Skip to main content
SpringerLink
Log in
Book cover

Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications pp 83–113Cite as

Fungal Diversity: Global Perspective and Ecosystem Dynamics

  • Chapter
  • First Online:

Abstract

All major biomes on earth contain a multitude of microorganisms; of this, a considerable proportion is shared by fungi in terms of abundance, genetic diversity, biomass and total biospheric DNA. In various ecosystems, fungi exist as pathogens, mutualists and decomposers and are of considerable ecological value as they influence nearly every component of the ecosystem services, viz. protection against pathogens, homeostatic balance, decomposition and other functions. Fungi are, however, functionally redundant in some ecosystems and endemic to certain bioregions. Next-generation sequencing has now uncovered unculturable fungal forms that has transformed our understanding towards their role in unexplored environments; cataloguing their diversity and study of their biogeographical patterns at local and global scale have become simpler. The data generated through advanced molecular approaches have introduced the concept of ‘mycobiome’ which was largely overlooked or considered as an integral yet small component of the ‘microbiome’ until now. In this chapter, we report new information that reveals various deterministic factors that shape fungal communities and their probable role in maintaining human, soil and plant health. Finally, we also discuss how the view of mycobiome has taken an independent shape and has more recently helped understand interkingdom interactions.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Allen EA, Hoch HC, Steadman JR, Stavely RJ (1991) Influence of leaf surface features on spore deposition and the epiphytic growth of phytopathogenic fungi. In: Andrews JH, Hirano SS (eds) Microbial ecology of leaves, Brock/Springer series in contemporary bioscience. Springer, New York

    Google Scholar 

  • Ambardar S, Singh HR, Gowda M, Vakhlu J (2016) Comparative metagenomics reveal phylum level temporal and spatial changes in mycobiome of below ground parts of Crocus sativus. PLoS One 11:e0163300

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Amend A (2014) From dandruff to deep-sea vents: malassezia-like fungi are ecologically hyper-diverse. PLoS Pathog 10(8):e1004277

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Andrews JH, Buck JW (2002) Adhesion of yeasts to leaf surfaces. In: Lindow SE, Hecht-Poinar EI, Elliott VJ (eds) Phyllosphere microbiology. APS Press, St. Paul, pp 53–68

    Google Scholar 

  • Araujo R (2014) Towards the genotyping of fungi: methods, benefits and challenges. Curr Fungal Infect Rep 8:203–210

    Article  Google Scholar 

  • Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: Are tropical leaves biodiversity hotspots? Ecology 88:541–549

    Article  PubMed  Google Scholar 

  • Arnold AE, Mejia LC, Kyllo D, Rojas EI, Maynard Z, Robbins N, Herre EA (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci 100:15649–15654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Averill C, Turner BL, Finzi AC (2014) Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505:543–545

    Article  CAS  PubMed  Google Scholar 

  • Aylor DE (2002) Aerobiology of fungi in relation to capture and release by plants. In: Lindow SE, Hecht-Poinar EI, Elliott VJ (eds) Phyllosphere microbiology. APS Press, St. Paul, pp 341–364

    Google Scholar 

  • Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288:4502–4512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Huerta-Cepas J (2018) Structure and function of the global topsoil microbiome. Nature 60(7717):233–237

    Article  CAS  Google Scholar 

  • Bai L, Cui J, Jie W, Cai B (2015) Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields. Microbiol Res 180:49–56

    Article  PubMed  Google Scholar 

  • Baier MC et al (2010) Knockdown of the symbiotic sucrose synthase tSucS1 affects arbuscule maturation and maintenance in mycorrhizal roots of Medicago truncatula. Plant Physiol 152:1000–1014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bar-On YM, Phillips R, Milo R (2018) The biomass distribution on Earth. Proc Natl Acad Sci USA 115(25):6506–6511

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bass D, Howe A, Brown N, Barton H, Demidova M, Michelle H, Li L, Sanders H, Watkinson SC, Willcock S, Richards TA (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc R Soc B Biol Sci 274:3069–3077

    Article  CAS  Google Scholar 

  • Belanger RR, Avis TJ (2002) Ecological processes and interactions occurring in leaf surface fungi. In: Lindow SE, Hecht-Poinar EI, Elliott VJ (eds) Phyllosphere microbiology. APS Press, St. Paul, pp 193–207

    Google Scholar 

  • Bender SF, Conen F, van der Heijden MGA (2015) Mycorrhizal effects on nutrient cycling, nutrient leaching and N2O production in experimental grassland. Soil Biol Biochem 80:283–292

    Article  CAS  Google Scholar 

  • Berg G, Grube M, Schloter M, Smalla K (2014) Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol 5:148

    PubMed  PubMed Central  Google Scholar 

  • Blachowicz A, Mayer T, Bashir M, Pieber TR, De León P, Venkateswaran K (2017) Human presence impacts fungal diversity of inflated lunar/Mars analog habitat. Microbiome 5(1):62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blackwell M (2011) The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438

    Article  PubMed  Google Scholar 

  • Blunt JW, Copp BR, Keyzers RA, Munro MH, Prinsep MR (2016) Marine natural products. Nat Prod Rep 33(3):382–431

    Article  CAS  PubMed  Google Scholar 

  • Bodenhausen N, Horton MW, Bergelson J (2013) Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8:e56329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bodenhausen N, Bortfeld-Miller M, Ackermann M, Vorholt JA (2014) A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PloS Gen 10:e1004283

    Article  CAS  Google Scholar 

  • Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nat Commun 1:48

    Article  PubMed  CAS  Google Scholar 

  • Botschuijver S, Roeselers G, Levin E, Jonkers DM, Welting O, Heinsbroek SEM, de Weerd HH, Boekhout T, Fornai M, Masclee AA et al (2017) Intestinal fungal dysbiosis is associated with visceral hypersensitivity in patients with irritable bowel syndrome and rats. Gastroenterology 153:1026–1039

    Article  PubMed  Google Scholar 

  • Bradley DJ, Gilbert GS, Martiny JBH (2008) Pathogens promote plant diversity through a compensatory response. Ecol Lett 11:461–469

    Article  PubMed  Google Scholar 

  • Busby PE, Ridout M, Newcombe G (2016) Fungal endophytes: modifiers of plant disease. Plant Mol Biol 90:645–655

    Article  CAS  PubMed  Google Scholar 

  • Cáceres MES, Dal Forno M, Barreto FMO and Aptroot A (2018) Unexpected basidiolichen diversity discovered in lowland Brazilian forests. S05-5 Abstract. symposium session 5. International Mycological Congress, p 35.

    Google Scholar 

  • Cassman NA, Leite MFA, Pan Y, de Hollander M, van Veen JA, Kuramae EE (2016) Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Sci Rep 6:23680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Chen Z, Guo R, Chen N, Lu H, Huang S, Wang J, Li L (2011) Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagn Microbiol Infect Dis 70:492–498

    Article  PubMed  Google Scholar 

  • Cicatiello P, Gravagnuolo AM, Gnavi G, Varese GC, Giardina P (2016) Marine fungi as source of new hydrophobins. Int J Biol Macromol 92:1229–1233

    Article  CAS  PubMed  Google Scholar 

  • Comandini O, Rinaldi AC, Kuyper TW (2012) Measuring and estimating ectomycorrhizal fungal diversity: a continuous challenge. In: Pagano M (ed) Mycorrhiza: occurrence in natural and restored environments. Nova Science Publishers, New York, pp 165–200

    Google Scholar 

  • Compant S, Clement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678

    Article  CAS  Google Scholar 

  • Cordier T, Robin C, Capdevielle X, Fabreguettes O, Desprez-Loustau ML, Vacher C (2012a) The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient. New Phytol 196:510–519

    Article  PubMed  Google Scholar 

  • Cordier T, Robin C, Capdeville X, Desprez-Loustau ML, Vacher C (2012b) Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecol 5:509–520

    Article  Google Scholar 

  • Cotton WR, Yuter S (2009) Principles of cloud and precipitation formation. In: Levin Z, Cotton WR (eds) Aerosol pollution impact on precipitation. Springer, Dordrecht, pp 13–43

    Chapter  Google Scholar 

  • Cox F, Newsham KK, Bol R, Dungait JA, Robinson CH (2016) Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. Ecol Lett 19:528–536

    Article  PubMed  Google Scholar 

  • Didari T, Mozaffari S, Nikfar S, Abdollahi M (2015) Effectiveness of probiotics in irritable bowel syndrome: updated systematic review with meta-analysis. World J Gastroenterol 21:3072–3084

    Article  PubMed  PubMed Central  Google Scholar 

  • Doyle SM, Sangwan N, Wang G, Gilbert JA, Christner BC, Zhu TF (2018) Metagenomic analysis of basal ice from an Alaskan glacier. Microbiome 6(1):123

    Article  PubMed  PubMed Central  Google Scholar 

  • Drake H, Ivarsson M (2017) The role of anaerobic fungi in fundamental biogeochemical cycles in the deep biosphere. Fungal Biol Rev. https://doi.org/10.1016/j.fbr.2017.10.001

    Article  Google Scholar 

  • Drappatz J, Schiff D, Kesari S, Norden AD, Wen PY (2007) Medical Management of Brain Tumor Patients. Neurol Clin 25:1035–1071

    Article  PubMed  Google Scholar 

  • Ehrmann J, Ritz K (2014) Plant: soil interactions in temperate multi-cropping production systems. Plant Soil 376:1–29

    Article  CAS  Google Scholar 

  • Elbert W, Taylor PE, Andreae MO, Pöschl U (2007) Contribution of fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions. Atmos Chem Phys 7:4569–4588

    Article  CAS  Google Scholar 

  • Enaud R, Vandenborght LE, Coron N, Bazin T, Prevel R, Schaeverbeke T et al (2018) The mycobiome: a neglected component in the microbiota-gut-brain axis. Microorganisms 6(1):22

    Article  PubMed Central  CAS  Google Scholar 

  • Falih AMK, Wainwright M (1995) Nitrification in-vitro by a range of filamentous fungi and yeasts. Lett Appl Microbiol 21:18–19

    Article  CAS  PubMed  Google Scholar 

  • Ferguson BA, Dreisbach TA, Parks CG, Filip GM, Schmitt CL (2003) Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon. Can J Forensic Res 33:612–623

    Article  Google Scholar 

  • Findlay SEG, Dye S, Kuehn KA (2002) Microbial growth and nitrogen retention in litter of Phragmites australis compared to Typha angustifolia. Wetlands 22:616–625

    Article  Google Scholar 

  • Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M (2013) NIH Intramural Sequencing Center Comparative Sequencing Program, KongHH, Segre JA: Topographic diversity of fungal and bacterial communities inhuman skin. Nature 498:367–370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe SG, Partida-Martínez LP (2016) The cacti microbiome: interplay between habitat-filtering and host- specificity. Front Microbiol 7:891. https://doi.org/10.3389/fmicb.2016.00150

    Article  Google Scholar 

  • Foster JA, Rinaman L, Cryan JF (2017) Stress & the gut-brain axis: regulation by the microbiome. Neurobiol Stress 7:124–136

    Article  PubMed  PubMed Central  Google Scholar 

  • Fröhlich-Nowoisky J, Pickersgill DA, Després VR, Pöschl U (2009) High diversity of fungi in air particulate matter. Proc Natl Acad Sci 106(31):12814–11281

    Article  PubMed  PubMed Central  Google Scholar 

  • Fuller R (1989) Probiotics in man and animals. J Appl Bacteriol 66:365–378

    Article  CAS  PubMed  Google Scholar 

  • Gang G-H, Cho G, Kwak YS, Park EH (2017) Distribution of rhizosphere and endosphere fungi on the first-class endangered plant Cypripedium japonicum. Mycobiology 45:97–100

    Article  PubMed  PubMed Central  Google Scholar 

  • Genre A, Chabaud M, Timmers T, Bonfante P, Barker DG (2005) Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection. Plant Cell 17:3489–3499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathol 6:e1000713

    Article  CAS  Google Scholar 

  • Gosiewski T, Salamon D, Szopa M, Sroka A, Malecki MT, Bulanda M (2014) Quantitative evaluation of fungi of the genus Candida in the feces of adult patients with type 1 and 2 diabetes-a pilot study. Gut Pathog 6(1):43

    Article  PubMed  PubMed Central  Google Scholar 

  • Gouba N, Drancourt M (2015) Digestive tract mycobiota: a source of infection. Med Mal Infect 45:9–16

    Article  CAS  PubMed  Google Scholar 

  • Gouba N, Raoult D, Drancourt M (2014) Gut microeukaryotes during anorexia nervosa: a case report. BMC Res Notes 7:33

    Article  PubMed  PubMed Central  Google Scholar 

  • Grosberg RK, Vermeij GJ, Wainwright PC (2012) Biodiversity in water and on land. Curr Biol 22:R900–R903

    Article  CAS  PubMed  Google Scholar 

  • Gulis V, Kuehn K, Suberkropp K (2006) The role of fungi in carbon and nitrogen cycles in freshwater ecosystems. In: Gadd GM (ed) Fungi in biogeochemical cycles. Cambridge University Press, Cambridge, pp 404–435

    Chapter  Google Scholar 

  • Guyon P, Graham B, Roberts GC, Mayol-Bracero OL, Maenhaut W, Artaxo P et al (2004) Sources of optically active aerosol particles over the Amazon forest. Atmos Environ 38:1039–1051

    Article  CAS  Google Scholar 

  • Haga DI, Burrows SM, Iannone R, Wheeler MJ, Mason RH, Chen J et al (2014) Ice nucleation by fungal spores from the classes Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes, and the effect on the atmospheric transport of these spores. Atmos Chem Phys 14:8611–8630

    Article  CAS  Google Scholar 

  • Halbwachs H, Simmel J (2018) Some like it hot, some not–tropical and arctic mushrooms. Fungal Biol Rev 32:143–l55

    Article  Google Scholar 

  • Haleem Khan AA, Mohan Karuppayil S (2012) Fungal pollution of indoor environments and its management. Saudi J Biol Sci 19:405–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hassan SED (2017) Plant growth-promoting activities for bacterial and fungal endophytes isolated from medicinal plant of Teucrium polium L. J Adv Res 8:687–695

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hassett MO, Fischer MWF, Money NP (2015) Mushrooms as rainmakers: how spores act as nuclei for raindrops. PLoS One 10:e0140407. https://doi.org/10.1371/journal.pone.0140407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95:641–655

    Article  Google Scholar 

  • Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432

    Article  Google Scholar 

  • Hawksworth DL, Lücking R (2017) Fungal diversity revisited: 2.2 to 3.8 million species. In: Heitman J, Howlett BJ, Crous PW, Stukenbrock EH, James TY, Gow NAR (eds) The fungal kingdom. The American Society for Microbiology, Washington, DC, pp 79–95

    Google Scholar 

  • Heald CL, Spracklen DV (2009) Atmospheric budget of primary biological aerosol particles from fungal spores. Geophys Res Lett 36:L09806

    Article  CAS  Google Scholar 

  • Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA (2015) Complementary amplicon-based genomic approaches for the study of fungal communities in humans. PLoS One 10(2):e0116705

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Helmus MR, Savage K, Diebel MW, Maxted JT, Ar I (2007) Separating the determinants of phylogenetic community structure. Ecol Lett 10:917–925

    Article  PubMed  Google Scholar 

  • Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD (2013) Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 8:e66019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huffnagle GB, Noverr MC (2013) The emerging world of the fungal microbiome. Trends Microbiol 21(7):334–341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huseyin CE, O’toole PW, Cotter PD, Scanlan PD (2017) Forgotten fungi—the gut mycobiome in human health and disease. FEMS Microbiol Rev 41:479–511

    Article  CAS  PubMed  Google Scholar 

  • Husman T (1996) Health effects of indoor-air microorganisms. Scand J Work Environ Health 22:5–13

    Article  CAS  PubMed  Google Scholar 

  • Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP et al (2012) Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 336(6086):1314–1317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ishibashi K, Fukazawa R, Miura NN, Adachi Y, Ogawa S, Ohno N (2014) Diagnostic potential of antibody titres against Candida cell wall β-glucan in Kawasaki disease. Clin Exp Immunol 177(1):161–167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska et al (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822

    Article  CAS  PubMed  Google Scholar 

  • Jansa J, Finlay R, Wallender H, Smith AF, Smith SE (2010) Role of mycorrhizal symbioses in phosphorus cycling. In: Phosphorus in action, Soil biology series. Springer, Heidelberg, pp 137–168

    Google Scholar 

  • Javot H, Penmetsa RV, Terzaghi N, Cook DR, Harrison MJA (2007) Medicago truncatula phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis. Proc Natl Acad Sci 104:1720–1725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeffery IB, O’Toole PW, Öhman L, Claesson MJ, Deane J, Quigley EMM, Simrén M (2012) An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 61:997–1006

    Article  PubMed  Google Scholar 

  • Jumpponen A, Jones KL (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186:496–513

    Article  CAS  PubMed  Google Scholar 

  • Kendrick B (2001) Fungi: ecological importance and impact on humans. In: e LS. https://doi.org/10.1002/9780470015902.a0000369.pub2

    Chapter  Google Scholar 

  • Kinkel LL (1997) Microbial population dynamics on leaves. Annu Rev Phytopathol 35:327–347

    Article  CAS  PubMed  Google Scholar 

  • Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R et al (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci 108:4578–4585

    Article  CAS  PubMed  Google Scholar 

  • Kosuta S et al (2003) Diffusible factor from arbuscular mycorrhizal fungi induces symbiosis-specific MtENOD11 expression in roots of Medicago truncatula. Plant Physiol 131:952–962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krauss GJ, Solé M, Krauss G, Schlosser D, Wesenberg D, Bärlocher F (2011) Fungi in freshwaters: ecology, physiology and biochemical potential. FEMS Microbiol Rev 35:620–651

    Article  CAS  PubMed  Google Scholar 

  • Kuhn H, Kuster H, Requena N (2010) Membrane steroid-binding protein 1 induced by a diffusible fungal signal is critical for mycorrhization in Medicago truncatula. New Phytol 185:716–733

    Article  CAS  PubMed  Google Scholar 

  • Landenmark HKE, Forgan DH, Cockell CS (2015) An estimate of the total DNA in the biosphere. PLoS Biol 13:e1002168

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Laughlin RJ, Stevens RJ (2002) Evidence for fungal dominance of denitrification and codenitrification in a grassland soil. Soil Sci Soc Am J 66:1540–1548

    Article  CAS  Google Scholar 

  • Le Van A, Quaiser A, Duhamel M, Michon-Coudouel S, Dufrense A, Vandenkoornhuyse P (2017) Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera. Peer J 5:e3454. https://doi.org/10.7717/peerj.3454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levetin E (2002) Bioaerosols in agricultural and outdoor settings. In: Bitton G (ed) Encyclopedia of environmental microbiology. Wiley, New York, pp 404–416

    Google Scholar 

  • Levetin E, Dorsey K (2006) Contribution of leaf surface fungi to the air spora. Aerobiologia 22:3–12

    Article  Google Scholar 

  • Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D et al (2015) Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 18(4):489–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li A, Fahey TJ (2013) Nitrogen translocation to fresh litter in northern hardwood forest. Ecosystems 16:521–528

    Article  CAS  Google Scholar 

  • Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Locey KJ, Lennon JT (2016) Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A 113:5970–5975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Markmann K, Giczey G, Parniske M (2008) Functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria. PLoS Biol 6:497–506

    Article  CAS  Google Scholar 

  • Martin F et al (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92

    Article  CAS  PubMed  Google Scholar 

  • May RM (1988) How many species are there on earth? Science 241:1441–1449

    Article  CAS  PubMed  Google Scholar 

  • McKenzie H, Main J, Pennington CR, Parratt D (1990) Antibody to selected strains of Saccharomyces cerevisiae (baker’s and brewer’s yeast) and Candida albicans in Crohn’s disease. Gut 31(5):536–538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Methvin BR, Suberkropp K (2003) Annual production of leaf-decaying fungi in 2 streams. J North Am Benth Soc 22:554–564

    Article  Google Scholar 

  • Mitter B, Petric A, Shin MW, Chain PS, Hauberg-Lotte L, Reinhold-Hurek B et al (2013) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120

    Article  PubMed  PubMed Central  Google Scholar 

  • Mogilnicka I, Ufnal M (2018) Gut mycobiota and fungal metabolites in human homeostasis. Curr Drug Targets 20(2):232–240

    Article  CAS  Google Scholar 

  • Möhler O, DeMott PJ, Vali G, Levin Z (2007) Microbiology and atmospheric processes: the role of biological particles in cloud physics. Biogeosci Discuss 4:1059–1071

    Article  Google Scholar 

  • Money NP (2011) Mushroom. Oxford University Press, Oxford

    Book  Google Scholar 

  • Monteiro RA, Balsanelli E, Wassem R, Marin AM, Brusamarello-Santos LCC, Schmidt MA, Tadra-Sfeir MZ, Pankievicz VCS, Cruz LM, Chubatsu LS, Pedrosa FO, Souza EM (2012) Herbaspirillum-plant interactions: microscopical, histological and molecular aspects. Plant Soil 356:175–196

    Article  CAS  Google Scholar 

  • Moradi R, Nosrati R, Zare H, Tahmasebi T, Saderi H, Owlia P (2018) Screening and characterization of in-vitro probiotic criteria of Saccharomyces and Kluyveromyces strains. Iranian J Microbiol 10:123–131

    Google Scholar 

  • Moser M (1993) Fungal growth and fructification under stress conditions. Ukraine Bot J 50:5e11

    Google Scholar 

  • Mu C, Yang Y, Zhu W (2016) Gut microbiota: the brain peacekeeper. Front Microbiol 7:345

    PubMed  PubMed Central  Google Scholar 

  • Mukherjee PK, Chandra J, Retuerto M, Sikaroodi M, Brown RE, Jurevic R, Ghannoum MA (2014) Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog 10:e1003996

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mumy KL, Chen X, Kelly CP, McCormick BA (2007) Saccharomyces boulardii interferes with Shigella pathogenesis by post-invasion signaling events. Am J Physiol Gastrointest Liver Physiol 294:G599–G609

    Article  PubMed  CAS  Google Scholar 

  • Nambu M, Kouno H, Aihara-Tanaka M, Shirai H, Takatori K (2009) Detection of fungi in indoor environments and fungus-specific IgE sensitization in allergic children. World Allergy Organ J 2(9):208

    Article  PubMed  PubMed Central  Google Scholar 

  • Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC et al (2017) The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5(1):153

    Article  PubMed  PubMed Central  Google Scholar 

  • Naumann M, Schussler A, Bonfante P (2010) The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. ISME J 4:862–871

    Article  PubMed  Google Scholar 

  • Newell SY (1993) Decomposition of shoots of a saltmarsh grass: methodology and dynamics of microbial assemblages. Adv Microb Ecol 13:301–326

    Article  Google Scholar 

  • Newton AC, Fitt BDL, Atkins SD, Walters DR, Daniell TJ (2010) Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions. Trends Microbiol 18:365–373

    Article  CAS  PubMed  Google Scholar 

  • O’Brien BL, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Oldroyd GE, Downie JA (2004) Calcium, kinases and nodulation signalling in legumes. Nat Rev Mol Cell Biol 5:566–576

    Article  CAS  PubMed  Google Scholar 

  • Onofri S, Seltimann L, de Hoog GS, Grube M, Barreca D, Ruisi S, Zucconi L (2007) Evolution and adaptation of fungi at boundaries of life. Adv Space Res 40:1657–1664

    Article  Google Scholar 

  • Pagano MC, Correa EJA, Duarte NF, Yelikbayev B, O’Donovan A, Gupta VK (2017) Advances in eco-efficient agriculture: the plant-soil mycobiome. Agriculture 7:14

    Article  CAS  Google Scholar 

  • Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5(7):e177

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6:763–775

    Article  CAS  PubMed  Google Scholar 

  • Paszowski U (2006) A journey through signaling in arbuscular mycorrhizal symbioses. Tansley Rev New Phytol 172:35–46

    Article  CAS  Google Scholar 

  • Pöschl U, Martin ST, Sinha B, Chen Q, Gunthe SS, Huffman JA et al (2010) Rainforest aerosols as biogenic nuclei of clouds and precipitation in the Amazon. Science 329:1513–1516

    Article  PubMed  CAS  Google Scholar 

  • Pumplin N et al (2010) Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis. Plant J 61:482–494

    Article  CAS  PubMed  Google Scholar 

  • Riccioni C et al (2008) Tuber melanosporum outcrosses: analysis of the genetic diversity within and among its natural populations under this new scenario. New Phytol 180:466–478

    Article  CAS  PubMed  Google Scholar 

  • Rima H, Steve L, Ismail F (2012) Antimicrobial and probiotic properties of yeasts: from fundamental to novel applications. Front Microbiol 3:421

    Google Scholar 

  • Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux JP, L’Haridon F (2016) The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol 210:1033–1043

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez MM, Pérez D, Chaves FJ, Esteve E, Marin-Garcia P, Xifra G, Vendrell J, Jové M, Pamplona R, Ricart W, Portero-Otin M (2015) Obesity changes the human gut mycobiome. Sci Rep 5:14600

    Article  CAS  Google Scholar 

  • Roy M, Watthana S, Stier A, Richard F, Vessabutr S, Selosse MA (2009) Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi. BMC Biol 7:51

    Article  PubMed  PubMed Central  Google Scholar 

  • Ross AA, Neufeld JD (2015) Microbial biogeography of a university campus. Microbiome 3(1):66

    Article  PubMed  PubMed Central  Google Scholar 

  • Sapkota R, Jorgensen LN, Nicolaisen M (2017) Spatiotemporal variation and networks in the mycobiome of the wheat canopy. Front Plant Sci 8:1357

    Article  PubMed  PubMed Central  Google Scholar 

  • Schappe T, Albornoz FE, Turner BL, Neat A, Condit R, Jones AF (2017) The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests. J Ecol 105:569–579

    Article  Google Scholar 

  • Schimann H, Bach C, Lengelle J, Louisanna E, Barantal S, Murat C, Buée M (2017) Diversity and structure of fungal communities in neotropical rainforest soils: the effect of host recurrence. Microb Ecol 73:310–320

    Article  PubMed  Google Scholar 

  • Schimel JP, Bennett J (2004) Nitrogen mineralization: challenges of a changing paradigm. Ecology 85:591–602

    Article  Google Scholar 

  • Schlaeppi K, Dombrowski N, Oter RG, Van Themaat EVL, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad USA 111:585–592

    Article  CAS  Google Scholar 

  • Selosse MA, Roy M (2009) Green plants that feed on fungi: facts and questions about mixotrophy. Trends Plant Sci 14:64–70

    Article  CAS  PubMed  Google Scholar 

  • Sessitsch A, Hardoim P, Doring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, van Overbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36

    Article  CAS  PubMed  Google Scholar 

  • Severance EG, Gressitt KL, Stallings CR, Katsafanas E, Schweinfurth LA, Savage CL, Adamos MB, Sweeney KM, Origoni AE, Khushalani S et al (2016) Candida albicans exposures, sex specificity and cognitive deficits in schizophrenia and bipolar disorder. NPJ Schizophr 2:16018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shoun H, Kim DH, Uchiyama H, Sugiyama J (1992) Denitrification by fungi. FEMS Microbiol Lett 94:277–281

    Article  CAS  Google Scholar 

  • Simonato F, Campanaro S, Lauro FM, Vezzi A, D’Angelo M, Vitulo N, Valle G, Bartlett DH (2006) Piezophilic adaptation: a genomic point of view. J Biotechnol 126:11–25

    Article  CAS  PubMed  Google Scholar 

  • Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Academic, New York

    Google Scholar 

  • Sokol H, Leducq V, Aschard H, Pham HP, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I et al (2017) Fungal microbiota dysbiosis in IBD. Gut 66:1039–1048

    Article  CAS  PubMed  Google Scholar 

  • Stolze-Rybczynski JL, Cui Y, Stevens MHH, Davis DJ, Fischer MW, Money NP (2009) Adaptation of the spore discharge mechanism in the Basidiomycota. PLoS One 4:e4163

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A, De Filippo C (2017) New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome 5:24

    Article  PubMed  PubMed Central  Google Scholar 

  • Suberkropp K (1995) The influence of nutrients on fungal growth, productivity, and sporulation during leaf breakdown in streams. Can J Bot 73(Suppl. 1):S1361–S1369

    Article  Google Scholar 

  • Suda W, Nagasaki A, Shishido M (2009) Powdery mildew-infection changes bacterial community composition in the phyllosphere. Microbes Environ 24:217–223

    Article  PubMed  Google Scholar 

  • Sun S, Li S, Avera BN, Strahm BD, Badgley BD (2017) Soil bacterial and fungal communities show distinct recovery patterns during forest ecosystem restoration. Appl Environ Microbiol. https://doi.org/10.1128/AEM.00966-17

  • Sundin GW (2002) Ultraviolet radiation on leaves: its influence on microbial communities and their adaptations. In: Lindow SE, Hecht-Poinar EI, Elliott VJ (eds) Phyllosphere microbiology. APS Press, St. Paul, pp 27–42

    Google Scholar 

  • Takata K, Tomita T, Okuno T, Kinoshita M, Koda T, Honorat JA et al (2015) Dietary yeasts reduce inflammation in central nerve system via microflora. Ann Clin Transl Neurol 2(1):56–66

    Article  CAS  PubMed  Google Scholar 

  • Takeda N et al (2009) Apoplastic plant subtilases support arbuscular mycorrhiza development in Lotus japonicus. Plant J 58:766–777

    Article  CAS  PubMed  Google Scholar 

  • Talbot JM, Bruns TD, Taylor JW, Smith DP, Branco S, Glassman SI, Erlandson S, Vilgalys R, Liao HL, Smith ME, Peay KG (2014) Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci U S A 111:6341–6346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tedersoo L, Nara K (2010) General latitudinal gradient of biodiversity is reversed in ectomycorrhizal fungi. New Phytol 185:351–354

    Article  PubMed  Google Scholar 

  • Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R et al (2014) Global diversity and geography of soil fungi. Science 346:1256688

    Article  PubMed  CAS  Google Scholar 

  • Tisthammer KH, Cobian GM, Amend AS (2016) Global biogeography of marine fungi is shaped by the environment. Fungal Ecol 19:39–46

    Article  Google Scholar 

  • Tiwari S, Thakur R, Shankar J (2015) Role of heat-shock proteins in cellular function and in the biology of fungi. Biotechnol Res Int 2015:132635

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Todd JD, Curson ARJ, Dupont CL, Nicholson P, Johnston AWB (2009) The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 11:1376–1385

    Article  CAS  PubMed  Google Scholar 

  • Tong X, Leung MH, Wilkins D, Lee PK (2017) City-scale distribution and dispersal routes of mycobiome in residences. Microbiome 5(1):131

    Article  PubMed  PubMed Central  Google Scholar 

  • Treseder KK, Lennon JT (2015) Fungal traits that drive ecosystem dynamics on land. Microbiol Mol Biol Rev 79:243–262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL (2014) Evolutionary histories of soil fungi are reflected in their large scale biogeography. Ecol Lett 17:1086–1093

    Article  PubMed  Google Scholar 

  • Trojanowska D, Zwolinska-Wcislo M, Tokarczyk M, Kosowski K, Mach T, Budak A (2010) The role of Candida in inflammatory bowel disease. Estimation of transmission of C albicans fungi in gastrointestinal tract based on genetic affinity between strains. Med Sci Monitor 16(10):CR451–CR457

    CAS  Google Scholar 

  • Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Underhill DM, Iliev ID (2014) The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol 4(405):416

    Google Scholar 

  • van der Heijden MGA, Martin FM, Selosse MA, Sanders IR (2015) Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol 205:1406–1423

    Article  PubMed  CAS  Google Scholar 

  • Vandenkoornhuyse P, Quaiser A, Duhamel M, Lê Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytol 206:1196–1206

    Article  PubMed  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840

    Article  CAS  PubMed  Google Scholar 

  • Walker JF, Aldrich-Wolfe L, Riffel A, Barbare H, Simpson NB, Trowbridge J, Jumpponen A (2011) Diverse Helotiales associated with the roots of three species of Arctic Ericaceae provide no evidence for host specificity. New Phytol 191:515–527

    Article  PubMed  Google Scholar 

  • Wardle DA, Lindahl BD (2014) Disentangling global soil fungal diversity. Science 346(6213):1052–1053

    Article  CAS  PubMed  Google Scholar 

  • Webster JR, Meyer JL (1997) Stream organic matter budgets. J North Am Benth Soc 16:3–161

    Article  Google Scholar 

  • Webster J, Davey RA, Turner JCR (1989) Vapour as the source of water in Buller’s drop. Mycol Res 93:297–302

    Article  Google Scholar 

  • Webster J, Davey RA, Smirnoff N, Fricke W, Hinde P, Tomos D et al (1995) Mannitol and hexoses are components of Buller’s drop. Mycol Res 99:833–838

    Article  CAS  Google Scholar 

  • Wilkins D, Leung MHY, Lee PKH (2016) Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes. Environ Microbiol 18:1754–1763

    Article  CAS  PubMed  Google Scholar 

  • Wilkinson HH, Siegel MR, Blankenship JD, Mallory AC, Bush LP, Schardl CL (2000) Contribution of fungal loline alkaloids to protection from aphids in a grass-endophyte mutualism. Mol Plant-Microbe Int 13:1027–1033

    Article  CAS  Google Scholar 

  • Woo C, Choa A, Siyu X, Yi S-M, Yamamoto N (2018) Taxonomic diversity of fungi deposited from the atmosphere. ISME J 12:2051–2060

    Article  PubMed  PubMed Central  Google Scholar 

  • Woodward FI, Lomas MR (2004) Vegetation dynamics – simulating response to climatic change. Biol Rev Camb Philos Soc 79:643–670

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto N, Bibby K, Qian J, Hospodsky D, Rismani-Yazdi H, Nazaroff WW et al (2012) Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J 6:1801–1811

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang T, Sun H, Shen C, Chu H (2016) Fungal assemblages in different habitats in an Erman’s Birch forest. Front Microbiol 7:1368. https://doi.org/10.3389/fmicb.2016.01368

    Article  PubMed  PubMed Central  Google Scholar 

  • Yano K et al (2008) CYCLOPS, a mediator of symbiotic intracellular accommodation. Proc Natl Acad Sci 105:20540–20545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zanello G, Meurens F, Berri M, Salmon H (2009) Saccharomyces boulardii effects on gastrointestinal diseases. Curr Issues Mol Biol 11(1):47

    CAS  PubMed  Google Scholar 

  • Zhang Q, Blaylock LA, Harrison MJ (2010) Two Medicago truncatula Half-ABC transporters are essential for arbuscule development in arbuscular mycorrhizal symbiosis. Plant Cell 22:1483–1497

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zoll J, Snelders E, Verweij PE, Melchers WJC (2016) Next generation sequencing in the mycology lab. Curr Fungal Infect Rep 10:37–42

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, India

    Apekcha Bajpai & Bhavdish N. Johri

  2. School of Life Science, Gujarat Central University, Gandhinagar, Gujarat, India

    Seema Rawat

Authors
  1. Apekcha Bajpai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Seema Rawat
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bhavdish N. Johri
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Division of Biological Sciences & Engineering, Netaji Subhas University of Technology, New Delhi, Delhi, India

    Tulasi Satyanarayana

  2. Department of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, India

    Bhavdish Narain Johri

  3. Division of Molecular Microbiology, Institute of Life Sciences, Bhubaneswar, Odisha, India

    Subrata Kumar Das

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bajpai, A., Rawat, S., Johri, B.N. (2019). Fungal Diversity: Global Perspective and Ecosystem Dynamics. In: Satyanarayana, T., Johri, B., Das, S. (eds) Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications. Springer, Singapore. https://doi.org/10.1007/978-981-13-8315-1_4

Download citation

Publish with us

Policies and ethics

Search

Navigation