Strong coupling of plant and fungal community structure across western Amazonian rainforests

ISME Journal

Volumn 7, Issue 9, 2013, Pages 1852-1861

  Peay, Kabir G ^a   Baraloto, Christopher ^b   Fine, Paul V A ^c  

^a STANFORD UNIVERSITY   (United States)

^b Campus Agronomique   (France)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

coexistence; diversity; Janzen Connell; natural enemies; negative feedback

Indexed keywords

RIBOSOMAL SPACER DNA;

ABUNDANCE; BIOSPHERE; BIOTA; COEXISTENCE; COMMUNITY COMPOSITION; COMMUNITY STRUCTURE; ENVIRONMENTAL CONDITIONS; FUNGUS; PLANT; PLANT COMMUNITY; PROKARYOTE; RAINFOREST; SAPROTROPHY; SPECIES RICHNESS; TREE; TROPICAL FOREST;

ARTICLE; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; ENVIRONMENT; FUNGUS; GENETICS; MICROBIOLOGY; MYCORRHIZA; PERU; PHYSIOLOGY; TREE; TROPIC CLIMATE;

BIODIVERSITY; DNA, RIBOSOMAL SPACER; ECOSYSTEM; ENVIRONMENT; FUNGI; MYCORRHIZAE; PERU; SOIL MICROBIOLOGY; TREES; TROPICAL CLIMATE;

AMAZON BASIN;

ANIMALIA; FUNGI; PROKARYOTA;

EID: 84883147832     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.66     Document Type: Article

References (72)

1. Amend A, Samson R, Seifert KA, Bruns TD. (2010). Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Aacd Sci USA 107: 13748-13753
2. Anderson MJ. (2001). A new method for non-parametric multivariate analysis of variance. Aust Ecol 26: 32-46
3. Arnold AE, Lutzoni F. (2007). Diversity and host range of foliar fungal endophytes: Are tropical leaves biodiversity hotspots? Ecology 88: 541-549
4. Arnold AE, Mejia LC, Kyllo D, Rojas EI, Maynard Z, Robbins N et al. (2003). Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci USA 100: 15649-15654
5. Augspurger CK. (1983). Seed dispersal of the tropical tree, Platypodium elegans, and the escape of its seedlings from fungal pathogens. J Ecol 71: 759-771
6. Baraloto C, Rabaud S, Molto Q, Blanc L, Fortunel C, Hérault B et al. (2011). Disentangling stand and environmental correlates of aboveground biomass in Amazonian forests. Global Change Biol 17: 2677-2688
7. Berbee ML. (2001). The phylogeny of plant and animal pathogens in the Ascomycota. Physiol Mol Plant Pathol 59: 165-187
8. Bever JD. (2002). Negative feedback within a mutualism: Host-specific growth of mycorrhizal fungi reduces plant benefit. Proc R Soc B 269: 2595-2601
9. Bisby GR. (1943). Geographical distribution of fungi. Bot Rev 9: 466-482
10. Branco S. (2010). Serpentine soils promote ectomycorrhizal fungal diversity. Mol Ecol 19: 5566-5576
11. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S et al. (2009). 454 Pyrosequencing analyses of forest soils reveals an unexpectedly high fungal diversity. New Phytologist 184: 449-456
12. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336
13. Comita LS, Muller-Landau HC, Aguilar S, Hubbell SP. (2010). Asymmetric density dependence shapes species abundances in a tropical tree community. Science 329: 330-332
14. Connell JH. (1971). On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. In: Den Boer PJ, Gradwell GR (eds). Dynamics of Populations. PUDOC: Wageningen, the Netherlands, pp 298-312
15. Connell JH. (1978). Diversity in tropical rain forests and coral reefs-high diversity of trees and corals is maintained only in a non-equilibrium state. Science 199: 1302-1310
16. Dadachova E, Casadevall A. (2008). Ionizing radiation: How fungi cope, adapt, and exploit with the help of melanin. Curr Opin Microbiol 11: 525-531
17. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200
18. Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461
19. Edwards IP, Zak DR. (2010). Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape. Mol Ecol 19: 1469-1482
20. Falkowski PG, Fenchel T, Delong EF. (2008). The microbial engines that drive Earth's biogeochemical cycles. Science 320: 1034-1039
21. Feinstein LM, Blackwood CB. (2012). Taxa-Area relationship and neutral dynamics influence the diversity of fungal communities on senesced tree leaves. Environ Microbiol 14: 1488-1499
22. Fine PVA, García-Villacorta R, Pitman NCA, Mesones I, Kembel SW. (2010). A floristic study of the white-sand forests of Peru. Ann Missouri Botanical Garden 97: 283-305
23. Fine PVA, Kembel SW. (2011). Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography 34: 552-565
24. Finlay BJ. (2002). Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063
25. Friesen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E. (2011). Microbially mediated plant functional traits. Annu Rev Ecol Evol Systematics 42: 23-46
26. Galante TE, Horton TR, Swaney DP. (2011). 95% of basidiospores fall within one meter of the cap- a field and modeling based study. Mycologia 103: 1175-1183
27. Gardes M, Bruns T. (1993). ITS primers with enhanced specificity for basidiomycetes-Application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118
28. Gaston KJ. (2000). Global patterns in biodiversity. Nature 405: 220-227
29. Gilbert GS, Ferrer A, Carranza J. (2002). Polypore fungal diversity and host density in a moist tropical forest. Biodiversity Conservation 11: 947-957
30. Gilbert GS, Sousa WP. (2002). Host specialization among wood-decay polypore fungi in a Caribbean mangrove forest. Biotropica 34: 396-404
31. Gilbert GS, Webb CO. (2007). Phylogenetic signal in plant pathogen-host range. PNAS 104: 4979-4983
32. Gilbert GS. (2002). Evolutionary ecology of plant diseases in natural ecosystems. Annu Rev Phytopathol 40: 13-43
33. Gillett JB. (1962). Pest pressure, an underestimated factor in evolution. Systematics Assoc Publ 4: 37-46
34. Green JL, Holmes AJ, Westoby M, Oliver I, Briscoe D, Dangerfield M et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature 432: 747-750
35. Gullison RE, Frumhoff PC, Canadell JG, Field CB, Nepstad DC, Hayhoe K et al. (2007). Tropical forests and climate policy. Science 316: 985-986
36. Hansen EM, Goheen EM. (2000). Phellinus weirii and other native root pathogens as determinants of forest structure and process in western North America. Annu Rev Phytopathol 38: 515-539
37. Harms KE,Wright SJ, Calderon O, Hernandez A, Herre EA. (2000). Pervasive density-dependent recruitment enhances seedling diversity in a tropical forest. Nature 404: 493-495
38. Hawksworth D. (1991). The fungal dimension of biodiversity-magnitude, significance and conservation. Mycol Res 95: 641-655
39. Hawksworth DL. (2012). Global species numbers of fungi: Are tropical studies and molecular approaches contributing to a more robust estimate? Biodiversity Conservation 21: 2425-2433
40. Henkel TW, Terborgh J, Vilgalys RJ. (2002). Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana. Mycol Res 106: 515-531
41. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM. (2004). A taxa-Area relationship for bacteria. Nature 432: 750-753
42. Hubbell SP. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press: Princeton, NJ, USA
43. Ihrmark K, Bodeker IT, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J et al. (2012). New primers to amplify the fungal ITS2 region-evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 82: 666-677
44. Izzo A, Agbowo J, Bruns TD. (2005). Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. New Phytologist 166: 619-630
45. Janzen DH. (1970). Herbivores and the number of tree species in tropical forests. Am Nat 104: 501-528
46. Klironomos JN. (2002). Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417: 67-70
47. Knight R, Reeder J. (2010). Denoising pyrosequencing reads by flowgram clustering. Nat Methods 7: 668-669
48. Koleff P, Gaston KJ, Lennon JJ. (2003). Measuring beta diversity for presence-Absence data. J Anim Ecol 72: 367-382
49. Liu X, Ligan M, Etienne RS, Wang Y, Staehlin C, Yu S. (2012). Experimental evidence for a phylogenetic Janzen-Connell effect in a subtropical forest. Ecol Lett 15: 111-118
50. Mangan SA, Schnitzer SA, Herre EA, Mack KML, Valencia MC, Sanchez EI et al. (2010). Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466: 752-755
51. Marengo J. (1998). Climatologia de la zona de Iquito, Peru. In: Kailliola R, Flores Paitan SGeoecologia y desarrollo Amazonico: Estudio integrado en la zona de Iquitos, Peru. University of Turku Press: Turku, pp 35-57
52. May R. (1991). A fondness for fungi. Nature 352: 475-476
53. McGuire KL, Fierer N, Bateman C, Treseder KK, Turner BL. (2012). Fungal community composition in neotropical rain forests: The influence of tree diversity and precipitation. Microb Ecol 63: 804-812
54. Peay KG, Kennedy PG, Bruns TD. (2008). Fungal community ecology: A hybrid beast with a molecular master. BioScience 58: 799-810
55. Peay KG, Kennedy PG, Davies SJ, Tan S, Bruns TD. (2010). Potential link between plant and fungal distributions in a dipterocarp rainforest: Community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. New Phytologist 185: 529-542
56. Peay KG, Schubert MG, Nguyen NH, Bruns TD. (2012). Measuring ectomycorrhizal fungal dispersal: Macroecological patterns driven by microscopic propagules. Mol Ecol 16: 4122-4136
57. Philips OL, Vargas PN, Monteagudo AL, Cruz AP, Zans MC, Sanchez WG et al. (2003). Habitat association among Amazonian tree species: A landscape-scale approach. J Ecol 91: 757-775
58. Queloz V, Sieber TN, Holdenrieder O, McDonald BA, Grünig CR. (2011). No biogeographical pattern for a root-Associated fungal species complex. Global Ecol Biogeography 20: 160-169
59. R Core Development Team (2009). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria
60. Smith ME, Douhan GW, Rizzo DM. (2007). Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a Quercus woodland. Mycorrhiza 18: 15-22
61. Smith ME, Henkel T, Aime MC, Fremier AK, Vilgalys R. (2011). Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforests. New Phytologist 192: 699-712
62. Smith ME, Henkel TW, Uehling JK, Fremier AK, Clarke HD, Vilgalys R. (2013). The ectomycorrhizal fungal community in a Neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea. PLoS One 8: E55160
63. Smith SE, Read DJ. (2008). Mycorrhizal Symbiosis, 3rd edn. Elsevier: San Francisco, CA, USA
64. Suh SO, Blackwell M, Kurtzman CP, Lachance MA. (2006). Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 98: 1006-1017
65. Tedersoo L, Mohammad B, Toots M, Diedhiou A, Henkel T, Kjoller R et al. (2012). Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. Mol Ecol 21: 4160-4170
66. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I et al. (2010). 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291-301
67. Terborgh J. (2012). Enemies maintain hyperdiverse tropical forests. Am Nat 179: 303-314
68. Toju H, Tanabe AS, Yamamoto S, Sato H. (2012). Highcoverage ITS primers for the DNA-based identification of Ascomycetes and Basidiomycetes in environmental samples. PLoS ONE 7: E40863
69. Tuomisto H, Ruokolainen K, Yli-Hall M. (2003). Dispersal, environment, and floristic variation of western Amazonian forests. Science 299: 241-244
70. van der Heijden MGA, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T et al. (1998). Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396: 69-72
71. Waldrop MP, Zak DR, Blackwood CB, Curtis CD, Tilman D. (2006). Resource availability controls fungal diversity across a plant diversity gradient. Ecol Lett 9: 1127-1135
72. Wright SJ. (2002). Plant diversity in tropical forests: A review of mechanisms of species coexistence. Oecologia 130: 1-14