Genomic evidence of symbiotic adaptations in fungus-associated bacteria

Daniyal Gohar; Kadri Põldmaa; Mari Pent; Saleh Rahimlou; Klara Cerk; Duncan Y.K. Ng; Falk Hildebrand; Mo Bahram

doi:10.1016/j.isci.2025.112253

Genomic evidence of symbiotic adaptations in fungus-associated bacteria

Daniyal Gohar^*, Kadri Põldmaa, Mari Pent, Saleh Rahimlou, Klara Cerk, Duncan Y.K. Ng, Falk Hildebrand, Mo Bahram^*

^*Corresponding author af dette arbejde

Institut for Agroøkologi - Plantepatologi og Mikrobiologi

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

Abstract

Fungi harbor diverse bacteria that engage in various relationships. While these relationships potentially influence fungal functioning, their underlying genetic mechanisms remain unexplored. Here, we aimed to elucidate the key genomic features of fungus-associated bacteria (FaB) by comparing 163 FaB genomes to 1,048 bacterial genomes from other hosts and habitats. Our analyses revealed several distinctive genomic features of FaB. We found that FaB are enriched in carbohydrate transport/metabolism- and motility-related genes, suggesting an adaptation for utilizing complex fungal carbon sources. They are also enriched in genes targeting fungal biomass, likely reflecting their role in recycling and rebuilding fungal structures. Additionally, FaB associated with plant-mutualistic fungi possess a wider array of carbon-acquisition enzymes specific to fungal and plant substrates compared to those residing with saprotrophic fungi. These unique genomic features highlight FaB’ potential as key players in fungal nutrient acquisition and decomposition, ultimately influencing plant-fungal symbiosis and ecosystem functioning.

Originalsprog	Engelsk
Artikelnummer	112253
Tidsskrift	iScience
Vol/bind	28
Nummer	4
ISSN	2589-0042
DOI	https://doi.org/10.1016/j.isci.2025.112253
Status	Udgivet - 1 apr. 2025

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title = "Genomic evidence of symbiotic adaptations in fungus-associated bacteria",

abstract = "Fungi harbor diverse bacteria that engage in various relationships. While these relationships potentially influence fungal functioning, their underlying genetic mechanisms remain unexplored. Here, we aimed to elucidate the key genomic features of fungus-associated bacteria (FaB) by comparing 163 FaB genomes to 1,048 bacterial genomes from other hosts and habitats. Our analyses revealed several distinctive genomic features of FaB. We found that FaB are enriched in carbohydrate transport/metabolism- and motility-related genes, suggesting an adaptation for utilizing complex fungal carbon sources. They are also enriched in genes targeting fungal biomass, likely reflecting their role in recycling and rebuilding fungal structures. Additionally, FaB associated with plant-mutualistic fungi possess a wider array of carbon-acquisition enzymes specific to fungal and plant substrates compared to those residing with saprotrophic fungi. These unique genomic features highlight FaB{\textquoteright} potential as key players in fungal nutrient acquisition and decomposition, ultimately influencing plant-fungal symbiosis and ecosystem functioning.",

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author = "Daniyal Gohar and Kadri P{\~o}ldmaa and Mari Pent and Saleh Rahimlou and Klara Cerk and Ng, {Duncan Y.K.} and Falk Hildebrand and Mo Bahram",

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doi = "10.1016/j.isci.2025.112253",

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AU - Gohar, Daniyal

AU - Põldmaa, Kadri

AU - Pent, Mari

AU - Rahimlou, Saleh

AU - Cerk, Klara

AU - Ng, Duncan Y.K.

AU - Hildebrand, Falk

AU - Bahram, Mo

PY - 2025/4/1

Y1 - 2025/4/1

N2 - Fungi harbor diverse bacteria that engage in various relationships. While these relationships potentially influence fungal functioning, their underlying genetic mechanisms remain unexplored. Here, we aimed to elucidate the key genomic features of fungus-associated bacteria (FaB) by comparing 163 FaB genomes to 1,048 bacterial genomes from other hosts and habitats. Our analyses revealed several distinctive genomic features of FaB. We found that FaB are enriched in carbohydrate transport/metabolism- and motility-related genes, suggesting an adaptation for utilizing complex fungal carbon sources. They are also enriched in genes targeting fungal biomass, likely reflecting their role in recycling and rebuilding fungal structures. Additionally, FaB associated with plant-mutualistic fungi possess a wider array of carbon-acquisition enzymes specific to fungal and plant substrates compared to those residing with saprotrophic fungi. These unique genomic features highlight FaB’ potential as key players in fungal nutrient acquisition and decomposition, ultimately influencing plant-fungal symbiosis and ecosystem functioning.

AB - Fungi harbor diverse bacteria that engage in various relationships. While these relationships potentially influence fungal functioning, their underlying genetic mechanisms remain unexplored. Here, we aimed to elucidate the key genomic features of fungus-associated bacteria (FaB) by comparing 163 FaB genomes to 1,048 bacterial genomes from other hosts and habitats. Our analyses revealed several distinctive genomic features of FaB. We found that FaB are enriched in carbohydrate transport/metabolism- and motility-related genes, suggesting an adaptation for utilizing complex fungal carbon sources. They are also enriched in genes targeting fungal biomass, likely reflecting their role in recycling and rebuilding fungal structures. Additionally, FaB associated with plant-mutualistic fungi possess a wider array of carbon-acquisition enzymes specific to fungal and plant substrates compared to those residing with saprotrophic fungi. These unique genomic features highlight FaB’ potential as key players in fungal nutrient acquisition and decomposition, ultimately influencing plant-fungal symbiosis and ecosystem functioning.

KW - Genomics

KW - Microbial genomics

KW - Microbial metabolism

KW - Microbiology

KW - Mycology

UR - http://www.scopus.com/inward/record.url?scp=105002138469&partnerID=8YFLogxK

U2 - 10.1016/j.isci.2025.112253

DO - 10.1016/j.isci.2025.112253

M3 - Journal article

AN - SCOPUS:105002138469

SN - 2589-0042

VL - 28

JO - iScience

JF - iScience

IS - 4

M1 - 112253

ER -

Genomic evidence of symbiotic adaptations in fungus-associated bacteria

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