Microbial biomarkers as indication of dynamic and heterogeneous urban water environments.

Water samples for the 16S rRNA gene and water quality analyses were collected from around 155 km of river segments surrounding the urban areas in Xi'an, China. Multiple statistical analyses showed that the dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the spring to the summer seasons were apparent but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed that the Chan and Zao Rivers, both more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in the summer. Multiple statistical analyses indicated that environmental variables had significant impacts on microbial communities. The geographical information system-based spatial analysis showed heterogeneity of microbial community distributions along the rivers. This study showed that the high-throughput sequencing analysis could identify some pathogenic bacteria that would significantly threaten public health and eco-environments in urban rivers.

Corrigendum: Activation of the NFκB signaling pathway in IL6+CSF3+ vascular endothelial cells promotes the formation of keloids.

[This corrects the article DOI: 10.3389/fbioe.2022.917726.].

Activation of the NFκB signaling pathway in IL6+CSF3+ vascular endothelial cells promotes the formation of keloids.

Background: Keloid is a disease caused by abnormal proliferation of skin fibres, the causative mechanism of which remains unclear. Method: In this study, endothelial cells of keloids were studied using scRNAseq combined with bulk-RNAseq data from keloids. The master regulators driving keloid development were identified by transcription factor enrichment analysis. The pattern of changes in vascular endothelial cells during keloid development was explored by inferring endothelial cell differentiation trajectories. Deconvolution of bulkRNAseq by CIBERSORTX verified the pattern of keloidogenesis. Immunohistochemistry for verification of the lesion process in keloid endothelial cells. Results: The endothelial cells of keloids consist of four main cell populations (MMP1+ Endo0, FOS + JUN + Endo1, IL6+CSF3+Endo2, CXCL12 + Endo3). Endo3 is an endothelial progenitor cell, Endo1 is an endothelial cell in the resting state, Endo2 is an endothelial cell in the activated state and Endo0 is an endothelial cell in the terminally differentiated state. Activation of the NFΚB signaling pathway is a typical feature of Endo2 and represents the early skin state of keloids. Conclusion: We have identified patterns of vascular endothelial cell lesions during keloidogenesis and development, and have found that activation of the NFΚB signaling pathway is an essential feature of keloid formation. These findings are expected to contribute to the understanding of the pathogenesis of keloids and to the development of new targeted therapeutic agents for the lesional characteristics of vascular endothelial cells.

Clarifying the beneficial effects of plant growth-promoting rhizobacteria for reducing abundances of antibiotic resistance genes during swine manure composting.

This study investigated the effects on antibiotic resistance genes (ARGs) and the related mechanisms of different plant growth-promoting rhizobacteria (PGPR) inoculation strategies during composting: no inoculation (CK), inoculation in initial phase (T1), inoculation in cooling phase (T2), and inoculation in both initial and cooling phases (T3). After composting, the total relative abundances (RAs) of ARGs decreased by 0.26 and 0.03 logs under T3 and T2, respectively, but increased by 0.05 and 0.22 logs under T1 and CK. The abundances of eight ARGs were lowest under T3, including some high risk ARGs with clinical importance. Bioavailable Cu significantly affected the readily removed ARGs, and PGPR inoculation decreased the bioavailability of Cu. T3 reduced the abundances of potential pathogen hosts, inhibited horizontal gene transfer by reducing the RAs of mobile gene elements (0.48 logs), and downregulated the expression of genes related to ARG propagation, thereby decreasing the ecological risk of ARGs.

Succession of diazotroph community and functional gene response to inoculating swine manure compost with a lignocellulose-degrading consortium.

Diazotroph community contributes to the nitrogen mass and improves the agronomic quality of composting product, but their responses to microbial inoculation during composting are unclear. In this study, the lignocellulose-degrading consortium was inoculated at different levels (0%: CK (control) and 10%: T) to investigate their effects on the variations in the diazotroph community and functional gene during composting. In the later composting phase, the nifH gene copy number was 17.50-25.28% higher in T than CK. The nitrogenase abundance in CK and T were 0.042% and 0.046% in composting product, respectively. Network analysis indicated that inoculation affected the co-occurrence patterns of the diazotroph community and changed the keystone species composition. Partial least-squares path modeling showed that available carbon sources and the succession of the diazotroph community mainly determined the increased abundance of nifH gene. Microbial inoculation stimulated the diazotrophs activities, and was conducive to the nitrogen production in composting product.

Influences of potassium solubilizing bacteria and K-feldspar on enzyme activities and metabolic activities of the bacterial communities in kiwifruit planting soil.

A pot experiment was conducted with kiwifruit planting soil to evaluate the impacts of potassium solubilizing bacteria (KSB) and K-feldspar on the soil nutrient levels, enzyme activities, and microecological environment. The effects were investigated of three inoculation treatments (T1: K-feldspar, T2: KSB, and T3: KSB with K-feldspar) and a non-inoculation treatment (CK) on the enzyme activities and the metabolic activities of the bacterial communities in kiwifruit rhizosphere soil. The results showed that the total nitrogen, available phosphorus, available potassium, and organic matter contents in T3 were 18.19%, 45.22%, 15.06%, and 4.17% higher, respectively, than those in CK at the end of the experiment (90 days). Compared with CK, T3 significantly increased the invertase, urease, acid phosphatase, and polyphenol oxidase activities. T3 had a higher kiwifruit root activity, but there were no significant differences among the four treatments (P > 0.05). T3 significantly altered the bacterial community diversity, increased the utilization of phenolic compounds and polymers, and decreased the utilization of amino acids. Redundancy analysis indicated that soil nutrients (total nitrogen, available phosphorus, and available potassium) and enzyme activities (urease and acid phosphatase) had more important effects on the metabolic activities of the bacterial communities. Co-inoculation enhanced the soil nutrients, enzyme activities, and bacterial community diversity. KSB co-inoculated with K-feldspar has the potential to improve the soil fertility, microbial metabolic activity and plant growth.

Succession of microbial communities and synergetic effects during bioremediation of petroleum hydrocarbon-contaminated soil enhanced by chemical oxidation.

Biotechnologies integrated with chemical techniques are promising in treating the soils contaminated by petroleum hydrocarbons. Experiments by applying the degrading consortium and the modified Fenton (MF) with the chelator sodium citrate simultaneously were carried out to investigate the effects of the MF reagents on the degradation of total petroleum hydrocarbons (TPHs), changes in enzyme activities and the succession of microbial communities at the 0, 20, 100 and 500 mmol/kg hydrogen peroxide concentration levels. The ratio between hydrogen peroxide, ferrous sulfate and sodium citrate in the MF reagents was 100:1:1. The results indicated that the degradation of TPHs conformed to first-order kinetics and MF treatments increased the total removal rates of TPHs (4.73-24.26%) and activated dehydrogenase and polyphenol oxidase activities. A shift in microbial communities from Proteobacteria to Bacteroidetes was observed during the enhanced bioremediation, and the predominant genus shifted from Pseudomonas with an average relative abundance (ARAs) of 76.61% at the beginning to Sphingobacterium with ARAs of 52.06% at the later stage. The MF reagents at the proper level could simplify the relationship among the community populations, alleviate their competition and strengthen their associations, which would optimize the removal efficiency.

Changes in structure and function of bacterial and fungal communities in open composting of Chinese herb residues.

In this study, dynamic changes in bacterial and fungal communities, metabolic characteristics, and trophic modes in Chinese herb residues open composting for 30 days were analyzed by using high-throughput sequencing, PICRUSt, and FUNGuild, respectively. Bacillaceae and Basidiomycota predominated at the early composting stage, while Proteobacteria and Ascomycota became the dominant phyla during the active phase. Aerobic composting had a significant effect on bacterial metabolic characteristics and fungal trophic modes over the composting time. The function of the bacterial communities changed from environmental information processing to metabolism. Fungal communities changed as well, with the pathogenic fungi decreasing and wood saprotrophs increasing. These results indicated that open composting of Chinese herb residues not only influenced microbial community structure but also changed metabolic characteristics and trophic modes, which became the internal dynamics of composting.

Effects of inoculating with lignocellulose-degrading consortium on cellulose-degrading genes and fungal community during co-composting of spent mushroom substrate with swine manure.

Composting is used widely for recycling spent mushroom substrate (SMS). This study investigated the effects of inoculating a lignocellulose-degrading consortium at two levels comprising 0% (control: CK) and 10% (T) on the fungal community and cellulose-degrading genes during SMS co-composting with swine manure. Lignocellulose degradation rate in T was 8.77-34.45% higher compared with CK. Inoculation affected the distribution of the fungal community, increased the community diversity, and inhibited pathogens. Network analysis showed that inoculation changed the co-occurrence patterns of the fungal communities and made the co-composting system more stable. The relative abundances of glycoside hydrolase genes GH3E (fungal GH3), GH6, and GH7 were 0.45, 0.09, and 0.39 logs higher in T, respectively, than CK. Partial least-squares path modeling suggested that the variations in cellulose-degrading genes were driven mainly by changes in the fungal community during co-composting. Therefore, the lignocellulose-degrading consortium accelerated the transformation of lignocellulose to facilitate safer composting.

Effects of inoculation with lignocellulose-degrading microorganisms on antibiotic resistance genes and the bacterial community during co-composting of swine manure with spent mushroom substrate.

Composting is usually employed to treat livestock manure, and inoculation with lignocellulose-degrading microorganisms can enhance the quality of compost. In this study, lignocellulose-degrading microorganisms were inoculated at two levels (uninoculated control = 0%, and T treatment = 10%) during co-composting of swine manure with spent mushroom substrate, and their effects on antibiotic resistance genes (ARGs) and the bacterial community were investigated. Inoculation with lignocellulose-degrading microorganisms caused greater decreases in 6/11 ARGs and 3/4 mobile genetic elements than the control. The total relative abundances of ARGs increased by 0.23 logs in the control but decreased by 0.08 logs in the T treatment after co-composting. The bacterial community was clustered according to the composting time in the two treatments, where inoculation mainly affected the bacterial community during the mesophilic phase. Redundancy analysis and network analysis showed that the bacterial community succession had important effects on the variations in ARGs. Inoculation with lignocellulose-degrading microorganisms led to the reduction of ARGs, which was significantly correlated with the abundances of potential host bacteria for ARGs. Thus, inoculation with lignocellulose-degrading microorganisms could decrease the risk of ARGs spreading and make compost products more security.

Effects of compost containing oxytetracycline on enzyme activities and microbial communities in maize rhizosphere soil.

Veterinary antibiotics can enter agricultural fields via the application of livestock manure containing antibiotics. However, the response of soil microorganisms to compost containing antibiotics is not well understood. A 120-day pot experiment was conducted to investigate the impact of compost containing oxytetracycline (OTC) on the enzyme activities and microbial communities in maize rhizosphere soil. Swine manure was artificially spiked with OTC at four concentrations, 35, 70, 105, and 140 mg kg-1, and combined with straw to produce compost. The compost products were applied to soil planted with maize. Rhizosphere soil samples were collected on days 1, 15, 30, 60, and 120. The results indicated that the urease activities first increased and then declined, while in contrast, the alkaline phosphatase activities first decreased and then increased slightly. Catalase exhibited dose-related activation during the maize growth period. At the end of the experiment, the soil enzyme activities were similar to their initial values, indicating that the soil enzymes showed a level of recovery. The carbon metabolic activity levels were higher in the soils with high OTC concentrations than in the control, whereas the Shannon diversity index was higher in the control soil. The results of principal component analysis (PCA) indicated that the application of compost containing OTC shifted the structure of the soil microbial community and negatively affected its stability. These results suggest that the compost containing OTC exerted selective pressure on enzyme activities and microbial communities in maize rhizosphere soil and decreased their resilience to antibiotic pollution.