Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems

Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were <i>Proteobacteria</i>, <i>Actinobacteria</i>, and <i>Acidobacteria</i>; the dominant archaea were <i>Crenarchaeota</i>; and the dominant fungi were <i>Ascomycota</i>. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were <i>CeoB</i>, <i>AcrB</i>, and <i>MexF. Paraburkholderia</i>, <i>Rhodococcus</i>, <i>Bradyrhizobium,</i> and <i>Agromyces</i> were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems. IMPORTANCE Currently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.