Antibiotic resistance genes (ARGs) have moved from the environmental resistome into human commensals and pathogens, driven by human selection with antimicrobial agents. These genes have increased in abundance in humans and domestic animals, to become common components of waste streams. Estuarine habitats lie between terrestrial/freshwater and marine ecosystems, acting as natural filtering points for pollutants. Here, we have profiled ARGs in sediments from 18 estuaries over 4,000 km of coastal China using high-throughput quantitative polymerase chain reaction, and investigated their relationship with bacterial communities, antibiotic residues and socio-economic factors. ARGs in estuarine sediments were diverse and abundant, with over 200 different resistance genes being detected, 18 of which were found in all 90 sediment samples. The strong correlations of identified resistance genes with known mobile elements, network analyses and partial redundancy analysis all led to the conclusion that human activity is responsible for the abundance and dissemination of these ARGs. Such widespread pollution with xenogenetic elements has environmental, agricultural and medical consequences.

Composting is widely used for recycling of urban sewage sludge to improve soil properties, which represents a potential pathway of spreading antibiotic resistant bacteria and genes to soils. However, the dynamics of antibiotic resistance genes (ARGs) and the underlying mechanisms during sewage sludge composting were not fully explored. Here, we used high-throughput quantitative PCR and 16S rRNA gene based illumina sequencing to investigate the dynamics of ARGs and bacterial communities during a lab-scale in-vessel composting of sewage sludge. A total of 156 unique ARGs and mobile genetic elements (MGEs) were detected encoding resistance to almost all major classes of antibiotics. ARGs were detected with significantly increased abundance and diversity, and distinct patterns, and were enriched during composting. Marked shifts in bacterial community structures and compositions were observed during composting, with Actinobacteria being the dominant phylum at the late phase of composting. The large proportion of Actinobacteria may partially explain the increase of ARGs during composting. ARGs patterns were significantly correlated with bacterial community structures, suggesting that the dynamic of ARGs was strongly affected by bacterial phylogenetic compositions during composting. These results imply that direct application of sewage sludge compost on field may lead to the spread of abundant ARGs in soils.

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Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.

Biochar has been suggested to improve acidic soils and to mitigate greenhouse gas emissions. However, little has been done on the role of biochar in ameliorating acidified soils induced by overuse of nitrogen fertilizers. In this study, we designed a pot trial with an acidic soil (pH 4.48) in a greenhouse to study the interconnections between microbial community, soil chemical property changes, and N 2 O emissions after biochar application. The results showed that biochar increased plant growth, soil pH, total carbon, total nitrogen, C/N ratio, and soil cation exchange capacity. The results of high-throughput sequencing showed that biochar application increased α-diversity significantly and changed the relative abundances of some microbes that are related with carbon and nitrogen cycling at the family level. Biochar amendment stimulated both nitrification and denitrification processes, while reducing N 2 O emissions overall. Results of redundancy analysis indicated biochar could shift the soil microbial community by changing soil chemical properties, which modulate N-cycling processes and soil N 2 O emissions. The significantly increased nosZ transcription suggests that biochar decreased soil N 2 O emissions by enhancing its further reduction to N 2 .

Microbe-mediated arsenic (As) biotransformation in paddy soils determines the fate of As in soils and its availability to rice plants, yet little is known about the microbial communities involved in As biotransformation. Here, we revealed wide distribution, high diversity, and abundance of arsenite (As(III)) oxidase genes (aioA), respiratory arsenate (As(V)) reductase genes (arrA), As(V) reductase genes (arsC), and As(III) Sadenosylmethionine methyltransferase genes (arsM) in 13 paddy soils collected across Southern China. Sequences grouped with As biotransformation genes are mainly from rice rhizosphere bacteria, such as some Proteobacteria, Gemmatimonadales, and Firmicutes. A significant correlation of gene abundance between arsC and arsM suggests that the two genes coexist well in the microbial As resistance system. Redundancy analysis (RDA) indicated that soil pH, EC, total C, N, As, and Fe, C/N ratio, SO 4 2− -S, NO 3 − -N, and NH 4 + -N were the key factors driving diverse microbial community compositions. This study for the first time provides an overall picture of microbial communities involved in As biotransformation in paddy soils, and considering the wide distribution of paddy fields in the world, it also provides insights into the critical role of paddy fields in the As biogeochemical cycle. ■ INTRODUCTIONChina is the world's largest rice producer, accounting for about 30% of the total world production (http://beta.irri.org/ statistics), mostly in Southern China.1 As a highly toxic metalloid, arsenic (As) contamination in paddy fields has emerged as a serious health concern worldwide, 2 especially considering that the anaerobic conditions in paddy soils are conducive to As mobilization, 3,4 resulting in a markedly enhanced bioavailability of As to rice plants. 5 It is now recognized that consumption of rice constitutes a large proportion of the dietary intake of As for the populations in China and other Asian countries. 6−8 Microbes are the key drivers for As biotransformation in paddy soils, catalyzing arsenate (As(V)) reduction, arsenite (As(III)) oxidation and methylation.9 Microcosm studies have demonstrated that microbes capable of As reduction, oxidation, and methylation often coexist in paddy soils, and their relative abundance and activity determine the fate of As in the paddy environment and the bioavailability of As to plants. 10−12 There are two known microbial pathways for As(V) reduction, the respiratory pathway mediated by arrA genes 13 and the detoxification pathway mediated by arsC genes.14 As(III) oxidation is catalyzed by As(III) oxidases, which are encoded by aioA and aioB genes for the two subunits of the enzyme 15 and have been identified in several heterotrophic and chemoautotrophic microorganisms. 16 Moreover, As(III) can be methylated by microbes into various organic As species. 17Arsenic biomethylation is catalyzed by As(III) S-adenosylmethionine methyltransferase (ArsM), which is encoded by arsM genes.18

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Speeding up antibiotic susceptibility testing (AST) is urgently needed in clincial settings to guide fast and tailored antibiotic prescription before treatment. It remains a big challenge to achieve a sample-to-AST answer within a half working day directly from a clinical sample. Here we develop single-cell Raman spectroscopy coupled with heavy water labeling (Raman-D 2 O) as a rapid activity-based AST approach directly applicable for clinical urine samples. By rapidly transferring (15 min) bacteria in clinical urine for AST, the total assay time from receiving urine to binary susceptibility/resistance (S/R) readout was shortened to only 2.5 h. Moreover, by overcoming the nonsynchronous responses between microbial activity and microbial growth, together with setting a new S/R cutoff value based on relative C−D ratios, S/R of both pathogenic isolates and three clinical urines against antibiotics of different action mechanisms determined by Raman-D 2 O were all consistent with the slow standard AST assay used in clincial settings. This work promotes clinical practicability and faciliates antibiotic stewardship.