Antioxidant enzymes and reactive oxygen species level of the Achromobacter xylosoxidans bacteria during hydrocarbons biotransformation

Potential of Chinese Yam (Dioscorea polystachya Turczaninow) By-Product as a Feed Additive in Largemouth Bass (Micropterus salmoides): Turning Waste into Valuable Resources

Chinese yam (Dioscorea polystachya Turczaninow) by-product produced in the water extraction process is commonly directly discarded resulting in a waste of resources and environmental pollution. However, the value of Chinese yam by-product which still contains effective ingredients is far from being fully realized; hence, it has the potential to be a safe and effective feed additive in aquaculture. To investigate the impacts of Chinese yam by-product on growth performance, antioxidant ability, histomorphology, and intestinal microbiota of Micropterus salmoides, juvenile fish (initial weight 13.16 ± 0.05 g) were fed diets supplemented with 0% (control), 0.1% (S1), 0.4% (S2), and 1.6% (S3) of Chinese yam by-product for 60 days. The results showed that no significant difference was found in weight gain, specific growth rate, and survival among all the experimental groups (P > 0.05). Feed conversion ratios of the S1 and S3 groups were significantly lower than those in the control group (P < 0.05). SOD activity of the S3 group and GSH contents of Chinese yam by-product groups were significantly higher than those in the control group (P < 0.05). MDA levels of the S2 and S3 groups were significantly lower than those in the control group and the S1 group (P < 0.05). Besides, Chinese yam by-product could protect liver and intestine health, as well as increase the abundance of beneficial bacteria and decrease the abundance of potential pathogens. This study suggests that Chinese yam by-product has the potential to be used as a functional feed additive in aquaculture, providing a reference for efficient recovery and utilization of by-products from plant sources during processing and culturing high-quality aquatic products.

The role of oxidative stress in genome destabilization and adaptive evolution of bacteria

The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.

Transcriptomic profiling reveals the molecular responses of Rhodococcus aetherivorans DMU1 to skatole stress

Skatole is a typical malodor compound in animal wastes. Several skatole-degrading bacterial strains have been obtained, whereas the molecular response of strains to skatole stress has not been well elucidated. Herein, the skatole degradation by a Gram-positive strain Rhodococcus aetherivorans DMU1 was investigated. Strain DMU1 showed high efficiency in skatole degradation under the conditions of 25-40 °C and pH 7.0-10.0. It could utilize various aromatics, including cresols, phenol, and methylindoles, as the sole carbon source for growth, implying its potential in the bioremediation application of animal wastes. Transcriptomic sequencing revealed that 328 genes were up-regulated and 640 genes were down-regulated in strain DMU1 when grown in the skatole-containing medium. Skatole increased the gene expression levels of antioxidant defense systems and heat shock proteins. The expression of ribosome-related genes was significantly inhibited which implied the growth inhibition of skatole. A rich set of oxidoreductases were changed, and a novel gene cluster containing the flavoprotein monooxygenase and ring-hydroxylating oxygenase genes was highly up-regulated, which was probably involved in skatole upstream degradation. The upregulation pattern of this gene cluster was further verified by qRT-PCR assay. Furthermore, skatole should be mainly degraded via the catechol ortho-cleavage pathway with cat25170 as the functional gene. The gene cat25170 was cloned and expressed in E. coli BL21(DE3). Pure enzyme assays showed that Cat25170 could catalyze catechol with Km 9.96 μmol/L and kcat 12.36 s-1.

Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use

For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.

Advances on tailored biochar for bioremediation of antibiotics, pesticides and polycyclic aromatic hydrocarbon pollutants from aqueous and solid phases

Biochar is gaining incredible importance for remediation applications due to their attractive removal properties. Moreover, it is becoming ecofriendly, cost-effective and sustainable bioadsorbents towards replacing expensive activated carbons. Studies reveal biochar effectiveness for removal of important and potentially severe organic pollutants such as antibiotics and pesticides. Recent research advancements on biochar modification (physical, chemical and biological) opens greater opportunity to form tailored biochar with improved surface properties than their native forms for offering better removal efficiencies. Further attentions paid towards emergent new modification methods to cover broad-spectrum pollutants using tailored biochar. Current review aims to summarize recent updates upon biochar tailoring, comparative account of tailored biochars removal efficiencies with respect to their native forms and to provide in-depth discussion covering specific interactions of tailored biochars with antibiotics, polycyclic aromatic hydrocarbons (PAHs) and pesticides for their effective removals and degradation from polluted environments. Application of inducer compounds e.g., peroxymonosulfate and sodium percarbonate further improved the biochar role towards degradation of toxic organic pollutants into their less or nontoxic forms. Biochar engineered with specific metals enable them for the same role without inducer compounds. Moreover, microbial interactions with biochar not only improve the bioremediation level further but also degrade the pollutants from the environment and open up better environmental and socio-economic prospects. Application of green, cost-effective and sustainable biochar for remediation of environmentally potential organic pollutants offers economical treatment methods as well as safe environment. These benefits are inline with global trends towards developing a sustainable process for biocircular economy.

Comparative proteomics unravelled the hexachlorocyclohexane (HCH) isomers specific responses in an archetypical HCH degrading bacterium Sphingobium indicum B90A

Hexachlorocyclohexane (HCH) is a persistent organochlorine pesticide that poses threat to different life forms. Sphingobium indicum B90A that belong to sphingomonad is well-known for its ability to degrade HCH isomers (α-, β-, γ-, δ-), but effects of HCH isomers and adaptive mechanisms of strain B90A under HCH load remain obscure. To investigate the responses of strain B90A to HCH isomers, we followed the proteomics approach as this technique is considered as the powerful tool to study the microbial response to environmental stress. Strain B90A culture was exposed to α-, β-, γ-, δ-HCH (5 mgL^-1) and control (without HCH) taken for comparison and changes in whole cell proteome were analyzed. In β- and δ-HCH-treated cultures growth decreased significantly when compared to control, α-, and γ-HCH-treated cultures. HCH residue analysis corroborated previous observations depicting the complete depletion of α- and γ-HCH, while only 66% β-HCH and 34% δ-HCH were depleted from culture broth. Comparative proteome analyses showed that β- and δ-HCH induced utmost systemic changes in strain B90A proteome, wherein stress-alleviating proteins such as histidine kinases, molecular chaperons, DNA binding proteins, ABC transporters, TonB proteins, antioxidant enzymes, and transcriptional regulators were significantly affected. Besides study confirmed constitutive expression of linA, linB, and linC genes that are crucial for the initiation of HCH isomers degradation, while increased abundance of LinM and LinN in presence of β- and δ-HCH suggested the important role of ABC transporter in depletion of these isomers. These results will help to understand the HCH-induced damages and adaptive strategies of strain B90A under HCH load which remained unravelled to date.

Cadmium enhances conjugative plasmid transfer to a fresh water microbial community

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd²⁺) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd²⁺ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd²⁺ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd²⁺ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd²⁺ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd²⁺ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd²⁺ in aquatic environments.

The mechanisms of biochar interactions with microorganisms in soil

Biochar, a carbonaceous material, is increasingly used in the remediation of the anthropogenically polluted soils and the restoration of their ecological functions. However, the interaction mechanisms among biochar, inorganic and organic soil properties and soil biota are still not very clear. The effect of biochar on soil microorganisms is very diverse. Several mechanisms of these interactions were suggested. However, a well acceptable mechanism of biochar effect on soil microorganisms is still missing. Therefore, efforts were made to examine and proposed a mechanism of the interactions between biochar and microorganisms, as well as existing problems of biochar impacts on main groups of soil enzymes, the composition of the microbiota and the detoxification (heavy metals) and degradation (polycyclic aromatic hydrocarbons) of soil pollutants. The data on the process of biochar colonization by microorganisms and the effect of volatile pyrolysis products released by biochar on the soil microbiota were analysed in detail. The effects of biochar on the physico-chemical properties of soils, the content of mineral nutrients and the response of microbial communities to these changes are also discussed. The information provided here may contribute to the solution of the feasibility, effectiveness and safety of the biochar questions to enhance the soil fertility and to detoxify pollutants in soils.

Antibacterial effects of low-temperature plasma generated by atmospheric-pressure plasma jet are mediated by reactive oxygen species

Emergence and spread of antibiotic resistance calls for development of non-chemical treatment options for bacterial infections. Plasma medicine applies low-temperature plasma (LTP) physics to address biomedical problems such as wound healing and tumor suppression. LTP has also been used for surface disinfection. However, there is still much to be learned regarding the effectiveness of LTP on bacteria in suspension in liquids, and especially on porous surfaces. We investigated the efficacy of LTP treatments against bacteria using an atmospheric-pressure plasma jet and show that LTP treatments have the ability to inhibit both gram-positive (S. aureus) and gram-negative (E. coli) bacteria on solid and porous surfaces. Additionally, both direct LTP treatment and plasma-activated media were effective against the bacteria suspended in liquid culture. Our data indicate that reactive oxygen species are the key mediators of the bactericidal effects of LTP and hydrogen peroxide is necessary but not sufficient for antibacterial effects. In addition, our data suggests that bacteria exposed to LTP do not develop resistance to further treatment with LTP. These findings suggest that this novel atmospheric-pressure plasma jet could be used as a potential alternative to antibiotic treatments in vivo.

Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis

In this study, we compared the expression of CYP153, sodA, sodC, and recA genes and ROS generation in hydrocarbon-degrading Rhodococcus erythropolis in the presence of cyclohexane, naphthalene, and diesel fuel. The expression of cytochrome P450, sodA (encoding Fe/Mn superoxide dismutase), recA, and superoxide anion radical generation rate increased after the addition of all studied hydrocarbons. The peak of CYP153, sodA, and recA gene expression was registered in the presence of naphthalene. The same substrate upregulated the Cu/Zn superoxide dismutase gene, sodC. Cyclohexane generated the highest level of superoxide anion radical production. Hydrogen peroxide accumulated in the medium enriched with diesel fuel. Taken together, hydrocarbon biotransformation leads to oxidative stress and upregulation of antioxidant enzymes and CYP153 genes, and increases DNA reparation levels in R. erythropolis cells.