Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity.
PacBio
environmental DNA
high‐throughput sequencing
metabarcoding
neotropical biodiversity
third‐generation sequencing
Journal
Ecology and evolution
ISSN: 2045-7758
Titre abrégé: Ecol Evol
Pays: England
ID NLM: 101566408
Informations de publication
Date de publication:
Jul 2020
Jul 2020
Historique:
received:
13
03
2020
revised:
09
05
2020
accepted:
26
05
2020
entrez:
8
8
2020
pubmed:
8
8
2020
medline:
8
8
2020
Statut:
epublish
Résumé
Fungi are a key component of tropical biodiversity. However, due to their inconspicuous and largely subterranean nature, they are 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 (phytophysiognomy) emerges as the strongest factor 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.
Identifiants
pubmed: 32760545
doi: 10.1002/ece3.6477
pii: ECE36477
pmc: PMC7391351
doi:
Types de publication
Journal Article
Langues
eng
Pagination
7509-7524Informations de copyright
© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Déclaration de conflit d'intérêts
The authors declare no conflict of interest.
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D48-50
pubmed: 26657633
Mol Ecol. 2012 Apr;21(8):1789-93
pubmed: 22486819
PeerJ. 2018 Sep 25;6:e5661
pubmed: 30280033
New Phytol. 2010 Jan;185(2):351-4
pubmed: 20088976
Science. 2004 Jun 11;304(5677):1629-33
pubmed: 15192218
Environ Microbiol Rep. 2016 Oct;8(5):774-779
pubmed: 27348848
Nat Rev Genet. 2016 May 17;17(6):333-51
pubmed: 27184599
Bioscience. 2017 Jun 1;67(6):534-545
pubmed: 28608869
J Biogeogr. 2011 Nov;38(11):2136-2149
pubmed: 22247585
Science. 2010 Nov 12;330(6006):927-31
pubmed: 21071659
Science. 2014 Nov 28;346(6213):1256688
pubmed: 25430773
Environ Microbiol Rep. 2017 Oct;9(5):668-675
pubmed: 28799713
Appl Environ Microbiol. 2009 Dec;75(23):7537-41
pubmed: 19801464
ISME J. 2013 Sep;7(9):1852-61
pubmed: 23598789
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Commun. 2017 Oct 30;8(1):1188
pubmed: 29084957
Phytopathology. 1997 Sep;87(9):888-91
pubmed: 18945058
Nat Methods. 2013 Oct;10(10):996-8
pubmed: 23955772
Nucleic Acids Res. 2019 Jan 8;47(D1):D259-D264
pubmed: 30371820
Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6034-6039
pubmed: 29760058
Science. 2013 Nov 15;342(6160):850-3
pubmed: 24233722
Mol Ecol. 2012 Sep;21(17):4160-70
pubmed: 22568722
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Mol Ecol. 2017 Dec;26(24):6960-6973
pubmed: 29113014
Front Microbiol. 2019 May 17;10:983
pubmed: 31191462
New Phytol. 2016 Jul;211(2):404-10
pubmed: 27040897
Sci Rep. 2019 Dec 16;9(1):19205
pubmed: 31844092
Appl Environ Microbiol. 2009 Aug;75(15):5111-20
pubmed: 19502440
Nat Rev Microbiol. 2019 Jan;17(2):95-109
pubmed: 30442909
FEMS Microbiol Lett. 2009 Jul;296(1):97-101
pubmed: 19459974
New Phytol. 2010 Apr;186(2):281-5
pubmed: 20409185
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6241-6
pubmed: 22454494
PeerJ. 2016 Oct 18;4:e2584
pubmed: 27781170
J Mol Evol. 2008 Feb;66(2):167-74
pubmed: 18259800
BMC Genomics. 2012 Jul 24;13:341
pubmed: 22827831
Mol Ecol Resour. 2017 Nov;17(6):e234-e240
pubmed: 28544559
PLoS Comput Biol. 2014 Apr 03;10(4):e1003531
pubmed: 24699258
An Acad Bras Cienc. 2008 Mar;80(1):101-14
pubmed: 18345379
New Phytol. 2018 Feb;217(3):1370-1385
pubmed: 28906012
Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89
pubmed: 26542840
ISME J. 2010 Oct;4(10):1340-51
pubmed: 20445636
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Mol Ecol. 2016 Jan;25(2):630-47
pubmed: 26642189
Nucleic Acids Res. 2018 Jan 4;46(D1):D41-D47
pubmed: 29140468