Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes.

Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to nontarget organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides-glyphosate, glufosinate, and dicamba-increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and ARGs. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across 11 provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage.

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.

Dynamics and functions of biomarker taxa determine substrate-specific organic waste composting.

Bacteria are an influential component of diverse composting microbiomes, but their structure and underlying dynamics are poorly understood. This study analyzed the bacterial communities of 577 compost datasets globally and constructed a substrate-dependent catalog with more than 15 million non-redundant 16S rRNA gene sequences. Using a random-forest machine-learning model, 30 biomarker taxa were identified that accurately distinguish between the food, sludge and manure waste composting microbiomes (accuracy >98 %). These biomarker taxa were closely associated with carbon and nitrogen metabolic processes, during which they contributed to the predominant stochastic process and are influenced by different factors in the substrate-specific composts. This is corroborated by the community topological characteristics, which feature the biomarkers as keystone taxa maintaining the bacterial network stability. These findings provide a theoretical basis to identify and enhance the biomarker-functional bacteria for optimizing the composting performance of different organic wastes.

Incomplete degradation of aromatic-aliphatic copolymer leads to proliferation of microplastics and antibiotic resistance genes.

Biodegradable plastics (BDPs) have attracted extensive attention as an alternative to conventional plastics. BDPs could be mineralized by composting, while the quality of compost affected by the presence of BDPs and the residual microplastics (MPs) has not been well evaluated. This study aimed to explore the MPs release potential and environmental implications of commercial BDPs (aromatic-aliphatic copolymer) films in uncontrolled composting. Results showed that the molecular weight of BDPs decreased by >60% within 60 d. However, the non-extracted organic matter and wet-sieving measurements indicated that MPs continuously released and accumulated during regular composting. The average MPs release potential (0.1-5 mm) was 134.6 ± 18.1 particles/mg (BDPs), which resulted in 103-104 particles/g dw in compost. The plastisphere of MPs showed a significantly higher (0.95-16.76 times) abundance of antibiotic resistance genes (ARGs), which resulted in the rising (1.34-2.24 times) of ARGs in compost heaps, in comparison to the control groups. Overall, BDPs promote the spread of ARGs through the selective enrichment of bacteria and horizontal transfer from released MPs. These findings confirmed that BDPs could enhance the release potential of MPs and the dissemination of ARGs, which would promote the holistic understanding and environmental risk of BDPs.

From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems.

Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, ß = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (104 ∼ 108 copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.

[Effects of Three Commonly Used Herbicides on Bacterial Antibiotic Resistance].

The spread of antibiotic resistance has become a serious threat to global public health. Recently, several studies have found that non-antibiotic chemicals can promote the generation and spread of bacterial antibiotic resistance. However, the effects of herbicides on the antibiotic resistance of bacteria remain unclear. In this study, Escherichia coli DH5α was used as the model strain to explore the effects of three commonly used herbicides (glyphosate, glufosinate, and dicamba) on the antibiotic resistance under soil environmental concentrations. The results showed that herbicide exposure affected the sensitivity of E. coli DH5α to antibiotics and significantly improved the resistance of E. coli DH5α to gentamicin (glyphosate > dicamba > glufosinate). After 30 d of herbicide exposure, the E. coli mutant strains enhanced the resistance to tetracycline, chloramphenicol, and aminoglycoside antibiotics, and the minimum inhibitory concentration of streptomycin was increased by 19.8 times. The whole-genome sequencing results illustrated that herbicides induced several previously well-characterized mutations associated with membrane proteins (ompF and papC), fimbriae proteins (yraH), and ribosomes (rpsL) related to antibiotic resistance. Together, the results showed that herbicides can enhance the antibiotic resistance of bacteria via inducing genetic mutations, thereby promoting the potential risk of the spread of antibiotic resistance genes in the environment.

Linking microbial community structure with molecular composition of dissolved organic matter during an industrial-scale composting.

This study explored the interactions between dissolved organic matter (DOM) composition and microbial community structure during an industrial-scale composting by Fourier transform ion cyclotron resonance mass spectrometry and 16S rRNA sequencing analysis. The results revealed that DOM from matured compost contained primarily lignins/carboxylic-rich alicyclic molecules (73.6%), the higher double bond equivalent (5.97) and aromaticity index (0.18), indicating that the molecular composition of DOM had changed substantially. Drastic changes in microbial community structure were also observed along with the DOM transformation process of composting. Network analysis further indicated that Caldicoprobacter, Bacillus, and Dechloromonas were associated with the most DOM subcategories. Caldicoprobacter could degrade carbohydrates, Bacillus accelerated the humification by transforming N-containing compounds, and Dechloromonas could degrade polycyclic aromatic hydrocarbons distributed in low O/C. These findings are helpful for understanding the molecular mechanisms of DOM transformation and humification of sludge composting.

Enhanced removal of antibiotic resistance genes and mobile genetic elements during sewage sludge composting covered with a semi-permeable membrane.

Transmission of antibiotic resistance genes (ARGs) via air media, such as particulate matter, has been intensively investigated due to human exposure through inhalation. However, whether particulate matter originating from the atmospheric environment of composting plants can impact ARG abundance during composting is unknown. Here, we investigated the effects of the atmospheric environment of composting plants on ARG abundance during sewage sludge composting using semi-permeable membrane-covered thermophilic composting (smTC) and conventional thermophilic composting (cTC). After smTC treatment, the total abundances of ARGs and mobile genetic elements (MGEs) decreased by 42.1 % and 38.1 % compared with those of the initial phase, respectively, but they increased by 4.5- and 1.6-fold after cTC, respectively. This result suggested that smTC was more efficient at decreasing ARGs and MGEs than cTC, mainly due to a significant reduction in bacterial contamination from the atmospheric environment of composting plants that accelerated the resurgence of ARGs and MGEs. Furthermore, culture experiments demonstrated that the abundance and diversity of antibiotic-resistant bacteria during the mature phase of smTC were also significantly (P <  0.05) lower than those in the cTC treatment. Thus, covering composting with a semi-permeable membrane could decrease the risk of ARGs spreading.

Hyperthermophilic composting reduces nitrogen loss via inhibiting ammonifiers and enhancing nitrogenous humic substance formation.

Composting is an efficient and economic approach used to convert organic waste into organic fertilizers. However, the substantial nitrogen loss during the composting process is one of the major disadvantages of conventional thermophilic composting (cTC). Here, we demonstrated for the first time that hyperthermophilic composting (hTC) was able to mitigate nitrogen loss by 40.9% compared to cTC after 44 days of composting in a full-scale plant. Results demonstrate a decrease in NH3 volatilization (52.4%), together with an inhibitory effect on protease (19.4-87.5%) and urease (9.1-75.2%) enzyme activities and the ammonification rate (5.2-80.1%) for hTC. Additionally, this study found that hTC could accelerate the humification process, thereby enhancing the formation of the recalcitrant nitrogen reservoir (mainly in the form of nitrogenous humic substances) and reducing the substrate for ammonification reactions. These findings suggest that hTC can significantly reduce nitrogen loss and provide insights into the role of humic substances in nitrogen retention in composting systems.