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Barnes, Christopher James; van der Gast, Christopher J.; Burns, Caitlin A.; McNamara, Niall P.; Bending, Gary D. (2016)
Publisher: Frontiers Media
Languages: English
Types: Article
Subjects: root-associated fungi, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, soil fungi, temporal variation in microbial communities, Microbiology, mycorrhizal fungi, Original Research, QK, Biology and Microbiology, Journal Article, fungal ecology, Ecology and Environment
Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.\ud
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    • Allen, M. (1992). Mycorrhizal Functioning: An Integrative Plant-Fungal Process. Berlin: Springer Science & Business Media.
    • An, G.-H., Miyakawa, S., Kawahara, A., Osaki, M., and Ezawa, T. (2008). Community structure of arbuscular mycorrhizal fungi associated with pioneer grass species Miscanthus sinensis in acid sulfate soils: habitat segregation along pH gradients. Soil Sci. Plant Nutr. 54, 517-528. doi: 10.1111/j.1747- 0765.2008.00267.x
    • Avis, P. G., Dickie, I. A., and Mueller, G. M. (2006). A 'dirty' business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Mol. Ecol. 15, 873-882. doi: 10.1111/j.1365- 294X.2005.02842.x
    • Bahram, M., Põlme, S., Kõljalg, U., Zarre, S., and Tedersoo, L. (2012). Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran. New Phytol. 193, 465-473. doi: 10.1111/j.1469-8137.2011. 03927.x
    • Becklin, K. M., Pallo, M. L., and Galen, C. (2012). Willows indirectly reduce arbuscular mycorrhizal fungal colonization in understorey communities. J. Ecol. 100, 343-351. doi: 10.1111/j.1365-2745.2011.01903.x
    • Berendsen, R. L., Pieterse, C. M. J., and Bakker, P. A. H. M. (2012). The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478-486. doi: 10.1016/j.tplants.2012.04.001
    • Berg, G., and Smalla, K. (2009). Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68, 1-13. doi: 10.1111/j.1574-6941.2009. 00654.x
    • Bergemann, S. E., and Miller, S. L. (2002). Size, distribution, and persistence of genets in local populations of the late-stage ectomycorrhizal basidiomycete, Russula brevipes. New Phytol. 156, 313-320. doi: 10.1046/j.1469-8137.2002.00507.x
    • Blaalid, R., Carlsen, T., Kumar, S., Halvorsen, R., Ugland, K. I., Fontana, G., et al. (2012). Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing: primary succession of root-associated fungi. Mol. Ecol. 21, 1897-1908. doi: 10.1111/j.1365- 294X.2011.05214.x
    • Braak, C., and ter Šmilauer, P. (2002). “CANOCO reference manual and CanoDraw for Windows user's guide: software for canonical community ordination (version 4.5),” in Section on Permutation Methods (New York, NY: Microcomputer Power).
    • Bragg, L., Stone, G., Imelfort, M., Hugenholtz, P., and Tyson, G. W. (2012). Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat. Methods 9, 425-426. doi: 10.1038/nmeth.1990
    • Bray, J. R., and Curtis, J. T. (1957). An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27, 325-349. doi: 10.2307/ 1942268
    • Bremner, J. M., and Keeney, D. R. (1965). Steam distillation methods for determination of ammonium, nitrate and nitrite. Anal. Chim. Acta 32, 485-495. doi: 10.1016/S0003-2670(00)88973-4
    • Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of highthroughput community sequencing data. Nat. Methods 7, 335-336. doi: 10.1038/nmeth.f.303
    • Chakravarty, P., and Unestam, T. (1987). Differential influence of ectomycorrhizae on plant growth and disease resistance in Pinus sylvestris seedlings. J. Phytopathol. 120, 104-120. doi: 10.1111/j.1439-0434.1987.tb04423.x
    • Corredor, A. H., Rees, K. V., and Vujanovic, V. (2014). Host genotype and health status influence on the composition of the arbuscular mycorrhizal fungi in Salix bioenergy plantations. Forest Ecol. Manag. 314, 112-119. doi: 10.1016/j.foreco.2013.12.002
    • Corredor, A. H., Van Rees, K., and Vujanovic, V. (2012). Changes in root-associated fungal assemblages within newly established clonal biomass plantations of Salix spp. For. Ecol. Manag. 282, 105-114. doi: 10.1016/j.foreco.2012.06.045
    • Davison, J., Moora, M., Öpik, M., Adholeya, A., Ainsaar, L., Bâ, A., et al. (2015). Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349, 970-973. doi: 10.1126/science.aab1161
    • Deacon, K., and Fleming, L. V. (1992). “Interactions of ectomycorrhizal fungi,” in Mycorrhizal Functioning: An Integrative Plant-Fungal Process, ed. M. F. Allen (London: Chapman and Hall), 249-300.
    • De Beeck, M. O., Lievens, B., Busschaert, P., Declerck, S., Vangronsveld, J., and Colpaert, J. V. (2014). Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS ONE 9:e97629. doi: 10.1371/journal.pone.0097629
    • Dumbrell, A. J., Ashton, P. D., Aziz, N., Feng, G., Nelson, M., Dytham, C., et al. (2011). Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol. 190, 794-804. doi: 10.1111/j.1469-8137.2010.03636.x
    • Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461
    • Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. doi: 10.1093/bioinformatics/ btr381
    • Espinoza, J. G., Briceño, E. X., Keith, L. M., and Latorre, B. A. (2008). Canker and twig dieback of blueberry caused by Pestalotiopsis spp. and a Truncatella sp. in Chile. Plant Dis. 92, 1407-1414. doi: 10.1094/PDIS-92-10- 1407
    • Finlay, B. J., and Clarke, K. J. (1999). Ubiquitous dispersal of microbial species. Nature 400, 828-828. doi: 10.1038/23616
    • Foissner, W. (1999). Protist diversity: estimates of the near-imponderable. Protist 150, 363-368. doi: 10.1016/S1434-4610(99)70037-4
    • Foissner, W. (2006). Biogeography and dispersal of micro-organisms: a review emphasizing protists. Acta Protozool. 45, 111-136.
    • Fowler, J., Cohen, L., and Jarvis, P. (1998). Practical Statistics for Field Biology. Chichester: John Wiley & Sons Ltd.
    • Fujiyoshi, M., Yoshitake, S., Watanabe, K., Murota, K., Tsuchiya, Y., Uchida, M., et al. (2011). Successional changes in ectomycorrhizal fungi associated with the polar willow Salix polaris in a deglaciated area in the High Arctic. Svalbard. Polar Biol. 34, 667-673. doi: 10.1007/s00300-010-0922-9
    • Garcia, K., Delteil, A., Conéjéro, G., Becquer, A., Plassard, C., Sentenac, H., et al. (2014). Potassium nutrition of ectomycorrhizal Pinus pinaster: overexpression of the Hebeloma cylindrosporum HcTrk1 transporter affects the translocation of both KC and phosphorus in the host plant. New Phytol. 201, 951-960. doi: 10.1111/nph.12603
    • Gardes, M., and Bruns, T. D. (1993). ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol. 2, 113-118. doi: 10.1111/j.1365-294X.1993. tb00005.x
    • Gosling, P., Mead, A., Proctor, M., Hammond, J. P., and Bending, G. D. (2013). Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient. New Phytol. 198, 546-556. doi: 10.1111/nph. 12169
    • Green, J. L., Holmes, A. J., Westoby, M., Oliver, I., Briscoe, D., Dangerfield, M., et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature 432, 747-750. doi: 10.1038/nature03034
    • Griffiths, R. I., Thomson, B. C., James, P., Bell, T., Bailey, M., and Whiteley, A. S. (2011). The bacterial biogeography of British soils. Environ. Microbiol. 13, 1642-1654. doi: 10.1111/j.1462-2920.2011.02480.x
    • Hazard, C., Gosling, P., van der Gast, C. J., Mitchell, D. T., Doohan, F. M., and Bending, G. D. (2013). The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale. ISME J. 7, 498-508. doi: 10.1038/ismej.2012.127
    • Henriksen, A., and Selmer-Olsen, A. R. (1970). Automatic methods for determining nitrate and nitrite in water and soil extracts. Analyst 95, 514-518. doi: 10.1039/AN9709500514
    • Hibbett, D. S. (2007). After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century. Mycol. Res. 111, 1001-1018. doi: 10.1016/j.mycres.2007. 01.012
    • Hilton, S., Bennett, A. J., Keane, G., Bending, G. D., Chandler, D., Stobart, R., et al. (2013). Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline. PLoS ONE 8:e59859. doi: 10.1371/journal.pone.0059859
    • Högberg, M. N., Briones, M. J. I., Keel, S. G., Metcalfe, D. B., Campbell, C., Midwood, A. J., et al. (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, 485-493. doi: 10.1111/j.1469-8137.2010. 03274.x
    • Högberg, M. N., and Högberg, P. (2002). Extramatrical ectomycorrhizal mycelium contributes one-third of microbial biomass and produces, together with associated roots, half the dissolved organic carbon in a forest soil. New Phytol. 154, 791-795. doi: 10.1046/j.1469-8137.2002.00417.x
    • Högberg, P., Nordgren, A., Buchmann, N., Taylor, A. F. S., Ekblad, A., Högberg, M. N., et al. (2001). Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 411, 789-792. doi: 10.1038/35081058
    • Horn, S., Caruso, T., Verbruggen, E., Rillig, M. C., and Hempel, S. (2014). Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales. ISME J. 8, 2231-2242. doi: 10.1038/ismej.2014.72
    • Husband, R., Herre, E. A., Turner, S. L., Gallery, R., and Young, J. P. W. (2002). Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest. Mol. Ecol. 11, 2669-2678. doi: 10.1046/j.1365-294X.2002.01647.x
    • Ihrmark, K., Bödeker, I. T. M., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., et al. (2012). New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 82, 666-677. doi: 10.1111/j.1574-6941.2012. 01437.x
    • Jones, M. D., Durall, D. M., and Tinker, P. B. (1990). Phosphorus relationships and production of extrametrical hyphae by two types of willow ectomycorrhizas at different soil phosphorus levels. New Phytol. 115, 259-267. doi: 10.1111/j.1469- 8137.1990.tb00451.x
    • Jumpponen, A., Jones, K. L., David Mattox, J., and Yaege, C. (2010). Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol. Ecol. 19, 41-53. doi: 10.1111/j.1365-294X.2009.04483.x
    • Kivlin, S. N., Hawkes, C. V., and Treseder, K. K. (2011). Global diversity and distribution of arbuscular mycorrhizal fungi. Soil Biol. Biochem. 43, 2294-2303. doi: 10.1016/j.soilbio.2011.07.012
    • Lang, C., Seven, J., and Polle, A. (2010). Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed Central European forest. Mycorrhiza 21, 297-308. doi: 10.1007/s00572- 010-0338-y
    • Last, F. T., Mason, P. A., Ingleby, K., and Fleming, L. V. (1984). Succession of fruitbodies of sheathing mycorrhizal fungi associated with Betula pendula. For. Ecol. Manag. 9, 229-234. doi: 10.1016/0378-1127(84)90050-1
    • Leski, T., Aucˇina, A., Skridaila, A., Pietras, M., Riepšas, E., and Rudawska, M. (2010). Ectomycorrhizal community structure of different genotypes of Scots pine under forest nursery conditions. Mycorrhiza 20, 473-481. doi: 10.1007/s00572-010-0298-2
    • Lilleskov, E. A., Bruns, T. D., Horton, T. R., Taylor, D., and Grogan, P. (2004). Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities. FEMS Microbiol. Ecol. 49, 319-332. doi: 10.1016/j.femsec.2004.04.004
    • Lilleskov, E. A., Fahey, T. J., Horton, T. R., and Lovett, G. M. (2002). Belowground ectomycorrhizal fungal community change over a nitrogen deposition gradient in Alaska. Ecology 83, 104-115. doi: 10.1890/0012- 9658(2002)083[0104:BEFCCO]2.0.CO;2
    • Liu, J., Maldonado-Mendoza, I., Lopez-Meyer, M., Cheung, F., Town, C. D., and Harrison, M. J. (2007). Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots. Plant J. 50, 529-544. doi: 10.1111/j.1365- 313X.2007.03069.x
    • Martiny, J. B. H., Eisen, J. A., Penn, K., Allison, S. D., and HornerDevine, M. C. (2011). Drivers of bacterial b-diversity depend on spatial scale. Proc. Natl. Acad. Sci. U.S.A. 108, 7850-7854. doi: 10.1073/pnas.1016 308108
    • Matheny, P. B., Curtis, J. M., Hofstetter, V., Aime, M. C., Moncalvo, J.-M., Ge, Z.- W., et al. (2006). Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98, 982-995. doi: 10.3852/mycologia.98.6.982
    • Mundra, S., Halvorsen, R., Kauserud, H., Müller, E., Vik, U., and Eidesen, P. B. (2015). Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation. New Phytol. 205, 1587-1597. doi: 10.1111/nph. 13216
    • Niklaus, P. A., Glockler, E., Siegwolf, R., and Korner, C. (2001). Carbon allocation in calcareous grassland under elevated CO2: a combined 13C pulse-labelling/soil physical fractionation study. Funct. Ecol. 15, 43-50. doi: 10.1046/j.1365-2435.2001.00485.x
    • Olsen, S. R. (1954). Estimation of Available Phosphorus in Soils by Extraction with Sodium Bicarbonate. Washington, DC: U.S. Department of Agriculture.
    • Peay, K. G., Kennedy, P. G., Davies, S. J., Tan, S., and Bruns, T. D. (2010). Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. New Phytol. 185, 529-542. doi: 10.1111/j.1469- 8137.2009.03075.x
    • Phillips, R. L., Zak, D. R., Holmes, W. E., and White, D. C. (2002). Microbial community composition and function beneath temperate trees exposed to elevated atmospheric carbon dioxide and ozone. Oecologia 131, 236-244. doi: 10.1007/s00442-002-0868-x
    • Phillips, R. P., and Fahey, T. J. (2007). Fertilization effects on fineroot biomass, rhizosphere microbes and respiratory fluxes in hardwood forest soils. New Phytol. 176, 655-664. doi: 10.1111/j.1469-8137.2007.02204.x
    • Pickles, B. J., Genney, D. R., Potts, J. M., Lennon, J. J., Anderson, I. C., and Alexander, I. J. (2010). Spatial and temporal ecology of Scots pine ectomycorrhizas. New Phytol. 186, 755-768. doi: 10.1111/j.1469- 8137.2010.03204.x
    • Pilloni, G., Granitsiotis, M. S., Engel, M., and Lueders, T. (2012). Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS ONE 7:e40467. doi: 10.1371/journal.pone.0040467
    • Põlme, S., Bahram, M., Yamanaka, T., Nara, K., Dai, Y. C., Grebenc, T., et al. (2013). Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale. New Phytol. 198, 1239-1249. doi: 10.1111/nph.12170
    • Rytter, R.-M., and Hansson, A.-C. (1996). Seasonal amount, growth and depth distribution of fine roots in an irrigated and fertilized Salix viminalis L. plantation. Biomass Bioenergy 11, 129-137. doi: 10.1016/0961-9534(96)00023-2
    • Smith, S. E., and Read, D. J. (2010). Mycorrhizal Symbiosis. Cambridge, MA: Academic Press.
    • Swaty, R. L., Gehring, C. A., Van Ert, M., Theimer, T. C., Keim, P., and Whitham, T. G. (1998). Temporal variation in temperature and rainfall differentially affects ectomycorrhizal colonization at two contrasting sites. New Phytol. 139, 733-739. doi: 10.1046/j.1469-8137.1998.00234.x
    • Tanaka, K., Endo, M., Hirayama, K., Okane, I., Hosoya, T., and Sato, T. (2011). Phylogeny of discosia and seimatosporium, and introduction of adisciso and immersidiscosia genera nova. Persoonia 26, 85-98. doi: 10.3767/003158511X576666
    • Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., et al. (2014). Global diversity and geography of soil fungi. Science 346:1256688. doi: 10.1126/science.1256688
    • Tedersoo, L., Bahram, M., Toots, M., Diédhiou, A. G., Henkel, T. W., Kjøller, R., et al. (2012). Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. Mol. Ecol. 21, 4160-4170. doi: 10.1111/j.1365- 294X.2012.05602.x
    • Tedersoo, L., Ramirez, K. S., Nilsson, R. H., Kaljuvee, A., Kõljalg, U., and Abarenkov, K. (2015). Standardizing metadata and taxonomic identification in metabarcoding studies. Giga Sci. 4:34. doi: 10.1186/s13742-015- 0074-5
    • Toljander, J. F., Eberhardt, U., Toljander, Y. K., Paul, L. R., and Taylor, A. F. S. (2006). Species composition of an ectomycorrhizal fungal community along a local nutrient gradient in a boreal forest. New Phytol. 170, 873-884. doi: 10.1111/j.1469-8137.2006.01718.x
    • van den Wollenberg, A. L. (1977). Redundancy analysis an alternative for canonical correlation analysis. Psychometrika 42, 207-219. doi: 10.1007/BF022 94050
    • van der Gast, C. J., Gosling, P., Tiwari, B., and Bending, G. D. (2011). Spatial scaling of arbuscular mycorrhizal fungal diversity is affected by farming practice. Environ. Microbiol. 13, 241-249. doi: 10.1111/j.1462-2920.2010. 02326.x
    • Verbruggen, E., Van Der Heijden, M. G., Weedon, J. T., Kowalchuk, G. A., and Röling, W. F. (2012). Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils. Mol. Ecol. 21, 2341-2353. doi: 10.1111/j.1365-294X.2012.05534.x
    • Visser, S. (1995). Ectomycorrhizal fungal succession in jack pine stands following wildfire. New Phytol. 129, 389-401. doi: 10.1111/j.1469-8137.1995.tb04309.x
    • Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07
    • Yu, L., Nicolaisen, M., Larsen, J., and Ravnskov, S. (2012). Succession of rootassociated fungi in Pisum sativum during a plant growth cycle as examined
    • by 454 pyrosequencing. Plant Soil 358, 225-233. doi: 10.1007/s11104-012-
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