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

Abstract

Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 m. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far no study investigated if such bacteria exist in terrestrial environments like e.g. soil. 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. A set of co-culture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The co-culture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that bacteria are present in the soil that can pass through a 0.1 m filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, are able to induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. ImportanceAnalysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 m. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments e.g. soil. By applying a novel isolation method, we show that such bacteria also exist in soil. The isolated bacteria was identified as Hylemonella gracilis. Co-culture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when co-cultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1 m filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.