A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1 based on iTRAQ

Arsenic effectively improves the degradation of fluorene by Rhodococcus sp. 2021 under the combined pollution of arsenic and fluorene

The performance of bacterial strains in executing degradative functions under the coexistence of heavy metals/heavy metal-like elements and organic contaminants is understudied. In this study, we isolated a fluorene-degrading bacterium, highly arsenic-resistant, designated as strain 2021, from contaminated soil at the abandoned site of an old coking plant. It was identified as a member of the genus Rhodococcus sp. strain 2021 exhibited efficient fluorene-degrading ability under optimal conditions of 400 mg/L fluorene, 30 °C, pH 7.0, and 250 mg/L trivalent arsenic. It was noted that the addition of arsenic could promote the growth of strain 2021 and improve the degradation of fluorene - a phenomenon that has not been described yet. The results further indicated that strain 2021 can oxidize As3+ to As5+; here, approximately 13.1% of As3+ was converted to As5+ after aerobic cultivation for 8 days at 30 °C. The addition of arsenic could greatly up-regulate the expression of arsR/A/B/C/D and pcaG/H gene clusters involved in arsenic resistance and aromatic hydrocarbon degradation; it also aided in maintaining the continuously high expression of cstA that codes for carbon starvation protein and prmA/B that codes for monooxygenase. These results suggest that strain 2021 holds great potential for the bioremediation of environments contaminated by a combination of arsenic and polycyclic aromatic hydrocarbons. This study provides new insights into the interactions among microbes, as well as inorganic and organic pollutants.

Metagenomic analysis reveals the distribution, function, and bacterial hosts of degradation genes in activated sludge from industrial wastewater treatment plants

For comprehensive insights into the bacterial community and its functions during industrial wastewater treatment, with a particular emphasis on its pivotal role in the bioremediation of organic pollutants, this study utilized municipal samples as a control group for metagenomic analysis. This approach allowed us to investigate the distribution, function, and bacterial hosts of biodegradation genes (BDGs) and organic degradation genes (ODGs), as well as the dynamics of bacterial communities during the industrial wastewater bioprocess. The results revealed that BDGs and ODGs associated with the degradation of benzoates, biphenyls, triazines, nitrotoluenes, and chlorinated aromatics were notably more abundant in the industrial samples. Specially, genes like clcD, linC, catE, pcaD, hbaB, hcrC, and badK, involved in the peripheral pathways for the catabolism of aromatic compounds, benzoate transport, and central aromatic intermediates, showed a significantly higher abundance of industrial activated sludge (AS) than municipal AS. Additionally, the BDG/ODG co-occurrence contigs in industrial samples exhibited a higher diversity in terms of degradation gene carrying capacity. Functional analysis of Clusters of Orthologous Groups (COGs) indicated that the primary function of bacterial communities in industrial AS was associated with the category of "metabolism". Furthermore, the presence of organic pollutants in industrial wastewater induced alterations in the bacterial community, particularly impacting the abundance of key hosts harboring BDGs and ODGs (e.g. Bradyrhizobium, Hydrogenophaga, and Mesorhizobium). The specific hosts of BDG/ODG could explain the distribution characteristics of degradation genes. For example, the prevalence of the Adh1 gene, primarily associated with Mesorhizobium, was notably more prevalent in the industrial AS. Overall, this study provides valuable insights into the development of more effective strategies for the industrial wastewater treatment and the mitigation of organic pollutant contamination.

The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare

The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.

Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review

Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.

Current and emerging trends in bioaugmentation of organic contaminated soils: A review

Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.

Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants that are ubiquitous in the environment. Numerous bacteria have evolved to have degrading genes or pathways to degrade PAHs. Stenotrophomonas maltophilia strain W18 was found to be able to degrade PAHs. Including 43 other complete genome sequences of S. maltophilia strains, we performed a comparative genomic analysis of 44 S. maltophilia strains by running OrthoFinder. A KEGG pathway enrichment analysis of environmental and clinical isolates of S. maltophilia revealed that environmental isolates tended to enhance gene functions such as "energy metabolism," "amino acid metabolism," "xenobiotic biodegradation and metabolism," and "folding, sorting, and degradation." The pangenome of the 44 S. maltophilia strains was open, while the core genome was estimated to reach a steady plateau. Based on gene annotations, we inferred that most of the degradation potential came from the core genome of S. maltophilia, while character genes and accessory genes also contributed to the degradation ability of S. maltophilia W18. The genes expression level of core genes, character genes and accessory genes were proved by RT-qPCR experiment, and accessory genes encoding alcohol dehydrogenase were upregulated most compared with genes with similar functions. We performed a credible comparative genomic analysis of S. maltophilia strains. S. maltophilia W18 was set as a model PAH-degrading bacterium of this species in this study, which would provide guidance for understanding and predicting the degradation mechanisms of other PAH-degrading S. maltophilia strains lacking complete genome data or waiting to be determined. IMPORTANCE This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable. The gene functions of how S. maltophilia environmental isolates are enhanced for adaptation to various natural environments compared with clinical isolates have been revealed. Combined with a pangenome analysis and RT-qPCR results, we have proved that core genes, character genes, and accessory genes are all involved in PAH degradation. Accessory genes encoding alcohol dehydrogenase were upregulated most compared with core and character genes with similar functions, which suggests that PAH metabolization potential might be enhanced by horizontal gene transfer.

Experimental study on the biodegradation of naphthalene and phenanthrene by functional bacterial strains in the riparian soil of a binary system

Polycyclic aromatic hydrocarbons (PAHs) such as naphthalene (Nap) and phenanthrene (Phe) are organic pollutants of concern owing to their toxicity, carcinogenicity, and teratogenicity. Biodegradation is considered the most economical and efficient process to remediate Nap and Phe. The riparian zone between a river and a riparian aquifer, which is rich in indigenous microorganisms, may be important for PAH remediation. However, few studies have evaluated the ability of indigenous microorganisms to remove Nap and Phe. In this study, focusing on the typical PAHs (Nap and Phe) as target pollutants, the genus-level community structure of Nap- and Phe-degrading bacteria was identified. Batch static and dynamic biodegradation experiments were conducted to explore the biodegradation mechanisms of Nap and Phe in the riparian zone and identify the factors influencing Nap and Phe biodegradation in the binary system (i.e., where Nap and Phe are simultaneously present). According to the genus-level community structure test results, the dominant bacterial genus in the binary system was mainly the Phe-degrading bacteria. The Nap and Phe-biodegradation percentages were 19.20% lower and 19.49% higher, respectively, in the binary system than in the unitary system. The results indicated that functional bacteria can degrade Nap and Phe, and that Nap weakly promoted Phe biodegradation. Additionally, the initial Nap and Phe concentration ratio, hydraulic gradient, and temperature affected Nap and Phe biodegradation. Dynamic biodegradation experiments showed that the biodegradation percentage decreased as the hydraulic gradient increased, and biodegradation percentage of Phe was always higher than that of Nap. According to the results of the dynamic laboratory experiments, the removal percentages of Nap and Phe by indigenous riparian-zone microorganisms were 6.21-16.73% and 13.95-24.45%, respectively. The findings in this study will be useful for alleviation of Nap and Phe pollution in groundwater and will facilitate determination of appropriate treatment measures for groundwater exposed to this type of pollution.

Enhanced bioremediation of 2,3',4,4',5-pentachlorodiphenyl by consortium GYB1 immobilized on sodium alginate-biochar

2,3',4,4',5-pentachlorodiphenyl (PCB 118), a dioxin-like PCB, is often detected in the environment and is difficult to be aerobically biodegraded. In this study, a novel polychlorinated biphenyl degrading consortium GYB1 that can metabolize PCB 118 was successfully obtained by acclimatization process. To enhance the application performance of free bacterial cells, consortium GYB1 was immobilized with sodium alginate and biochar to prepare SC-GYB1 beads. Orthogonal experiments indicated that the optimal composition of the beads (0.2 g) was 2.0% sodium alginate (SA) content, 2.0% wet weight of cells and 1.5% biochar content, which can degrade 50.50% PCB 118 in 5 d. Immobilization shortened the degradation half-life of 1 mg/L PCB 118 by consortium GYB1 from 8.14 d to 3.79 d and made the beads more robust to respond to environmental stress. The SC-GYB1 beads could even keep considerable PCB degradation ability under 200 mg/L Cd²⁺ stress. According to 16S rRNA gene analysis, Pseudomonas and Stenotrophomonas played the dominant role in consortium GYB1. And embedding obviously altered the community structure and the key bacterial genera during the PCB removal process. Therefore, the immobilization of bacteria consortium by sodium alginate-biochar enhanced the biodegradation of PCB 118, which will provide new insights into functional microorganisms' actual application for PCB restoration.

iTRAQ-based quantitative proteomic analysis of the antimicrobial mechanism of lactobionic acid against Staphylococcus aureus

Staphylococcus aureus is a common pathogenic microorganism that causes foodborne diseases. Lactobionic acid (LBA) is a natural polyhydroxy acid widely used in the food industry. To understand the antibacterial action of LBA against S. aureus better and identify 274 differentially expressed proteins upon LBA treatment, an isobaric tag was used for relative and absolute quantification-based quantitative proteomics. Combined with ultrastructural observations, results suggested that LBA inhibited S. aureus by disrupting cell wall and membrane integrity, regulating adenosine triphosphate binding cassette transporter expression, affecting cellular energy metabolism, attenuating S. aureus virulence and reducing infection, and decreasing the levels of proteins involved in stress and starvation responses. Quantitative real-time polymerase chain reaction analysis was used to validate the proteomic data. The results provide new insights into the inhibitory effects of LBA on S. aureus and suggest that LBA application may be a promising method to ensure food and pharmaceutical product safety.