Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.

Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).

Organic Fertilizer Application Mediates Tomato Defense Against Pseudomonas syringae pv. Tomato, Possibly by Reshaping the Soil Microbiome.

Bacterial speck caused by Pseudomonas syringae pv. tomato is a serious foliar disease on tomato. However, it is still unknown how organic fertilizers application mediates plant defense against foliar pathogens by altering the composition of the soil microbial community. We conducted a 2-cycle pot experiment involving chemical and organic fertilizers and tracked tomato foliar pathogen incidence. Using microbiome sequencing, we then compared the differences in bulk and rhizosphere microbial communities. The results showed that, compared with soils amended with chemical fertilizer, soils amended with organic fertilizer gradually and significantly presented a reduction in tomato foliar disease, and the bacterial richness and diversity significantly increased. Moreover, the bacterial and fungal compositions of the bulk soil and rhizosphere soil of the organic fertilizer and chemical fertilizer treatments were different from each other. More importantly, the abundance of some potentially beneficial bacteria, such as Luteolibacter, Glycomyces, Flavobacterium, and Flavihumibacter, increased in the organic fertilizer-amended soil, and these genera were significantly negatively correlated with the incidence of tomato foliar disease. These results suggest that organic fertilizers can alter the taxonomy of the soil microbiome and that some specific beneficial microbial communities may play an important role in reducing the infection of foliar pathogens by inducing plant resistance.

Removal of antibiotic resistance genes during livestock wastewater treatment processes: Review and prospects.

Antibiotic resistance genes (ARGs) are emerging pollutants that have received extensive attention. Many different types of ARGs exist in livestock wastewater. If not effectively treated, they can threaten animal production, public health and the ecological safety of the surrounding environment. To address the high risk of livestock wastewater contamination by ARGs, the effects of different wastewater treatment processes on ARGs and their influencing factors and mechanisms are reviewed herein. Additionally, the current problems associated with removal of ARGs are discussed, and future research is proposed.