Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure

Abstract

Bacteria and antibiotic resistance genes (ARGs) in vegetables may influence human gut microbiome and ultimately human health. However, little is known about how vegetable microbiomes and ARGs respond to exposure of anthropogenic antibiotics from crop irrigation water. This study investigated bacterial community assembly and ARG profiles in lettuce (Lactuca sativa) shoots and roots, rhizosphere soil, and bulk soil irrigated with antibiotics-containing water, using 16S rRNA amplicon sequencing and high throughput real-time qPCR, respectively. With antibiotic exposure alpha diversity values remained unchanged for the rhizosphere soil and lettuce roots, but were significantly decreased for the bulk soil and lettuce shoots (p < 0.05). Based on calculations of normalized stochastic ratio (NST), bacterial community assembly was more stochastic in the rhizosphere soil (83%-86%) and bulk soil (81%-84%) than in the lettuce roots (45%-48%). These results suggest a stronger deterministic control of plant roots in bacterial community assembly. Antibiotic exposure did not substantially change the stochasticity of the bacterial communities, despite the NST values were significantly increased by ~3% (p < 0.05) for the rhizosphere soil and lettuce roots and significantly decreased by ~3% (p < 0.05) for the bulk soil, when comparing treatments with and without antibiotics. The levels of Methylophilaceae and Beijerinckiaceae were significantly different between the antibiotic and antibiotics-free treatments. Antibiotic exposure consistently increased the abundance of mobile genetic elements (MGEs) in the rhizosphere soil, but not in other samples. No consistent changes in ARGs were observed with and without antibiotic exposure. Finally, the correlation network analysis revealed that the rhizosphere soil may be a hotspot for interactions between ARGs, MGEs, bacterial communities, and antibiotic residues.

Keywords: Antibiotic resistance genes; Antibiotics; Bacterial community; Lettuce; Soil.