Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

TY - JOUR

T1 - Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

AU - Tyc, Olaf

AU - Kulkarni, Purva

AU - Ossowicki, Adam

AU - Tracanna, Vittorio

AU - Medema, Marnix H.

AU - van Baarlen, Peter

AU - van IJcken, W. F. J.

AU - Verhoeven, Koen J. F.

AU - Garbeva, Paolina

N1 - Data archiving: raw data available upon request. Whole-genome sequence at NCBI GenBank. Raw reads of transcriptomics data at Sequence Read Archive. Metabolomics raw data at metabolights.

PY - 2022

Y1 - 2022

N2 - Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. 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-μm 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-μm 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.

AB - Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. 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-μm 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-μm 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.

UR - https://www.ncbi.nlm.nih.gov/nuccore/CP031395

UR - https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA483535

UR - http://www.ebi.ac.uk/metabolights/MTBLS5841

U2 - 10.1128/msystems.00574-22

DO - 10.1128/msystems.00574-22

M3 - Article

SN - 2379-5077

JO - mSystems

JF - mSystems

M1 - e00574-22

ER -