Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil
Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coe...
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Online Access: | https://doi.org/10.3389/fmicb.2018.03243 https://doaj.org/article/7327f4313058431baa13c09dae422f2c |
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ftdoajarticles:oai:doaj.org/article:7327f4313058431baa13c09dae422f2c 2023-05-15T14:53:08+02:00 Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil Magdalena Wutkowska Anna Vader Sunil Mundra Elisabeth J. Cooper Pernille B. Eidesen 2019-01-01T00:00:00Z https://doi.org/10.3389/fmicb.2018.03243 https://doaj.org/article/7327f4313058431baa13c09dae422f2c EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fmicb.2018.03243/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2018.03243 https://doaj.org/article/7327f4313058431baa13c09dae422f2c Frontiers in Microbiology, Vol 9 (2019) below-ground processes fungal trophic mode fungal functional group snow regime arctic vegetation snow fences Microbiology QR1-502 article 2019 ftdoajarticles https://doi.org/10.3389/fmicb.2018.03243 2022-12-31T08:31:14Z Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one’s study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic. Article in Journal/Newspaper Arctic Svalbard Directory of Open Access Journals: DOAJ Articles Arctic Svalbard Frontiers in Microbiology 9 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
below-ground processes fungal trophic mode fungal functional group snow regime arctic vegetation snow fences Microbiology QR1-502 |
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below-ground processes fungal trophic mode fungal functional group snow regime arctic vegetation snow fences Microbiology QR1-502 Magdalena Wutkowska Anna Vader Sunil Mundra Elisabeth J. Cooper Pernille B. Eidesen Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
topic_facet |
below-ground processes fungal trophic mode fungal functional group snow regime arctic vegetation snow fences Microbiology QR1-502 |
description |
Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one’s study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic. |
format |
Article in Journal/Newspaper |
author |
Magdalena Wutkowska Anna Vader Sunil Mundra Elisabeth J. Cooper Pernille B. Eidesen |
author_facet |
Magdalena Wutkowska Anna Vader Sunil Mundra Elisabeth J. Cooper Pernille B. Eidesen |
author_sort |
Magdalena Wutkowska |
title |
Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
title_short |
Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
title_full |
Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
title_fullStr |
Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
title_full_unstemmed |
Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil |
title_sort |
dead or alive; or does it really matter? level of congruency between trophic modes in total and active fungal communities in high arctic soil |
publisher |
Frontiers Media S.A. |
publishDate |
2019 |
url |
https://doi.org/10.3389/fmicb.2018.03243 https://doaj.org/article/7327f4313058431baa13c09dae422f2c |
geographic |
Arctic Svalbard |
geographic_facet |
Arctic Svalbard |
genre |
Arctic Svalbard |
genre_facet |
Arctic Svalbard |
op_source |
Frontiers in Microbiology, Vol 9 (2019) |
op_relation |
https://www.frontiersin.org/article/10.3389/fmicb.2018.03243/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2018.03243 https://doaj.org/article/7327f4313058431baa13c09dae422f2c |
op_doi |
https://doi.org/10.3389/fmicb.2018.03243 |
container_title |
Frontiers in Microbiology |
container_volume |
9 |
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1766324546043904000 |