Local distribution of Fungal communities in a tropical rain forest - PowerPoint PPT Presentation

Local distribution of Fungal communities in a tropical rain forest and its relation to plant cover ¡ Lucie Zinger , Heidy Schimann , and the METABAR team ATBC San Jose – June 2013 Unité Mixte de Recherche ECOlogie des FOrêts 1 ¡ de Guyane

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • Patterns of fungal diversity: recent advances – Evidences of dispersal limitations (Peay et al. 2010) – Contrasted patterns of species richness in relation to temperature/latitudes: Endophytic Fungi ECM Fungi è tropical hotspots è unimodal relationship (Arnold et al. 2007) (Tedersoo et al. 2012) Transformed species richness � 1

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • Patterns of fungal diversity: recent advances – Evidences of dispersal limitations (Peay et al. 2010) – Contrasted patterns of species richness in relation to temperature/latitudes – Uncertainties on their relationship with plant diversity Temperate ¡grasslands ¡ Tropical ¡forests ¡ Overall ¡fungal ¡community ¡ Selected ¡fungal ¡groups ¡ è Depends on ecosystem type? dominant fungal ecological strategies? (Waldrop et al. 2007, Peay et al. 2013) 1

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • Patterns of fungal diversity: recent advances – Evidences of dispersal limitations (Peay et al. 2010) – Contrasted patterns of species richness in relation to temperature/latitudes: depends on fungal lineages/functional guilds – Uncertainties on their relationship with plant diversity • Current limitations: – Usually characterized for EM/AM fungi only è Need for global vs. functional vision of fungal diversity patterns – Usually studied in temperate ecosystems è Similar patterns in hyperdiverse habitats? – Poorly studied at fine spatial scales è No understanding of small-scale processes 1

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • What is the fine-scale variation of fungal communities in a hyperdiverse ecosystem? – Spatial scale of variation: hectare, larger, lower? – Similar patterns for different fungal lineages? • Is there a relationship between fungal and plant diversity? – Overall – Depending on fungal lineages/ecological guilds? 2

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION � Nouragues Ecological Research Station � Nouragues ¡ H20 plot 3 ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • 100m x 100m plot • 5 m sampling grid è 361 sampling points 80 60 40 20 20 40 60 80 4 ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • Sample processing: a metabarcoding approach + NGS è High-throughput species identification with environmental DNA Reference ¡Database ¡ Environmental ¡ Metagenomic ¡ DNA ¡metabarcodes ¡ sample ¡ DNA ¡ Taxonomic ¡assignment ¡ ATCGCTA � TCGCTACG � GCTACAG � Clustering ¡ DNA ¡ GGCTAG ¡ PCR ¡amplifica3on ¡ extrac3on ¡ & ¡sequencing ¡ Con3ngency ¡table ¡of ¡MOTUs ¡ Monday ¡S7 ¡ ¡Taberlet ¡et ¡al ¡ ¡ Marker ¡used ¡ Eukaryota Fungi Plants Chloroplast DNA trnL 18S rRNA gene Internal Transcript (UAA) intron : P6 loop 5 Spacers (ITS1)

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • γ diversity and sampling representativeness AccumulaEon ¡curve ¡ RarefacEon ¡curve ¡ è ¡sequencing ¡depth ¡sufficient ¡for ¡both ¡markers ¡ ITS1 è ¡sampling ¡effort ¡sEll ¡insufficient ¡for ¡ITS1 ¡ 18S nb OTUs 10000 10000 ITS 18S 6000 6000 nb. of reads 1 391 145 839 023 nb. of OTUs 13 447 2 316 2000 2000 (97% seq. identity) (100% seq. identity) 0 0 0 50 150 250 350 0 400000 800000 1200000 nb reads nb sites Buée el al 2009 Lentendu et al 2011 Tedersoo et al 2010 Peay et al 2013 Temperate ¡soils ¡ Tropical soils nb. of OTUs ~ 1000 5100 312 1 776 (97% seq. identity) è Deeper description of fungal diversity 7

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION α diversity patterns RICHNESS SHANNON (nb. Of OTUs) (exp Shannon) Spearman R = 0.69, p < 0.01 ITS 18S OTUs Richness 120 80 60 40 20 50 100 150 200 250 ITS1 OTUs Richness 18S è Fungal diversity highly variable at the plot scale è Weak spatial autocorrelation è Patterns supported by the two markers used 8

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION β diversity patterns Nb. of comparisons ITS 18S Spearman R=0.47, p <0.01 18S Sorensen Distances Sorensen Pairwise Distances Nb. of OTUs ITS1 Sorensen Distances Occupancy (log10 nb samples when present) è Strong community turnover due to many localised taxa è Short distance spatial autocorrelation (<20 m) è Patterns supported by the two markers used 9

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION Fungal vs. Plant α and β diversity patterns Spearman r=0.34, p=0.04 Spearman r=0.07, p=0.37 nb. Fungal OTUs ITS1 18S nb. Plant OTUs (trnL P6 loop) Sorensen distances Spearman r =0.04, p=0.02 Spearman r=0.02, p=0.18 Fungal ITS1 18S Plant Sorensen distances (trnL P6 loop) è No obvious correlations between fungal and plant diversity 10

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION 3 groups of Fungal communities ≠ trophic strategy/mycelium exploration ranges - Agaricomycetes = ectomycorrhizal/saprophytes + high - Sordariomycetes: endophytes/pathogens + variable - Glomeromycetes = symbiotic endomycorrhizal + low 11

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION Relationships with plants with plants by focusing on different fungal groups α diversity β diversity Agaricomycetes nb Fungal OTUs (18S) Spearman r = 0.59, p=0.01 Sorensen distances (18S) Fungal nb Plant OTUs (tnrL P6 loop) Plant Sorensen distances (tnrL P6 loop) è No correlations in terms of alpha diversity 12 è Strong correlation Agaricomycetes vs. plant β diversity patterns

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION • High + non uniform patterns of diversity ( α and β ) • No clear relationships with global plant diversity è spatial scale è plant diversity does not drive fungal diversity locally è different responses of different fungal groups ( Agaricomycetes) • Metabarcoding approach ➔ access deep inventories on multiple taxa ➔ test ecological hypotheses on fungal communities Limits • taxonomic assignation of OTUs, for both plants and fungi (incomplete databases for tropical species) • Dealing with rare OTUs: which threshold apply when analysing at the community level ? • Which factors and what kind of interactions ? Need for environmental data 13

Aurélie Bonin Jérôme Chave Eric Coissac Philippe Gaucher Ludovic Gielly Johan Pansu Amaia Pelozuelo Angelika Studeny Pierre Taberlet Gilles Rayé Maxime Réjou- Méchain Mélanie Roy Audrey Sagne

Alpha ¡div ¡3 ¡groups ¡ ¡ 17 ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION Home-made pipeline Genbank ¡/ ¡Local ¡ File ¡1 ¡ ¡ File ¡2 ¡ ¡ Sequences ¡ 5’ ¡reads ¡ 3’ ¡reads ¡ Paired-­‑end ¡ assembling ¡ Database ¡construc3on ¡ Tags ¡and ¡Primers ¡ ¡ Reads ¡dereplica3on ¡ Taxonomical ¡assigna3on ¡ (=OTUs ¡100% ¡similarity) ¡ Errors ¡dele3ons ¡ (size, ¡N, ¡variants) ¡ Con3ngency ¡tables ¡of ¡ Clustering ¡ ITS ¡only ¡ OTUs ¡ (LCS ¡+ ¡MCL) ¡