production titer, yield, and conversion ratio of PA reached 10.81 g/L, 5.92 g/g cells, and 0.56 g/g glycerol, representing increases of 22.0%, 23.8%, and 21.7%, respectively. We also investigated the effects of introducing these acid resistance elements on the transcript levels of related enzymes. The results showed that the expression of genes in the engineered pathways affected the expression of the other genes. Additionally, the intracellular pools of amino acids were altered as different genes were overexpressed, which may further contribute to the enhanced PA production. This study provides an effective strategy for improving PA production in propionibacteria; this strategy may be useful for the production of other organic acids. Biotechnol. Bioeng. 2016;113: 1294-1304. © 2015 Wiley Periodicals, Inc.

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract

Rodent-derived strains of Lactobacillus reuteri densely colonize the forestomach of mice and possess several genes whose predicted functions constitute adaptations towards an acidic environment. The objective of this study was to systematically determine which genes of L. reuteri 100-23 contribute to tolerance towards host gastric acid secretion. Genes predicted to be involved in acid resistance were inactivated, and their contribution to survival under acidic conditions was confirmed in model gastric juice. Fitness of five mutants that showed impaired in vitro acid resistance were then compared through competition experiments in ex-germ-free mice that were either treated with omeprazole, a proton-pump inhibitor that suppresses acid secretion in the stomach, or left untreated. This analysis revealed that the urease cluster was the predominant factor in mediating resistance to gastric acid production. Population levels of the mutant, which were substantially decreased in untreated mice, were almost completely restored through omeprazole, demonstrating that urease production in L. reuteri is mainly devoted to overcome gastric acid. The findings provide novel information on the mechanisms by which L. reuteri colonizes its gastric niche and demonstrate that in silico gene predictions and in vitro tests have limitations for predicting the ecological functions of colonization factors in bacterial symbionts.

Effects of acetic acid and arginine on pH elevation and growth of Bacillus licheniformis in an acidified cucumber juice medium

Bacillus licheniformis has been shown to cause pH elevation in tomato products having an initial pH below 4.6 and metabiotic effects that can lead to the growth of pathogenic bacteria. Because of this, the organism poses a potential risk to acidified vegetable products; however, little is known about the growth and metabolism of this organism in these products. To clarify the mechanisms of pH change and growth of B. licheniformis in vegetable broth under acidic conditions, a cucumber juice medium representative of a noninhibitory vegetable broth was used to monitor changes in pH, cell growth, and catabolism of sugars and amino acids. For initial pH values between pH 4.1 to 6.0, pH changes resulted from both fermentation of sugar (lowering pH) and ammonia production (raising pH). An initial pH elevation occurred, with starting pH values of pH 4.1 to 4.9 under both aerobic and anaerobic conditions, and was apparently mediated by the arginine deiminase reaction of B. licheniformis. This initial pH elevation was prevented if 5 mM or greater acetic acid was present in the brine at the same pH. In laboratory media, under favorable conditions for growth, data indicated that growth of the organism was inhibited at pH 4.6 with protonated acetic acid concentrations of 10 to 20 mM, corresponding to 25 to 50 mM total acetic acid; however, growth inhibition required greater than 300 mM citric acid (10-fold excess of the amount in processed tomato products) products under similar conditions. The data indicate that growth and pH increase by B. licheniformis may be inhibited by the acetic acid present in most commercial acidified vegetable products but not by the citric acid in many tomato products.

Adaptive responses of Bacillus cereus ATCC14579 cells upon exposure to acid conditions involve ATPase activity to maintain their internal pH

This study examined the involvement of ATPase activity in the acid tolerance response (ATR) of Bacillus cereus ATCC14579 strain. In the current work, B. cereus cells were grown in anaerobic chemostat culture at external pH (pH_e ) 7.0 or 5.5 and at a growth rate of 0.2 h^-1 . Population reduction and internal pH (pH_i ) after acid shock at pH 4.0 was examined either with or without ATPase inhibitor N,N'-dicyclohexylcarbodiimide (DCCD) and ionophores valinomycin and nigericin. Population reduction after acid shock at pH 4.0 was strongly limited in cells grown at pH 5.5 (acid-adapted cells) compared with cells grown at pH 7.0 (unadapted cells), indicating that B. cereus cells grown at low pH_e were able to induce a significant ATR and Exercise-induced increase in ATPase activity. However, DCCD and ionophores had a negative effect on the ability of B. cereus cells to survive and maintain their pH_i during acid shock. When acid shock was achieved after DCCD treatment, pH_i was markedly dropped in unadapted and acid-adapted cells. The ATPase activity was also significantly inhibited by DCCD and ionophores in acid-adapted cells. Furthermore, transcriptional analysis revealed that atpB (ATP beta chain) transcripts was increased in acid-adapted cells compared to unadapted cells before and after acid shock. Our data demonstrate that B. cereus is able to induce an ATR during growth at low pH. These adaptations depend on the ATPase activity induction and pH_i homeostasis. Our data demonstrate that the ATPase enzyme can be implicated in the cytoplasmic pH regulation and in acid tolerance of B. cereus acid-adapted cells.

A new chemically defined medium for the growth and sporulation of Bacillus cereus strains in anaerobiosis

A new chemically defined liquid medium, MODS, was developed for the aerobic growth and anaerobic growth and sporulation of Bacillus cereus strains. The comparison of sporulation capacity of 18 strains of B. cereus has shown effective growth and spore production in anaerobiosis..

Coping with low pH: molecular strategies in neutralophilic bacteria

As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.

Identification of regulated genes conferring resistance to high concentrations of glyphosate in a new strain of Enterobacter

Glyphosate is a widely used herbicide that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity. Most plants and microbes are sensitive to glyphosate. However, transgenic-resistant crops that contain a modified epsps obtained from the resistant microbes have been commercially successful and therefore, new resistance genes and their adaptive regulatory mechanisms are of great interest. In this study, a soil-borne, glyphosate-resistant bacterium was selected and identified as Enterobacter. The EPSPS in this strain was found to have been altered to a resistant one. A total of 42 differentially expressed genes (DEGs) in the glyphosate were screened using microarray techniques. Under treatment, argF, sdhA, ivbL, rrfA-H were downregulated, whereas the transcripts of speA, osmY, pflB, ahpC, fusA, deoA, uxaC, rpoD and a few ribosomal protein genes were upregulated. Data were verified by quantitative real-time PCR on selected genes. All transcriptional changes appeared to protect the bacteria from glyphosate and associated osmotic, acidic and oxidative stresses. Many DEGs may have the potential to confer resistance to glyphosate alone, and some may be closely related to the shikimate pathway, reflecting the complex gene interaction network for glyphosate resistance.