Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting.

The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.

Comparing the variations and influencing factors of CH4 emissions from paddies and wetlands under CO2 enrichment: A data synthesis in the last three decades.

Understanding and quantifying the impact of elevated tropospheric carbon dioxide concentration (e [CO2]) on methane (CH4) globally is important for effectively assessing and mitigating climate warming. Paddies and wetlands are the two important sources of CH4 emissions. Yet, a quantitative synthetic investigation of the effects of e [CO2] on CH4 emissions from paddies and wetlands on a global scale has not been conducted. Here, we conducted a meta-analysis of 488 observation cases from 40 studies to assess the long-term effects of e [CO2] (ambient [CO2]+ 53-400 µmol mol-1) on CH4 emissions and to identify the relevant key drivers. On aggregate, e [CO2] increased CH4 emissions by 25.7% (p < 0.05) from paddies but did not affect CH4 emissions from wetlands (-3.29%; p > 0.05). The e [CO2] effects on paddy CH4 emissions were positively related to that on belowground biomass and soil-dissolved CH4 content. However, these factors under e [CO2] resulted in no significant change in CH4 emissions in wetlands. Particularly, the e [CO2]-induced abundance of methanogens increased in paddies but decreased in wetlands. In addition, tillering number of rice and water table levels affected e [CO2]-induced CH4 emissions in paddies and wetlands, respectively. On a global scale, CH4 emissions changed from an increase (+0.13 and + 0.86 Pg CO2-eq yr-1) under short-term e [CO2] into a decrease and no changes (-0.22 and + 0.03 Pg CO2-eq yr-1) under long-term e [CO2] in paddies and wetlands, respectively. This suggested that e [CO2]-induced CH4 emissions from paddies and wetlands changed over time. Our results not only shed light on the different stimulative responses of CH4 emissions to e [CO2] from paddy and wetland ecosystems but also suggest that estimates of e [CO2]-induced CH4 emissions from global paddies and wetlands need to account for long-term changes in various regions.

Fertilizer-induced N2O and NO emissions in tea gardens and the main controlling factors: A recent three-decade data synthesis.

Tea gardens have been widely documented to be hotspots for nitrogen (N) oxide emissions (i.e., nitrous oxide (N2O) and nitric oxide (NO)). However, a quantitative understanding of N oxide emissions related to different fertilizer regimes and the main controlling factors is lacking. Here, we performed a meta-analysis of 56 peer-reviewed publications on N oxide emissions from global tea gardens over the past three decades. Overall, fertilization increased N2O and NO emissions (p < 0.001) by 584 % and 790 %, respectively. The stimulating effect of fertilizer on N2O and NO emissions was mainly related to high N application rates. Furthermore, organic fertilizer treatment, combined fertilizer treatment, biochar amendment, and inhibitor amendment reduced N2O emissions (p < 0.05) by 63 %, 64 %, 69 %, and 94 %, respectively, relative to chemical fertilizer treatment. For NO emissions, only biochar amendment decreased fertilizer-driven stimulation (by 80 %, p < 0.05). Notably, the dominant factors that influenced fertilizer-induced N2O and NO emissions in tea gardens were fertilization regimes, climatic conditions, and soil properties. On a global scale, fertilization increased mean N2O and NO emissions (p < 0.05) from global tea gardens by 44.5 Gg N yr-1 and 34.3 Gg N yr-1, respectively, whereas compared with no amendment application, inhibitors reduced N2O emissions (p < 0.05) by 32.2 Gg N yr-1 and biochar reduced NO emissions (p < 0.05) by 23.6 Gg N yr-1. Our results suggest that to obtain maximum ecological and economic benefits, appropriate N fertilizer and biochar and inhibitor amendments should be applied for site-specific mitigation purposes, and long-term, multiarea, in situ experiments and microbial mechanism studies should be conducted.

Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.

Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.

Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes.

Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), ß-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.

Double-edged effects of elevating temperature on the aging of exogenous arsenic in flooded paddy soils.

Temperature variation can have a significant impact on arsenic (As) bioavailability in paddy soils. However, details regarding the transformation of exogenous As during the aging process in paddy soils at various temperatures remain unclear. This work investigated the effects of temperature on the As extractability and As species transformation of three paddy soils spiked with exogenous arsenate at 60 mg kg-1 under flooded aging and explored the related chemical and microbial mechanisms. The results showed that 0.05 M NH4H2PO4-extractable As decreased over time during flooded aging for 192 days, and it decreased by approximately one-third at 35 °C compared with 15 °C and 25 °C at the same aging time, indicating that higher temperatures facilitated the decrease in As extractability. As(V) reduction mainly occurred at 35 °C because the abundance and As(V)-reducing capacity of the predominant indigenous bacteria, the Bacillus sp strains, and the abundance of the arrA gene were significantly higher than those at 15 °C and 25 °C. The reduction of As(V) to As(III) and aging occurred simultaneously. The kinetic models were established, and the rate constants of the reduction and aging processes were obtained. Soil properties significantly affected the aging and reduction processes of extractable As(V). Our study indicated that elevating temperature had dual effects on the environmental risk of As in the flooded aging process. The previous definition of "aging" based on cationic metals needs to be updated according to the transformation characteristics of As species in flooded conditions. Our results addressed the necessity of impeding the reduction of As(V) in paddy soils under global warming.

Key microbial clusters and environmental factors affecting the removal of antibiotics in an engineered anaerobic digestion system.

To identify the key microbial clusters and influencing factors involved in antibiotic removal from engineered anaerobic digestion (AD) systems, the dynamic characteristics of antibiotics, physiochemical factors, microbial communities and functional genes were investigated by 16S rRNA and metagenome sequencing. The results showed that antibiotic removal occurred mainly in the first 21 days, and sulfonamides had the highest removal rate. The key microbial clusters related to the biodegradation of antibiotics consisted mainly of Firmicutes and Bacteroidetes. The key enzymes consisted of deaminases, peptidases, C-N ligases, decarboxylases and alkyl-aryl transferases. Structural equation modelling indicated that low concentrations of propionic acid promoted the biodegradation activities of key microbial clusters in the first 21 days, but their activities were inhibited by the accumulated propionic acid after 21 days. Thus, propionic acid should be regulated in engineered AD systems to prevent the adverse effect of acid inhibition on antibiotic-degrading bacteria.

Antibiotic degradation dominates the removal of antibiotic resistance genes during composting.

To identify the key hosts involved in horizontal gene transfer (HGT) and vertical gene transfer (VGT) of antibiotic resistance genes (ARGs) and to determine the extent to and ways in which environmental properties contribute to ARG removal, the changes in ARG profile and key hosts during biogas residue and pig manure composting were investigated using metagenomic sequencing coupled with network analysis. Composting significantly reduced the abundances of ARGs other than bacA. Seventy and 41 hosts from Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes were associated with HGT and VGT, respectively. The key environmental properties were determined using structural equation modelling. Antibiotics directly affected HGT and determined ARG removal. Temperature indirectly affected HGT, mainly by influencing the degradation of antibiotics. BacA was associated only with hosts involved in VGT, which may lead to its low removal rate. These findings specify the priority and pathway of antibiotics and temperature affecting ARG profile.

Pollution characteristics of livestock faeces and the key driver of the spread of antibiotic resistance genes.

The increasing prevalence of antibiotic resistance genes (ARGs) in livestock and poultry faeces has attracted considerable amounts of attention. However, in the actual breeding environment, the key driver of the spread of ARGs and which bacteria are involved remain unclear. This study investigated 19 antibiotics and 4 heavy metals in 147 animal faeces. The results showed that piglet faeces exhibited the highest levels of antibiotics and heavy metals. Twelve ARGs, 4 mobile genetic elements (MGEs) and bacterial communities of piglet faeces from 6 pig farms were further assessed to determine the key driver and relevant mechanism of the spread of ARGs. Sulphonamides (SAs) explained 36.5% of the variance (P < 0.05) of the bacterial community and were significantly related to 8 genes (P < 0.01), indicating that SAs dominated the spread of ARGs and should be tightly supervised. Structural equation modelling (SEM) indicated that SAs increased the abundance of ARGs via two pathways: horizontal transfer of ARGs (involving 10 genera) and vertical transfer of ARGs (involving 26 genera). These results improve our understanding of the potential hosts involved in the spread of ARGs, suggesting that monitoring of the above potential hosts is also important in animal feeding practice.