Tree Ecosystem: Microbial Dynamics and Functionality

  • Samiksha Joshi
  • Manvika Sahgal
  • Salil K. Tewari
  • Bhavdish N. Johri


Trees constitute a dominant component of the agroforestry ecosystem. The forests are dynamic ecological reservoirs. Microbial dynamics in a forest are usually governed by the fires, insect outbreaks, climatic or seasonal variations, and anthropogenic activities occurring across tens to thousands of years. Microbial ecological studies revealed that microbe species are important drivers of various processes taking place in forests as well as respond to these changes. Microbial dynamic studies have been undertaken in temperate and boreal forests, whereas tropical forests are yet to be explored and characterized. Still there is a lack of information and knowledge in this area. The description of the microbial communities is incomplete or biased. Also, scanty information is available on ectomycorrhiza (ECM) and saprophytic wood-decomposing fungi. The microbial taxa actively participating in forest ecosystem services have not yet identified. This chapter describes intensive studies that have been carried out on microbial activity; their interactions with trees and other forest biota are required.


Microbial communities Forests Ectomycorrhiza Decomposing fungi Ecosystem services 



The authors would like to thank the financial assistance provided by ICAR and GOI. They also want to thank the State Forest Department of Tanakpur and Lachiwala range in Uttarakhand for allowing the sampling of natural sisso forests.


  1. Adams AS, Jordan MS, Adams SM (2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. Int Soc Microb Ecol 5:1323–1331Google Scholar
  2. Arnstadt T, Hoppe B, Kahl T et al (2016) Dynamics of fungal community composition, decomposition and resulting deadwood properties in logs of Fagus sylvatica, Picea abies and Pinus sylvestris. Forest Ecol and Manag 382:129–142CrossRefGoogle Scholar
  3. Ashton MS, Tyrrell ML, Spalding D, Gentry B (eds) (2012) Managing forest carbon in a changing climate. Springer Netherlands. Accessed on 29 Jan 2019Google Scholar
  4. Augusto L, Ranger J, Binkley D et al (2002) Impact of several common tree species of European temperate forests on soil fertility. Ann Forest Sci 59(3):233–253CrossRefGoogle Scholar
  5. Augusto L, De Schrijver A, Vesterdal L et al (2015) Influences of evergreen gymnosperm and deciduous angiosperm tree species on the functioning of temperate and boreal forests. Biol Rev 90(2):444–466PubMedCrossRefGoogle Scholar
  6. Bai Y, Eijsink VG, Kielak AM et al (2016) Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 18(1):38–49PubMedCrossRefGoogle Scholar
  7. Bailey BA, Bae H, Strem MD et al (2006) Fungal and plant gene expression during the colonization of cacao seedlings by endophytic isolates of four Trichoderma species. Planta 224(6):1449–1464PubMedCrossRefGoogle Scholar
  8. Bailey BA, Bae H, Strem MD et al (2008) Antibiosis, mycoparasitism, and colonization success for endophytic Trichoderma isolates with biological control potential in Theobroma cacao. Biol Control 46(1):24–35CrossRefGoogle Scholar
  9. Bakker MG, Otto-Hanson L, Lange AJ et al (2013) Plant monocultures produce more antagonistic soil Streptomyces communities than high-diversity plant communities. Soil Biol Biochem 65:304–312CrossRefGoogle Scholar
  10. Bal A, Anand R, Berge O et al (2012) Isolation and identification of diazotrophic bacteria from internal tissues of Pinuscontorta and Thujaplicata. Can J of For Res 42(4):807–813CrossRefGoogle Scholar
  11. Baldrian P (2008) Wood-inhabiting ligninolytic basidiomycetes in soils: ecology and constraints for applicability in bioremediation. Fungal Ecol 1(1):4–12CrossRefGoogle Scholar
  12. Baldrian P, Kolarik M, Stursova M et al (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. Int Soci Microb Ecol J 6(2):248–258Google Scholar
  13. Baldrian P, Snajdr J, Merhautova V et al (2013) Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change. Soil Biol Biochem 56:60–68CrossRefGoogle Scholar
  14. Baldrian P, Zrustova P, Tlaskal V et al (2016) Fungi associated with decomposing deadwood in a natural beech-dominated forest. Fungal Ecol 23:109–122CrossRefGoogle Scholar
  15. Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nat 515(7528):505CrossRefGoogle Scholar
  16. Barengo N, Sieber TN, Holdenrieder O (2000) Diversity of endophytic mycobiota in leaves and twigs of pubescent birch (Betula pubescens). Sydowia 52(2):305–320Google Scholar
  17. Barlocher F, Boddy L (2016) Aquatic fungal ecol—how does it differ from terrestrial? Fungal Ecol 19:5–13CrossRefGoogle Scholar
  18. Bartossek R, Nicol GW, Lanzen A et al (2010) Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiol 12(4):1075–1088PubMedCrossRefGoogle Scholar
  19. Bawa KS, Kress WJ, Nadkarni NM, Lele S, Raven PH, Janzen DH et al (2004) Tropical ecosystems into the 21st century. Science 306(5694):227–228PubMedCrossRefGoogle Scholar
  20. Bebber DP, Watkinson SC, Boddy L et al (2011) Simulated nitrogen deposition affects wood decomposition by cord-forming fungi. Oecol 167(4):1177–1184CrossRefGoogle Scholar
  21. Beck A, Persoh D, Rambold G (2014) First evidence for seasonal fluctuations in lichen-and bark-colonising fungal communities. Folia Microbiol 59(2):155–157CrossRefGoogle Scholar
  22. Beier S, Bertilsson S (2013) Bacterial chitin degradation—mechanisms and ecophysiological strategies. Front Microbiol 4:149PubMedPubMedCentralCrossRefGoogle Scholar
  23. Berlemont R, Martiny AC (2015) Genomic potential for polysaccharide deconstruction in bacteria. Appl Environ Microbiol 81(4):1513–1519PubMedPubMedCentralCrossRefGoogle Scholar
  24. Berthrong S, Yeager CM, Gallegos-Graves L et al (2014) Nitrogen fertilization has a stronger effect on soil N-fixing bacterial communities than elevated atmospheric CO2. Appl Environ Microbiol 80(10):3103–3112PubMedPubMedCentralCrossRefGoogle Scholar
  25. Bhadra B, Rao RS, Singh PK (2008) Yeasts and yeast-like fungi associated with tree bark: diversity and identification of yeasts producing extracellular endoxylanases. Curr Microbiol 56:489–494PubMedCrossRefGoogle Scholar
  26. Bills GF, Polishook JD (1991) Microfungi from Carpinus caroliniana. Can J Bot 69(7):1477–1482CrossRefGoogle Scholar
  27. Bisht R, Chaturvedi S, Srivastava R et al (2009) Effect of arbuscular mycorrhizal fungi, Pseudomonas fluorescens and Rhizobium leguminosarum on the growth and nutrient status of Dalbergia sissoo Roxb. Tropical Ecol 50(2):231Google Scholar
  28. Boddey RM, Döbereiner J (1995) Nitrogen fixation associated with grasses and cereals: recent progress and perspectives for the future. In: Nitrogen economy in tropical soils. Springer, Dordrecht, pp 241–250CrossRefGoogle Scholar
  29. Boddy L (1992) Microenvironmental aspects of xylem defenses to wood decay fungi. In: Defense mechanisms of woody plants against fungi. Springer, Berlin/Heidelberg, pp 96–132CrossRefGoogle Scholar
  30. Boddy L, Rayner ADM (1983) Ecological roles of basidiomycetes forming decay communities in attached oak branches. New Phytol 93(1):77–88CrossRefGoogle Scholar
  31. Bohannan BJ, Hughes J (2003) New approaches to analyzing microbial biodiversity data. Curr Opin Microbiol 6(3):282–287PubMedCrossRefGoogle Scholar
  32. Bonito G, Reynolds H, Robeson MS (2014) Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol 23(13):3356–3370PubMedCrossRefGoogle Scholar
  33. Bowers RM, McLetchie S, Knight R (2011) Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. Int Soc Microb Ecol J 5:601–612Google Scholar
  34. Brabcová V, Nováková M, Davidová A, Baldrian P (2016) Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community. New Phytologist 210(4):1369–1381PubMedCrossRefGoogle Scholar
  35. Bragina A, Berg C, Berg G (2015) The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity. Mol Ecol 24:4795–4807PubMedCrossRefGoogle Scholar
  36. Bravo-Velasquez E, Hedger J (1988) The effect of ecological disturbance on competition between Crinipellis perniciosa and other tropical fungi. Proc R Soc Edinburgh, Sect B Biol Sci 94:159–166CrossRefGoogle Scholar
  37. Brzostek ER, Greco A, Drake JE et al (2013) Root carbon inputs to the rhizosphere stimulate extracellular enzyme activity and increase nitrogen availability in temperate forest soils. Biogeochem 115(1-3):65–76CrossRefGoogle Scholar
  38. Buckeridge KM, Grogan P (2010) Deepened snow increases late thaw biogeochemical pulses in mesic low arctic tundra. Biogeochem 101(1-3):105–121CrossRefGoogle Scholar
  39. Buée M, Vairelles D, Garbaye J (2005) Year-round monitoring of diversity and potential metabolic activity of the ectomycorrhizal community in a beech (Fagus silvatica) forest subjected to two thinning regimes. Mycorrhiza 15(4):235–245PubMedCrossRefGoogle Scholar
  40. Buée M, Courty PE, Mignot D et al (2007) Soil niche effect on species diversity and catabolic activities in an ectomycorrhizal fungal community. Soil Biol Biochem 39:1947–1955CrossRefGoogle Scholar
  41. Buée M, De Boer W, Martin F et al (2009) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321(1-2):189–212CrossRefGoogle Scholar
  42. Buée M, Maurice JP, Zeller B et al (2011) Influence of tree species on richness and diversity of epigeous fungal communities in a French temperate forest stand. Fungal Ecol 4:22–31CrossRefGoogle Scholar
  43. Büntgen U, Tegel W, Egli S et al (2011) Truffles and climate change. Front Ecol Env 9(3):150–151CrossRefGoogle Scholar
  44. Cabello P, Roldan MD, Moreno-Vivian C (2004) Nitrate reduction and the nitrogen cycle in archaea. Microbiology 150(11):3527–3546PubMedCrossRefPubMedCentralGoogle Scholar
  45. Carrell AA, Frank C (2015) Bacterial endophyte communities in the foliage of coast redwood and giant sequoia Front Microbiol;6:1008Google Scholar
  46. Carroll G (1995) Forest endophytes: pattern and process. Can J Bot 73(S1):1316–1324CrossRefGoogle Scholar
  47. Carroll GC, Carroll FE (1978) Studies on the incidence of coniferous needle endophytes in the Pacific Northwest. Can J Bot 56(24):3034–3043CrossRefGoogle Scholar
  48. Chao A (1984) Nonparametric estimation of the number of classes in a population Scandinavian. J Stat:265–270Google Scholar
  49. Chazdon RL, Colwell RK, Denslow JS et al (1998) Statistical methods for estimating species richness of woody regeneration in primary and secondary rain forests of northeastern Costa Rica. No Man Biosph 20:285–309Google Scholar
  50. Chen Y, Wen X, Sun Y et al (2014) Mulching practices altered soil bacterial community structure and improved orchard productivity and apple quality after five growing seasons. Sci Hort 172:248–257CrossRefGoogle Scholar
  51. Churchland C, Grayston SJ (2014) Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling. Front Microbiol 5:261PubMedPubMedCentralCrossRefGoogle Scholar
  52. Clay K (1988) Fungal endophytes of grasses: a defensive mutualism between plants and fungi. Ecol 69(1):10–16CrossRefGoogle Scholar
  53. Clemmensen KE, Bahr A, Ovaskainen O et al (2013) Roots and associated fungi drive long-term carbon sequestration in boreal forest. Sci 339(6127):1615–1618CrossRefGoogle Scholar
  54. Cleveland CC, Townsend AR, Schimel DS (1999) Global patterns of terrestrial biological nitrogen (N2) fixation in natural ecosystems. Global Biogeochem Cy 13(2):623–645CrossRefGoogle Scholar
  55. Clissmann F, Fiore-Donno AM, Hoppe B, Krüger D, Kahl T, Unterseher M, Schnittler M (2015) First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs. FEMS Microbiol Ecol 91(6)Google Scholar
  56. Cobb RC, Filipe JA, Meentemeyer RK et al (2012) Ecosystem transformation by emerging infectious disease: loss of large tanoak from California forests. J Ecol 100(3):712–722CrossRefGoogle Scholar
  57. Coince A, Cordier T, Lengellé J (2014) Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns. PloS One 9(6):e100668PubMedPubMedCentralCrossRefGoogle Scholar
  58. Colagiero M, Pentimone I, Rosso LC et al (2017) A metagenomic study on the effect of aboveground plant cover on soil bacterial diversity. In: Soil biological communities and ecosystem resilience. Springer, Cham, pp 97–106CrossRefGoogle Scholar
  59. Collignon C, Calvaruso C, Turpault MP (2011) Temporal dynamics of exchangeable K, Ca and Mg in acidic bulk soil and rhizosphere under Norway spruce (Piceaabies abies Karst) and beech (Fagus sylvatica L) stands. Plant and Soil 349(1-2):355–366CrossRefGoogle Scholar
  60. Colliver BB, Stephenson T (2000) Production of nitrogen oxide and dinitrogen oxide by autotrophic nitrifiers. Biotechnol Adv 18(3):219–232PubMedCrossRefGoogle Scholar
  61. Cong J, Yang Y, Liu X et al (2015) Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession. Sci Rep 5:10007PubMedPubMedCentralCrossRefGoogle Scholar
  62. Corneo PE, Pellegrini A, Cappellin L et al (2013) Microbial community structure in vineyard soils across altitudinal gradients and in different seasons. FEMS Microbiol Ecol 84(3):588–602PubMedCrossRefGoogle Scholar
  63. Courty PE, Franc A, Pierrat JC et al (2008) Temporal changes in the ectomycorrhizal community in two soil horizons of a temperate oak forest. Appl Environ Microbiol 74(18):5792–5801PubMedPubMedCentralCrossRefGoogle Scholar
  64. Da Silva MF, Carreira LMM, Tavares AS, Ribeiro IC, Jardim MAG, Lobo MDAGA, Oliveira J (1989) As leguminosas da Amazo#nia Brasileira-Lista Pre$via Acta Bota [nica]. Anais do XXXIX Congresso Nacional de Botanica 2:193–237Google Scholar
  65. Davey ML, Heegaard E, Halvorsen R (2012) Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing. New Phytol 195:844–846PubMedCrossRefGoogle Scholar
  66. de Araujo Pereira AP, de Andrade PA, Bini D, Durrer A, Robin A, Bouillet JP, Andreote FD, Cardoso EJ (2017) Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium. PLoS One 12(7):e0180371CrossRefGoogle Scholar
  67. De Boer HJ, Kool A, Broberg A et al (2005a) Anti-fungal and anti-bacterial activity of some herbal remedies from Tanzania. J Ethnopharmacol 96(3):461–469PubMedCrossRefGoogle Scholar
  68. De Boer W, Folman LB, Summerbell RC et al (2005b) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29(4):795–811PubMedCrossRefGoogle Scholar
  69. De Gannes V, Eudoxie G, Hickey WJ (2014) Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils. PLoS One 9(2):e89568PubMedPubMedCentralCrossRefGoogle Scholar
  70. Delhomme N, Sundstrom G, Zamani N (2015) Serendipitous meta-transcriptomics: the fungal community of Norway spruce (Picea abies). PLoS One 10(9):e0139080PubMedPubMedCentralCrossRefGoogle Scholar
  71. Demanèche S, Philippot L, David MM et al (2009) Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach. Appl Environ Microbiol 75(2):534–537PubMedCrossRefPubMedCentralGoogle Scholar
  72. Devi NB, Yadava PS (2006) Seasonal dynamics in soil microbial biomass C, N and P in a mixed-oak forest ecosystem of Manipur, North-east India. App Soil Ecol 31(3):220–227CrossRefGoogle Scholar
  73. Domke GM, Perry CH, Walters BF et al (2016) Estimating litter carbon stocks on forest land in the United States. Sci Total Environ 557:469–478PubMedCrossRefPubMedCentralGoogle Scholar
  74. Dupuy B, Diahuissie A, Doumbia F et al (1997) Effet de deux types d’éclaircie en foret dense ivoirienne. Bois Forets Des Tropiques 253:5–19Google Scholar
  75. Edwards M, Johns DG, Licandro P et al (2006) Ecological status report: results from the CPR survey 2004/2005. SAHFOS Tech Rep (3):1–8Google Scholar
  76. Edwards AC, Scalenghe R, Freppaz M (2007) Changes in the seasonal snow cover of alpine regions and its effect on soil processes. Quat Int 162:172–181CrossRefGoogle Scholar
  77. Eichlerová I, Homolka L, Žifčáková L, Lisá L, Dobiášová P, Baldrian P (2015) Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. Fungal Ecol 13:10–22CrossRefGoogle Scholar
  78. Ekblad A, Wallander H, Godbold DL et al (2013) The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling. Plant Soil 366(1-2):1–27CrossRefGoogle Scholar
  79. El Komy MH, Saleh AA, Eranthodi A, Molan YY (2015) Characterization of novel Trichoderma asperellum isolates to select effective biocontrol agents against tomato Fusarium wilt. Plant Pathol J 31:50–60PubMedCrossRefGoogle Scholar
  80. Esson KC, Lin X, Kumaresan D et al (2016) Alpha and gamma proteobacterial methanotrophs co-dominate the active methane oxidizing communities in an acidic boreal peat bog. Appl Environ Microbiol. 82:2363–2371PubMedPubMedCentralCrossRefGoogle Scholar
  81. Fierer N, Jackson RB (2006) The diversity and Biogeogr of soil bacterial communities. Proc Natl Acad Sci 103(3):626–631PubMedCrossRefGoogle Scholar
  82. Folman LB, Klein Gunnewiek PJ, Boddy L et al (2008) Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil. FEMS Microbiol Ecol 63(2):181–191PubMedCrossRefGoogle Scholar
  83. Foster NW, Bhatti JS (2006) Forest ecosystems: nutrient cycling Encyclopedia of soil science. Taylor Francis Group, New York, pp 718–721Google Scholar
  84. Founoune H, Duponnois R, Ba AM et al (2002) Influence of the dual arbuscular endomycorrhizal/ectomycorrhizal symbiosis on the growth of Acacia holosericea (A. Cunn. ex G. Don) in glasshouse conditions. Ann Forest Sci 59(1):93–98CrossRefGoogle Scholar
  85. Fransson P, Andersson A, Norström S et al (2016) Ectomycorrhizal exudates and pre-exposure to elevated CO2 affects soil bacterial growth and community structure. Fungal Ecol 20:211–224CrossRefGoogle Scholar
  86. Frey SD, Drijber R, Smith H et al (2008) Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biol Biochem 40(11):2904–2907CrossRefGoogle Scholar
  87. Frey B, Niklaus PA, Kremer J et al (2011) Heavy machinery traffic impacts methane emission, abundance of methanogens and community structure in oxic forest soils. Appl Environ Microbiol 77:6060–6068PubMedPubMedCentralCrossRefGoogle Scholar
  88. Fukami T, Dickie IA, Paula W et al (2010) Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol Lett 13(6):675–684PubMedCrossRefGoogle Scholar
  89. Gaby JC, Buckley DH (2011) A global census of nitrogenase diversity. Environ Microbiol 13(7):1790–1799PubMedCrossRefPubMedCentralGoogle Scholar
  90. Galloway JN, Dentener FJ, Capone DG (2004) Nitrogen cycles: past, present, and future. Biogeochemistry 70(2):153–226CrossRefGoogle Scholar
  91. García-Fraile P, Menéndez E, Rivas R (2015) Role of bacterial biofertilizers in agriculture and forestry. Bioengineering 2:183–205CrossRefGoogle Scholar
  92. Gennaro M, Gonthier P, Nicolotti G (2003) Fungal endophytic communities in healthy and declining Quercus robur L and Q. cerris L trees in northern Italy. J Phytopathol 151(10):529–534CrossRefGoogle Scholar
  93. Gibson L, Lee TM, Koh LP et al (2011) Primary forests are irreplaceable for sustaining tropical biodiversity. Nat 478:378–381CrossRefGoogle Scholar
  94. Giordano L, Gonthier P, Varese GC (2009) Mycobiota inhabiting sapwood of healthy and declining Scots pine (Pinus sylvestris L) trees in the Alps. Fungal Divers 38:69–83Google Scholar
  95. Goldmann K, Schöning I, Buscot F (2015) Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems. Front Microbiol 6:1300PubMedPubMedCentralCrossRefGoogle Scholar
  96. Grayston SJ, Griffith GS, Mawdsley JL et al (2001) Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem 33(4-5):533–551CrossRefGoogle Scholar
  97. Grube M, Cernava T, Soh J et al (2015) Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. Int Soci Microb Ecol J 9:412–424Google Scholar
  98. Grünig CR, Duò A, Sieber TN (2006) Population genetic analysis of Phialocephala fortinii sl and Acephala applanata in two undisturbed forests in Switzerland and evidence for new cryptic species. Fungal Genet Biol 43(6):410–421PubMedCrossRefGoogle Scholar
  99. Grünig CR, Queloz V, Sieber TN et al (2008) Dark septate endophytes (DSE) of the Phialocephala fortinii slAcephala applanata species complex in tree roots: classification, population biology, and ecology. Botany 86(12):1355–1369CrossRefGoogle Scholar
  100. Hacquard S, Schadt CW (2015) Towards a holistic understanding of the beneficial interactions across the Populus microbiome. New Phytol 205(4):1424–1430PubMedCrossRefGoogle Scholar
  101. Haichar ZF, Marol C, Berge O et al (2008) Plant host habitat and root exudates shape soil bacterial community structure. Int Soci Microb Ecol 2(12):1221Google Scholar
  102. Hammond DS (2005) Guianan forest dynamics: geomorphographic control and tropical forest change across diverging landscapes In: Hammond DS, ed. Tropical forests of the Guiana shield; ancient forests in a modern world. CABI Publishing, Wallingford, pp 343–379Google Scholar
  103. Hannula SE, Morrien E, de Hollander M et al (2017) Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. Int Soci Microb Ecol J 11(10):2294Google Scholar
  104. Hardoim PR, van Overbeek LS, Berg G (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol R 79:293–320CrossRefGoogle Scholar
  105. Hartmann M, Howes CG, VanInsberghe D et al (2012) Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests. Int Soci Microb Ecol J 6(12):2199–2218Google Scholar
  106. Hartmann M, Niklaus PA, Zimmermann S et al (2014) Resistance and resilience of the forest soil microbiome to logging-associated compaction. Int Soci Microb Ecol J 8(1):226Google Scholar
  107. Hawkes CV, Kivlin SN, Rocca JD (2011) Fungal community responses to precipitation Global Change. Biol 17(4):1637–1645Google Scholar
  108. Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95(6):641–655CrossRefGoogle Scholar
  109. Hawksworth DL (2012) Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate? Biodivers Conserv 21(9):2425–2433CrossRefGoogle Scholar
  110. Hayatsu M, Tago K, Saito M (2008) Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci Plant Nutr 54(1):33–45CrossRefGoogle Scholar
  111. Hibbett DS, Ohman A, Glotzer D et al (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25(1):38–47CrossRefGoogle Scholar
  112. Hieber M, Gessner MO (2002) Contribution of stream detrivores, fungi, and bacteria to leaf breakdown based on biomass estimates. Ecol 83(4):1026–1038CrossRefGoogle Scholar
  113. Hill TC, Walsh KA, Harris JA, Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43(1):1–11PubMedCrossRefGoogle Scholar
  114. Hiscox J, Savoury M, Muller CT (2015) Priority effects during fungal community establishment in beech wood. Int Soci Microb Ecol J 9(10):2246Google Scholar
  115. Hoffland E, Kuyper TW, Wallander H (2004) The role of fungi in weathering. Front Ecol Environ 2(5):258–264CrossRefGoogle Scholar
  116. Högberg P (1986) Soil nutrient availability, root symbioses and tree species composition in tropical Africa. J Trop Ecol 2:359–372CrossRefGoogle Scholar
  117. Högberg P, Nordgren A, Buchmann N et al (2001) Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 411:789–792PubMedCrossRefGoogle Scholar
  118. Högberg MN, Briones MJ, Keel SG (2010) Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest. New Phytol 187(2):485–493PubMedCrossRefGoogle Scholar
  119. Hoppe B, Kruger D, Kahl T (2015) A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies. Sci Rep 5:9456PubMedPubMedCentralCrossRefGoogle Scholar
  120. Hottola J, Ovaskainen O, Hanski I (2009) A unified measure of the number, volume and diversity of dead trees and the response of fungal communities. J Ecol 97(6):1320–1328CrossRefGoogle Scholar
  121. Houlton BZ, Wang YP, Vitousek PM et al (2008) A unifying framework for dinitrogen fixation in the terrestrial biosphere. Nature 454(7202):327PubMedCrossRefGoogle Scholar
  122. Hughes JB, Hellmann JJ, Ricketts TH et al (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67(10):4399–4406PubMedPubMedCentralCrossRefGoogle Scholar
  123. Ingham ER (1999) The soil biology primer chapter 1. The soil foodweb. NRCS Soil Quality Institute, USDA, p 48Google Scholar
  124. Ishida TA, Nara K, Hogetsu T (2007) Host effects on ectomycorrhizal fungal communities: insight from eight host species in mixed conifer–broadleaf forests. New Phytol 174(2):430–440PubMedPubMedCentralCrossRefGoogle Scholar
  125. Izumi H, Anderson IC, Alexander IJ et al (2006) Endobacteria in some ectomycorrhiza of Scots pine (Pinus sylvestris). FEMS Microbiol Ecol 56(1):34–43PubMedCrossRefGoogle Scholar
  126. Jeanbille M, Buée M, Bach C (2016) Soil parameters drive the structure, diversity and metabolic potentials of the bacterial communities across temperate beech forest soil sequences. Microb Ecol 71(2):482–493PubMedCrossRefGoogle Scholar
  127. Johnston SR, Boddy L, Weightman AJ (2016) Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol:92–179Google Scholar
  128. Jones CM, Stres B, Rosenquist M et al (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25(9):1955–1966PubMedCrossRefGoogle Scholar
  129. Jönsson MT, Edman M, Jonsson BG (2008) Colonization and extinction patterns of wood-decaying fungi in a boreal old-growth Picea abies forest. J Ecol 96(5):1065–1075CrossRefGoogle Scholar
  130. Joshi S (2018) Rhizospheric bacterial diversity in different Dalbergia sissoo Roxb provenances PhD thesis, G.B. Pant University of Agriculture & Technology, UK, IndiaGoogle Scholar
  131. Jost L (2007) Partitioning diversity into independent alpha and beta components. Ecology 88:2427–2439PubMedCrossRefGoogle Scholar
  132. Jumpponen ARI, Trappe JM (1998) Dark septate endophytes: a review of facultative biotrophic root-colonizing fungi. New Phytol 140(2):295–310CrossRefGoogle Scholar
  133. Jung J, Yeom J, Han J et al (2012) Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils. J Microbiol 50(3):365–373PubMedCrossRefGoogle Scholar
  134. Kaiser C, Koranda M, Kitzler B et al (2010) Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil. New Phytol 187(3):843–858PubMedPubMedCentralCrossRefGoogle Scholar
  135. Kaiser C, Fuchslueger L, Koranda M et al (2011) Plants control the seasonal dynamics of microbial N cycling in a beech forest soil by belowground C allocation. Ecology 92(5):1036–1051PubMedCrossRefGoogle Scholar
  136. Kauserud H, Heegaard E, Buntgen U et al (2012) Warming-induced shift in European mushroom fruiting phenology. Proc Natl Acad Sci 109:14488–14493PubMedCrossRefGoogle Scholar
  137. Kersten P, Cullen D (2007) Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 44(2):77–87PubMedCrossRefGoogle Scholar
  138. Kluber LA, Smith JE, Myrold DD (2011) Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi. Soil Biol Biochem 43(5):1042–1050CrossRefGoogle Scholar
  139. Kohler A, Kuo A, Nagy LG (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 47:410–U176CrossRefGoogle Scholar
  140. Koleff P, Gaston KJ, Lennon JJ (2003) Measuring beta diversity for presence–absence data. J Anim Ecol 72(3):367–382CrossRefGoogle Scholar
  141. Korkama T, Fritze H, Pakkanen A et al (2007) Interactions between extraradical ectomycorrhizal mycelia, microbes associated with the mycelia and growth rate of Norway spruce (Picea abies) clones. New Phytol 173(4):798–807PubMedCrossRefGoogle Scholar
  142. Kostka JE, Weston DJ, Glass JB (2016) The Sphagnum microbiome: new insights from an ancient plant lineage. New Phytol 211:57–64PubMedCrossRefGoogle Scholar
  143. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55(1):485–529PubMedCrossRefGoogle Scholar
  144. Kowalski KP, Bacon C, Bickford W et al (2015) Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes. Front Microbiol 6:95PubMedPubMedCentralCrossRefGoogle Scholar
  145. Kubartova A, Ottosson E, Dahlberg A et al (2012) Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing. Mol Ecol 21(18):4514–4532PubMedCrossRefGoogle Scholar
  146. Küffer N, Senn-Irlet B (2005) Influence of forest management on the species richness and composition of wood-inhabiting basidiomycetes in Swiss forests. Biodivers Conserv 14(10):2419–2435CrossRefGoogle Scholar
  147. Kuffner M, Hai B, Rattei T et al (2012) Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol 82(3):551–562PubMedPubMedCentralCrossRefGoogle Scholar
  148. Kulhánkova A, Béguiristain T, Moukoumi J et al (2006) Spatial and temporal diversity of wood decomposer communities in different forest stands, determined by ITS rDNA targeted TGGE. Annals Forest Sci 63(5):547–556CrossRefGoogle Scholar
  149. Kuzyakov Y, Blagodatskaya E (2015) Microbial hotspots and hot moments in soil: concept & review. Soil Biol Biochem 83:184–199CrossRefGoogle Scholar
  150. Laessøe T, Lodge DJ (1994) Three host-specific Xylaria species. Mycol:436–446Google Scholar
  151. Landeweert R, Hoffland E, Finlay RD et al (2001) Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. Trends Ecol Evol 16(5):248–254PubMedCrossRefGoogle Scholar
  152. Lang C, Seven J, Polle A (2011) Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed Central European forest. Mycorrhiza 21(4):297–308PubMedCrossRefGoogle Scholar
  153. Lau MC, Stackhouse BT, Layton AC et al (2015) An active atmospheric methane sink in high Arctic mineral cryosols. Int Soci Microb Ecol J 9(8):1880Google Scholar
  154. Lauber CL, Strickland MS, Bradford MA et al (2008) The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 40(9):2407–2415CrossRefGoogle Scholar
  155. Lauber CL, Hamady M, Knight R et al (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75(15):5111–5120PubMedPubMedCentralCrossRefGoogle Scholar
  156. Laverman AM, Speksnijder AGCL, Braster M et al (2001) Spatiotemporal stability of an ammonia-oxidizing community in a nitrogen-saturated forest soil. Microb Ecol 42(1):35–45PubMedCrossRefGoogle Scholar
  157. Lazzaro A, Hilfiker D, Zeyer J (2015) Structures of microbial communities in alpine soils: seasonal and elevational effects. Front Microbiol 6:1330PubMedPubMedCentralCrossRefGoogle Scholar
  158. Lederberg J (2006) The microbe’s contribution to biology-50 years after. Int Microbiol 9(3):155PubMedGoogle Scholar
  159. Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nat 442(7104):806CrossRefGoogle Scholar
  160. Lejon DP, Chaussod R, Ranger J et al (2005) Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb Ecol 50(4):614–625PubMedCrossRefGoogle Scholar
  161. Lewis G, Schrire B, Mackinder B, Lock M (2005) Legumes of the World, Royal Botanic Gardens, Kew:p592Google Scholar
  162. Libois Q, PicardG FJL, Arnaud L et al (2013) Influence of grain shape on light penetration in snow. The Cryosphere 7(6):1803–1818CrossRefGoogle Scholar
  163. Lilleskov EA, Fahey TJ, Horton TR et al (2002) Belowground ectomycorrhizal fungal community change over a nitrogen deposition gradient in Alaska. Ecology 83(1):104–115CrossRefGoogle Scholar
  164. Lindahl BD, Tunlid A (2015) Ectomycorrhizal fungi–potential organic matter decomposers, yet not saprotrophs. New Phytol 205(4):1443–1447PubMedCrossRefGoogle Scholar
  165. Lindahl B, Stenlid JAN, Olsson S et al (1999) Translocation of 32P between interacting mycelia of a wood-decomposing fungus and ectomycorrhizal fungi in microcosm systems. New Phytol 144(1):183–193CrossRefGoogle Scholar
  166. Lindahl BD, Ihrmark K, Boberg J et al (2007) Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytol 173(3):611–620PubMedPubMedCentralCrossRefGoogle Scholar
  167. Lindahl BD, De Boer W, Finlay RD (2010) Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi. Int Soci Microb Ecol J 4(7):872Google Scholar
  168. Lindner DL, Banik MT (2011) Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycology 103(4):731–740CrossRefGoogle Scholar
  169. Lipson DA, Schmidt SK, Monson RK (1999) Links between microbial population dynamics and nitrogen availability in an alpine ecosystem. Ecol 80(5):1623–1631CrossRefGoogle Scholar
  170. Lipson DA, Schadt CW, Schmidt SK (2002) Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt. Microb Ecol 43(3):307–314PubMedCrossRefPubMedCentralGoogle Scholar
  171. Lladó S, Zifcakova L, Vetrovsky T et al (2016) Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition. Biol Fert Soils 52(2):251–260CrossRefGoogle Scholar
  172. Lladó S, López-Mondéjar R, Baldrian P (2017) Forest soil Bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol Mol Biol Rev 81(2)Google Scholar
  173. Long X, Chen C, Xu Z et al (2012) Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO2. Soil Biol Biochem 46:163–171CrossRefGoogle Scholar
  174. López-Bucio J, Pelagio-Flores R, Herrera-Estrell A (2015) Trichoderma as biostimulant: exploiting the multilevel properties of a plant beneficial fungus. Sci. Hortic. 196:109–123CrossRefGoogle Scholar
  175. Lopez-Mondejar R, Voriskova J, Vetrovsky T et al (2015) The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics. Soil Biol Biochem 87:43–50CrossRefGoogle Scholar
  176. López-Mondejar R, Zühlke D, Becher D et al (2016) Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 6:25279PubMedPubMedCentralCrossRefGoogle Scholar
  177. Lukesova T, Kohout P, Vetrovsky T (2015) The potential of dark septate endophytes to form root symbioses with ectomycorrhizal and ericoid mycorrhizal middle European forest plants. PLoS One 10:e124752CrossRefGoogle Scholar
  178. Malchair S, Carnol M (2012) AOB community structure and richness under European beech, sessile oak, Norway spruce and Douglas fir at three temperate forest sites. Plant Soil 366:521–535CrossRefGoogle Scholar
  179. Marupakula S, Mahmood S, Finlay RD (2016) Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi. Environ Microbiol 18(5):1470–1483PubMedCrossRefGoogle Scholar
  180. McLaren JR, Turkington R (2011) Plant identity influences decomposition through more than one mechanism. PLoS One 6(8)PubMedPubMedCentralCrossRefGoogle Scholar
  181. McLaughlin DJ, Hibbett DS, Lutzoni F et al (2009) The search for the fungal tree of life. Trends Microbiol 17(11):488–497PubMedCrossRefGoogle Scholar
  182. McMahon SM, Harrison SP, Armbruster WS et al (2011) Improving assessment and modelling of climate change impacts on global terrestrial biodiversity. Trends Ecol Evol 26(5):249–259PubMedCrossRefGoogle Scholar
  183. Mirza BS, Potisap C, Nüsslein K et al (2014) Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest. Appl Environ Microbiol 80(1):281–288PubMedPubMedCentralCrossRefGoogle Scholar
  184. Monson RK, Lipson DL, Burns SP et al (2006) Winter forest soil respiration controlled by climate and microbial community composition. Nat 439(7077):711CrossRefGoogle Scholar
  185. Moreira FMS, Franco AA (1994) Rhizobia-host interactions in tropical ecosystems in Brazil. In: Sprent JI, McKey D (eds) Advances in legume systematics, Part 5: the nitrogen factor, vol 5. R BotGard, Kew, pp 63–74Google Scholar
  186. Moyes AB, Kueppers LM, Pett-Ridge J et al (2016) Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer. New Phytol 210(2):657–668PubMedCrossRefPubMedCentralGoogle Scholar
  187. Müller MM, Valjakka R, Suokko A et al (2001) Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers. Mol Ecol 10(7):1801–1810PubMedCrossRefPubMedCentralGoogle Scholar
  188. Nacke H, Goldmann K, Schöning I et al (2016) Fine spatial scale variation of soil microbial communities under European beech and Norway spruce. Front Microbiol 7:2067PubMedPubMedCentralCrossRefGoogle Scholar
  189. Nazaries L, Murrell JC, Millard P et al (2013) Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol 15(9):2395–2417PubMedCrossRefPubMedCentralGoogle Scholar
  190. Newcombe G, Martin F, Kohler A (2010) Defense and nutrient mutualisms in Populus. In: Genetics and genomics of populus. Springer, New York, pp 247–277CrossRefGoogle Scholar
  191. Newton RJ, Jones SE, Eiler A et al (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol R 75:14–49CrossRefGoogle Scholar
  192. Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14(5):207–212PubMedCrossRefPubMedCentralGoogle Scholar
  193. Nitrogen Cycling Down: https://organicsoiltechnologycom/nitrogen-cycling-downhtmlGoogle Scholar
  194. Noguez AM, Arita HT, Escalante AE et al (2005) Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Global Ecol Biogeogr 14(3):241–248CrossRefGoogle Scholar
  195. Okubo T, Tsukui T, Maita H et al (2012) Complete genome sequence of Bradyrhizobium sp S23321: insights into symbiosis evolution in soil oligotrophs. Microb Environ 27(3):306–315CrossRefGoogle Scholar
  196. Öpik M, Moora M, Zobel M (2008) High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest. New Phytol 179:867–876PubMedCrossRefPubMedCentralGoogle Scholar
  197. Orellana LH, Rodriguez-R LM, Higgins S et al (2014) Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle. Mol Biol 5(3):e01193–e01114Google Scholar
  198. Osono T (2007) Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecol Res 22(6):955–974CrossRefGoogle Scholar
  199. Pajares S, Bohannan BJ (2016) Ecology of nitrogen fixing, nitrifying, and denitrifying microorganisms in tropical forest soils. Front Microbiol 7:1045PubMedPubMedCentralGoogle Scholar
  200. Parfitt D, Hunt J, Dockrell D et al (2010) Do all trees carry the seeds of their own destruction? PCR reveals numerous wood decay fungi latently present in sapwood of a wide range of angiosperm trees. Fungal Ecol 3(4):338–346CrossRefGoogle Scholar
  201. Peh KSH, Corlett RT, Bergeron Y (2015) Routledge Handbook of Forest Ecology. RoutledgeGoogle Scholar
  202. Peršoh D (2015) Plant-associated fungal communities in the light of meta’omics. Fungal Divers 75:1–25CrossRefGoogle Scholar
  203. Pester M, Rattei T, Flechl S et al (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14(2):525–539PubMedPubMedCentralCrossRefGoogle Scholar
  204. Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agro 96:249–305CrossRefGoogle Scholar
  205. Philpott TJ, Prescott CE, Chapman WK et al (2014) Nitrogen translocation and accumulation by a cord-forming fungus (Hypholomaf asciculare) into simulated woody debris. Forest Ecol Manag 315:121–128CrossRefGoogle Scholar
  206. Piri T (1996) The spreading of the S type of Heterobasidion annosum from Norway spruce stumps to the subsequent tree stand. Eur J Forest Pathol 26(4):193–204CrossRefGoogle Scholar
  207. Pons TL, Perreijn K, Van Kessel C et al (2007) Symbiotic nitrogen fixation in a tropical rainforest: 15N natural abundance measurements supported by experimental isotopic enrichment. New Phytol 173(1):154–167PubMedCrossRefGoogle Scholar
  208. Prescott CE, Grayston SJ (2013) Tree species influence on microbial communities in litter and soil: current knowledge and research needs. Forest Ecol Manag 309:19–27CrossRefGoogle Scholar
  209. Prevost-Boure NC, Maron PA, Ranjard L et al (2011) Seasonal dynamics of the bacterial community in forest soils under different quantities of leaf litter. Appl Soil Ecol 47(1):14–23CrossRefGoogle Scholar
  210. Priyanka J, Koel M (2015) Diversity study of nitrate reducing bacteria from soil samples-a metagenomics approach. J Comp Sci Syst Biol 8(4):191Google Scholar
  211. Puig H, Riera B, Lescure JP (1990) Phytomasse et productivite. Bois Forets Des Tropiques 220:25–32Google Scholar
  212. Purahong W, Hoppe B, Kahl T et al (2014) Changes within a single land-use category alter microbial diversity and community structure: Molecular evidence from wood-inhabiting fungi in forest ecosystems. J Environ Manag 139:109–119CrossRefGoogle Scholar
  213. Purahong W, Kapturska D, Pecyna MJ et al (2015) Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation. Microb Ecol 69(4):905–913PubMedCrossRefGoogle Scholar
  214. Rachid CTCC, Balieiro FC, Peixoto RS et al (2013) Mixed plantations can promote microbial integration and soil nitrate increases with changes in the N cycling genes. Soil Biol Biochem 66:146–153CrossRefGoogle Scholar
  215. Rajala T, Peltoniemi M, Pennanen T et al (2010) Relationship between wood-inhabiting fungi determined by molecular analysis (denaturing gradient gel electrophoresis) and quality of decaying logs. Can J Forest Res 40(12):2384–2397CrossRefGoogle Scholar
  216. Rajala T, Peltoniemi M, Hantula J et al (2011) RNA reveals a succession of active fungi during the decay of Norway spruce logs. Fungal Ecol 4(6):437–448CrossRefGoogle Scholar
  217. Rajala T, Peltoniemi M, Pennanen T et al (2012) Fungal community dynamics in relation to substrate quality of decaying Norway spruce (Picea abies [L] Karst) logs in boreal forests. FEMS Microbiol Ecol 81(2):494–505PubMedCrossRefGoogle Scholar
  218. Rajala T, Tuomivirta T, Pennanen T et al (2015) Habitat models of wood inhabiting fungi along a decay gradient of Norway spruce logs. Fungal Ecol 18:48–55CrossRefGoogle Scholar
  219. Rakesh M (2013) Chronic N-amended soils exhibit an altered bacterial community structure in Harvard Forest, MA, USA. FEMS Microbiol Ecol 83(2):478–493CrossRefGoogle Scholar
  220. Rasche F, Knapp D, Kaiser C et al (2011) Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. Int Soci Microb Ecol J 5(3):389Google Scholar
  221. Rayner AD, Boddy L (1988) Fungal decomposition of wood. Its biology and ecology. Wiley, New YorkGoogle Scholar
  222. Redford AJ, Bowers RM, Knight R et al (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12(11):2885–2893PubMedPubMedCentralCrossRefGoogle Scholar
  223. Reed SC, Townsend AR, Cleveland CC et al (2010) Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecol 164(2):521–531CrossRefGoogle Scholar
  224. Reed BM, Sarasan V, Kane M et al (2011) Biodiversity conservation and conservation biotechnology tools. In vitro Cell Dev Biol-Pl 47(1):1–4CrossRefGoogle Scholar
  225. Renvall P (1995) Community structure and dynamics of wood-rotting Basidiomycetes on decomposing conifer trunks in northern Finland. Karstenia 35:1–51CrossRefGoogle Scholar
  226. Riley R, Salamov AA, Brown DW et al (2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci111(27):9923-9928Google Scholar
  227. Rincón A, Pueyo JJ (2010) Effect of fire severity and site slope on diversity and structure of the ectomycorrhizal fungal community associated with post-fire regenerated Pinus pinaster Ait seedlings. Forest Ecol Manag 260(3):361–369CrossRefGoogle Scholar
  228. Rineau F, Roth D, Shah F et al (2012) The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. Environ Microbiol 14(6):1477–1487PubMedPubMedCentralCrossRefGoogle Scholar
  229. Rodrigues KF (1993) Endophytic species of Xylaria: cultural and isozymic studies. Sydowia 45:116–138Google Scholar
  230. Rodriguez RJ, White JF Jr, Arnold AE et al (2009) Fungal endophytes: diversity and functional roles. New Phytol 182(2):314–330CrossRefGoogle Scholar
  231. Rosling A, Landeweert R, Lindahl BD et al (2003) Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytol 159(3):775–783CrossRefGoogle Scholar
  232. Rossman AY, Palm-Hernández ME (2008) Systematics of plant pathogenic fungi: why it matters. Plant Dis 92(10):1376–1386PubMedCrossRefGoogle Scholar
  233. Rotthauwe JH, Witzel KP, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 63(12):4704–4712PubMedPubMedCentralGoogle Scholar
  234. Rousk J, Baath E, Brookes PC et al (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. Int Soci Microb Ecol J 4(10):1340Google Scholar
  235. Rousk J, Brookes PC, Baath E (2011) Fungal and bacterial growth responses to N fertilization and pH in the 150-year ‘Park Grass’ UK grassland experiment. FEMS Microbiol Ecol 76(1):89–99PubMedCrossRefGoogle Scholar
  236. Rytioja J, Hilden K, Yuzon J et al (2014) Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Molr Biol Rev 78(4):614–649CrossRefGoogle Scholar
  237. Sabatier D (1994) Diversité des arbres et du peuplement forestier en Guyane. Gestion de l’écosysteme forestier et aménagement de l’espace régional, pp 41–47Google Scholar
  238. Savi F, Di Bene C, Canfora L et al (2016) Environmental and biological controls on CH4 exchange over an evergreen Mediterranean forest. Agri Forest Meteorol 226:67–79CrossRefGoogle Scholar
  239. Schilling JS, Kaffenberger JT, Liew FJ et al (2015) SigNat wood modifications reveal decomposer community history. PloS one 10(3):e0120679PubMedPubMedCentralCrossRefGoogle Scholar
  240. Schloss PD, Delalibera I, Handelsman J (2006) Bacteria associated with the guts of two wood-boring beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae). Environ Entomol 35:625–629CrossRefGoogle Scholar
  241. Schmalenberger A, Duran AL, Bray AW et al (2015) Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals. Sci Rep 5:12187PubMedPubMedCentralCrossRefGoogle Scholar
  242. Schmidt SK, Lipson DA (2004) Microbial growth under the snow: implications for nutrient and allelochemical availability in temperate soils. Plant Soil 259(1–2):1–7CrossRefGoogle Scholar
  243. Schmidt O, Horn MA, Kolb S (2015) Temperature impacts differentially on the methanogenic food web of cellulose supplemented peatland soil. Environ Microbiol 17:720–734PubMedCrossRefGoogle Scholar
  244. Seibold S, Bassler C, Brandl R et al (2015) Experimental studies of dead-wood biodiversity—a review identifying global gaps in knowledge. Biol Conserv 191:139–149CrossRefGoogle Scholar
  245. Selosse MA, Vohník M, Chauvet E (2008) Out of the rivers: are some aquatic hyphomycetes plant endophytes? New Phytol 178(1):3–7PubMedCrossRefGoogle Scholar
  246. Serkebaeva YM, Kim Y, Liesack W (2013) Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a Northern Wetland, with focus on poorly studied phyla and candidate divisions. PLoS One 8:e63394CrossRefGoogle Scholar
  247. Shannon CE, Weaver W (1949) The mathematical theory of communication. Urbana: University of Illinois Press, ChampaignGoogle Scholar
  248. Shaw LJ, Nicol GW, Smith Z et al (2006) Nitrosospira spp can produce nitrous oxide via a nitrifier denitrification pathway. Environ Microbiol 8(2):214–222PubMedCrossRefGoogle Scholar
  249. Shoun H, Kim DH, Uchiyama H et al (1992) Denitrification by fungi. FEMS Microbiol Lett 94(3):277–281CrossRefGoogle Scholar
  250. Sieber TN, Rys J, Holdenrieder O (1999) Mycobiota in symptomless needles of Pinusmugo ssp uncinata. Mycol Res 103(3):306–310CrossRefGoogle Scholar
  251. Sieber-Canavesi F, Sieber TN (1993) Successional patterns of fungal communities in needles of European silver fir (Abies alba Mill). New Phytol 125(1):149–161CrossRefGoogle Scholar
  252. Simard SW, Beiler KJ, Bingham MA et al (2012) Mycorrhizal networks: mechanisms, ecology and modeling. Fungal Biol Rev 26(1):39–60CrossRefGoogle Scholar
  253. Simpson EH (1949) Measurement of diversity. Nature 163:688CrossRefGoogle Scholar
  254. Song Y, Chen D, Lu K et al (2015) Enhanced tomato disease resistance primed by arbuscular mycorrhizal fungus. Front Plant Sci 6:786PubMedPubMedCentralGoogle Scholar
  255. Sprent JL (1995) Legume trees and shrubs in the tropics N2-fixation in perspective. Soil Biol Biochem 27:401–407CrossRefGoogle Scholar
  256. Sprent JI (2005) Nodulated legume trees. In: Werner D, Newton WE (eds) Nitrogen fixation in agriculture, forestry, ecology and the environment. Springer, New York, pp 113–141Google Scholar
  257. Sprent JI (2009) Legume nodulation: global perspective. Wiley-Blackwell, OxfordGoogle Scholar
  258. Stenlid J, Penttila R, Dahlberg A (2008) Wood-decay basidiomycetes in boreal forests: distribution and community development. In: British mycological society symposia series, vol 28. Academic, pp 239–262Google Scholar
  259. Stokland JN, Siitonen J, Jonsson BG (2012) Biodiversity in dead wood Cambridge University PressGoogle Scholar
  260. Stork NE, Coddington JA, Colwell RK et al (2009) Vulnerability and resilience of tropical forest species to land-use change. Conserv Biol 23:1438–1447PubMedCrossRefGoogle Scholar
  261. Stursova M, Snajdr J, Cajthaml T (2014) When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback. Int Soci for Microb Ecol J 8:1920–1931Google Scholar
  262. Sutherland JM, and Sprent JI (1993) Nitrogen fixation by legume trees Symbiosis in Nitrogen fixing trees. 33-63Google Scholar
  263. Svensson M, Johansson V, Dahlberg A (2016) The relative importance of stand and dead wood types for wood dependent lichens in managed boreal forests. Fungal Ecol 20:166–174CrossRefGoogle Scholar
  264. Szink I, Davis EL, Ricks KD et al (2016) New evidence for broad trophic status of leaf endophytic fungi of Quercus gambelii. Fungal Ecol 22:2–9CrossRefGoogle Scholar
  265. Szukics U, Hackl E, Zechmeister-Boltenstern S et al (2012) Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils. Microbiol Res 167(2):103–109PubMedCrossRefGoogle Scholar
  266. Talbot JM, Bruns TD, Taylor JW et al (2014) Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci 111:6341–6346PubMedCrossRefGoogle Scholar
  267. Tanaka M, Nara K (2009) Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizae. FEMS Microbiol Ecol 69(3):329–343PubMedCrossRefGoogle Scholar
  268. Taylor AE, Zeglin LH, Wanzek TA et al (2012) Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials. Int Soci Microb Ecol J 6(11):2024Google Scholar
  269. Tedersoo L, Suvi T, Jairus T (2008) Forest microsite effects on community composition of ectomycorrhizal fungi on seedlings of Picea abies and Betula pendula. Environ Microbiol 10(5):1189–1201PubMedCrossRefGoogle Scholar
  270. Tedersoo L, May TW, Smith ME (2010) Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20:217–263PubMedCrossRefGoogle Scholar
  271. Tedersoo L, Bahram M, Polme S et al (2014) Global diversity and geography of soil fungi. Sci 346:1078–1087Google Scholar
  272. Tedersoo L, Bahram M, Cajthaml T et al (2016) Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. Int Soci Microb Ecol J 10(2):346–362Google Scholar
  273. Ter Steege H, Sabatier D, Castellanos H et al (2000) An analysis of the floristic composition and diversity of Amazonian forests including those of the Guiana Shield. J Tropical Ecol 16:801–828CrossRefGoogle Scholar
  274. Thomson BC, Tisserant E, Plassart P et al (2015) Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites. Soil Biol Biochem 88:403–413CrossRefGoogle Scholar
  275. Tiedje JM, Sexstone AJ, Myrold DD et al (1983) Denitrification: ecological niches, competition and survival. Anton Leeuw 48(6):569–583CrossRefGoogle Scholar
  276. Treseder KK, Lennon JT (2015) Fungal traits that drive ecosystem dynamics on land. Microbiol Mol Biol Rev 79(2):243–262PubMedPubMedCentralCrossRefGoogle Scholar
  277. Treseder KK, Vitousek PM (2001) Effects of soil nutrient availability on investment in acquisition of N and P in Hawaiian rain forests. Ecol 82(4):946–954CrossRefGoogle Scholar
  278. Treusch AH, Leininger S, Kletzin A et al (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7(12):1985–1995PubMedCrossRefGoogle Scholar
  279. Trivedi P, Trivedi C, Grinyer J (2016) Harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria. Front Plant Sci 7:1423PubMedPubMedCentralGoogle Scholar
  280. Tuomisto H (2010) A diversity of beta diversities: straightening up a concept gone awry Part 1 Defining beta diversity as a function of alpha and gamma diversity. Ecography 33:2–22CrossRefGoogle Scholar
  281. Turner BL, Yavitt JB, Harms KE et al (2013) Seasonal changes and treatment effects on soil inorganic nutrients following a decade of fertilizer addition in a lowland tropical forest. Soil Sci Soci Am J 77(4):1357–1369CrossRefGoogle Scholar
  282. Unterseher M, Reiher A, Finstermeier K et al (2007) Species richness and distribution patterns of leaf-inhabiting endophytic fungi in a temperate forest canopy. Mycol Prog 6(3):201–212CrossRefGoogle Scholar
  283. Unterseher M, Persoh D, Schnittler M (2013) Leaf-inhabiting endophytic fungi of European Beech (Fagus sylvatica L) co-occur in leaf litter but are rare on decaying wood of the same host. Fungal Divers 60(1):43–54CrossRefGoogle Scholar
  284. Urbanova M, Snajdr J, Baldrian P (2015) Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees. Soil Biol Biochem 84:53–64CrossRefGoogle Scholar
  285. Uroz S, Calvaruso C, Turpault MP et al (2009) Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 17(8):378–387PubMedCrossRefGoogle Scholar
  286. Uroz S, Oger P, Morin E et al (2012) Distinct ectomycorrhizospheres share similar bacterial communities as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 78:3020–3024PubMedPubMedCentralCrossRefGoogle Scholar
  287. Uroz S, Ioannidis P, Lengelle J et al (2013) Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. PLoS One 8(2):e55929PubMedPubMedCentralCrossRefGoogle Scholar
  288. Uroz S, Oger P, Tisserand E et al (2016) Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci Rep 6:27756PubMedPubMedCentralCrossRefGoogle Scholar
  289. Valaskova V, De Boer W, Gunnewiek PJK et al (2009) Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood. Int Soci Microb Ecol J 3(10):1218Google Scholar
  290. Van Cleve K, Chapin FS, Dyrness CT et al (1991) Element cycling in taiga forests: state-factor control. BioSci 41(2):78–88CrossRefGoogle Scholar
  291. Van Der Heijden MG, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11(3):296–310CrossRefGoogle Scholar
  292. Van der Wal A, Ottosson E, de Boer W (2015) Neglected role of fungal community composition in explaining variation in wood decay rates. Ecol 96(1):124–133CrossRefGoogle Scholar
  293. Van Dyk JS, Pletschke BI (2012) A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes factors affecting enzymes, conversion and synergy. Biotechnol Adv 30(6):1458–1480PubMedCrossRefPubMedCentralGoogle Scholar
  294. Van Insberghe D, Maas KR, Cardenas E et al (2015) Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils. Int Soci Microb Ecol J 9(11):2435Google Scholar
  295. Vik U, Logares R, Blaalid R et al (2013) Different bacterial communities in ectomycorrhizae and surrounding soil. Sci Rep 3:3471PubMedPubMedCentralCrossRefGoogle Scholar
  296. Vitousek PM, Cassman K, Cleveland C et al (2002) Towards an ecological understanding of biological nitrogen fixation. Biogeochem 57:1–45CrossRefGoogle Scholar
  297. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840PubMedCrossRefPubMedCentralGoogle Scholar
  298. Voriskova J, Baldrian P (2013) Fungal community on decomposing leaf litter undergoes rapid successional changes. Int Soci Microb Ecol J 7(3):477Google Scholar
  299. Vořiškova J, Brabcova V, Cajthaml T et al (2014) Seasonal dynamics of fungal communities in a temperate oak forest soil. New Phytol 201(1):269–278PubMedCrossRefGoogle Scholar
  300. Walker JK, Cohen H, Higgins LM et al (2014) Testing the link between community structure and function for ectomycorrhizal fungi involved in a global tripartite symbiosis. New Phytol 202(1):287–296CrossRefGoogle Scholar
  301. Wallenstein MD, Hall EK (2012) A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning. Biogeochem 109(1-3):35–47CrossRefGoogle Scholar
  302. Wang Y, Li C, Wang Q et al (2016) Environmental behaviors of phenolic acids dominated their rhizodeposition in boreal poplar plantation forest soils. J Soils Sediments 16:1858–1870CrossRefGoogle Scholar
  303. Wardle DA, Walker LR, Bardgett RD (2004) Ecosystem properties and forest decline in contrasting long-term chronosequences. Science 305(5683):509–513PubMedCrossRefGoogle Scholar
  304. Wells JM, Boddy L (1995) Phosphorus translocation by saprotrophic basidiomycete mycelial cord systems on the floor of mixed deciduous woodland. Mycol Res 99(8):977–980CrossRefGoogle Scholar
  305. Whittaker RH (1960) Vegetation of the Siskiyou mountains, Oregon and California. Ecol Monogr 30(3):279–338CrossRefGoogle Scholar
  306. Wu F, Yang W, Zhang J et al (2010) Litter decomposition in two subalpine forests during the freeze–thaw season. Acta Oecol 36(1):135–140CrossRefGoogle Scholar
  307. Wubet T, Christ S, Schoning I et al (2012) Differences in soil fungal communities between European beech (Fagus sylvatica L) dominated forests are related to soil and understory vegetation. PloS One 7(10):e47500PubMedPubMedCentralCrossRefGoogle Scholar
  308. Xia M, Talhelm AF, Pregitzer KS (2015) Fine roots are the dominant source of recalcitrant plant litter in sugar mapledominated northern hardwood forests. New Phytol 208:715–726PubMedPubMedCentralCrossRefGoogle Scholar
  309. Yahara T, Javadi F, Onoda Y et al (2013) Global legume diversity assessment: concepts, key indicators, and strategies. Taxon 62(2):249–266CrossRefGoogle Scholar
  310. Yamashita S, Hattori T, Abe H (2010) Host preference and species richness of wood-inhabiting aphyllophoraceous fungi in a cool temperate area of Japan. Mycol 102(1):11–19CrossRefGoogle Scholar
  311. Zehr JP, Jenkins BD, Short SM et al (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5(7):539–554PubMedCrossRefPubMedCentralGoogle Scholar
  312. Zhalnina K, de Quadros PD, Camargo FA et al (2012) Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol 3:210PubMedPubMedCentralCrossRefGoogle Scholar
  313. Zhou J, Deng Y, Shen L et al (2016) Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun 7:12083PubMedPubMedCentralCrossRefGoogle Scholar
  314. Žifčáková L, Dobiasova P, Kolarova Z et al (2011) Enzyme activities of fungi associated with Picea abies needles. Fungal Ecol 4(6):427–436CrossRefGoogle Scholar
  315. Žifčáková L, Vetrovsky T, Howe A (2016) Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ Microbiol 18:288–301PubMedCrossRefPubMedCentralGoogle Scholar
  316. Zinger L, Lejon DP, Baptist F et al (2011) Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS One 75:5863–5870Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Samiksha Joshi
    • 1
  • Manvika Sahgal
    • 1
  • Salil K. Tewari
    • 2
  • Bhavdish N. Johri
    • 3
  1. 1.Department of MicrobiologyG. B. Pant University of Agriculture & TechnologyPantnagarIndia
  2. 2.Department of Genetics and Plant BreedingG. B. Pant University of Agriculture & TechnologyPantnagarIndia
  3. 3.Department of BiotechnologyBarkatullah UniversityBhopalIndia

Personalised recommendations