Skip to main content

Advertisement

SpringerLink
Log in

Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi

  • Original Article
  • Published:
Mycorrhiza Aims and scope Submit manuscript

Abstract

The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L (2016) Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev 40:686–700

    Article  PubMed  Google Scholar 

  • Bates D, Mächler M, Bolker B, Walker S (2015) Fitting linear mixed-effects models using lme4. J Stat Softw 67:1–48

    Article  Google Scholar 

  • Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic Acids Res 41:D36–D42

    Article  CAS  PubMed  Google Scholar 

  • Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27:233–243

    Article  PubMed  PubMed Central  Google Scholar 

  • Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–59

    Article  CAS  PubMed  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bradley IM, Pinto AJ, Guest JS (2016) Design and evaluation of Illumina MiSeq-compatible, 18S rRNA gene-specific primers for improved characterization of mixed phototrophic communities. Appl Environ Microbiol 82:5878–5891

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown SP, Callaham MA, Oliver AK, Jumpponen A (2013) Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiol Ecol 86:557–566

    Article  CAS  PubMed  Google Scholar 

  • Burke CM, Darling AE (2016) A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq. Peer J 4:e2492

    Article  PubMed  PubMed Central  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinf 10:421

    Article  Google Scholar 

  • Cline LC, Zak DR, Upchurch RA, Freedman ZB, Peschel AR (2017) Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe. Ecol Lett 20:202–211

    Article  PubMed  Google Scholar 

  • Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771

    Article  CAS  PubMed  Google Scholar 

  • Cui XC, Hu JL, Wang JH, Yang JS, Lin XG (2016) Reclamation negatively influences arbuscular mycorrhizal fungal community structure and diversity in coastal saline-alkaline land in Eastern China as revealed by Illumina sequencing. Appl Soil Ecol 98:140–149

    Article  Google Scholar 

  • Davison J, Moora M, Öpik M, Adholeya A, Ainsaar L, Bâ A, Burla S, Diedhiou AG, Hiiesalu I, Jairus T, Johnson NC, Kane A, Koorem K, Kochar M, Ndiaye C, Pärtel M, Reier Ü, Saks Ü, Singh R, Vasar M, Zobel M (2015) Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349:970–973

    Article  CAS  PubMed  Google Scholar 

  • Davison J, Öpik M, Zobel M, Vasar M, Metsis M, Moora M (2012) Communities of arbuscular mycorrhizal fungi detected in forest soil are spatially heterogeneous but do not vary throughout the growing season. PLoS One 7:e41938

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • del Campo J, Sieracki ME, Molestina R, Keeling P, Massana R, Ruiz-Trillo I (2014) The others: our biased perspective of eukaryotic genomes. Trends Ecol Evol 29:252–259

    Article  PubMed  PubMed Central  Google Scholar 

  • Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36:e105

    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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia K, Doidy J, Zimmermann SD, Wipf D, Courty PE (2016) Take a trip through the plant and fungal transportome of mycorrhiza. Trends Plant Sci 21:937–950

    Article  CAS  PubMed  Google Scholar 

  • Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12:245

    Article  PubMed  PubMed Central  Google Scholar 

  • Glassman SI, Peay KG, Talbot JM, Smith DP, Chung JA, Taylor JW, Vilgalys R, Bruns TD (2015) A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern. New Phytol 205:1619–1631

    Article  CAS  PubMed  Google Scholar 

  • Hart MM, Aleklett K, Chagnon PL, Egan C, Ghignone S, Helgason T, Lekberg Y, Öpik M, Pickles BJ, Waller L (2015) Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. New Phytol 207:235–247

    Article  PubMed  Google Scholar 

  • Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5:183–188

    Article  CAS  PubMed  Google Scholar 

  • Johansen RB, Johnston P, Mieczkowski P, Perry GLW, Robeson MS, Burns BR, Vilgalys R (2016) A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities. Fungal Ecol 23:141–155

    Article  Google Scholar 

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kenward MG, Roger JH (1997) Small sample inference for fixed effects from restricted maximum likelihood. Biometrics 53:983–997

    Article  CAS  PubMed  Google Scholar 

  • Lee HK, Lee CK, Tang JW, Loh TP, Koay ES (2016) Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer. Sci Rep 6:33318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee J, Lee S, Young JPW (2008) Improved PCR primers form the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 65:339–349

    Article  CAS  PubMed  Google Scholar 

  • Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, Mu D, Pang E, Cao H, Cha H, Lin T, Zhou Q, Shang Y, Li Y, Sharma T, van Velzen R, de Ruijter N, Aanen DK, Win J, Kamoun S, Bisseling T, Geurts R, Huang S (2014) Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet 10:e1004078

    Article  PubMed  PubMed Central  Google Scholar 

  • Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjoller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H (2013) Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide. New Phytol 199:288–299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu M, Zheng R, Bai SL, Bai Y, Wang JG (2017) Slope aspect influences arbuscular mycorrhizal fungus communities in arid ecosystems of the Daqingshan Mountains, Inner Mongolia, North China. Mycorrhiza 27:189–200

    Article  PubMed  Google Scholar 

  • Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963

    Article  PubMed  PubMed Central  Google Scholar 

  • Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD (2012) PANDAseq: paired-end assembler for illumina sequences. BMC Bioinf 13:31

    Article  CAS  Google Scholar 

  • Medinger R, Nolte V, Pandey RV, Jost S, Ottenwälder B, Schlötterer C, Boenigk J (2010) Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19:32–40

    Article  PubMed  PubMed Central  Google Scholar 

  • Minoche AE, Dohm JC, Himmelbauer H (2011) Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol 12:R112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW (2014) Improved multiple displacement amplification (iMDA) and ultraclean reagents. BMC Genomics 15:443

    Article  PubMed  PubMed Central  Google Scholar 

  • Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 39:e90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL (2011) Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 12:106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Niklas N, Pröll J, Danzer M, Stabentheiner S, Hofer K, Gabriel C (2013) Routine performance and errors of 454 HLA exon sequencing in diagnostics. BMC Bioinf 14:176

    Article  Google Scholar 

  • Oksanen J, Blanchet GF, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2016) Vegan: community ecology package. R package version 2:3–5 https://CRAN.R-project.org/package=vegan

    Google Scholar 

  • Oliver AK, Brown SP, Callaham MA, Jumpponen A (2015) Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15%. Fungal Ecol 15:86–89

    Article  Google Scholar 

  • Ondov BD, Bergman NH, Phillippy AM (2011) Interactive metagenomic visualization in a web browser. BMC Bioinf 12:385

    Article  Google Scholar 

  • Öpik M, Davison J, Moora M, Zobel M (2014) DNA-based detection and identification of Glomeromycota: the virtual taxonomy of environmental sequences. Botany 92:135–147

    Article  Google Scholar 

  • Öpik M, Davison J (2016) Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity. Fungal Ecol 24B:106–113

    Article  Google Scholar 

  • Öpik M, Metsis M, Weedon JT, Zobel M, Moora M (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol 184:424–437

    Article  PubMed  Google Scholar 

  • Öpik M, Moora M, Liira J, Zobel M (2006) Composition of root-colonizing arbuscular mycorrhizal fungal communities in different ecosystems around the globe. J Ecol 94:778–790

    Article  Google Scholar 

  • Öpik M, Moora M, Zobel M, Saks Ü, Wheatley R, Wright F, Daniell T (2008) High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest. New Phytol 179:867–876

    Article  PubMed  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 188:223–241

    Article  PubMed  Google Scholar 

  • Öpik M, Zobel M, Cantero JJ, Davison J, Facelli JM, Hiiesalu I, Jairus T, Kalwij JM, Koorem K, Leal ME, Liira J, Metsis M, Neshataeva V, Paal J, Phosri C, Põlme S, Reier Ü, Saks Ü, Schimann H, Thiéry O, Vasar M, Moora M (2013) Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi. Mycorrhiza 23:411–430

    Article  PubMed  Google Scholar 

  • Orchard S, Hilton S, Bending GD, Dickie IA, Standish RJ, Gleeson DB, Jeffery RP, Powell JR, WALKER C, Bass D, Monk J, Simonin A, Ryan MH (2017) Fine endophytes (Glomus Tenue) are related to Mucoromycotina, not Glomeromycota. New Phytol 213:481–486

    Article  PubMed  Google Scholar 

  • Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35:e130

    Article  PubMed  PubMed Central  Google Scholar 

  • Parikh HI, Koparde VN, Bradley SP, Buck GA, Sheth NU (2016) MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. BMC Bioinf 17:491

    Article  Google Scholar 

  • Perkins TT, Tay CY, Thirriot F, Marshall B (2013) Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes. PLoS One 8:e67539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Picher ÁJ, Budeus B, Wafzig O, Krüger C, García-Gómez S, Martínez-Jiménez MI, Díaz-Talavera A, Weber D, Blanco L, Schneider A (2016) TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol. Nat Commun 7:13296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pozo MJ, Lopez-Raez JA, Azcon-Aguilar C, Garcia-Garrido JM (2015) Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses. New Phytol 205:1431–1436

    Article  CAS  PubMed  Google Scholar 

  • Randle-Boggis RJ, Helgason T, Sapp M, Ashton PD (2016) Evaluating techniques for metagenome annotation using simulated sequence data. FEMS Microbiology Ecology 92:fiw095

  • Reeder J, Knight R (2009) The 'rare biosphere': a reality check. Nat Methods 6:636–637

    Article  CAS  PubMed  Google Scholar 

  • Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng Des Sel 12:85–94

    Article  CAS  Google Scholar 

  • Saks Ü, Davison J, Öpik M, Vasar M, Moora M, Zobel M (2014) Root-colonizing and soil-borne communities of arbuscular mycorrhizal fungi in a temperate forest understory. Botany 92:277–285

    Article  Google Scholar 

  • Salvioli A, Ghignone S, Novero M, Navazio L, Bagnaresi P, Bonfante P (2016) Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential. ISME J 10:130–144

    Article  CAS  PubMed  Google Scholar 

  • Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G (2012) Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 13:682–695

    Article  CAS  PubMed  Google Scholar 

  • Schlaeppi K, Bender SF, Mascher F, Russo G, Patrignani A, Camenzind T, Hemple S, Rilling MC, van der Heijden MGA (2016) High-resolution community profiling of arbuscular mycorrhizal fungi. New Phytol 212:780–791

    Article  CAS  PubMed  Google Scholar 

  • Schmidt PA, Bálint M, Greshake B, Bandow C, Römbke J, Schmitt I (2013) Illumina metabarcoding of a soil fungal community. Soil Biol Biochem 65:128–132

    Article  CAS  Google Scholar 

  • Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805

    Article  CAS  PubMed  Google Scholar 

  • Simon L, Lalonde M, Bruns TD (1992) Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots. Appl Environ Microbiol 58:291–295

    CAS  PubMed  PubMed Central  Google Scholar 

  • Smith SE, Read DJ (2008) Mycorrhizal symbiosis. Academic Press, Amsterdam

    Google Scholar 

  • Spatafora JW, Chang Y, Benny GL, Lazarus KL, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE (2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108:1028–1046

    Article  PubMed  Google Scholar 

  • Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C (2016) A survey of the gene repertoire of Gigaspora Rosea unravels conserved features among Glomeromycota for obligate biotrophy. Front Microbiol 7:233

    PubMed  PubMed Central  Google Scholar 

  • Taylor JD, Helgason T, Öpik M (2017) Molecular community ecology of arbuscular mycorrhizal fungi. In: Dighton J, White JF, eds. The fungal community: its organization and role in the ecosystem, 4th edn. CRC Press, 00

  • Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson H, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding of fungi. MycoKeys 10:1–43

    Article  Google Scholar 

  • 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 Phytol 188:291–301

    Article  CAS  PubMed  Google Scholar 

  • Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 18:1979–1990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thiéry O, Vasar M, Jairus T, Davison J, Roux C, Kivistik PA, Metspalu A, Milani L, Saks Ü, Moora M, Zobel M (2016) Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent. Mol Ecol 25:2816–2832

    Article  PubMed  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics-a guide from sampling to data analysis. Microb Inf Exp 2:3

    Article  Google Scholar 

  • Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Becard G, Bonfante P, Paszkowski U, Shachar-Hill Y, Tuskan GA, JPW Y, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 110:20117–20122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Treseder KK (2016) Model behavior of arbuscular mycorrhizal fungi: predicting soil carbon dynamics under climate change. Botany 94:417–423

    Article  CAS  Google Scholar 

  • van der Heijden MGA, de Bruin S, Luckerhoff L, van Logtestijn RSP, Schlaeppi K (2015) A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment. ISME J 10:389–399

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang C, White PJ, Li CJ (2016) Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site. Mycorrhiza 27:369–381

    Article  CAS  PubMed  Google Scholar 

  • Xu TL, Veresoglou SD, Chen YL, Rillig MC, Xiang D, Ondrej D, Hao ZP, Liu L, Deng Y, Hu YJ, Chen WP, Wang JT, He JZ, Chen BD (2016) Plant community, geographic distance and abiotic factors play different roles in predicting AMF biogeography at the regional scale in northern China. Environ Microbiol Rep 8:1048–1057

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics 30:614–620

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was funded by grants from the Estonian Research Council (grant IUT 20-28), the European Regional Development Fund (Centre of Excellence EcolChange) and ERA-NET Cofund BiodivERsA project SoilMan. Preparatory procedures for 454 sequencing were performed by BiotaP Ltd. (Tallinn, Estonia). RA and MR were supported by the EU ERDF through the Estonian Centre of Excellence in Genomics and Translational Medicine (project no. 2014-2020.4.01.15-0012) and by the Estonian Ministry of Education and Research (institutional grant IUT34-11). We are grateful to the Estonian Genome Centre for technical support.

Author information

Authors and Affiliations

  1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia

    Martti Vasar, John Davison, Teele Jairus, Mari Moora, Martin Zobel & Maarja Öpik

  2. Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Str, 51010, Tartu, Estonia

    Reidar Andreson & Maido Remm

  3. Estonian Biocentre, 23b Riia Str, 51010, Tartu, Estonia

    Reidar Andreson

  4. Department of Biology, University of York, York, YO10 5DD, UK

    J. P. W. Young

Authors
  1. Martti Vasar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Reidar Andreson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John Davison
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Teele Jairus
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mari Moora
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Maido Remm
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. P. W. Young
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Martin Zobel
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Maarja Öpik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Martti Vasar.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

ESM 1

(PDF 1495 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Vasar, M., Andreson, R., Davison, J. et al. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza 27, 761–773 (2017). https://doi.org/10.1007/s00572-017-0791-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00572-017-0791-y

Keywords

Search

Navigation