Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
Antonie Van Leeuwenhoek. 2023 Jul;116(7):667-685. doi: 10.1007/s10482-023-01834-z. Epub 2023 May 8.
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
细胞外 DNA 使环境微生物发生转化是一种被忽视的水平基因转移和进化机制。它通过垂直转移和接合转移引发外源性基因的获取，并传播抗生素耐药性。我们结合混合培养生物技术和 Hi-C 测序来阐明废水微生物的转化，该转化使用合成质粒进行，该质粒编码 GFP 和卡那霉素抗性基因，在暴露于卡那霉素的恒化器混合培养物中，卡那霉素的浓度代表废水、肠道和污染环境（0.01-2.5-50-100mg/L）。我们发现，亲缘关系较远的革兰氏阴性菌（Runella：102 个 Hi-C 连接，Bosea：35 个，Gemmobacter：33 个和 Zoogloea：24 个）和革兰氏阳性菌（Microbacterium sp.：90 个）在高抗生素暴露（50mg/L）下被外源质粒转化。此外，抗生素压力将氨基糖苷类抗生素抗性基因的起源从基因组 DNA 转移到在微生物中积累的质粒上的移动遗传元件上。这些结果揭示了 Hi-C 测序在捕捉和监测微生物组内异种元素转移方面的强大功能。
