Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis

Microbial community analysis of aquatic environments showed that an important component of microbial diversity consists of bacteria with cell sizes smaller than ~0.1 m. However, so far no study investigated if such bacteria with small cell sizes exist in terrestrial environments as well. Here, we isolated soil bacteria that passed through a 0.1 m filter, by applying a novel isolation and culturing approach. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. We performed a set of interaction assays with phylogenetically distant soil bacteria with larger cell and genome size. The interaction assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Furthermore, we observed that H. gracilis is able to change the behavior of interacting bacteria without direct cell-cell contact. Transcriptomics and metabolomics analysis was performed with the aim to explain the mechanisms of these interactions. Our study indicates that soil bacteria that can pass through a 0.1 M filter may have been overlooked in soil microbial communities and that such bacteria are able to induce transcriptional and metabolomics responses in other soil-bacteria. Furthermore, we revealed that the interaction allowed utilization of substrates that are not utilized by monocultures.