Metabarcoding for plant pathologists

References

• Abdala Asbun A, Besseling MA, Balzano S, van Bleijswijk JDL, Witte HJ, Villanueva L, Engelmann JC. 2020. Cascabel: a scalable and versatile amplicon sequence data analysis pipeline delivering reproducible and documented results. Front Genet. 11:489357. doi: 10.3389/fgene.2020.489357.
   PubMed Web of Science ®Google Scholar
• Abellan-Schneyder I, Matchado MS, Reitmeier S, Sommer A, Sewald Z, Baumbach J, List M, Neuhaus K. 2021. Primer, pipelines, parameters: issues in 16S rRNA gene sequencing. mSphere. 6(1):e01202–20. doi: 10.1128/mSphere.01202-20.
   PubMed Web of Science ®Google Scholar
• Aitchison J, Barceló-Vidal C, Martín-Fernández JA, Pawlowsky-Glahn V. 2000. Logratio analysis and compositional distance. Math Geol. 32(3):271–5. doi: 10.1023/A:1007529726302.
   Google Scholar
• Allen B, Kon M, Bar-Yam Y. 2009. A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. Am Nat. 174(2):236–243. doi: 10.1086/600101.
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2.
   PubMed Web of Science ®Google Scholar
• Anslan S, Bahram M, Hiiesalu I, Tedersoo L. 2017. PipeCraft: flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data. Mol Ecol Resour. 17(6):e234–e240. doi: 10.1111/1755-0998.12692.
   PubMed Web of Science ®Google Scholar
• Anslan S, Mikryukov V, Armolaitis K, Ankuda J, Lazdina D, Makovskis K, Vesterdal L, Schmidt IK, Tedersoo L. 2021. Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms. PeerJ. 9:e12254. doi: 10.7717/peerj.12254.
   PubMed Web of Science ®Google Scholar
• Apprill A, McNally S, Parsons R, Weber L. 2015. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol. 75(2):129–137. doi: 10.3354/ame01753.
   Web of Science ®Google Scholar
• Arrigoni E, Antonielli L, Pindo M, Pertot I, Perazzolli M. 2018. Tissue age and plant genotype affect the microbiota of apple and pear bark. Microbial Res. 211:57–68. doi: 10.1016/j.micres.2018.04.00204.002.
   PubMedGoogle Scholar
• Bastida F, Eldridge DJ, García C, Kenny Png G, Bardgett RD, Delgado-Baquerizo M. 2021. Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes. IMSE J. 15(7):2081–91. doi: 10.1038/s41396-021-00906-0.
   Google Scholar
• Beckers B, Op De Beeck M, Weyens N, Boerjan W, Vangronsveld J. 2017. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome. 5:1–7. doi: 10.1186/s40168-017-0241-2.
   PubMed Web of Science ®Google Scholar
• Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10(1):189. doi: 10.1186/1471-2180-10-189.
   PubMed Web of Science ®Google Scholar
• Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E. 2005. Defining operational taxonomic units using DNA barcode data. Philos T R Soc B. 360(1462):1935–1943. doi: 10.1098/rstb.2005.1725.
   PubMed Web of Science ®Google Scholar
• Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. 2022. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour. 22(4):1231–1246. doi: 10.1111/1755-0998.13512.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi: 10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857. doi: 10.1038/s41587-019-0209-9.
   PubMed Web of Science ®Google Scholar
• Boutigny A-L, Gautier A, Basler R, Dauthieux F, Leite S, Valade R, Aguayo J, Ioos R, Laval V, Melcher U. 2019. Metabarcoding targeting the EF1 alpha region to assess Fusarium diversity on cereals. PLoS ONE. 14(1):e0207988. doi: 10.1371/journal.pone.0207988.
   PubMed Web of Science ®Google Scholar
• Buchner D, Macher T-H, Leese F, Alkan C. 2022. APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. Bioinformatics. 38(20):4817–4819. doi: 10.1093/bioinformatics/btac588.
   PubMed Web of Science ®Google Scholar
• Bukin YS, Galachyants YP, Morozov I, Bukin S, Zakharenko A, Zemskaya T. 2019. The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci Data. 6(1):190007. doi: 10.1038/sdata.2019.7.
   PubMedGoogle Scholar
• Bullington LS, Lekberg Y, Larkin BG. 2021. Insufficient sampling constrains our characterization of plant micro biomes. Sci Rep. 11(1):3645. doi: 10.1038/s41598-021-83153-9.
   PubMed Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Holmes SP. 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11(12):2639–2643. doi: 10.1038/ismej.2017.119.
   PubMed Web of Science ®Google Scholar
• 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(7):581. doi: 10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK. 2019. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 47(18):e103. doi: 10.1093/nar/gkz569.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. P Natl Acad Sci. 108(supplement_1):4516–4522. doi: 10.1073/pnas.1000080107.
   PubMed Web of Science ®Google Scholar
• Chao A, Gotelli NJ, Hsieh T, Sander EL, Ma K, Colwell RK, Ellison AM. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol Monogr. 84(1):45–67. doi: 10.1890/13-0133.1.
   Web of Science ®Google Scholar
• Chen W, Zhang CK, Cheng Y, Zhang S, Zhao H, Casiraghi M. 2013. A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS ONE. 8(8):e70837. doi: 10.1371/journal.pone.0070837.
   PubMed Web of Science ®Google Scholar
• Costello M, Fleharty M, Abreu J, Farjoun Y, Ferriera S, Holmes L, Granger B, Green L, Howd T, Mason T, et al. 2018. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. Bmc Genom. 19(1):332. doi:10.1186/s12864-018-4703.
   PubMedGoogle Scholar
• Daly AJ, Baetens JM, De Baets B. 2018. Ecological diversity: measuring the unmeasurable. Mathematics. 6(7):119. doi: 10.3390/math6070119.
   Web of Science ®Google Scholar
• Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. 2018. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 6(1):226. doi: 10.1186/s40168-018-0605-2.
   PubMedGoogle Scholar
• De Boer SH, López MM. 2012. New grower-friendly methods for plant pathogen monitoring. Annu Rev Phytopathol. 50(1):197–218. doi: 10.1146/annurev-phyto-081211-172942.
   PubMedGoogle Scholar
• Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, et al. 2018. Towards robust and repeatable sampling methods in eDNA-based studies. Mol Ecol Resour. 18(5):940–952. doi:10.1111/1755-0998.12907.
   Web of Science ®Google Scholar
• Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. 2017. Nextflow enables reproducible computational workflows. Nat Biotechnol. 35(4):316–319. doi: 10.1038/nbt.3820.
   PubMed Web of Science ®Google Scholar
• Dixon P. 2003. VEGAN, a package of R functions for community ecology. J Veg Sci. 14(6):927–930. doi: 10.1111/j.1654-1103.2003.tb02228.x.
   Web of Science ®Google Scholar
• Dopheide A, Xie D, Buckley TR, Drummond AJ, Newcomb RD, Bunce M. 2019. Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity. Methods Ecol Evol. 10(1):120–133. doi: 10.1111/2041-210X.13086.
   Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26(19):2460–2461. doi: 10.1093/bioinformatics/btq461.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2016. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv: 081257.
   Google Scholar
• Edgar RC, Valencia A. 2018. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics. 34(14):2371–2375. doi: 10.1093/bioinformatics/bty113.
   PubMed Web of Science ®Google Scholar
• Edwards RA, Rohwer F. 2005. Viral metagenomics. Nat Rev Microbiol. 3(6):504–510. doi: 10.1038/nrmicro1163.
   PubMed Web of Science ®Google Scholar
• Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. 2019. Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends Microbiol. 27(2):105–117. doi: 10.1016/j.tim.2018.11.003.
   PubMed Web of Science ®Google Scholar
• Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G, et al. 2018. FROGS: find, rapidly, OTUs with Galaxy solution. Bioinformatics. 34(8):1287–1294. doi: 10.1093/bioinformatics/btx791.
   PubMed Web of Science ®Google Scholar
• Fierer N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 15(10):579–590. doi: 10.1038/nrmicro.2017.87.
   PubMed Web of Science ®Google Scholar
• Fiore-Donno AM, Human ZR, Štursová M, Mundra S, Morgado L, Kauserud H, Baldrian P, Bonkowski M. 2022. Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition. Soil Biol Biochem. 168:108628. doi: 10.1016/j.soilbio.2022.108628.
   Web of Science ®Google Scholar
• Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature. 484(7393):186–194. doi: 10.1038/nature10947.
   PubMed Web of Science ®Google Scholar
• Foster ZSL, Albornoz FE, Fieland VJ, Larsen MM, Jones FA, Tyler BM, Nguyen HDT, Burgess TI, Riddell C, Voglmayr H, et al. 2022. A new oomycete metabarcoding method using the rps10 gene. Phytobiomes J. 6(3):214–226. doi:10.1094/PBIOMES-02-22-0009-R.
   Google Scholar
• Foster ZSL, Chamberlain S, Grünwald NJ. 2018. Taxa: an R package implementing data standards and methods for manipulation of taxonomic data. F1000Res. 7:272. doi: 10.12688/f1000research.14013.2 2.
   PubMedGoogle Scholar
• Foster ZS, Sharpton TJ, Grünwald NJ, Poisot T. 2017. Metacoder: an R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol. 13(2):e1005404. doi: 10.1371/journal.pcbi.1005404.
   PubMed Web of Science ®Google Scholar
• Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 28(23):3150–3152. doi: 10.1093/bioinformatics/bts565.
   PubMed Web of Science ®Google Scholar
• Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, Schonrogge K, Bunce M. 2015. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol. 6(8):973–980. doi: 10.1111/2041-210X.12399.
   PubMed Web of Science ®Google Scholar
• Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. 2020. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res. 48(W1):W395–W402. doi: 10.1093/nar/gkaa434.
   PubMed Web of Science ®Google Scholar
• Janda JM, Abbott SL. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 45(9):2761–2764. doi: 10.1128/JCM.01228-07.
   PubMed Web of Science ®Google Scholar
• Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinform. 15:1–2. doi: 10.1186/1471-2105-15-182.
   PubMed Web of Science ®Google Scholar
• Jost L. 2006. Entropy and diversity. Oikos. 113(2):363–375. doi: 10.1111/j.2006.0030-1299.14714.x.
   Web of Science ®Google Scholar
• Kemp BM, Smith DG. 2005. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int. 154(1):53–61. doi: 10.1016/j.forsciint.2004.11.017.
   PubMed Web of Science ®Google Scholar
• Kluyver T, Ragan-Kelley B, Pérez F, Granger B, Bussonnier M, Frederic J, Kelley K, Hamrick J, Grout J, Corlay S, et al. 2016. Jupyter notebooks – a publishing format for reproducible computational workflows. In: Loizides F Scmidt B, editors. Positioning and power in academic publishing: players, agents and agendas. IOS Press; pp. 87–90. https://eprints.soton.ac.uk/403913/.
   Google Scholar
• Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 22(21):5271–5277. doi:10.1111/mec.12481.
   PubMed Web of Science ®Google Scholar
• Laforest-Lapointe I, Messier C, Kembel SW. 2016. Tree phyllosphere bacterial communities: exploring the magnitude of intra-and inter-individual variation among host species. PeerJ. 24:e2367. doi: 10.7717/peerj.2367.
   Google Scholar
• Latz MA, Grujcic V, Brugel S, Lycken J, John U, Karlson B, Andersson A, Andersson AF. 2022. Short‐and long‐read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing. Mol Ecol Resour. 22(6):2304–18. doi: 10.1111/1755-0998.13623.
   PubMed Web of Science ®Google Scholar
• Lin H, Peddada SD. 2020. Analysis of compositions of microbiomes with bias correction. Nat Commun. 11:3514. doi: 10.1038/s41467-020-17041-7.
   PubMed Web of Science ®Google Scholar
• Loos D, Zhang L, Beemelmanns C, Kurzai O, Panagiotou G. 2021. DAnIEL: a user-friendly web server for fungal ITS amplicon sequencing data. Front Microbiol. 12. doi: 10.3389/fmicb.2021.720513.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12):550. doi: 10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 71(12):8228–8235. doi: 10.1128/AEM.71.12.8228-8235.2005.
   PubMed Web of Science ®Google Scholar
• Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. 2011. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5(2):169–172. doi: 10.1038/ismej.2010.133.
   PubMed Web of Science ®Google Scholar
• Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR. 1996. The ribosomal database project (RDP). Nucleic Acids Res. 24(1):82–85. doi: 10.1093/nar/24.1.82.
   PubMed Web of Science ®Google Scholar
• Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17(1):10–12. doi: 10.14806/ej.17.1.200.
   Google Scholar
• McLaren MR, Willis AD, Callahan BJ. 2019. Consistent and correctable bias in metagenomic sequencing experiments. Elife. 8:e46923. doi: 10.7554/eLife.46923.
   PubMed Web of Science ®Google Scholar
• McNear DH Jr. 2013. The rhizosphere-roots, soil and everything in between. Nature Ed Knowl. 4(3):1.
   Google Scholar
• Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, et al. 2021. Sustainable data analysis with Snakemake. F1000Res. 10:33. doi: 10.12688/f1000research.29032.2.
   PubMedGoogle Scholar
• Munoz‐Ucros J, Zwetsloot MJ, Cuellar‐Gempeler C, Bauerle TL, Wandrag E. 2021. Spatiotemporal patterns of rhizosphere microbiome assembly: from ecological theory to agricultural application. J Appl Ecol. 58(5):894–904. doi: 10.1111/1365-2664.13850.
   Web of Science ®Google Scholar
• Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. 2016. Funguild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20:241–248. doi: 10.1016/j.funeco.2015.06.006.
   Web of Science ®Google Scholar
• Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B. 2018. Minimizing polymerase biases in metabarcoding. Mol Ecol Resour. 18(5):927–939. doi: 10.1111/1755-0998.12895.
   Web of Science ®Google Scholar
• Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. 2019. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol. 17(2):95–109. doi: 10.1038/s41579-018-0116-y.
   PubMed Web of Science ®Google Scholar
• Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K-H, Kõljalg U, Fairhead C. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE. 1(1):e59. doi: 10.1371/journal.pone.0000059.
   PubMed Web of Science ®Google Scholar
• Oksanen J 2010. Vegan: community ecology package. http://CRAN.R-project.org/package=vegan.
   Google Scholar
• Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol. 188(1):223–241. doi: 10.1111/j.1469-8137.2010.03334.x.
   PubMed Web of Science ®Google Scholar
• Özkurt E, Fritscher J, Soranzo N, DYK N, Davey RP, Bahram M, Hildebrand F. 2022. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome. 10(1):176. doi: 10.1186/s40168-022-01365-1.
   PubMed Web of Science ®Google Scholar
• Palmer JM, Jusino MA, Banik MT, Lindner DL. 2018. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ. 6:e4925. doi: 10.7717/peerj.4925.
   PubMed Web of Science ®Google Scholar
• Parada AE, Needham DM, Fuhrman JA. 2016. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 18(5):1403–1414. doi: 10.1111/1462-2920.13023.
   PubMed Web of Science ®Google Scholar
• Paulson JN, Stine OC, Bravo HC, Pop M. 2013. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 10(12):1200–1202. doi: 10.1038/nmeth.2658.
   PubMed Web of Science ®Google Scholar
• Pervaiz ZH, Contreras J, Hupp BM, Lindenberger JH, Chen D, Zhang Q, Wang C, Twigg P, Saleem M. 2020. Root microbiome changes with root branching order and root chemistry in peach rhizosphere soil. Rhizosphere. 16:100249. doi: 10.1016/j.rhisph.2020.100249.
   Web of Science ®Google Scholar
• Pielou EC. 1966. The measurement of diversity in different types of biological collections. J Theor Biol. 13:131–144. doi: 10.1016/0022-5193(66)90013-0.
   Web of Science ®Google Scholar
• Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L. 2021. Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms. 9(1):188. doi: 10.3390/microorganisms9010188.
   PubMed Web of Science ®Google Scholar
• Prince AM, Andrus L. 1992. PCR: how to kill unwanted DNA. Biotechniques. 12(3):358–360.
   PubMed Web of Science ®Google Scholar
• Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM, Zhou J. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microb. 67(2):880–887. doi: 10.1128/AEM.67.2.880-887.2001.
   PubMed Web of Science ®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(Database issue):D590–D596. doi: 10.1093/nar/gks1219.
   PubMed Web of Science ®Google Scholar
• Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. 2017. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 35(9):833–844. doi: 10.1038/nbt.3935.
   PubMed Web of Science ®Google Scholar
• Richter-Heitmann T, Eickhorst T, Knauth S, Friedrich MW, Schmidt H. 2016. Evaluation of strategies to separate root-associated microbial communities: a crucial choice in rhizobiome research. Front Microbiol. 7. doi: 10.3389/fmicb.2016.00773.
   PubMed Web of Science ®Google Scholar
• Riit T, Tedersoo L, Drenkhan R, Runno-Paurson E, Kokko H, Anslan S. 2016. Oomycete-specific ITS primers for identification and metabarcoding. MycoKeys. 14:17–30. doi: 10.3897/mycokeys.14.9244.
   Google Scholar
• R Markdown: dynamic documents for R. 2023. https://github.com/rstudio/rmarkdown.
   Google Scholar
• Robertson BL, Brown JA, McDonald T, Jaksons P. 2013. BAS: balanced acceptance sampling of natural resources. Biometrics. 69(3):776–784. doi: 10.1111/biom.12059.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26(1):139–140. doi: 10.1093/bioinformatics/btp616.
   PubMed Web of Science ®Google Scholar
• Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 4:e2584. doi: 10.7717/peerj.2584.
   PubMed Web of Science ®Google Scholar
• Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, Harkins TT, Cookson BT, Hoffman NG, Löffler FE. 2014. Performance comparison of Illumina and Ion Torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol. 80(24):7583–7591. doi: 10.1128/AEM.02206-14.
   PubMed Web of Science ®Google Scholar
• Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12(1):87. doi: 10.1186/s12915-014-0087-z.
   PubMed Web of Science ®Google Scholar
• Sanzani SM, Destri Nicosia MG L, Faedda R, Cacciola SO, Schena L. 2014. Use of quantitative PCR detection methods to study biocontrol agents and phytopathogenic fungi and oomycetes in environmental samples. J Phytopathol. 162(1):1–13. doi: 10.1111/jph.12147.
   Web of Science ®Google Scholar
• Sapkota R, Jørgensen LN, Nicolaisen M. 2017. Spatiotemporal variation and networks in the mycobiome of the wheat canopy. Front Plant Sci. 2(8):1357. doi: 10.3389/fpls.2017.01357.
   Google Scholar
• Sapkota R, Nicolaisen M. 2015. An improved high throughput sequencing method for studying oomycete communities. J Microbiol Meth. 110:33–39. doi: 10.1016/j.mimet.2015.01.013.
   PubMed Web of Science ®Google Scholar
• Sapp M, Lewis E, Moss S, Barrett B, Kirk S, Elphinstone JG, Denman S. 2016. Metabarcoding of bacteria associated with the acute oak decline syndrome in England. Forests. 7(5):95. doi: 10.3390/f7050095.
   Web of Science ®Google Scholar
• Schloss PD. 2020. Reintroducing mothur: 10 years later. McBain AJ, editor. Appl Environ Microbiol. 86(2):e02343–19. doi:10.1128/AEM.02343-19.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 75(23):7537–7541. doi: 10.1128/AEM.01541-09.
   PubMed Web of Science ®Google Scholar
• Schrader C, Schielke A, Ellerbroek L, Johne R. 2012. PCR inhibitors–occurrence, properties and removal. J Appl Microbiol. 113(5):1014–1026. doi: 10.1111/j.1365-2672.2012.05384.x.
   PubMed Web of Science ®Google Scholar
• Shannon CE. 1948. A mathematical theory of communication. Bell Syst Tech J. 27(3):379–423. doi: 10.1002/j.1538-7305.1948.tb01338.x.
   Google Scholar
• Simpson EH. 1949. Measurement of diversity. Naturen. 163(4148):688–688. doi: 10.1038/163688a0.
   Google Scholar
• Sow A, Brévault T, Benoit L, Chapuis M-P, Galan M, Coeur D’acier A, Delvare G, Sembène M, Haran J. 2019. Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding. Sci Rep. 9(1):1–12. doi: 10.1038/s41598-019-40243-z.
   PubMedGoogle Scholar
• Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. 2020. Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline. Front Microbiol. 11:550420. doi: 10.3389/fmicb.2020.550420.
   PubMed Web of Science ®Google Scholar
• Sylla J, Alsanius BW, Krüger E, Reineke A, Strohmeier S, Wohanka W. 2013. Leaf microbiota of strawberries as affected by biological control agents. Phytopathology. 103(10):1001–1011. doi: 10.1094/PHYTO-01-13-0014-R.
   PubMed Web of Science ®Google Scholar
• Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol. 21(8):2045–2050. doi: 10.1111/j.1365-294X.2012.05470.x.
   PubMed Web of Science ®Google Scholar
• Tedersoo L, Albertsen M, Anslan S, Callahan B, Druzhinina IS. 2021. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Appl Environ Microbiol. 87(17):e00626–21. doi: 10.1128/AEM.00626-21.
   PubMed Web of Science ®Google Scholar
• Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. 2022. Best practices in metabarcoding of fungi: from experimental design to results. Mol Ecol. 31(10):2769–2795. doi: 10.1111/mec.16460.
   PubMed Web of Science ®Google Scholar
• Tedersoo L, Lindahl B. 2016. Fungal identification biases in microbiome projects. Env Microbiol Rep. 8(5):774–779. doi: 10.1111/1758-2229.12438.
   PubMed Web of Science ®Google Scholar
• Theil S, Rifa E. 2021. rANOMALY: AmplicoN wOrkflow for microbial community anaLysis. F1000Res. 10(7): doi: 10.12688/f1000research27268.1.
   PubMedGoogle Scholar
• U’Ren JM, Riddle JM, Monacell JT, Carbone I, Miadlikowska J, Arnold AE. 2014. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Mol Ecol Resour. 14(5):1032–1048. doi: 10.1111/1755-0998.12252.
   PubMed Web of Science ®Google Scholar
• Vasar M, Davison J, Neuenkamp L, Sepp S-K, Young JPW, Moora M, Öpik M. 2021. User-friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences. Mol Ecol Resour. 21(4):1380–1392. doi: 10.1111/1755-0998.13340.
   PubMed Web of Science ®Google Scholar
• Wagner MR, Lundberg DS, Del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T. 2016. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun. 7(1):12151. doi: 10.1038/ncomms12151.
   PubMedGoogle 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(16):5261–5267. doi: 10.1128/AEM.00062-07.
   PubMed Web of Science ®Google Scholar
• Warwick RM, Clarke KR. 1995. New ‘biodiversity’ measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser. 129:301–305. doi: 10.3354/meps129301.
   Web of Science ®Google Scholar
• White T, Bruns T, Lee S, Taylor J, Innis M, Gelfand D, Sninsky J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. Vol. 31. London (UK): Academic Press; pp. 315–322.
   Google Scholar
• Xie Y, Allaire JJ, Grolemund G. 2018. R Markdown: the definitive guide. Boca Raton (FL): Chapman and Hall/CRC. https://bookdown.org/yihui/rmarkdown.
   Google Scholar
• Xie Y, Dervieux C, Riederer E. 2020. R Markdown cookbook. Boca Raton (FL): Chapman and Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.
   Google Scholar
• Zafeiropoulos H, Viet HQ, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E. 2020. PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience. 9(3):giaa022. doi: 10.1093/gigascience/giaa022.
   PubMed Web of Science ®Google Scholar
• Zhang J, Kobert K, Flouri T, Stamatakis A. 2014. PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics. 30(5):614–620. doi: 10.1093/bioinformatics/btt593.
   PubMed Web of Science ®Google Scholar