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Transcriptomic markers of fungal growth, respiration and carbon-use efficiency

Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with pract...

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Autores principales: Hasby, Fahri A, Barbi, Florian, Manzoni, Stefano, Lindahl, Björn D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374604/
https://www.ncbi.nlm.nih.gov/pubmed/34338746
http://dx.doi.org/10.1093/femsle/fnab100
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author Hasby, Fahri A
Barbi, Florian
Manzoni, Stefano
Lindahl, Björn D
author_facet Hasby, Fahri A
Barbi, Florian
Manzoni, Stefano
Lindahl, Björn D
author_sort Hasby, Fahri A
collection PubMed
description Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-β-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach.
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spelling pubmed-83746042021-08-20 Transcriptomic markers of fungal growth, respiration and carbon-use efficiency Hasby, Fahri A Barbi, Florian Manzoni, Stefano Lindahl, Björn D FEMS Microbiol Lett Research Letter Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-β-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach. Oxford University Press 2021-08-02 /pmc/articles/PMC8374604/ /pubmed/34338746 http://dx.doi.org/10.1093/femsle/fnab100 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Letter
Hasby, Fahri A
Barbi, Florian
Manzoni, Stefano
Lindahl, Björn D
Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title_full Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title_fullStr Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title_full_unstemmed Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title_short Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
title_sort transcriptomic markers of fungal growth, respiration and carbon-use efficiency
topic Research Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374604/
https://www.ncbi.nlm.nih.gov/pubmed/34338746
http://dx.doi.org/10.1093/femsle/fnab100
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