| Title: | Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis |
| Author(s): | Tyc O; Kulkarni P; Ossowicki A; Tracanna V; Medema MH; van Baarlen P; van IWFJ; Verhoeven KJF; Garbeva P; |
| Address: | "Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, Netherlands. Goethe University, Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt, Germany. Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, Netherlands. Institute of Biology, Above-Belowground Interactions Group, Leiden University, Leiden, Netherlands. Wageningen University, Department of Plant Sciences, Bioinformatics Group, Wageningen, Netherlands. University Cologne, Institut fur Pflanzenwissenschaften, Cologne, Germany. Wageningen University, Department of Animal Sciences, Host-Microbe Interactomics, Wageningen, Netherlands. Center for Biomics, Erasmus University Medical Center, Rotterdam, Netherlands. Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Netherlands. Department of Plant and Environmental Sciences, Faculty of Natural and Life Sciences, University of Copenhagen, Copenhagen, Denmark" |
| DOI: | 10.1128/msystems.00574-22 |
| ISSN/ISBN: | 2379-5077 (Electronic) 2379-5077 (Linking) |
| 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 mum. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-mum filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture 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 in soil there are bacteria that can pass through a 0.1-mum filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can 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. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 mum. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured 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-mum filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities" |
| Keywords: | *Soil Metabolome Symbiosis *Comamonadaceae Gram-negative bacteria Hylemonella sp.interspecific interactions metabolome analysis metabolomics transcriptome analysis transcriptomics volatile organic compounds; |
| Notes: | "MedlineTyc, Olaf Kulkarni, Purva Ossowicki, Adam Tracanna, Vittorio Medema, Marnix H van Baarlen, Peter van IJcken, W F J Verhoeven, Koen J F Garbeva, Paolina eng Research Support, Non-U.S. Gov't 2022/12/21 mSystems. 2023 Feb 23; 8(1):e0057422. doi: 10.1128/msystems.00574-22. Epub 2022 Dec 20" |
