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

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

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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 Unit Mixte de Recherche ECOlogie des FOrts 1 de

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Local distribution of Fungal communities in a tropical rain forest and its relation to plant cover ¡

Lucie Zinger , Heidy Schimann, and the METABAR team

Unité Mixte de Recherche

ECOlogie des FOrêts de Guyane

1 ¡

ATBC San Jose – June 2013

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SLIDE 2
  • Patterns of fungal diversity: recent advances

– Evidences of dispersal limitations (Peay et al. 2010) – Contrasted patterns of species richness in relation to temperature/latitudes:

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

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ECM Fungi è unimodal relationship

(Tedersoo et al. 2012)

Endophytic Fungi è tropical hotspots

(Arnold et al. 2007)

Transformed species richness

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SLIDE 3
  • 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

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

1

è Depends on ecosystem type? dominant fungal ecological strategies?

(Waldrop et al. 2007, Peay et al. 2013)

Temperate ¡grasslands ¡ Tropical ¡forests ¡ Overall ¡fungal ¡community ¡ Selected ¡fungal ¡groups ¡

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SLIDE 4
  • 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

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

1

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SLIDE 5
  • 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?

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

2

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SLIDE 6

Nouragues ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

3 ¡

Nouragues Ecological Research Station

  • H20 plot
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  • 100m x 100m plot
  • 5 m sampling grid

è 361 sampling points

20 40 60 80 20 40 60 80

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

4 ¡

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ATCGCTA TCGCTACG GCTACAG GGCTAG ¡

PCR ¡amplifica3on ¡ & ¡sequencing ¡ DNA ¡ extrac3on ¡ Environmental ¡ sample ¡ Metagenomic ¡ DNA ¡ DNA ¡metabarcodes ¡ Reference ¡Database ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

5

Chloroplast DNA trnL (UAA) intron: P6 loop

Plants

Internal Transcript Spacers (ITS1) 18S rRNA gene

Eukaryota Fungi

Taxonomic ¡assignment ¡ Clustering ¡ Con3ngency ¡table ¡of ¡MOTUs ¡

  • Sample processing: a metabarcoding approach + NGS

è High-throughput species identification with environmental DNA

Marker ¡used ¡

Monday ¡S7 ¡ ¡Taberlet ¡et ¡al ¡ ¡

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  • γ diversity and sampling representativeness

è Deeper description of fungal diversity

è ¡sequencing ¡depth ¡sufficient ¡for ¡both ¡markers ¡ è ¡sampling ¡effort ¡sEll ¡insufficient ¡for ¡ITS1 ¡

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

7

50 150 250 350 2000 6000 10000

nb sites nb reads

400000 800000 1200000 2000 6000 10000 ITS1 18S

AccumulaEon ¡curve ¡

nb OTUs

RarefacEon ¡curve ¡

ITS 18S

  • nb. of reads

1 391 145 839 023

  • nb. of OTUs

13 447

(97% seq. identity)

2 316

(100% seq. identity)

Buée el al 2009 Lentendu et al 2011 Tedersoo et al 2010 Peay et al 2013

Temperate ¡soils ¡ Tropical soils

  • nb. of OTUs

(97% seq. identity)

~ 1000 5100 312 1 776

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SLIDE 10

α diversity patterns

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

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50 100 150 200 250 20 40 60 80 120

ITS1 OTUs Richness 18S OTUs Richness

RICHNESS

(nb. Of OTUs)

SHANNON

(exp Shannon)

18S ITS

Spearman R = 0.69, p < 0.01

è Fungal diversity highly variable at the plot scale è Weak spatial autocorrelation è Patterns supported by the two markers used

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β diversity patterns

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

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Spearman R=0.47, p <0.01

è Strong community turnover due to many localised taxa è Short distance spatial autocorrelation (<20 m) è Patterns supported by the two markers used

18S Sorensen Distances ITS1 Sorensen Distances

  • Nb. of comparisons
  • Nb. of OTUs

Sorensen Pairwise Distances Occupancy (log10 nb samples when present)

ITS 18S

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Fungal vs. Plant α and β diversity patterns

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

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è No obvious correlations between fungal and plant diversity

  • nb. Plant OTUs (trnL P6 loop)
  • nb. Fungal OTUs

ITS1 Fungal Sorensen distances ITS1 Spearman r=0.34, p=0.04 Spearman r=0.07, p=0.37 Spearman r =0.04, p=0.02 Spearman r=0.02, p=0.18 18S Plant Sorensen distances (trnL P6 loop) 18S

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3 groups of Fungal communities ≠ trophic strategy/mycelium exploration ranges

  • Agaricomycetes = ectomycorrhizal/saprophytes +

high

  • Sordariomycetes: endophytes/pathogens +

variable

  • Glomeromycetes = symbiotic endomycorrhizal +

low

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

11

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Relationships with plants with plants by focusing on different fungal groups

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

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α diversity β diversity

è No correlations in terms of alpha diversity è Strong correlation Agaricomycetes vs. plant β diversity patterns

Agaricomycetes

Plant Sorensen distances (tnrL P6 loop) Fungal Sorensen distances (18S) nb Plant OTUs (tnrL P6 loop) nb Fungal OTUs (18S) Spearman r = 0.59, p=0.01

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  • 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

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

13

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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

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Alpha ¡div ¡3 ¡groups ¡ ¡

17 ¡

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

CONTEXT QUESTIONS MAT & MET RESULTS CONCLUSION

Home-made pipeline