Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship

ABSTRACT Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this rel...

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Autores principales:	Candice L. Swift, Katherine B. Louie, Benjamin P. Bowen, Casey A. Hooker, Kevin V. Solomon, Vasanth Singan, Chris Daum, Christa P. Pennacchio, Kerrie Barry, Vaithiyalingam Shutthanandan, James E. Evans, Igor V. Grigoriev, Trent R. Northen, Michelle A. O’Malley
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	RNA-seq transcriptomics cocultivation secondary metabolism fungi anaerobe Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/839aff9d79a84a08aa87d725f0873150
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spelling	oai:doaj.org-article:839aff9d79a84a08aa87d725f08731502021-11-10T18:37:51ZCocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship10.1128/mBio.01442-212150-7511https://doaj.org/article/839aff9d79a84a08aa87d725f08731502021-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01442-21https://doaj.org/toc/2150-7511ABSTRACT Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria Fibrobacter succinogenes strain UWB7 with the anaerobic gut fungi Anaeromyces robustus or Caecomyces churrovis on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription. A. robustus upregulated components of its secondary metabolism in the presence of Fibrobacter succinogenes strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both A. robustus and C. churrovis cocultures upregulated S-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present. F. succinogenes strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that A. robustus and C. churrovis produce antimicrobials when exposed to rumen bacteria and, more broadly, that anaerobic gut fungi are a source of novel antibiotics. IMPORTANCE Anaerobic fungi are outnumbered by bacteria by 4 orders of magnitude in the herbivore rumen. Despite their numerical disadvantage, they are resilient members of the rumen microbiome. Previous studies mining the genomes of anaerobic fungi identified genes encoding enzymes to produce natural products, which are small molecules that are often antimicrobials. In this work, we cocultured the anaerobic fungus Anaeromyces robustus or Caecomyes churrovis with rumen bacteria Fibrobacter succinogenes strain UWB7 and sequenced fungal and bacterial active genes via transcriptome sequencing (RNA-seq). Consistent with production of a fungal defense compound, bacteria upregulated genes encoding drug efflux pumps, which often export toxic molecules, and fungi upregulated genes encoding biosynthetic enzymes of natural products. Furthermore, tandem mass spectrometry detected an unknown fungal metabolite enriched in the coculture. Together, these findings point to an antagonistic relationship between anaerobic fungi and rumen bacteria resulting in the production of a fungal compound with potential antimicrobial activity.Candice L. SwiftKatherine B. LouieBenjamin P. BowenCasey A. HookerKevin V. SolomonVasanth SinganChris DaumChrista P. PennacchioKerrie BarryVaithiyalingam ShutthanandanJames E. EvansIgor V. GrigorievTrent R. NorthenMichelle A. O’MalleyAmerican Society for MicrobiologyarticleRNA-seqtranscriptomicscocultivationsecondary metabolismfungianaerobeMicrobiologyQR1-502ENmBio, Vol 12, Iss 4 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA-seq transcriptomics cocultivation secondary metabolism fungi anaerobe Microbiology QR1-502
spellingShingle	RNA-seq transcriptomics cocultivation secondary metabolism fungi anaerobe Microbiology QR1-502 Candice L. Swift Katherine B. Louie Benjamin P. Bowen Casey A. Hooker Kevin V. Solomon Vasanth Singan Chris Daum Christa P. Pennacchio Kerrie Barry Vaithiyalingam Shutthanandan James E. Evans Igor V. Grigoriev Trent R. Northen Michelle A. O’Malley Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
description	ABSTRACT Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria Fibrobacter succinogenes strain UWB7 with the anaerobic gut fungi Anaeromyces robustus or Caecomyces churrovis on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription. A. robustus upregulated components of its secondary metabolism in the presence of Fibrobacter succinogenes strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both A. robustus and C. churrovis cocultures upregulated S-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present. F. succinogenes strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that A. robustus and C. churrovis produce antimicrobials when exposed to rumen bacteria and, more broadly, that anaerobic gut fungi are a source of novel antibiotics. IMPORTANCE Anaerobic fungi are outnumbered by bacteria by 4 orders of magnitude in the herbivore rumen. Despite their numerical disadvantage, they are resilient members of the rumen microbiome. Previous studies mining the genomes of anaerobic fungi identified genes encoding enzymes to produce natural products, which are small molecules that are often antimicrobials. In this work, we cocultured the anaerobic fungus Anaeromyces robustus or Caecomyes churrovis with rumen bacteria Fibrobacter succinogenes strain UWB7 and sequenced fungal and bacterial active genes via transcriptome sequencing (RNA-seq). Consistent with production of a fungal defense compound, bacteria upregulated genes encoding drug efflux pumps, which often export toxic molecules, and fungi upregulated genes encoding biosynthetic enzymes of natural products. Furthermore, tandem mass spectrometry detected an unknown fungal metabolite enriched in the coculture. Together, these findings point to an antagonistic relationship between anaerobic fungi and rumen bacteria resulting in the production of a fungal compound with potential antimicrobial activity.
format	article
author	Candice L. Swift Katherine B. Louie Benjamin P. Bowen Casey A. Hooker Kevin V. Solomon Vasanth Singan Chris Daum Christa P. Pennacchio Kerrie Barry Vaithiyalingam Shutthanandan James E. Evans Igor V. Grigoriev Trent R. Northen Michelle A. O’Malley
author_facet	Candice L. Swift Katherine B. Louie Benjamin P. Bowen Casey A. Hooker Kevin V. Solomon Vasanth Singan Chris Daum Christa P. Pennacchio Kerrie Barry Vaithiyalingam Shutthanandan James E. Evans Igor V. Grigoriev Trent R. Northen Michelle A. O’Malley
author_sort	Candice L. Swift
title	Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
title_short	Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
title_full	Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
title_fullStr	Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
title_full_unstemmed	Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship
title_sort	cocultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationship
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/839aff9d79a84a08aa87d725f0873150
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Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship

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