Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems

Jonathan Parra; Scott A. Jarmusch; Katherine R. Duncan

doi:10.1111/1462-2920.16635

Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems

Jonathan Parra, Scott A. Jarmusch, Katherine R. Duncan

Strathclyde Institute Of Pharmacy And Biomedical Sciences

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Abstract

Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free‐living Pseudonocardia remains understudied. This study applies a multi‐omics approach to investigate the chemical ecology of free‐living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry‐based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free‐living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.

Original language	English
Article number	e16635
Number of pages	11
Journal	Environmental Microbiology
Volume	26
Issue number	6
Early online date	20 Jun 2024
DOIs	https://doi.org/10.1111/1462-2920.16635
Publication status	Published - 20 Jun 2024

Funding

We would like to thank Beatriz Camara for supplying strain VO44-3 as well as Paul Jensen for strain CNS-139. We also thank Matt Hutchings and Leighton Pritchard for their insightful comments on this work. Jonathan Parra was supported by Programa de Innovaci\u00F3n y Capital Humano para la Competitividad (PINN) of Ministerio de Ciencia Tecnolog\u00EDa y Telecomunicaciones, Costa Rica, grant 2-1-4-17-1-037. Scott A. Jarmusch received support from the Danish National Research Foundation (DNRF137). We would also like to acknowledge funding from the Novo Nordisk Foundation (grant NNF19OC0055625) for the infrastructure \u2018Imaging microbial language in biocontrol (IMLiB).\u2019 Finally, we acknowledge the DTU Metabolomics Core for the usage of MSI equipment. We would like to thank Beatriz Camara for supplying strain VO44\u20103 as well as Paul Jensen for strain CNS\u2010139. We also thank Matt Hutchings and Leighton Pritchard for their insightful comments on this work. Jonathan Parra was supported by Programa de Innovaci\u00F3n y Capital Humano para la Competitividad (PINN) of Ministerio de Ciencia Tecnolog\u00EDa y Telecomunicaciones, Costa Rica, grant 2\u20101\u20104\u201017\u20101\u2010037. Scott A. Jarmusch received support from the Danish National Research Foundation (DNRF137). We would also like to acknowledge funding from the Novo Nordisk Foundation (grant NNF19OC0055625) for the infrastructure \u2018Imaging microbial language in biocontrol (IMLiB).\u2019 Finally, we acknowledge the DTU Metabolomics Core for the usage of MSI equipment.

Keywords

actinomycetes
chemical ecology
phylogeny
antagonistic interactions

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1111/1462-2920.16635Licence: CC BY 4.0

Parra-etal-EM-2024-Multi-omics-analysis-of-antagonistic-interactions-among-free-living-PseudonocardiaFinal published version, 1.93 MBLicence: CC BY 4.0

Cite this

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title = "Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems",

abstract = "Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free‐living Pseudonocardia remains understudied. This study applies a multi‐omics approach to investigate the chemical ecology of free‐living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry‐based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free‐living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.",

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AB - Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free‐living Pseudonocardia remains understudied. This study applies a multi‐omics approach to investigate the chemical ecology of free‐living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry‐based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free‐living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.

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KW - chemical ecology

KW - phylogeny

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JF - Environmental Microbiology

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ER -

Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems

Abstract

Funding

Keywords

UN SDGs

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