Abstract
Metabarcoding of environmental samples is nowadays an established method in biodiversity research. When it comes to studying fungal populations in various ecotypes, fruit body inventories are the traditional method to assess the diversity of fungal communities. In this study, both methods—metabarcoding of soil samples and a traditional fruit body inventory—were conducted on 144 sample plots in an altitudinal gradient in the Bavarian Forest (Germany) and the results were compared. Metabarcoding detected significantly more species than the traditional fruit body inventory. The majority of taxa recorded in the fruit body inventory belonged to the Basidiomycota, whereas in the metabarcoding data, the distribution of species between Basidiomycota and Ascomycota was approximately balanced. Species of several orders forming inconspicuous or hypogeous fruit bodies were detected only by metabarcoding, while several wood decomposers were recorded only in the fruit body inventory. The proportion of detected wood-colonising species with melanized spores was considerably higher with metabarcoding than with the fruit body inventory, where more than 70% of recorded wood-colonisers had hyaline spores. Based on the metabarcoding data, a decline of species richness with increasing altitude was evident, but this was not visible in the fruit body inventory data. Detrended correspondence analyses yielded similar results for relative species community similarities with both survey methods.
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Data availability
Survey data of metabarcoding, including coordinates and collection dates are archived in NCBI BioSamples under Submission ID SUB11928789 and SUB9332799.The datasets generated by the fruit body inventory or analysed during the current study available from the corresponding author on reasonable request.
References
Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87:99–108. https://doi.org/10.1007/s00253-010-2585-4
Blaschke M, Siemonsmeier A (2021) Pilzartengemeinschaften im Höhengradienten. Z Mykol 87(2):363–385
Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/s41587-019-0209-9
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303
Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM (2018) Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol 22:2461–2476. https://doi.org/10.1111/mec.14694
Dahl MB, Shchepin O, Schunk C, Menzel A, Novozhilov YK, Schnittler M (2018) A four year survey reveals a coherent pattern between occurrence of fruit bodies and soil amoebae populations for nivicolous myxomycetes. Sci Rep 8:11662. https://doi.org/10.1038/s41598-018-30131-3
Dahl MB, Brejnrod AD, Russel J, Sørensen SJ, Schnittler M (2019) Different degrees of niche differentiation for bacteria, fungi, and myxomycetes within an elevational transect in the German Alps. Microb Ecol 78:764–780. https://doi.org/10.1007/s00248-019-01347-1
Flessa F, Harjes J, Cáceres ME, Rambold G (2021) Comparative analyses of sooty mould communities from Brazil and Central Europe. Mycol Prog 20(7):869–887. https://doi.org/10.1007/s11557-021-01700-0
Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R, Hansen AJ, Læssøe T, Heilmann-Clausen J (2019) Man against machine: do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients? Biol Conserv 233:201–212. https://doi.org/10.1016/j.biocon.2019.02.038
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes–application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118. https://doi.org/10.1111/j.1365-294X.1993.tb00005.x
Geml J, Gravendeel B, van der Gaag KJ, Neilen M, Lammers Y, Raes N, Semenova TA, de Knijff P, Noordeloos ME (2014a) The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. PLoS ONE 9(6):e99852. https://doi.org/10.1371/journal.pone.0099852
Geml J, Pastor N, Fernandez L, Pacheco S, Semenova TA, Becerra AG, Wicaksono CY, Nouhra ER (2014b) Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient. Mol Ecol 23(10):2452–2472. https://doi.org/10.1111/mec.12765
Gkoutselis GM, Rohrbach S, Harjes J, Obst M, Brachmann A, Horn M, Rambold G (2021) Microplastics accumulate fungal pathogens in terrestrial ecosystems. Sci Rep 11:13214. https://doi.org/10.1038/s41598-021-92405-7
Guerreiro MA, Brachmann A, Begerow D, Peršoh D (2018) Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter. Fungal Divers 8:237–251. https://doi.org/10.1007/s13225-017-0390-4
Harjes J, Janssen TML, Gkoutselis G, Okach DO, Siemonsmeier A, Kinge RT, Blaschke M, Rambold G (submitted) Relations of betweenness centrality and topological coefficient of ectomycorrhizome and soil fungal saprobiome networks may be indicative for total C sequestration trends in soil. Fungal Diversity.
Kranabetter JM, Friesen J, Gamiet S, Kroeger P (2009) Epigeous fruiting bodies of ectomycorrhizal fungi as indicators of soil fertility and associated nitrogen status of boreal forests. Mycorrhiza 19:535–548. https://doi.org/10.1007/s00572-009-0255-0
Nearing JT, Douglas GM, Comeau AM, Langille MGI (2018) Denoising the denoisers: an independent evaluation of microbiome sequence error-correction approaches. PeerJ 6:e5364. https://doi.org/10.7717/peerj.5364
Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Koljalg U, Abarenkov K (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47(D1):D259–D264. https://doi.org/10.1093/nar/gky1022
Oksanen J (2011) Multivariate analysis of ecological communities in R: vegan tutorial. R Package Version 1:1–43
Ovaskainen O, Schigel D, Ali-Kovero H, Auvinen P, Paulin L, Nordén B, Nordén J (2013) Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi. ISME J 7(9):1696–1709. https://doi.org/10.1038/ismej.2013.61
Porter TM, Skillman JE, Moncalvo JM (2008) Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Mol Ecol 17(13):3037–3050. https://doi.org/10.1111/j.1365-294X.2008.03813.x
Purahong W, Wubet T, Lentendu G, Hoppe B, Jariyavidyanont K, Arnstadt T, Baber K, Otto P, Kellner H, Hofrichter M, Bauhus J, Weisser WW, Krüger D, Schulze E-D, Kahl T, Buscot F (2018) Determinants of deadwood-inhabiting fungal communities in temperate forests: Molecular evidence from a large scale deadwood decomposition experiment. Front Microbiol 9:2120. https://doi.org/10.3389/fmicb.2018.02120
R Core Team (2019) R: A language and environment for statistical computing. – R foundation for statistical computing, Wien. http://www.R-project.org/ [Accessed 12 Mar 2020].
Schmidt-Stohn G, Oertel B (2015) Warum DNA-Sequenzierungen an Pilzen auch für Amateur-Mykologen wichtig sind. J JEC 17:75–88
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109(16):6241–6246. https://doi.org/10.1073/pnas.1117018109
Siemonsmeier A, Förster B, Blaschke M (2020) Forest structures and carbon storage in managed and unmanaged forests along an altitudinal gradient in a central European low mountain range. Waldökologie, Landschaftsforschung und Naturschutz – Forest Ecology. Landsc Res Nat Conserv 19:71–88
Siles JA, Margesin R (2016) Abundance and diversity of bacterial, archaeal, and fungal communities along an altitudinal gradient in alpine forest soils: what are the driving factors? Microb Ecol 72:207–220. https://doi.org/10.1007/s00248-016-0748-2
Thomsen PF, Willerslev E (2015) Environmental DNA–an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18. https://doi.org/10.1016/j.biocon.2014.11.019
White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press Inc, New York, pp 315–322
Zamora JC, Ekman S (2020) Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacyonaemataceae fam. nov. Persoonia 44:161–205. https://doi.org/10.3767/persoonia.2020.44.07
Zinger L, Lejon DPH, Baptist F, Bouasria A, Aubert S, Geremia RA, Choler P (2011) Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS ONE. https://doi.org/10.1371/journal.pone.0019950
Acknowledgements
The authors thank Finn Wahl (Bavarian State Institute of Forestry, Freising, Germany) for assistance with trait mapping, Johannes Matt (Nature Park Bavarian Forest) for assistance in the field work, Theresa M. L. Janssen and Gerasimos Gkoutselis (University of Bayreuth, Dept. of Mycology) for assistance in the laboratory. Furthermore, we want to thank the two anonymous reviewers for their valuable comments on the manuscript.
Funding
This study was conducted within the research project “Höhengradient” funded by the Forest Climate Fund, sponsored by the Federal Ministry of Food and Agriculture and the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety, Germany (References: 22WC412201, 22WC412203).
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This project was designed by AS, MB and GR. The fruit body monitoring campaigns were designed by MB and the sampling campaigns and lab workflow for the metabarcoding part by GR and JH. Metabarcoding samples were collected by DO and processed by JH who also analysed the sequence data. The combined analysis of both datasets was conducted by MB and AS. The manuscript was drafted by MB and AS with additions of JH and further elaborated by all co-authors. All authors read and approved the final manuscript.
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Communicated by Yusuf Akhter.
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Blaschke, M., Siemonsmeier, A., Harjes, J. et al. Comparison of survey methods for fungi using metabarcoding and fruit body inventories in an altitudinal gradient. Arch Microbiol 205, 269 (2023). https://doi.org/10.1007/s00203-023-03606-9
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DOI: https://doi.org/10.1007/s00203-023-03606-9