FAO (2010) Global forest resources assessment 2010. http://www.fao.org/forest-resources-assessment/en/
Bradford MA, Berg B, Maynard DS, Wieder WR, Wood SA (2016) Understanding the dominant controls on litter decomposition. J. Ecol. 104:229–238. https://doi.org/10.1111/1365-2745.12507
CAS
Article
Google Scholar
Berg B, Laskowski R (2006) Litter decomposition: a guide to carbon and nutrient turnover. Elsevier
David JF (2014) The role of litter-feeding macroarthropods in decomposition processes: a reappraisal of common views. Soil Biol. Biochem. 76:109–118. https://doi.org/10.1016/j.soilbio.2014.05.009
CAS
Article
Google Scholar
Persson T, Bååth E, Clarholm M et al (1980) Trophic structure, biomass dynamics and carbon metabolism of soil organisms in a Scots pine forest. Oikos 32:419–459. https://doi.org/10.2307/20112829
CAS
Article
Google Scholar
Berg B, Hannus K, Popoff T, Theander O (1982) Changes in organic chemical components of needle litter during decomposition. Long-term decomposition in a Scots pine forest. I. Can. J. Bot. 60:1310–1319
CAS
Article
Google Scholar
Staaf H, Berg B (1982) Accumulation and release of plant nutrients in decomposing Scots pine litter. Long-term decomposition in a Scots pine forest. II. Can. J. Bot. 60:1561–1568. https://doi.org/10.1139/b82-199
CAS
Article
Google Scholar
Berg B (1986) Nutrient release from litter and humus in coniferous forest soils—a mini review. Scand. J. For. Res. 1:359–369
Article
Google Scholar
Berg B (1988) Dynamics of nitrogen (15N) in decomposing Scots pine (Pinus sylvestris) needle litter. Long-term decomposition in a Scots pine forest. VI. Can. J. Bot. 66:1539–1546
CAS
Article
Google Scholar
Bardgett RD (2005) The biology of soil: a community and ecosystem approach. Oxford University Press
Cepáková Š, Frouz J (2015) Changes in chemical composition of litter during decomposition: a review of published 13C NMR spectra. J. Soil Sci. Plant Nutr. 15:805–815
Google Scholar
Ponge J-FF (1991) Succession of fungi and fauna during decomposition of needles in a small area of Scots pine litter. Plant Soil 138:99–113. https://doi.org/10.1007/BF00011812
Article
Google Scholar
Tokumasu S, Aoki T, Oberwinkler F (1994) Fungal succession on pine needles in Germany. Mycoscience 35:29–37. https://doi.org/10.1007/BF02268525
Article
Google Scholar
Berg MP, Kniese J, Bedaux J, Verhoef H (1998) Dynamics and stratification of bacteria and fungi in the organic layers of a scots pine forest soil. Biol. Fertil. Soils 26:268–284. https://doi.org/10.1007/s003740050378
Article
Google Scholar
Aneja MK, Sharma S, Fleischmann F, Stich S, Heller W, Bahnweg G, Munch JC, Schloter M (2006) Microbial colonization of beech and spruce litter—influence of decomposition site and plant litter species on the diversity of microbial community. Microb. Ecol. 52:127–135. https://doi.org/10.1007/s00248-006-9006-3
Article
PubMed
Google Scholar
Schneider T, Keiblinger KM, Schmid E, Sterflinger-Gleixner K, Ellersdorfer G, Roschitzki B, Richter A, Eberl L, Zechmeister-Boltenstern S, Riedel K (2012) Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME J. 6:1749–1762. https://doi.org/10.1038/ismej.2012.11
CAS
Article
PubMed
PubMed Central
Google Scholar
Voříšková J, Baldrian P (2013) Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J. 7:477–486. https://doi.org/10.1038/ismej.2012.116
CAS
Article
PubMed
Google Scholar
Urbanová M, Šnajdr J, Baldrian P (2015) Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees. Soil Biol. Biochem. 84:53–64. https://doi.org/10.1016/j.soilbio.2015.02.011
CAS
Article
Google Scholar
Tláskal V, Voříšková J, Baldrian P et al (2016) Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia. FEMS Microbiol. Ecol. 92:fiw177. https://doi.org/10.1093/femsec/iw177
Article
PubMed
Google Scholar
Purahong W, Wubet T, Lentendu G, Schloter M, Pecyna MJ, Kapturska D, Hofrichter M, Krüger D, Buscot F (2016) Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition. Mol. Ecol. 25:4059–4074. https://doi.org/10.1111/mec.13739
CAS
Article
PubMed
Google Scholar
Dilly O, Munch J-C (1996) Microbial biomass content, basal respiration and enzyme activities during the course of decomposition of leaf litter in a black alder (Alnus glutinosa (L.) Gaertn.) forest. Soil Biol. Biochem. 28:1073–1081. https://doi.org/10.1016/0038-0717(96)00075-2
CAS
Article
Google Scholar
Baldrian P (2017) Forest microbiome: diversity, complexity, and dynamics. FEMS Microbiol. Rev. 41:109–130. https://doi.org/10.1093/femsre/fuw040
CAS
Article
PubMed
Google Scholar
Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. University of California Press
Melillo JM, Aber JD, Linkins AE, Ricca A, Fry B, Nadelhoffer KJ (1989) Carbon and nitrogen dynamics along the decay continuum: plant litter to soil organic matter. Plant Soil 115:189–198. https://doi.org/10.1007/BF02202587
Article
Google Scholar
Baldrian P, Kolařík M, Štursová M, Kopecký J, Valášková V, Větrovský T, Žifčáková L, Šnajdr J, Rídl J, Vlček Č, Voříšková J (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6:248–258. https://doi.org/10.1038/ismej.2011.95
CAS
Article
PubMed
Google Scholar
Žifčáková L, Větrovský T, Howe A, Baldrian P (2016) Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ. Microbiol. 18:288–301. https://doi.org/10.1111/1462-2920.13026
CAS
Article
PubMed
Google Scholar
Osono T (2006) Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Can. J. Microbiol. 52:701–716. https://doi.org/10.1139/w06-023
CAS
Article
PubMed
Google Scholar
Voříšková J, Brabcová V, Cajthaml T, Baldrian P (2014) Seasonal dynamics of fungal communities in a temperate oak forest soil. New Phytol. 201:269–278. https://doi.org/10.1111/nph.12481
CAS
Article
PubMed
Google Scholar
Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65
CAS
Article
Google Scholar
Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765–4774. doi: 0021–9193/98/$04.00+0
Steele HL, Streit WR (2005) Metagenomics: advances in ecology and biotechnology. FEMS Microbiol. Lett. 247:105–111. https://doi.org/10.1016/j.femsle.2005.05.011
CAS
Article
PubMed
Google Scholar
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:R245–R249
CAS
Article
Google Scholar
Rondon MR, Bettermann AD, Brady SF et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541–2547
CAS
Article
Google Scholar
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 Microbiol. Ecol. 80:735–746. https://doi.org/10.1111/j.1574-6941.2012.01343.x
CAS
Article
PubMed
Google Scholar
Tsai Y-L, Olson BH (1992) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Apllied Environ. Microbiol. 58:754–757
CAS
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:590–596. https://doi.org/10.1093/nar/gks1219
CAS
Article
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41:1–11. https://doi.org/10.1093/nar/gks808
CAS
Article
Google Scholar
IDT (2014) IDT Oligo Analyzer. http://eu.idtdna.com/calc/analyzer
Faircloth BC, Glenn TC (2012) Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One 7:e42543. https://doi.org/10.1371/journal.pone.0042543
CAS
Article
PubMed
PubMed Central
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537–7541. https://doi.org/10.1128/AEM.01541-09
CAS
Article
PubMed
PubMed Central
Google Scholar
Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb. Ecol. 67:635–647. https://doi.org/10.1007/s00248-013-0344-7
CAS
Article
PubMed
PubMed Central
Google Scholar
Gołębiewski M, Całkiewicz J, Creer S, Piwosz K (2017) Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary. Environ. Microbiol. Rep. 9:129–143. https://doi.org/10.1111/1758-2229.12509
CAS
Article
PubMed
Google Scholar
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38. https://doi.org/10.1186/1471-2105-12-38
Article
PubMed
PubMed Central
Google Scholar
Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12:1889–1898. https://doi.org/10.1111/j.1462-2920.2010.02193.x
CAS
Article
PubMed
PubMed Central
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. https://doi.org/10.1093/bioinformatics/btr381
CAS
Article
PubMed
PubMed Central
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261–5267. https://doi.org/10.1128/AEM.00062-07
CAS
Article
PubMed
PubMed Central
Google Scholar
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WHCF, Lara E, le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:597–604. https://doi.org/10.1093/nar/gks1160
CAS
Article
Google Scholar
Sheneman L, Evans J, Foster JA (2006) Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22:2823–2824. https://doi.org/10.1093/bioinformatics/btl478
CAS
Article
PubMed
Google Scholar
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228–8235. https://doi.org/10.1128/AEM.71.12.8228-8235.2005
CAS
Article
PubMed
PubMed Central
Google Scholar
Horn HS (1966) Measurement of “overlap” in comparative ecological studies. Am. Nat. 100:419–424. https://doi.org/10.1086/282436
Article
Google Scholar
Bray RJ, Curtis JT (1957) An ordination of the upland forest communities of southern Winsconin. Ecol. Monogr. 27:325–349. https://doi.org/10.2307/1942268
Article
Google Scholar
Oksanen J, Blanchet FG, Kindt R, et al (2013) Vegan: community ecology package. R package, https://cran.r-project.org/web/packages/vegan/index.html
ter Braak CJF, Schaffers AP (2004) Co-correspondence analysis: a new ordination method to relate two community compositions. Ecology 85:834–846. https://doi.org/10.1890/03-0021
Article
Google Scholar
Simpson GL (2009) Cocorresp: co-correspondence analysis ordination methods. R package, https://github.com/gavinsimpson/cocorresp
Langille M, Zaneveld J, Caporaso JG et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814–821. https://doi.org/10.1038/nbt.2676
CAS
Article
PubMed
PubMed Central
Google Scholar
DeSantis TZ, Hugenholtz P, Larsen N et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069–5072. https://doi.org/10.1128/AEM.03006-05
CAS
Article
PubMed
PubMed Central
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124. https://doi.org/10.1093/bioinformatics/btu494
CAS
Article
PubMed
PubMed Central
Google Scholar
R Core Team (2016) R: a language and environment for statistical computing. https://www.r-project.org/
Harrell Jr FE, with contributions from Charles Dupont, many others. (2014) Hmisc: Harrell miscellaneous. R package, https://cran.r-project.org/web/packages/Hmisc/index.html
McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. https://doi.org/10.1371/journal.pone.0061217
CAS
Article
PubMed
PubMed Central
Google Scholar
Deja-Sikora E (2012) Search for bacterial cadmium, zinc, lead, copper and chromium resistance genes in metagenome of soils polluted with heavy metals. Nicolaus Copernicus University
Krsek M, Wellington EMH (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J. Microbiol. Methods 39:1–16. https://doi.org/10.1016/S0167-7012(99)00093-7
CAS
Article
PubMed
Google Scholar
Bomberg M, Montonen L, Timonen S (2010) Anaerobic Eury- and Crenarchaeota inhabit ectomycorrhizas of boreal forest Scots pine. Eur. J. Soil Biol. 46:356–364. https://doi.org/10.1016/J.EJSOBI.2010.09.002
Article
Google Scholar
Larsen BB, Miller EC, Rhodes MK, Wiens JJ (2017) Inordinate fondness multiplied and redistributed: the number of species on earth and the new pie of life. Q. Rev. Biol. 92:229–265. https://doi.org/10.1086/693564
Article
Google Scholar
Carrell AA, Frank AC (2014) Pinus flexilis and Picea engelmannii share a simple and consistent needle endophyte microbiota with a potential role in nitrogen fixation. Front. Microbiol. 5: . doi: https://doi.org/10.3389/fmicb.2014.00333
Millberg H, Boberg J, Stenlid J (2015) Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden. Fungal Ecol. 17:126–139. https://doi.org/10.1016/j.funeco.2015.05.012
Article
Google Scholar
Boberg JB, Ihrmark K, Lindahl BD (2011) Decomposing capacity of fungi commonly detected in Pinus sylvestris needle litter. Fungal Ecol. 4:110–114. https://doi.org/10.1016/J.FUNECO.2010.09.002
Article
Google Scholar
Osono T, Hirose D (2011) Colonization and lignin decomposition of pine needle litter by Lophodermium pinastri. For. Pathol. 41:156–162. https://doi.org/10.1111/j.1439-0329.2010.00648.x
Article
Google Scholar
van der PAS JB, Slater-hayes JD, Gadgil PD, Bulman L (1984) Cyclaneusma (Naemacyclus) needle-cast of Pinus radiata in New Zealand. 2: reduction in growth of the host, and its economic implication. New Zeal J For Sci 14:197–209
Vestgarden L (2001) Carbon and nitrogen turnover in the early stage of Scots pine (Pinus sylvestris L.) needle litter decomposition: effects of internal and external nitrogen. Soil Biol. Biochem. 33:465–474. https://doi.org/10.1016/S0038-0717(00)00187-5
CAS
Article
Google Scholar
Crous PW, Quaedvlieg W, Hansen K, Hawksworth DL, Groenewald JZ (2014) Phacidium and Ceuthospora (Phacidiaceae) are congeneric: taxonomic and nomenclatural implications. IMA Fungus 5:173–193. https://doi.org/10.5598/imafungus.2014.05.02.02
Article
PubMed
PubMed Central
Google Scholar
Farr DF, Rossman AY (2018) Fungal databases, U.S. National Fungus Collecsions, ARS, USDA. https://nt.ars-grin.gov/fungaldatabases. Accessed 1 Feb 2018
Wiseman MS, Kim YK, Dugan FM, Rogers JD, Xiao CL (2016) A new postharvest fruit rot in apple and pear caused by Phacidium lacerum. Plant Dis. 100:32–39. https://doi.org/10.1094/PDIS-02-15-0158-RE
CAS
Article
Google Scholar
Berg B, McClaugherty C (2003) Plant litter. Decomposition, humus formation, carbon sequestration. Springer-Verlag Berlin Heidelberg, Berlin Heidelberg
Google Scholar
Bae Y-S, Knudsen GR (2001) Influence of a fungus-feeding nematode on growth and biocontrol efficacy of Trichoderma harzianum. Phytopathology 91:301–306. https://doi.org/10.1094/PHYTO.2001.91.3.301
CAS
Article
PubMed
Google Scholar
Taktek S, Trépanier M, Servin PM, St-Arnaud M, Piché Y, Fortin JA, Antoun H (2015) Trapping of phosphate solubilizing bacteria on hyphae of the arbuscular mycorrhizal fungus Rhizophagus irregularis DAOM 197198. Soil Biol. Biochem. 90:1–9. https://doi.org/10.1016/j.soilbio.2015.07.016
CAS
Article
Google Scholar
Baldrian P, Zrůstová P, Tláskal V, Davidová A, Merhautová V, Vrška T (2016) Fungi associated with decomposing deadwood in a natural beech-dominated forest. Fungal Ecol. 23:109–122. https://doi.org/10.1016/j.funeco.2016.07.001
Article
Google Scholar
Berg B, Matzner E (1997) Effect of N deposition on decomposition of plant litter and soil organic matter in forest systems. Environ. Rev. 5:1–25
CAS
Article
Google Scholar
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications. pp 315–322
Wakelin SA, Colloff MJ, Harvey PR, Marschner P, Gregg AL, Rogers SL (2007) The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize. FEMS Microbiol. Ecol. 59:661–670. https://doi.org/10.1111/j.1574-6941.2006.00235.x
CAS
Article
PubMed
Google Scholar
Neefs J-M, Van de Peer Y, De Rijk P et al (1993) Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21:3025–3049
CAS
Article
Google Scholar
Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C (2014) Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 9:e87624. https://doi.org/10.1371/journal.pone.0087624
CAS
Article
PubMed
PubMed Central
Google Scholar