High diversity and rapid spatial turnover of integron gene cassettes in soil

Abstract

Summary Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

“…These studies were developed with samples from different environments and using different approaches. However, "extreme" environments like Antarctica have been relatively poorly explored (Ghaly et al, 2019 ; Gillings, 2014 ; Stokes et al, 2001 ).…”

Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities

“…Finally, exploring gene cassettes provides a window into the functional diversity of the bacterial pangenome. Gene cassettes have been found to be extraordinarily abundant and diverse in every environment surveyed [20][21][22][23][24][25][26].…”

“…Cassette-targeted amplicon sequencing has been used previously, with varying returns in gene cassette recovery [20][21][22][23][24][25][26][27]. As sequencing technologies have improved, the ability to capture a greater diversity of gene cassettes has also increased [20,26].…”

The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology

“…Many of the horizontally acquired genes that confer resistance are ancient (Recchia and Hall, 1997;Perron et al, 2015). These mobile resistance genes are part of the vast library of genes capable of conferring adaptive phenotypes, and form the floating genome shared amongst the microbiota (Shapiro, 2010;Aminov, 2011;Ghaly et al, 2019). These genes can move between individuals of the same species and between the cells of different species.…”