Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types.

The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.

Lower soil nitrogen-oxide emissions associated with enhanced denitrification under replacing mineral fertilizer with manure in orchard soils.

Emerging evidence suggests that replacing mineral fertilizers with organic livestock manure can effectively suppress reactive gaseous nitrogen (N) emissions from soils. However, the extent of this mitigation potential and the underlying microbial mechanisms in orchards remain unclear. To address this knowledge gap, we measured nitrous and nitric oxide (N2O and NO) emissions, microbial N cycling gene abundance, and N2O isotopomer ratios in pear and citrus orchards under three different fertilization regimes: no fertilization, mineral fertilizer, and manure plus mineral fertilizer. The results showed that although manure application caused large transient peaks of N2O, it reduced cumulative emissions of N2O and NO by an average of 20 % and 17 %, respectively, compared to the mineral fertilizer treatment. Partial replacement of mineral fertilizers with manure enhanced the contribution of AOA to nitrification and reduced the contribution of AOB, thus reducing N2O emissions from nitrification. Isotope analysis suggested that the pathway for N2O production in the soils of both orchards was dominated by bacterial denitrification and nitrifier denitrification. The manure treatment reduced the ratio of denitrification products. Additionally, the dual isotope mixing model results indicated that partially replacing mineral fertilizers with manure could promote soil denitrification, resulting in more N2O being reduced. N-oxide emissions were on average 67 % higher in the pear orchard than in the citrus orchard, probably due to the differences in soil physicochemical properties and growth habits between the two orchards. These findings underscore the potential of partially replacing mineral fertilizers with organic manure in orchards to reduce gaseous N emissions, contributing to the transition towards environmentally sustainable and climate-smart agricultural practices.

Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties.

Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.