Phenotypic Variation and Genomics of Bdellovibrio Predatory Bacteria from the Built Environment

Abstract

Bdellovibrio are predatory bacteria that attack and kill Gram‐negative bacteria. They are found in a range of environments, including soil, water, and living organisms, but little is known about Bdellovibrio in the built environment. Surfaces, such as drains, are ideal for biofilm formation, which may provide stable prey sources for predatory bacteria. Investigating Bdellovibrio from the built environment will broaden our understanding of variation in prey range and predation efficiency and contribute to the development of predatory bacteria as biocontrol agents for use in settings such as hospital buildings.To test for the presence of predatory bacteria in built environment sites, we collected swab samples, extracted metagenomic DNA, and performed PCR with Bdellovibrio‐specific primers. Using this approach, we detected evidence of Bdellovibrio in a janitorial closet drain at Providence College. To obtain pure isolates, we made enrichments by combining swab samples from the drain with either Raoultella, a Gram‐negative bacterium previously isolated from a freshwater site, or E. coli ML35. Six predatory bacteria isolates were obtained using Raoultella as prey, and one was obtained using E. coli. Plaque features of each isolate on double agar overlay plates varied in size, shape, and appearance.To classify the isolates, we sequenced the 16S rRNA gene and found that the ~1300 bp sequence was identical for all isolates. This 16S rRNA gene sequence has 95%‐96% identity to Bdellovibrio bacteriovorus, suggesting the isolates are within the Bdellovibrio genus. We then generated short read sequencing data for each isolate using Illumina and performed de novo assembly using SPAdes. These assemblies yielded 2–11 contigs. Using the isolate with two contigs as a reference, we aligned each draft assembly and found at least 99% nucleotide identity across the full length of each contig. Given the identical 16S rRNA genes and the high sequence similarity among draft genome assemblies, this suggests that all seven Bdellovibrio isolates from the drain are representatives of a clonal population, but they are demonstrating plasticity in plaque phenotype. An alternative hypothesis is that small differences in gene sequences or gene content underlie the variation in plaque phenotype. To test these hypotheses, we are working on generating a complete genome using long read sequencing with PacBio.To understand variation in prey range, we challenged three of the Bdellovibrio isolates from the drain with eight Gram‐negative prey. Each isolate attacked the same two prey strains (Raoultella and E. coli ML35). This narrow prey range suggests that these Bdellovibrio may be prey specialists. We are isolating multiple prey strains from the drain to provide insight into plaque phenotype and prey range variation. Moving forward we will test predation efficiency using a variety of Gram‐negative bacteria. This work will contribute to our understanding and development of predatory bacteria and may inform their use in biofilm control and as an antibiotic alternative.Support or Funding InformationResearch reported in this poster was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number 2 P20 GM103430 and startup funding from Providence College.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.