Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting

As a major reservoir of antibiotics,animal manure contributes a lot to the augmented environmental pressure of antibiotic resistance genes(ARGs).This might be the first study to explore the effects of different ventilation types on the control of ARGs and to identify the relationships between archaeal communities and ARGs during the composting of dairy manure.Several ARGs were quantified via Real-time qPCR and microbial communities including bacteria and archaea were analyzed by High-throughput sequencing during vacuum-type composting(VTC) and positive-pressure composting(PPC).The total detected ARGs and class I integrase gene(intI1) under VTC were significantly lower than that under PPC during each stage of the composting(p <0.001).The relative abundance of potential human pathogenic bacteria(HPB) which were identified based on sequencing information and correlation analysis decreased by 74.6% and 91.4% at the end of PPC and VTC,respectively.The composition of archaeal communities indicated that methane-producing archaea including Methanobrevibacter,Methanocorpusculum and Methanosphaera were dominant throughout the composting.Redundancy analysis suggested that Methanobrevibacter and Methanocorpusculum were positively correlated with all of the detected ARGs.Network analysis determined that the possible hosts of ARGs were different under VTC and PPC,and provided new sights about potential links between archaea and ARGs.Our results showed better performance of VTC in reducing ARGs and potential HPB and demonstrated that some archaea could also be influential hosts of ARGs,and caution the risks of archaea carrying ARGs.

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress

Polycyclic aromatic hydrocarbons(PAHs)are ubiquitous priority pollutants that cause great damage to the natural environment and health.Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment.Here,microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community.We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils,and consistent trends were discovered in soils at different latitudes.The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments.In contrast,the abundance of Patescibacteria with a highly streamlined and smaller genome decreased,implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant.Moreover,we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nid A gene along the concentration gradients in the co-occurrence network.Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes,with significant consequences for community stability and potential biodegradation strategies.