Harnessing landfill-derived Bacillus subtilis (LLS-04) for bio-electrodegradation of di-butyl phthalate: Comprehensive toxicity assessment across multiple biological models

Di-butyl phthalate (DBP), a pervasive environmental contaminant, poses significant ecological and health risks due to its persistence and toxicity. This study investigates the potential of a landfill-derived Bacillus subtilis strain (LLS-04) in bio-electrodegradation of DBP, alongside a comprehensive toxicity assessment across multiple biological models. Bio-electrodegradation efficiency was compared to biodegradation and electrodegradation, revealing that bio-electrodegradation achieved a remarkable 98.57 % reduction in DBP concentration significantly outperforming the other methods. This enhanced degradation was attributed to improved microbial activity and enzyme production, as indicated by higher protein content and increased esterase and dehydrogenase activities in the bio-electrodegradation system. The optimized conditions facilitated efficient degradation, with HPLC-MS/MS analysis confirming the breakdown of DBP into non-toxic end products via a proposed metabolic pathway. A comprehensive toxicity assessment, including in-silico analysis, in-vitro cytotoxicity and brine shrimp lethality assays, demonstrated a significant reduction in toxicity of BES treated effluent compared to DBP untreated effluent. Furthermore, in-vivo toxicity studies using animal model supported these findings, demonstrating reduced toxicity in the BES treated effluent compared to the DBP untreated effluent. Overall, these findings highlight the potential application of bio-electrodegradation in bioremediation strategies for phthalate pollution, offering an effective solution for reducing both DBP concentration and its environmental toxicity.

Deletion of YJL218W reduces salt tolerance of Saccharomyces cerevisiae

The YJL218W open reading frame may be involved in peroxisomal biogenesis. However, whether it mediates salt tolerance is unclear. We found that after knockdown of YJL218W in Saccharomyces cerevisiae (S. cerevisiae), its salt tolerance was reduced and cell death was increased. Transcriptome sequencing and analysis further revealed that YJL218W knockdown mediated significant changes in the expression of 1432 messenger RNA (mRNAs), of which 603 were upregulated. KEGG enrichment analysis and polymerase chain reaction (PCR) assay indicated that YJL218W mediated the regulation of peroxisome-related genes. Therefore, YJL218W may regulate salt stress in S. cerevisiae by regulating peroxisome assembly.

Exploring the Roles of Dietary Herbal Essential Oils in Aquaculture: A Review

The aquaculture sector is one of the main activities contributing to food security for humanity around the globe. However, aquatic animals are susceptible to several farming stressors involved in deteriorated growth performance, reduced productivity, and eventually high mortality rates. In some countries still, antibiotics and chemotherapies are comprehensively applied to control biotic stressors. Aside from the apparent benefits, the continuous usage of antibiotics develops bacterial resistance, deteriorates bacterial populations, and accumulates these compounds in the aquatic environment. Alternatively, environmentally friendly additives were used to avoid the direct and indirect impacts on the aquatic ecosystem and human health. In aquaculture, medicinal herbs and extracts are extensively used and approved for their growth-promoting, anti-inflammatory, and antioxidative properties. Herbal essential oils contain many bioactive components with powerful antibacterial, antioxidative, and immunostimulant potentials, suggesting their application for aquatic animals. Essential oils can be provided via diet and can benefit aquatic animals by improving their well-being and health status. The use of essential oils in aquafeed has been studied in a variety of aquatic animals to determine their beneficial roles and optimum doses. The outputs illustrated that herbal essential oils are exciting alternatives to antibiotics with prominent growth promotion, antioxidative, and immunostimulant roles. Herein, we reviewed the beneficial roles of essential oils in aquaculture. This review also aims to describe trends in herbal essential oils use, mainly in commercial fish species, and to analyze different factors that affect essential oils’ efficacy on the growth performance, antioxidative, and immune responses of finfish species.

Crp/fnr family protein binds to promoters of atxA and sodmn genes that regulate the expression of exotoxins in Bacillus anthracis

Bacillus anthracis produces a tripartite exotoxin, which is regulated by AtxA. Sodmn is constitutively expressed during invasion. Crp/Fnr family transcriptional regulators are known to bind promoters of toxin regulators as well as constitutively expressed genes during pathogenesis. B. anthracis fnr gene was cloned, over-expressed in E. coli and recombinant protein was purified. Oligomeric nature of recombinant rFnr protein was studied by diamide treatment and DTT reduction. DNA binding of rFnr protein was studied by EMSA. We observed that rFnr exists in both monomeric and oligomeric forms. It was found that rFnr was able to oligomerize after diamide treatment which was reversible through DTT reduction. Promoter regions of atxA and sodmn show binding to monomeric form of rFnr, however, dimeric form was unable to bind. Fnr might be playing a role in regulation of toxin gene expression via regulation of atxA gene. It can also be involved in regulation of pathogenesis by regulating the sodmn expression. Oligomerization can act as an ON/OFF switch for the Fnr mediated regulation.

Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains

We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H₂O₂-sensitive phenotype.

Essential Oils as Stress-Reducing Agents for Fish Aquaculture: A Review

In fish, stressful events initiate a hormone cascade along the hypothalamus-pituitary-interrenal and hypothalamus-sympathetic-chromaffin (HSC) axis to evoke several physiological reactions in order to orchestrate and maintain homeostasis. Several biotic and abiotic factors, as well as aquaculture procedures (handling, transport, or stocking density), activated stress system inducing negative effects on different physiological processes in fish (growth, reproduction, and immunity). In order to reduce these consequences, the use of essential oils (EOs) derived from plants has been the focus of aquaculture studies due to their diverse properties (e.g., anesthetic, antioxidant, and antimicrobial), which have been shown to reduce biochemical and endocrine alterations and, consequently, to improve the welfare status. Recently, several studies have shown that biogenic compounds isolated from different EOs present excellent biological activities, as well as the nanoencapsulated form of these EOs may potentiate their effects. Overall, EOs presented less side effects than synthetic compounds, but their stress-reducing efficacy is related to their chemical composition, concentration or chemotype used. In addition, their species-specific actions must be clearly established since they can act as stressors by themselves if their concentrations and chemotypes used are not suitable. For this reason, it is necessary to assess the effect of these natural compound mixtures in different fish species, from marine to freshwater, in order to find the ideal concentration range and the way for their administration to obtain the desired biological activity, without any undesired side effects. In this review, the main findings regarding the use of different EOs as stress reducers will be presented to highlight the most important issues related to their use to improve fish welfare in aquaculture.

Alternative sigma factor B (σB) and catalase enzyme contribute to Staphylococcus epidermidis biofilm's tolerance against physico-chemical disinfection

Staphylococcus epidermidis is the predominant cause of recalcitrant biofilm-associated infections, which are often highly resistant to antibiotics. Thus, the use of physico-chemical agents for disinfection offers a more effective approach to the control of S. epidermidis biofilm infections. However, the underlying tolerance mechanisms employed by S. epidermidis biofilm against these physico-chemical disinfectants remain largely unknown. The expression of a σ^B-dependent gene, alkaline shock protein 23 (asp23) and catalase activity by S. epidermidis biofilm and planktonic cells exposed to heat (50 °C), 0.8 M sodium chloride (NaCl), 5 mM sodium hypochlorite (NaOCl) or 50 μM hydrogen peroxide (H₂O₂) for 60 minutes were compared. Significantly higher asp23 expression levels were observed in biofilms exposed to 50 °C, 5 mM NaOCl or 50 μM H₂O₂ compared to the corresponding planktonic cells (p < 0.05). Conversely, asp23 expression levels in biofilm and planktonic cells exposed to 0.8 M NaCl were not significantly different (p > 0.05). Further, biofilms exposed to 50 °C, 0.8 M NaCl, 5 mM NaOCl or 50 μM H₂O₂ exhibited significantly higher catalase activity than the planktonic cells (p < 0.05). These results suggest that activities of σ^B and catalase may be involved in the tolerance of S. epidermidis biofilm against physico-chemical disinfection.

Late-Exponential Gene Expression in codY-Deficient Bacillus anthracis in a Host-Like Environment

CodY is a pleiotropic regulator commonly found in Gram-positive bacteria and regulates various biological processes during the stringent response in a nutrient-limiting environment. CodY also participates in virulence factor expression in many low G+C Gram-positive pathogens, as observed in Bacillus anthracis. However, the mechanism by which B. anthracis CodY regulates metabolism and virulence factors in response to environmental changes is unclear. Here, we attempted to identify the link between CodY and B. anthracis regulation with codY-deficient and codY-overexpressing mutants using high-throughput transcriptional analysis. Growth pattern analyses of codY mutants in both rich and minimal media showed defects in early cell proliferation, with opposite patterns in the early stationary phase: CodY overexpression prolonged bacterial growth, whereas deletion inhibited growth. RNA sequencing of codY-deficient B. anthracis showed both positive and negative changes in the gene expression of proteases and virulence factors as well as genes related to stringent response-related metabolism and biosynthetic processing. We also found that changes in codY expression could alter virulence gene expression of B. anthracis, suggesting modes of regulation in its virulence in a CodY concentration-dependent manner. Collectively, we conclude from these results that CodY can both positively and negatively regulate its regulon via direct and/or indirect approaches, and that its mode of regulation may be concentration dependent.

Effect of malachite green toxicity on non target soil organisms

Although malachite green (MG), is banned in Europe and US for its carcinogenic and teratogenic effect, the dye being cheap, is persistently used in various countries for fish farming, silk, dye, leather and textile industries. Current research, however, fails to elucidate adequate knowledge concerning the effects of MG in our ecosystem. In the present investigation, for the first time, an attempt has been made to study the effects of MG on soil biota by testing Bacillus subtilis, Azotobacter chroococcum, Saccharomyces cerevisiae, Penicillium roqueforti, Eisenia fetida and seeds of three crop plants of different families. Various tests were conducted for determining cytotoxicity, genotoxicity, acute toxicity, morphological and germination effect. Our data confirmed MG toxicity on fungi and bacteria (gram positive and gram negative organisms) showing elevated level of ROS. Genotoxicity caused in the microorganisms was detected by DNA polymorphism and fragmentation. Also, scanning electron microscopy data suggests that the inhibitory effect of MG to these beneficial microbes in the ecosystem might be due to pore formation in the cell and its eventual disruption. Filter paper and artificial soil test conducted on earthworms demonstrated a LC 50 of 2.6 mg cm(-2) and 1.45 mg kg(-1) respectively with severe morphological damage. However, seed germination of Mung bean, Wheat and Mustard was found to be unaffected in presence of MG up to 100 mL(-1) concentration. Thus, understanding MG toxicity in non target soil organisms and emphasis on its toxicological effects would potentially explicate its role as an environmental contaminant.

Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress

Acidovorax avenae subsp. avenae is the causal agent of bacterial brown stripe disease in rice. In this study, we characterized a novel horizontal transfer of a gene cluster, including tetR, on the chromosome of A. avenae subsp. avenae RS-1 by genome-wide analysis. TetR acted as a repressor in this gene cluster and the oxidative stress resistance was enhanced in tetR-deletion mutant strain. Electrophoretic mobility shift assay demonstrated that TetR regulator bound directly to the promoter of this gene cluster. Consistently, the results of quantitative real-time PCR also showed alterations in expression of associated genes. Moreover, the proteins affected by TetR under oxidative stress were revealed by comparing proteomic profiles of wild-type and mutant strains via 1D SDS-PAGE and LC-MS/MS analyses. Taken together, our results demonstrated that tetR gene in this novel gene cluster contributed to cell survival under oxidative stress, and TetR protein played an important regulatory role in growth kinetics, biofilm-forming capability, superoxide dismutase and catalase activity, and oxide detoxicating ability.

Transcriptomic and phenotypic analysis of paralogous spx gene function in Bacillus anthracis Sterne

Spx of Bacillus subtilis is a redox-sensitive protein, which, under disulfide stress, interacts with RNA polymerase to activate genes required for maintaining thiol homeostasis. Spx orthologs are highly conserved among low %GC Gram-positive bacteria, and often exist in multiple paralogous forms. In this study, we used B. anthracis Sterne, which harbors two paralogous spx genes, spxA1 and spxA2, to examine the phenotypes of spx null mutations and to identify the genes regulated by each Spx paralog. Cells devoid of spxA1 were sensitive to diamide and hydrogen peroxide, while the spxA1 spoxA2 double mutant was hypersensitive to the thiol-specific oxidant, diamide. Bacillus anthracis Sterne strains expressing spxA1DD or spxA2DD alleles encoding protease-resistant products were used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses in order to uncover genes under SpxA1, SpxA2, or SpxA1/SpxA2 control. Comparison of transcriptomes identified many genes that were upregulated when either SpxA1DD or SpxA2DD was produced, but several genes were uncovered whose transcript levels increased in only one of the two SpxADD-expression strains, suggesting that each Spx paralog governs a unique regulon. Among genes that were upregulated were those encoding orthologs of proteins that are specifically involved in maintaining intracellular thiol homeostasis or alleviating oxidative stress. Some of these genes have important roles in B. anthracis pathogenesis, and a large number of upregulated hypothetical genes have no homology outside of the B. cereus/thuringiensis group. Microarray and RT-qPCR analyses also unveiled a regulatory link that exists between the two spx paralogous genes. The data indicate that spxA1 and spxA2 are transcriptional regulators involved in relieving disulfide stress but also control a set of genes whose products function in other cellular processes.

Bacillus anthracis harbors two paralogs of the global transcriptional regulator of stress response, SpxA. SpxA1 and SpxA2 contribute to disulfide stress tolerance, but only SpxA1 functions in resistance to peroxide. Transcriptome analysis uncovered potential SpxA1 and SpxA2 regulon members, which include genes activated by both paralogs. However, paralog-specific gene activation was also observed. Genes encoding glutamate racemase, CoA disulfide reductase, and products functioning in bacillithiol biosynthesis, are among the genes activated by the SpxA paralogs.