Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

The quantification and identification of new plasmid-acquiring
bacteria in representative mating conditions is critical to characterize
the risk of horizontal gene transfer in the environment. This study
aimed to quantify conjugation events resulting from manure application
to soils and identify the transconjugants resulting from these events.
Conjugation was quantified at multiple time points by plating and
flow cytometry, and the transconjugants were recovered by fluorescence-activated
cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants
were only observed within the first 4 days after manure application
and at values close to the detection limits of this experimental system
(1.00–2.49 log CFU/g of manured soil, ranging between 10–5 and 10–4 transconjugants-to-donor
ratios). In the pool of recovered transconjugants, we found amplicon
sequence variants (ASVs) of genera whose origin was traced to soils
(Bacillus and Nocardioides) and
manure (Comamonas and Rahnella).
This work showed that gene transfer from fecal to soil bacteria occurred
despite the less-than-optimal conditions faced by manure bacteria
when transferred to soils, but these events were rare, mainly happened
shortly after manure application, and the plasmid did not colonize
the soil community. This study provides important information to determine
the risks of AMR spread via manure application.