Hernández Marcela, Roy Shamik, Keevil C William, Dumont Marc G
School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
Environ Microbiome. 2023 Apr 18;18(1):34. doi: 10.1186/s40793-023-00489-7.
We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.
An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.
The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.
我们旨在通过将DNA稳定同位素探测（SIP）与高通量测序相结合，在英国农业土壤中鉴定能够在包括超广谱抗生素美罗培南在内的多种抗生素存在下生长的细菌。土壤在含头孢噻肟、美罗培南、环丙沙星和甲氧苄啶的O-水中孵育。对来自标记的“重”和未标记的“轻”SIP组分的宏基因组和16S rRNA基因的V4区域进行测序。
检测到与对照相比，用O-水处理的“重”组分中16S rRNA拷贝数增加。这些处理导致细菌群落组成存在差异。与抗生素孵育两天后，酸杆菌门（原嗜酸菌门）的成员高度丰富。孵育四天后，包括嗜麦芽窄食单胞菌在内的假单胞菌门（原变形菌门）很突出。此外，从“重”组分中获得了一个来自嗜麦芽窄食单胞菌属的宏基因组组装基因组（MAG-1，完整性90.7%）。最后，在未分类组装的“重 ”组分中鉴定出11个抗微生物抗性基因（ARG），在MAG-1中鉴定出10个ARG。相比之下，在未分类组装的“轻”组分中仅鉴定出两个ARG。
结果表明，这种农业土壤中存在非致病性土壤细菌以及潜在的临床病原体，并且从标记的群落中鉴定出了几种ARG，但这些群体之间是否会发生水平基因转移仍不清楚。
