Tuning interdomain conjugation toward in situ population modification in yeasts

The ability to modify and control natural and engineered microbiomes is
essential for biotechnology and biomedicine. Fungi are critical members of
most microbiomes, yet technology for modifying the fungal members of a
microbiome has lagged far behind that for bacteria. Interdomain
conjugation (IDC) is a promising approach, as DNA transfer from bacterial
cells to yeast enables in situ modification. While such genetic transfers
have been known to naturally occur in a wide range of eukaryotes, and are
thought to contribute to their evolution, IDC has been understudied as a
technique to control fungal or fungal-bacterial consortia. One major
obstacle to widespread use of IDC is its limited efficiency. In this work,
we utilize interactions between genetically tractable Escherichia coli and
Saccharomyces cerevisiae to control the incidence of IDC. We test the
landscape of population interactions between the bacterial donors and
yeast recipients to find that bacterial commensalism leads to maximized
IDC, both in culture and in mixed colonies. We demonstrate the capacity of
cell-to-cell binding via mannoproteins to assist both IDC incidence and
bacterial commensalism in culture, and model how these tunable controls
can predictably yield a range of IDC outcomes. Further, we demonstrate
that these lessons can be utilized to lastingly alter a recipient yeast
population, by both “rescuing” a poor-growing recipient population and
collapsing a stable population via a novel IDC-mediated CRISPR/Cas9
system.