Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing...

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Autores principales:	Andreas N. Schneider, John Sundh, Görel Sundström, Kerstin Richau, Nicolas Delhomme, Manfred Grabherr, Vaughan Hurry, Nathaniel R. Street
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	fungi metatranscriptomics ITS amplicon sequencing Norway spruce nutrient enrichment ectomycorrhiza Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1f0ed9d9056a4e8cb8f39137b1257016
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spelling	oai:doaj.org-article:1f0ed9d9056a4e8cb8f39137b12570162021-12-02T17:07:26ZComparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce10.1128/mSystems.00884-202379-5077https://doaj.org/article/1f0ed9d9056a4e8cb8f39137b12570162021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00884-20https://doaj.org/toc/2379-5077ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius. IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.Andreas N. SchneiderJohn SundhGörel SundströmKerstin RichauNicolas DelhommeManfred GrabherrVaughan HurryNathaniel R. StreetAmerican Society for MicrobiologyarticlefungimetatranscriptomicsITS amplicon sequencingNorway sprucenutrient enrichmentectomycorrhizaMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	fungi metatranscriptomics ITS amplicon sequencing Norway spruce nutrient enrichment ectomycorrhiza Microbiology QR1-502
spellingShingle	fungi metatranscriptomics ITS amplicon sequencing Norway spruce nutrient enrichment ectomycorrhiza Microbiology QR1-502 Andreas N. Schneider John Sundh Görel Sundström Kerstin Richau Nicolas Delhomme Manfred Grabherr Vaughan Hurry Nathaniel R. Street Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
description	ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius. IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.
format	article
author	Andreas N. Schneider John Sundh Görel Sundström Kerstin Richau Nicolas Delhomme Manfred Grabherr Vaughan Hurry Nathaniel R. Street
author_facet	Andreas N. Schneider John Sundh Görel Sundström Kerstin Richau Nicolas Delhomme Manfred Grabherr Vaughan Hurry Nathaniel R. Street
author_sort	Andreas N. Schneider
title	Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
title_short	Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
title_full	Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
title_fullStr	Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
title_full_unstemmed	Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
title_sort	comparative fungal community analyses using metatranscriptomics and internal transcribed spacer amplicon sequencing from norway spruce
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/1f0ed9d9056a4e8cb8f39137b1257016
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Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

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