Screening
mutant libraries (MLs) of bacteria for strains with specific
phenotypes is often a slow and laborious process that requires assessment
of tens of thousands of individual cell colonies after plating and
culturing on solid media. In this report, we develop a three-dimensional,
photodegradable hydrogel interface designed to dramatically improve
the throughput of ML screening by combining high-density cell culture
with precision extraction and the recovery of individual, microscale
colonies for follow-up genetic and phenotypic characterization. ML
populations are first added to a hydrogel precursor solution consisting
of polyethylene glycol (PEG) o-nitrobenzyl diacrylate
and PEG-tetrathiol macromers, where they become encapsulated into
13 μm thick hydrogel layers at a density of 90 cells/mm2, enabling parallel monitoring of 2.8 × 104 mutants per hydrogel. Encapsulated cells remain confined within
the elastic matrix during culture, allowing one to track individual
cells that grow into small, stable microcolonies (45 ± 4 μm
in diameter) over the course of 72 h. Colonies with rare growth profiles
can then be identified, extracted, and recovered from the hydrogel
in a sequential manner and with minimal damage using a high-resolution,
365 nm patterned light source. The light pattern can be varied to
release motile cells, cellular aggregates, or microcolonies encapsulated
in protective PEG coatings. To access the benefits of this approach
for ML screening, an Agrobacterium tumefaciens C58
transposon ML was screened for rare, resistant mutants able to grow
in the presence of cell free culture media from Rhizobium
rhizogenes K84, a well-known inhibitor of C58 cell growth.
Subsequent genomic analysis of rare cells (9/28,000) that developed
into microcolonies identified that seven of the resistant strains
had mutations in the acc locus of the Ti plasmid.
These observations are consistent with past research demonstrating
that the disruption of this locus confers resistance to agrocin 84,
an inhibitory molecule produced by K84. The high-throughput nature
of the screen allows the A. tumefaciens genome
(approximately 5.6 Mbps) to be screened to saturation in a single
experimental trial, compared to hundreds of platings required by conventional
plating approaches. As a miniaturized version of the gold-standard
plating assay, this materials-based approach offers a simple, inexpensive,
and highly translational screening technique that does not require
microfluidic devices or complex liquid handling steps. The approach
is readily adaptable to other applications that require isolation
and study of rare or phenotypically pure cell populations.