SEARCH

SEARCH BY CITATION

References

  • Agnelli A, Ascher J, Corti G, Ceccherini MT, Nannipieri P, Pietramellara G. 2004. Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biology & Biochemistry 36: 859868.
  • Andreetta A, Macci C, Ceccherini M, Cecchini G, Masciandaro G, Pietramellara G, Carnicelli S. 2012. Microbial dynamics in Mediterranean Moder humus. Biology and Fertility of Soils 48: 259270.
  • Aponte C, García LV, Marañón T, Gardes M. 2010. Indirect host effect on ectomycorrhizal fungi: leaf fall and litter quality explain changes in fungal communities on the roots of co-occurring Mediterranean oaks. Soil Biology & Biochemistry 42: 788796.
  • Bååth E. 2001. Estimation of fungal growth rates in soil using C-14-acetate incorporation into ergosterol. Soil Biology & Biochemistry 33: 20112018.
  • Baldrian P, Kolařík M, Štursová M, Kopecký J, Valášková V, Větrovský T, Žifčáková L, Šnajdr J, Rídl J, Vlček Č et al. 2012. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME Journal 6: 248258.
  • Baldrian P, Merhautová V, Cajthaml T, Petránková M, Šnajdr J. 2010. Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil. Biology and Fertility of Soils 46: 717726.
  • Baldrian P, Šnajdr J, Merhautová V, Dobiášová P, Cajthaml T, Valášková V. 2013a. Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change. Soil Biology & Biochemistry 56: 6068.
  • Baldrian P, Štursová M. 2011. Enzymes in forest soils. In: Shukla G, Varma A, eds. Soil enzymology. Berlin, Germany: Springer, 6173.
  • Baldrian P, Větrovský T, Cajthaml T, Dobiášova P, Petránkova M, Šnajdr J, Eichlerová I. 2013b. Estimation of fungal biomass in forest litter and soil. Fungal Ecology 6: 111.
  • Baldrian P, Voříšková J, Dobiášová P, Merhautová V, Lisá L, Valášková V. 2011. Production of extracellular enzymes and degradation of biopolymers by saprotrophic microfungi from the upper layers of forest soil. Plant and Soil 338: 115.
  • Berg B, McClaugherty C. 2003. Plant litter. Berlin, Germany: Springer.
  • Berg MP, Kniese JP, Verhoef HA. 1998. Dynamics and stratification of bacteria and fungi in the organic layers of a Scots pine forest soil. Biology and Fertility of Soils 26: 313322.
  • Björk RG, Björkman MP, Andersson MX, Klemedtsson L. 2008. Temporal variation in soil microbial communities in Alpine tundra. Soil Biology & Biochemistry 40: 266268.
  • Bödeker ITM, Nygren CMR, Taylor AFS, Olson A, Lindahl BD. 2009. Class II peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi. ISME Journal 3: 13871395.
  • Boer WD, Folman LB, Summerbell RC, Boddy L. 2005. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiology Reviews 29: 795811.
  • Bréda N, Maillard P, Montpied P, Brechet C, Garbaye J, Courty PE. 2013. Isotopic evidence in adult oak trees of a mixotrophic lifestyle during spring reactivation. Soil Biology & Biochemistry 58: 136139.
  • 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: 235245.
  • Clemmensen KE, Bahr A, Ovaskainen O, Dahlberg A, Ekblad A, Wallander H, Stenlid J, Finlay RD, Wardle DA, Lindahl BD. 2013. Roots and associated fungi drive long-term carbon sequestration in boreal forest. Science 339: 16151618.
  • Coince A, Cael O, Bach C, Lengellé J, Cruaud C, Gavory F, Morin E, Murat C, Marcais B, Bueé M. 2013. Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecology 6: 223235.
  • Courty P-E, Bréda N, Garbaye J. 2007. Relation between oak tree phenology and the secretion of organic matter degrading enzymes by Lactarius quietus ectomycorrhizas before and during bud break. Soil Biology & Biochemistry 39: 16551663.
  • Courty PE, Buéé M, Diedhiou AG, Frey-Klett P, Le Tacon F, Rineau F, Turpault MP, Uroz S, Garbaye J. 2010a. The role of ectomycorrhizal communities in forest ecosystem processes: new perspectives and emerging concepts. Soil Biology & Biochemistry 42: 679698.
  • Courty P-E, Franc A, Garbaye J. 2010b. Temporal and functional pattern of secreted enzyme activities in an ectomycorrhizal community. Soil Biology & Biochemistry 42: 20222025.
  • Courty PE, Franc A, Pierrat JC, Garbaye J. 2008. Temporal changes in the ectomycorrhizal community in two soil horizons of a temperate oak forest. Applied and Environmental Microbiology 74: 57925801.
  • Davey ML, Heegaard E, Halvorsen R, Ohlson M, Kauserud H. 2012. Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing. New Phytologist 195: 844856.
  • Dumbrell AJ, Ashton PD, Aziz N, Feng G, Nelson M, Dytham C, Fitter AH, Helgason T. 2011. Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytologist 190: 794804.
  • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 24602461.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 21942200.
  • Edwards IP, Zak DR. 2010. Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape. Molecular Ecology 19: 14691482.
  • Ekblad A, Wallander H, Godbold DL, Cruz C, Johnson D, Baldrian P, Björk RG, Epron D, Kieliszewska-Rokicka B, Kjøller R et al. 2013. The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling. Plant and Soil 366: 127.
  • FAO & JRC. 2012. Global forest land-use change 1990–2005, by Lindquist EJ, D'Annunzio R, Gerrand A, MacDicken K, Achard F, Beuchle R, Brink A, Eva HD, Mayaux P, San-Miguel-Ayanz J & Stibig H-J, eds. FAO Forestry Paper No. 169. Rome, FAO: Food and Agriculture Organization of the United Nations and European Commission Joint Research Centre.
  • van der Heijden MGA, Horton TR. 2009. Socialism in soil? The importance of mycorrhizal fungal networks for facilitation in natural ecosystems. Journal of Ecology 97: 11391150.
  • Hobbie EA. 2006. Carbon allocation to ectomycorrhizal fungi correlates with belowground allocation in culture studies. Ecology 87: 563569.
  • Högberg MN, Briones MJI, Keel SG, Metcalfe DB, Campbell C, Midwood AJ, Thornton B, Hurry V, Linder S, Näsholm T 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 Phytologist 187: 485493.
  • Jumpponen A, Jones KL, Blair J. 2010. Vertical distribution of fungal communities in tallgrass prairie soil. Mycologia 102: 10271041.
  • Jumpponen A, Jones KL, Mattox D, Yaege C. 2009. Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Molecular Ecology 19: 4153.
  • Kaiser C, Koranda M, Kitzler B, Fuchslueger L, Schnecker J, Schweiger P, Rasche F, Zechmeister-Boltenstern S, Sessitsch A, Richter A. 2010. Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil. New Phytologist 187: 843858.
  • Koide RT, Shumway DL, Xu B, Sharda JN. 2007. On temporal partitioning of a community of ectomycorrhizal fungi. New Phytologist 174: 420429.
  • Koleff P, Gaston KJ, Lennon JJ. 2003. Measuring beta diversity for presence–absence data. Journal of Animal Ecology 72: 367382.
  • Kuffner M, Hai B, Rattei T, Melodelima C, Schloter M, Zechmeister-Boltenstern S, Jandl R, Schindlbacher A, Sessitsch A. 2012. Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiology Ecology 82: 551562.
  • Landesman W, Dighton J. 2011. Shifts in microbial biomass and the bacteria : fungi ratio occur under field conditions within 3 h after rainfall. Microbial Ecology 62: 228236.
  • Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Hogberg P, Stenlid J, Finlay RD. 2007. Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytologist 173: 611620.
  • Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J et al. 2013. Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide. New Phytologist 199: 288299.
  • Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488: 8690.
  • Nilsson RH, Tedersoo L, Lindahl BD, Kjøller R, Carlsen T, Quince C, Abarenkov K, Pennanen T, Stenlid J, Bruns T et al. 2011. Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytologist 191: 314318.
  • O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology 71: 55445550.
  • Osono T. 2006. Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Canadian Journal of Microbiology 52: 701716.
  • Parrent JL, Vilgalys R. 2007. Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization. New Phytologist 176: 164174.
  • Reeder J, Knight R. 2010. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods 7: 668669.
  • Rineau F, Roth D, Shah F, Smits M, Johansson T, Canback B, Olsen PB, Persson P, Grell MN, Lindquist E et al. 2012. The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. Environmental Microbiology 14: 14771487.
  • Rosling A, Landeweert R, Lindahl BD, Larsson KH, Kuyper TW, Taylor AFS, Finlay RD. 2003. Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. New Phytologist 159: 775783.
  • Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J. 2008. Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Applied and Environmental Microbiology 74: 29022907.
  • Schadt CW, Martin AP, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301: 13591361.
  • Šnajdr J, Cajthaml T, Valášková V, Merhautová V, Petránková M, Spetz P, Leppänen K, Baldrian P. 2011. Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. FEMS Microbiology Ecology 75: 291303.
  • Šnajdr J, Valášková V, Merhautová V, Herinková J, Cajthaml T, Baldrian P. 2008. Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biology & Biochemistry 40: 20682075.
  • Steffen KT, Cajthaml T, Snajdr J, Baldrian P. 2007. Differential degradation of oak (Quercus petraea) leaf litter by litter-decomposing basidiomycetes. Research in Microbiology 158: 447455.
  • Štursová M, Žifčáková L, Leigh MB, Burgess R, Baldrian P. 2012. Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiology Ecology 80: 735746.
  • Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. 2010. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291301.
  • Uroz S, Ioannidis P, Lengelle J, Cébron A, Morin E, Buée M, Martin F. 2013. Functional assays and metagenomic analyses reveal differences between the microbial communities inhabiting the soil horizons of a Norway Spruce plantation. PLoS ONE 8: e55929.
  • Větrovský T, Baldrian P. 2013. Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biology and Fertility of Soils. doi:10.1007/s00374-013-0801-y.
  • Voříšková J, Baldrian P. 2013. Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME Journal 7: 477486.
  • Wallander H, Nilsson LO, Hagerberg D, Bååth E. 2001. Estimation of the biomass and seasonal growth of external mycelium of ectomycorrhizal fungi in the field. New Phytologist 151: 753760.
  • White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In: Innis MA, Gelfand DH, Sninsky JN, White TJ, eds. PCR protocols: a guide to methods and applications. New York, NY, USA: Academic Press, 315322.
  • Wittmann C, Kahkonen MA, Ilvesniemi H, Kurola J, Salkinoja-Salonen MS. 2004. Areal activities and stratification of hydrolytic enzymes involved in the biochemical cycles of carbon, nitrogen, sulphur and phosphorus in podsolized boreal forest soils. Soil Biology & Biochemistry 36: 425433.
  • Yang Y, Luo Y. 2011. Carbon : nitrogen stoichiometry in forest ecosystems during stand development. Global Ecology and Biogeography 20: 354361.