Diversity, spatial distribution and activity of fungi in freshwater ecosystems
High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process...
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doaj-1e01b683be284706b5cb77ee3a8de6492020-11-24T21:25:53ZengPeerJ Inc.PeerJ2167-83592019-02-017e624710.7717/peerj.6247Diversity, spatial distribution and activity of fungi in freshwater ecosystemsCécile Lepère0Isabelle Domaizon1Jean-Francois Humbert2Ludwig Jardillier3Mylène Hugoni4Didier Debroas5Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, FranceCARRTEL, Université Savoie Mont Blanc, INRA, Thonon Les Bains, FranceiEES Paris, Sorbonne Université, INRA, Paris, FranceUnité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, FranceCNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, Villeurbanne Cedex, FranceLaboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, FranceHigh-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.https://peerj.com/articles/6247.pdfFungiFreshwatersMeta-analysisDiversity |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cécile Lepère Isabelle Domaizon Jean-Francois Humbert Ludwig Jardillier Mylène Hugoni Didier Debroas |
spellingShingle |
Cécile Lepère Isabelle Domaizon Jean-Francois Humbert Ludwig Jardillier Mylène Hugoni Didier Debroas Diversity, spatial distribution and activity of fungi in freshwater ecosystems PeerJ Fungi Freshwaters Meta-analysis Diversity |
author_facet |
Cécile Lepère Isabelle Domaizon Jean-Francois Humbert Ludwig Jardillier Mylène Hugoni Didier Debroas |
author_sort |
Cécile Lepère |
title |
Diversity, spatial distribution and activity of fungi in freshwater ecosystems |
title_short |
Diversity, spatial distribution and activity of fungi in freshwater ecosystems |
title_full |
Diversity, spatial distribution and activity of fungi in freshwater ecosystems |
title_fullStr |
Diversity, spatial distribution and activity of fungi in freshwater ecosystems |
title_full_unstemmed |
Diversity, spatial distribution and activity of fungi in freshwater ecosystems |
title_sort |
diversity, spatial distribution and activity of fungi in freshwater ecosystems |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2019-02-01 |
description |
High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites. |
topic |
Fungi Freshwaters Meta-analysis Diversity |
url |
https://peerj.com/articles/6247.pdf |
work_keys_str_mv |
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