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Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity
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  • Camila Duarte Ritter,
  • Micah Dunthorn,
  • Sten Anslan,
  • Vitor de Lima,
  • Leho Tedersoo,
  • R. Henrik Nilsson,
  • Alexandre Antonelli
Camila Duarte Ritter
University of Duisburg-Essen
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Micah Dunthorn
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Sten Anslan
echnische Universität Braunschweig
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Vitor de Lima
Universidade Federal de Pernambuco
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Leho Tedersoo
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R. Henrik Nilsson
University of Gothenburg
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Alexandre Antonelli
Royal Botanic Gardens Kew
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Abstract

Fungi are a key component of tropical biodiversity. Due to their inconspicuous and largely subterranean nature, they are however usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomies) emerges as the strongest factor in explaining fungal community composition. Naturally open areas – campinas – are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi–plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short-reads can suffice for diversity and community comparison, long-reads add taxonomic precision and have the potential to reveal population diversity.

Peer review status:ACCEPTED

12 Mar 2020Submitted to Ecology and Evolution
14 Mar 2020Submission Checks Completed
14 Mar 2020Assigned to Editor
17 Mar 2020Reviewer(s) Assigned
07 Apr 2020Review(s) Completed, Editorial Evaluation Pending
14 Apr 2020Editorial Decision: Revise Minor
09 May 20201st Revision Received
09 May 2020Review(s) Completed, Editorial Evaluation Pending
09 May 2020Submission Checks Completed
09 May 2020Assigned to Editor
11 May 2020Reviewer(s) Assigned
26 May 2020Editorial Decision: Accept