Agroforestry pp 645-667 | Cite as

Microbial Biodiversity in Agroforestry Systems

  • K. R. Sridhar
  • D. J. Bagyaraj


Agroforestry system is a combination of trees with crops in the same area to have optimum beneficial ecological interactions among ecosystem components. One of the major ecosystem services of agroforestry is conservation of biodiversity in each geographic location owing to the alarming rate of destruction of forests and extent of soil perturbation worldwide. Microbial biodiversity as the hub of ecosystem facilitates sustainable agroforestry to mankind by providing food, fibre and non-timber forest products. Agroforestry system is one of the hopes for progress towards sustainable developments, ecosystem services through microbial diversity and improvement of soil health. The major candidates of importance in agroforestry include symbiotic nitrogen fixers, non-symbiotic nitrogen fixers, phosphate-mobilizing organisms (mainly mycorrhizal fungi) and disease-preventing endophytic microbes. Depending on the management and health of agroforestry, the microbial diversity boost towards tripartite or multiple associations (or consortia) with plant species, which leads to sustainable developments in favour of incalculable ecosystem services. The composition of microbial diversity could be managed based on the diversity of tree species and food crops considered for practice of agroforestry system. Global coordinated efforts in evaluation of microbial biodiversity result in greater understanding, management of agroforestry systems towards sustainability and reaping the benefit of ecosystem services.


Ecosystem service Microbial mutualism Mycorrhizal fungi Nitrogen fixation Soil health Sustainable agriculture 



One of the authors (KRS) is grateful to the University Grants Commission, New Delhi, for the award of UGC-BSR Faculty Fellowship.


  1. Almeida EF, Polizel RPH, Gomes LC, Xavier FA, Mendonça ES (1997) Biomassa microbiana em sistemas agroflorestais na zona da mata mineira. Rev Bras Agroecol 2:739–742Google Scholar
  2. Altieri AA (1999) The ecological role of biodiversity in agroecosystems. Agric Ecosys Environ 74:19–31CrossRefGoogle Scholar
  3. Ambarish CN, Sridhar KR (2014) Do the giant pill-millipedes (Arthrosphaera: Sphaerotheriida) disseminate arbuscular mycorrhizal spores in the Western Ghats? Symbiosis 64:91–95CrossRefGoogle Scholar
  4. Araujo ASF, Leite LFC, Iwata BF, Lira MA, Xavier GR, Figueiredo MVB (2012) Microbiological process in agroforestry systems. A review. Agron Sustain Dev 32:215–226CrossRefGoogle Scholar
  5. Avidano L, Gamalero E, Cossa GP, Carraro E (2005) Characterization of soil health in an Italian polluted site by using microorganisms as bio-indicators. Appl Soil Ecol 30:21–33CrossRefGoogle Scholar
  6. Bagyaraj DJ (1992) Vesicular arbuscular mycorrhiza: application in agriculture. In: Norris JR, Read DJ, Verma AK (eds) Methods in microbiology, vol 24. Academic Press, London, pp 359–374Google Scholar
  7. Bagyaraj DJ (2011) Microbial biotechnology for sustainable agriculture, horticulture and forestry. New India Publishing Agency, New Delhi, p 308Google Scholar
  8. Bagyaraj DJ (2014) Mycorrhizal fungi. Proc Indian Natl Sci Acad 80:415–428CrossRefGoogle Scholar
  9. Bagyaraj DJ (2015) Status paper on arbuscular mycorrhizal fungi. In: Harsh NS, Kumar A (eds) Advances in mycorrhiza and useful microbes in forestry, ICFRE state of knowledge series 2. Greenfields Publishers, Dehra Dun, pp 21–37Google Scholar
  10. Bagyaraj DJ, Thilagar G, Ravisha C, Kushalappa CG, Krishnamurthy KN, Vaast P (2015) Below ground microbial diversity as influenced by coffee agroforestry systems in the Western Ghats, India. Agric Ecosyst Environ 202:198–202CrossRefGoogle Scholar
  11. Bai J, Zhong C (1996) Management of Casuarina plantations in China. In: Pinyopusarerk K, Turnbull JW, Midgley SJ (eds) Current research and development in Casuarinas. CSIRO Forestry and Forest Products, Canberra, pp 196–199Google Scholar
  12. Bainard LD, Klironomos JN, Gorden AM (2011) Arbuscular mycorrhizal fungi in tree-based intercropping systems: a review of their abundance and diversity. Pedobiologia 54:57–61CrossRefGoogle Scholar
  13. Baker D, Torrey JG (1979) The isolation and cultivation of actinomicetous root nodule endophytes. In: Gordon JC, Wheeler CT, Perrin DA (eds) Symbiotic nitrogen fixation in the management of temperate forest. Oregon State University, Corvallis, pp 38–56Google Scholar
  14. Balakrishna AN, Lakshmipathy R, Bagyaraj DJ, Ashwin R (2016) Influence of alley copping system on AM fungi, microbial biomass C and yield of finger millet, peanut and pigeon pea. Agrofor Syst.
  15. Barea JM (1997) Mycorrhiza/bacteria interactions on plant growth promotion. In: Ogoshi A, Kobayashi L, Homma Y, Kodama F, Kondon N, Akino S (eds) Plant growth-promoting rhizobacteria, present status and future prospects. OCDE, Paris, pp 150–158Google Scholar
  16. Barea JM, Werner D, Azcon-Guilar C, Azcon R (2005) Interactions of arbuscular mycorrhiza and nitrogen-fixing symbiosis in sustainable agriculture. In: Werner D, Newton WE (eds) Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, Dordrecht, pp 199–222CrossRefGoogle Scholar
  17. Beena KR, Raviraja NS, Arun AB, Sridhar KR (2000) Diversity of arbuscular mycorrhizal fungi on the coastal sand dunes of the west coast of India. Curr Sci 79:1459–1466Google Scholar
  18. Bethlenfalvay GJ, Brown MS, Stafford AE (1985) Glycine-glomus-rhizobium symbiosis. II. Antagonistic effects between mycorrhizal colonization and nodulation. Plant Physiol 79:1054–1058PubMedPubMedCentralCrossRefGoogle Scholar
  19. Brown MS, Bethlenfalvay GJ (1987) Glycine-glomus-rhizobium-symbiosis: photosynthesis in nodulated, mycorrhizal or N-fertilized and P-fertilized soybean plants. Plant Physiol 85:120–123PubMedPubMedCentralCrossRefGoogle Scholar
  20. Brunner I (2001) Ectomycorrhizas: their role in forest ecosystems under the impact of acidifying pollutants. Perspect Plant Ecol Evol Syst 4:13–27CrossRefGoogle Scholar
  21. Bunning S, Jimenez JJ (2003) Indicators and assessment of soil biodiversity/soil ecosystem functioning for farmers and governments. OECD expert meeting on soil erosion and biodiversity, Rome, 25–28 MarchGoogle Scholar
  22. Callaham D, Del Tredici P, Torrey JG (1978) Isolation and cultivation in vitro of the actinomycete causing root nodulation in Comptonia. Science 199:899–902PubMedCrossRefGoogle Scholar
  23. Campbell CD, Chapman SJ, Cameron CM, Davidson MS, Potts JM (2003) A rapid microtitre plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl Environ Microbiol 69:3593–3599PubMedPubMedCentralCrossRefGoogle Scholar
  24. Cardoso MI, Kuyper TW (2006) Mycorrhizas and tropical soil fertility. Agric Ecosys Environ 116:72–84CrossRefGoogle Scholar
  25. Chakraborty U, Chakraborty B, Basnet M (2006) Plant growth promotion and induction of resistance in Camellia sinensis by Bacillus megaterium. J Basic Microbiol 46:186–195PubMedCrossRefGoogle Scholar
  26. Chauhan H, Bagyaraj DJ, Selvakumar G, Sundaram SP (2015) Novel plant growth promoting rhizobacteria-prospects and potential. Appl Soil Ecol 95:38–53CrossRefGoogle Scholar
  27. Chelius MK, Triplett EW (1999) Rapid detection of arbuscular mycorrhizae in roots and soil of an intensively managed turf grass system by PCR amplification of small subunit rDNA. Soil Biol Biochem 36:1873–1883Google Scholar
  28. Chen WX, Tan ZY, Gao JL, Li Y, Wang ET (1997) Rhizobium hainanense sp. nov., isolated from tropical legumes. Int J Syst Bacteriol 47:870–873PubMedCrossRefGoogle Scholar
  29. Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199:1302–1310PubMedCrossRefGoogle Scholar
  30. De Lajudie P, Willems A, Nick G, Moreira F, Molouba F, Hoste B, Torck U, Neyra M, Collins MD, Lindström K, Dreyfus B, Gillis M (1998) Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 48:369–382PubMedCrossRefGoogle Scholar
  31. Degens BP, Harris JA (1997) Development of a physiological approach to measuring the catabolic diversity of soil microbial communities. Soil Biol Biochem 29:1309–1320CrossRefGoogle Scholar
  32. Dell B, Malajczuk N, Bougher NL, Thomson G (1994) Development and function of Pisolithus and Scleroderma ectomycorrhizas formed in vivo with Allocasuarina, Casuarina and Eucalyptus. Mycorrhiza 5:129–138CrossRefGoogle Scholar
  33. Desai S, Kumar GP, Amalraj LD, Bagyaraj DJ, Ashwin R (2016) Exploring PGPR and AMF biodiversity for plant health management. In: Singh DP, Singh HB, Prabha R (eds) Microbial inoculants in sustainable agricultural productivity. Springer, New Delhi, pp 145–160CrossRefGoogle Scholar
  34. Dinkelaker B, Hengeler C, Marschner H (1995) Distribution and function of proteoid roots and other root clusters. Bot Acta 108:183–200CrossRefGoogle Scholar
  35. Dodd JC, Arias I, Koomen I, Hayman DS (1990) The management of populations of vesicular-arbuscular mycorrhizal fungi in acid-infertile soils of a savanna ecosystem. Plant Soil 122:229–240CrossRefGoogle Scholar
  36. Doran JW, Parkins TB (1996) Quantitative indicators of soil quality: a minimum data set. In: Doran JW, Jones AJ (eds) Methods for assessing soil quality. Soil Science Society of America, Madison, pp 25–38Google Scholar
  37. Dreyfus B, Garcia JL, Gillis M (1988) Characterization of Azorhizobium caulinodans gen. Nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int J Syst Bacteriol 38:89–98CrossRefGoogle Scholar
  38. Egeston-Warburton LM, Allen EB (2000) Shifts in arbuscular mycorrhizal communities along an anthropogenic nitrogen deposition gradient. Ecol Appl 10:484–496CrossRefGoogle Scholar
  39. Egli S, Mozafar A (2001) Eine Standard method zur Erfassung des Mykkorrhiza-Infektionspotenzials in Landwirtschaftsboden. Bull Voll Bod 5:6–7Google Scholar
  40. Forster SM (1980) The role of nitrogen fixation in aggregation and stabilization of dune sand. Proc Soc Gen Microbiol 7:106pGoogle Scholar
  41. Forster SM, Nicolson TH (1981) Microbial aggregation of sand in a maritime dune succession. Soil Biol Biochem 13:205–208CrossRefGoogle Scholar
  42. Freitas ADS, Sampaio EVSB, Santos CERS, Fernandes AR (2010) Biological nitrogen fixation in tree legumes of the Brazilian semi-arid caatinga. J Arid Environ 74:344–349CrossRefGoogle Scholar
  43. Fuentes-Ramírez LE, Bustillos-Cristales R, Tapia-Hernández A, Jiménez Salgado T, Wang ET, Martínez-Romero E, Caballero-Mellado J (2001) Novel nitrogen-fixing acetic bacteria, Gluconacetobacter johannae sp. nov. and Gluconacetobacter azotocaptans sp. nov., associated with coffee plants. J Syst Evol Microbiol 51:1305–1314CrossRefGoogle Scholar
  44. Gauthier D, Diem HG, Dommergues Y (1983) Preliminary results of research on Frankia and endomycorrhizae associated with Casuarina equisetifolia. In: Midgeley SJ, Turnbull JW, Johnson RD (eds) Casuarina ecology, management and utilization. CSIRO, Melbourne, pp 211–217Google Scholar
  45. Ghate SD, Sridhar KR (2016a) Contribution to the knowledge on macrofungi in mangroves of the Southwest India. Plant Biosyst 150:977–986CrossRefGoogle Scholar
  46. Ghate SD, Sridhar KR (2016b) Spatiotemporal diversity of macrofungi in the coastal sand dunes of Southwestern India. Mycosphere 7:458–472CrossRefGoogle Scholar
  47. Ghate SD, Sridhar KR, Karun NC (2014) Macrofungi on the coastal sand dunes of South-western India. Mycosphere 5:144–151CrossRefGoogle Scholar
  48. Giller KE, Beare MH, Lavelle P, Izac AMN, Swift MJ (1997) Agricultural intensification, soil biodiversity and agro-ecosystem function. Appl Soil Ecol 6:3–16CrossRefGoogle Scholar
  49. Glick BR, Patten CL, Holguin G, Penrose DM (1999) Biochemical and genetic mechanisms used by plant growth-promoting bacteria. Imperial College Press, London, pp 134–179CrossRefGoogle Scholar
  50. Han TX, Wang ET, Wu LJ, Chen WF, Gu JG, Gu CT, Tian CF, Chen WX (2008) Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int J Syst Evol Microbiol 58:1693–1699PubMedCrossRefGoogle Scholar
  51. Harvey CA, Villalobos JAG (2007) Agroforestry systems conserve species-rich but modified assemblages of tropical birds and bats. Biodivers Conserv 16:2257–2292CrossRefGoogle Scholar
  52. Hernández-Lucas I, Segovia L, Martínez-Romero E, Pueppke SG (1995) Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L. Appl Environ Microbiol 61:2775–2779PubMedPubMedCentralGoogle Scholar
  53. Herridge DF, Peoples MB, Boddey RM (2008) Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311:1–18CrossRefGoogle Scholar
  54. Izac AMN (2003) Economic aspects of soil fertility management and agroforestry practices. In: Schroth G, Sinclair F (eds) Trees crops and soil fertility: concepts and research methods. CABI, Wallingford, pp 13–37Google Scholar
  55. Jadhav BB, Gaynar DG (1995) Effect of Casuarina equisetifolia leaf litter leachates on germination and seedling growth of rice and cowpea. Allelopathy J 2:105–108Google Scholar
  56. Jesus EDC, Marsh TL, Tiedje JM, Moreira FMDS (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3:1004–1011CrossRefGoogle Scholar
  57. Jose S (2009) Agroforestry for ecosystem services and environmental benefits: an overview. Agrofor Syst 76:1–10CrossRefGoogle Scholar
  58. Kandeler E, Böhm KE (1996) Temporal dynamics of microbial biomass, xylanase activity, N-mineralization and potential nitrification in different tillage systems. Appl Soil Ecol 5:221–230Google Scholar
  59. Karun NC, Sridhar KR (2014) A preliminary study on macrofungal diversity in an arboretum and three plantations of the southwest coast of India. Curr Res Environ Appl Mycol 4:173–187CrossRefGoogle Scholar
  60. Karun NC, Sridhar KR (2016) Spatial and temporal diversity of macrofungi in the Western Ghats forests of India. Appl Ecol Environ Res 14:1–21CrossRefGoogle Scholar
  61. Kaur B, Gupta SR, Singh G (2000) Soil carbon, microbial activity and nitrogen availability in agroforestry systems on moderately alkaline soils in northern India. Appl Soil Ecol 15:283–294CrossRefGoogle Scholar
  62. Kaushik N, Kumar S, Chowdhary K (2016) Endophytic fungi: potential and prospects in plant health management. In: Chowdappa P, Sharma P, Singh D, Misra AK (eds) Prospectives of plant pathology in genomic era. Today & Tomorrow’s Printers and Publishers, New Delhi, pp 357–378Google Scholar
  63. Kling M, Jakobsen I (1998) Arbuscular mycorrhiza in soil quality assessment. Ambio 27:29–34Google Scholar
  64. Kremen C (2005) Managing ecosystem services: what do we need to know about their ecology? Ecol Lett 8:468–479PubMedCrossRefGoogle Scholar
  65. Kumar S, Adholeya A (2016) Impact of land use and soil types on arbuscular mycorrhizal fungal diversity in tropical soils of India. Afr J Microbiol Res 10:1595–1606CrossRefGoogle Scholar
  66. Kumar A, Shukla A, Hashmi S, Tewari RK (2007) Effect of trees on colonization of intercrops by vesicular arbuscular mycorrhizae in agroforestry systems. Ind J Agric Sci 77:291–298Google Scholar
  67. Lacombe S, Bradley RL, Hamel C, Beaulieu C (2009) Do tree-based intercropping of power and influence: the role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning. Can J Bot 82:1016–1045Google Scholar
  68. Lakshmipathy R, Balakrishna AN, Bagyaraj DJ (2012) Abundance and diversity of AMF across a gradient of land use intensity and their seasonal variations in Nilgiri biosphere of Western Ghats, India. J Agric Sci Technol 14:903–918Google Scholar
  69. Lalonde M (1979) A simple and rapid method for the isolation and cultivation in vitro and characterization of Frankia strains from Alnus root nodules. In: Gordon JC, Wheeler CT, Perrin DA (eds) Symbiotic nitrogen fixation in the management of temperate forests. Oregon State University, Corvallis, pp 403–419Google Scholar
  70. Lalonde M, Calvert HE, Pine S (1981) Isolation and use of Frankia strains in actinorhizae formation. In: Gibson AH, Newton WE (eds) Current perspectives in nitrogen fixation. Australian Academy of Sciences, Canberra, pp 296–299Google Scholar
  71. Leary JJK, Singleton PW, Borthakur D (2004) Canopy nodulation of the endemic tree legume Acacia koa in the mesic forests of Hawaii. Ecology 85:3151–3157CrossRefGoogle Scholar
  72. Leblanc HA, McGraw RL, Nygren P, Le Roux C (2005) Neotropical legume tree Inga edulis forms N2-fixing symbiosis with fast-growing Bradyrhizobium strains. Plant Soil 275:123–133CrossRefGoogle Scholar
  73. Lemoine MC, Gollotte A, Gianinazzi-Pearson V (1995) Localization of β (1-3) Glucan in walls of the endomycorrhizal fungi Glomus mosseae (Nicol. & Gerd.) Gerd. & Trappe and Acaulospora laevis Gerd. & Trappe during colonization of host roots. New Phytol 129:97–105CrossRefGoogle Scholar
  74. León YS, Melo ED, Sato G, Johnson-Maynard J, Lugo-Pérez J (2006) Earthworm populations, microbial biomass and coffee production in different experimental agroforestry management systems in Costa Rica. Carribb J Sci 42:397–409Google Scholar
  75. Lie TA, Göktan D, Engin M, Pijenborg J, Anlarsal E (1987) Coevolution of the legume-Rhizobium association. Plant Soil 100:171–181CrossRefGoogle Scholar
  76. Lloret L, Ormeno-Orillo E, Rincón R, Martínez-Romero J, Rogel-Hernández MA, Martínez-Romero E (2007) Ensifer mexicanus sp nov.: a new species nodulating Acacia angustisima (mill.) Kuntze in Mexico. Syst Appl Microbiol 30:280–290PubMedCrossRefGoogle Scholar
  77. Loy A, Taylor MW, Bodrossy L, Wagner M (2006) Applications of nucleic acid microarrays in soil microbial ecology. In: Cooper JE, Rao JR (eds) Molecular approaches for soil, rhizosphere and plant microorganism analysis. CAB International, Wellingford, pp 18–24CrossRefGoogle Scholar
  78. Mamatha G, Bagyaraj DJ, Jaganath S (2002) Inoculation of field-established mulberry and papaya with arbuscular mycorrhizal fungi and a mycorrhiza helper bacterium. Mycorrhiza 12:313–316PubMedCrossRefGoogle Scholar
  79. Martínez L, Caballero-Mellado J, Orozco J, Martínez-Romero E (2003) Diazotrophic bacteria associated with banana (Musa spp.) Plant Soil 255:35–47CrossRefGoogle Scholar
  80. Metzker M (2005) Emerging technologies in DNA sequencing. Genome Res 15:1767–1776PubMedCrossRefGoogle Scholar
  81. Moreira FMS (2008) Nitrogen-fixing leguminosae-nodulating bacteria. In: Moreira FMS, Huising EJ, Bignell DE (eds) A handbook of tropical soil biology. Earthscan, London, pp 107–130Google Scholar
  82. Moulin L, Chen W-M, Béna G, Dreyfus B, Boivin-Masson C (2002) Rhizobia: the family is expanding. In: Finan T, O’Brian M, Layzell D, Vessey K, Newton W (eds) Nitrogen fixation: global perspectives. CAB International, Wallingford, pp 61–65Google Scholar
  83. Mungai NW, Motavalli PP, Kremer RJ, Nelson KA (2005) Spatial variation of soil enzyme activities and microbial functional diversity in temperate alley cropping systems. Biol Fertil Soils 42:129–136CrossRefGoogle Scholar
  84. Mutabaruka R, Mutabaruka C, Fernandez I (2002) Research note: diversity of arbuscular mycorrhizal fungi spores in soils of smallholder agroforestry and monocultural coffee systems in Southwestern Ethiopia. Biol Fertil Soils 44:653–659Google Scholar
  85. Nair PKR (1989) Agroforestry systems in the tropics. Kluwer, Norwell, p 148CrossRefGoogle Scholar
  86. Nambiar PTC, Rupela OP, Kumar Rao JVDK (1988) Nodulation and nitrogen fixation in groundnut (Arachis hypogaea L), chickpea (Cicer arietinum) and pigeon pea (Cajanus cajan L Mi II sp.) In: Subbarao NS (ed) Biological nitrogen fixation-recent developments. Oxford/IBH Publishing, New Delhi, pp 53–70Google Scholar
  87. Natarajan K, Senthilarasu G, Kumaresan V, Riviere T (2005) Diversity in ectomycorrhizal fungi of a dipterocarp forest in Western Ghats. Curr Sci 88:1893–1895Google Scholar
  88. Nielsen MN, Winding A (2002). Microorganisms as indicators of soil health. National Environmental Research Institute, Technical report no. 388. National Environmental Research Institute, Denmark.
  89. Nygren P, Fernández MP, Harmand J-M, Leblanc HA (2012) Symbiotic dinitrogen fixation by trees: an underestimated resource in agroforestry systems? Nutr Cycl Agroecosyst 94:123–160CrossRefGoogle Scholar
  90. Oades JM (1984) Soil organic matter and structural stability: mechanisms and implications for management. Plant Soil 76:319–337CrossRefGoogle Scholar
  91. Palma JHN, Graves AR, Bunce RGH, Burgess PJ, Filippi R, Keesman K, van Keulen H, Liagre F, Mayus M, Moreno G, Reisner Y, Herzog F (2007) Modeling environmental benefits of silvoarable agroforestry in Europe. Agric Ecosyst Environ 119:320–334CrossRefGoogle Scholar
  92. Pande M, Tarafdar JC (2004) Arbuscular mycorrhizal fungal diversity in neem based agroforestry systems in Rajasthan. Appl Soil Eco 26:233–241CrossRefGoogle Scholar
  93. Pavithra M, Sridhar KR, Greeshma AA, Karun NC (2016) Spatial and temporal heterogeneity of macrofungi in the protected forests of Southwestern India. J Agric Technol 12:105–124Google Scholar
  94. Perry DA (1994) Forest ecosystems. Johns Hopkins University Press, Baltimore, p 649Google Scholar
  95. Pinho RC, Miller RP, Aflaia SS (2012) Agroforestry and improvement of soil fertility: a view from Amazonia. Appl Environ Soil Sci.
  96. Prasad R, Mertia RS (2005) Dehydrogenase activity and VAM fungi in tree-rhizosphere of agroforestry systems in Indian arid zone. Agrofor Syst 63:219–233CrossRefGoogle Scholar
  97. Prasad R, Kumar M, Verma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant-growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 247–260Google Scholar
  98. Quispel A, Burggraff AJP (1981) Frankia the diazotrophic endophyte from actinorhizas. In: Gibson AH, Newton WE (eds) Current perspectives in nitrogen fixation. Australian Academy of Sciences, Canberra, pp 229–236Google Scholar
  99. Radhakrishnan S, Varadharajan M (2016) Status of microbial diversity in agroforestry systems in Tamil Nadu, India. J Basic Microbiol 56:662–669PubMedCrossRefGoogle Scholar
  100. Rao TA, Meher-Homji VM (1985) Strand plant communities of the Indian sub-continent. Proc Indian Acad Sci (Plant Sci) 94:505–523Google Scholar
  101. Rose SL, Trappe JM (1980) Three new endomycorrhizal Glomus spp. associated with actinorhizal shrubs. Mycotaxon 10:413–420Google Scholar
  102. Rose SL, Youngberg CF (1981) Tripartite associations in snowbrush (Ceanothus velutinus): effect of vesicular-arbuscular mycorrhizae on growth, nodulation and nitrogen fixation. Can J Bot 59:34–39CrossRefGoogle Scholar
  103. Ruiz-Lozano JM, Collados C, Barea JM, Azcón R (2001) Arbuscular mycorrhizal symbiosis can alleviate drought-induced nodule senescence in soybean plants. New Phytol 151:493–502CrossRefGoogle Scholar
  104. Russo RO (2005) Nitrogen fixing trees with actinorhiza in forestry and agroforestry. In: Werner D, Newton WE (eds) Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, Dordrecht, pp 143–171CrossRefGoogle Scholar
  105. Saucedo-García A, Anaya AL, Espinosa-García FJ, González MC (2014) Diversity and communities of foliar endophytic fungi from different agroecosystems of Coffea arabica L. in two regions of Veracruz, Mexico. PLoS One 9:e98454PubMedPubMedCentralCrossRefGoogle Scholar
  106. Selim KA, El-Beih AA, Abdel-Rahman TM, El-Diwany AI (2012) Biology of endophytic fungi. Curr Res Environ Appl Mycol 2:31–82CrossRefGoogle Scholar
  107. Sharma SK, Ramesh A, Sharma MP, Joshi OP, Govaerts B, Steenwerth KL, Karlen DL (2010) Microbial community structure and diversity as indicators for evaluating soil quality. In: Lichtfouse E (ed) Biodiversity, biofuels, agroforestry and conservation agriculture. Springer, Dordrecht, pp 317–358CrossRefGoogle Scholar
  108. Shi L-L, Mortimer PE, Silk JWF, Zou X-M, Xu J, Feng W-T, Qiao L (2014) Variation in forest soil fungal diversity along a latitudinal gradient. Fungal Divers 64:305–315CrossRefGoogle Scholar
  109. Shukla A, Kumar A, Jha A, Tripathi VD (2010) The effect of soil moisture on growth and arbuscular mycorrhizal colonization of crops and tree seedlings in alfisol. Indian Phytopathol 63:411–417Google Scholar
  110. Silva IF, Neto SEA, Kusdra JF (2014) Biological activity of soils under systems of organic farming, agroforestry and pasture in the Amazon. Rev Ciĉnc Agron 45:427–432CrossRefGoogle Scholar
  111. Singer R, Gomez LD (1984) The basidiomycetes of Costa Rica. III. The genus Phylloporus (Boletaceae). Brenesia 22:163–181Google Scholar
  112. Sørensen J, Sessitsch A (2007) Plant-associated bacterial-lifestyle and molecular interactions. In: Van Elsas JD, Jansson JK, Trevors JT (eds) Modern soil microbiology. CRC, New York, pp 221–236Google Scholar
  113. Sprent JI (2002) Nodulation in legumes. Ann Bot 89:797–798CrossRefGoogle Scholar
  114. Sprent JI (2005) Nodulated legume trees. In: Werner D, Newton WE (eds) Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, Dordrecht, pp 113–141CrossRefGoogle Scholar
  115. Sprent JI (2009) Legume nodulation, a global perspective. Wiley-Blackwell, Oxford, p 181CrossRefGoogle Scholar
  116. Sridhar KR (2009) Fungi in the tree canopy – an appraisal. In: Rai M, Bridge P (eds) Applied mycology. CAB International, Wallingford, pp 73–91CrossRefGoogle Scholar
  117. Sridhar KR (2012) Aspect and prospect of endophytic fungi. In: Sati SC, Belwal M (eds) Microbes: diversity and biotechnology. Daya Publishing House, New Delhi, pp 43–62Google Scholar
  118. Sridhar KR (2016) Mycorrhizal fungi in restoration of coastal forests. In: Bagyaraj DJ, Jamaluddin (eds) Microbes for restoration of degraded ecosystems. New India Publishing Agency, New Delhi, pp 317–334Google Scholar
  119. Sridhar KR, Roy S, Sudheep NM (2011) Assemblage and diversity of arbuscular mycorrhizal fungi in mangrove plant species of the southwest coast of India. In: Metras JN (ed) Mangroves: ecology, biology and taxonomy. Nova Science Publishers, New York, pp 257–274Google Scholar
  120. Sturmer SL (2012) A history of the taxonomy and systematics of arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota. Mycorrhiza 22:247–258PubMedCrossRefGoogle Scholar
  121. Sulzbacher MA, Giachini AJ, Grebenc T, Silva BDB, Gurgel FE, Loiola MIB, Neves MA, Baseia IG (2013) A survey of an ectotrophic sand dune forest in the northeast Brazil. Mycosphere 4:1106–1116CrossRefGoogle Scholar
  122. Taylor MW, Loy A, Wagner M (2007) Microarrays for studying the composition and function of microbial communities. In: Seviour RJ, Blackall LL (eds) The microbiology of activated sludge. IWA Publishing, London, pp 397–411Google Scholar
  123. Tian Y, Cao F, Wang G, Zhang W, Yu W (2012) Soil microbiological properties and enzyme activities in ginkgo-tea agroforestry compared to monoculture. For Res 1:1–6Google Scholar
  124. Varma A, Verma S, Sudha, Sahay N, Bütehorn B, Franken P (1999) Piriformospora indica, a cultivable plant-growth-promoting root endophyte. Appl Environ Microbiol 65:2741–2744PubMedPubMedCentralGoogle Scholar
  125. Wang FQ, Wang ET, Lui J, Chen Q, Sui XH, Chen WF, Chen WX (2007) Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int J Syst Evol Microbiol 57:1192–1199PubMedCrossRefGoogle Scholar
  126. Warcup JH (1980) Ectomycorrhizal associations of Australian indigenous plants. New Phytol 85:531–535CrossRefGoogle Scholar
  127. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA (2002) High density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68:2535–2541PubMedPubMedCentralCrossRefGoogle Scholar
  128. Wirth SJ, Wolf GA (1992) Microplate colorimetric assay for endo-acting cellulase, xylanase, chitinase, 1, 3-beta-glucanase and amylase extracted from forest soil horizons. Soil Biol Biochem 24:511–519CrossRefGoogle Scholar
  129. Wolde-Meskel E, Terefework Z, Frostegård A, Lindström K (2005) Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 55:1439–1452PubMedCrossRefGoogle Scholar
  130. Yao MK, Tweddell RJ, Desilets H (2002) Effect of two vesicular-arbuscular mycorrhizal fungi on the growth of micropropagated potato plantlets and on the extent of disease caused by Rhizoctonia solani. Mycorrhiza 12:235–242PubMedCrossRefGoogle Scholar
  131. Zelles L (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterization of microbial communities in soil: a review. Biol Fertil Soil 29:111–129CrossRefGoogle Scholar
  132. Zhang X, Harper R, Karsisto M, Lindström K (1991) Diversity of Rhizobium bacteria isolated from the root nodules of leguminous trees. Int J Syst Bacteriol 41:104–113CrossRefGoogle Scholar
  133. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294PubMedCrossRefGoogle Scholar
  134. Zomer RJ, Trabucco A, Coe R, Place F (2009) Trees on farm: analysis of global extent and geographical patterns of agroforestry. ICRAF working paper # 89. World Agroforestry Centre, Nairobi, Kenya, pp 72Google Scholar

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© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  1. 1.Department of BiosciencesMangalore UniversityMangaloreIndia
  2. 2.Centre for Natural Biological Resources and Community DevelopmentBangaloreIndia

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