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

TL;DR

This study explores microbial diversity and antibiotic resistance genes in untouched karst sinkhole ecosystems, revealing unique microbial networks and resistance patterns.

Contribution

The study provides novel insights into microbial composition and antibiotic resistance genes in pristine karst tiankengs, previously unexplored environments.

Findings

Non-degraded tiankengs maintain complex and stable microbial networks dominated by Proteobacteria, Actinobacteria, and Acidobacteria.

ARGs like CeoB, AcrB, and MexF are prevalent, hosted mainly by Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces.

Soil factors influence microbial communities more than antibiotic resistance genes in these ecosystems.

Abstract

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 Proteobacteria,
Actinobacteria, and Acidobacteria; the
dominant archaea were Crenarchaeota; and the dominant fungi
were Ascomycota. 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 CeoB, AcrB, and
MexF. Paraburkholderia, Rhodococcus,
Bradyrhizobium, and Agromyces 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.

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.

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