Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns

Area of Science:

• Environmental microbiology
• Genomics
• Public health

Background:

• Antibiotic resistance genes (ARGs) can be present in rice grains.
• The primary sources of ARGs in rice grains (seed-associated vs. environmental) are not well understood.

Purpose of the Study:

• To investigate the relative contributions of seed-associated and environmental reservoirs to ARGs in rice grains.
• To characterize the ARG profiles in various rice tissues and surrounding environmental matrices.

Main Methods:

• Shotgun metagenomics was performed on rice tissues (grain, seed, leaf, stem, root) and environmental samples (soil, water, PM10).
• Source tracking (FEAST) was used to determine the attribution of microbial communities and ARGs.
• Phylogenetic screening and metagenome-assembled genomes (MAGs) were employed to analyze ARG linkages and mobility.

Main Results:

• 1019 ARG subtypes were detected across all samples.
• Seed sources contributed significantly to the grain microbiome (49.49%), but environmental sources were more dominant for the grain resistome (20.68%).
• 39 near-identical ARG linkages were identified, suggesting potential horizontal gene transfer (HGT) or vertical gene transfer (VGT).

Conclusions:

• Rice grain microbiomes show seedborne signatures, while the resistome is more strongly influenced by environmental factors.
• Identifying ARG reservoirs in rice systems is crucial for public health and agricultural safety.
• Further research into ARG mobility mechanisms (VGT/HGT) in rice ecosystems is warranted.