Traditionally, characterisation and comparison of AMF communities has been carried out by morphological identification of asexual spores in soil. In recent decades, molecular methods such as soil metabarcoding have become more popular than morphological identification of spores, but direct comparisons of the efficiency of both approaches have been rare. In this study, we compared AMF communities in soil samples from vegetable farms using both morphological and molecular methods (internal transcribed spacer, ITS, markers). In addition, we performed a systematic literature search and retrieved nine studies that analysed AMF communities using both approaches in the same soil samples, mostly in agroecosystems. Our results show that AMF communities determined by morphological spore-based identification are different than those determined by molecular genetic markers, but not as often claimed. In some cases, the morphological spore-based characterisation of spores revealed more diverse glomeromycotan communities. Moreover, in several cases the spore-based methods recovered taxa that the molecular methods did not, while in other cases the opposite was observed. The field and literature-based results of this study indicate that for a comprehensive and exhaustive characterisation of AMF communities it is necessary to combine both approaches. However, if the aim is to compare communities under different environmental conditions, both approaches provide comparable patterns.

Institute of Botany Czech Academy of Sciences Zámek 1 Průhonice 252 43 Czech Republic

Instituto Multidisciplinario de Biología Vegetal CONICET FCEFyN Universidad Nacional de Córdoba CC 495 Córdoba 5000 Argentina

Zobrazit více v PubMed

Abarenkov K et al (2021) Full UNITE + INSD dataset for eukaryotes. UNITE Community

Babalola BJ, Li J, Willing CE, Zheng Y et al (2022) Nitrogen fertilisation disrupts the Temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field. New Phytol 234(6):2057–2072. https://doi.org/10.1111/nph.18043 PubMed DOI

Bardgett RD, Van Der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515(7528):505–511. https://doi.org/10.1038/nature13855 PubMed DOI

Berruti A, Lumini E, Bianciotto V (2017) AMF components from a microbial inoculum fail to colonize roots and lack soil persistence in an arable maize field. Symbiosis 72:73–80. https://doi.org/10.1007/s13199-016-0442-7 DOI

Bidondo LF, Colombo RP, Recchi M, Silvani VA, Pérgola M, Martínez A, Godeas AM (2018) Detection of arbuscular mycorrhizal fungi associated with Pecan (Carya illinoinensis) trees by molecular and morphological approaches. MycoKeys 42:73–88. https://doi.org/10.3897/mycokeys.42.26118 DOI

Błaszkowski J (2012) Glomeromycota. W. Szafer Institute of Botany, Polish Academy of Sciences

Blaxter M, Mann J, Chapman T et al (2005) Defining operational taxonomic units using DNA barcode data. Philos T R Soc B 360(1462):1935–1943. https://doi.org/10.1098/rstb.2005.1725 DOI

Brundrett MC (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154(2):275–304. https://doi.org/10.1046/j.1469-8137.2002.00397.x PubMed DOI

Calaça FJS, Bustamante M (2022) Richness of arbuscular mycorrhizal fungi (Glomeromycota) along a vegetation gradient of Brazilian Cerrado: responses to seasonality, soil types, and plant communities. Mycol Prog 21(2):1–15. https://doi.org/10.1007/s11557-022-01785-1 DOI

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. https://doi.org/10.1038/ismej.2017.119 PubMed DOI PMC

Carini P, Marsden PJ, Leff JW, Morgan EE, Strickland MS, Fierer N (2016) Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol 2:1624. https://doi.org/10.1038/nmicrobiol.2016.242 DOI

Chagnon PL, Bainard LD (2015) Using molecular biology to study mycorrhizal fungal community ecology: limits and perspectives. Plant Signal Behav 10(7):e1046668. https://doi.org/10.1080/15592324.2015.1046668 PubMed DOI PMC

Cofré MN, Ferrari AE, Becerra A, Domínguez L, Wall LG, Urcelay C (2017) Effects of cropping systems under no-till agriculture on arbuscular mycorrhizal fungi in Argentinean Pampas. Soil Use Manag 33(2):364–378. https://doi.org/10.1111/sum.12349 DOI

Colombo RP, Fernandez Bidondo L et al (2014) Diversity of arbuscular mycorrhizal fungi in soil from the Pampa Ondulada, Argentina, assessed by pyrosequencing and morphological techniques. Can J Microbiol 60(12):819–827. https://doi.org/10.1139/cjm-2014-0364 PubMed DOI

Conti G, Urcelay C, Gundel PE, Piñeiro G (2025) The potential of arbuscular mycorrhizal fungi to improve soil organic carbon in agricultural ecosystems: A meta-analytical approach. Funct Ecol 00:1–15. https://doi.org/10.1111/1365-2435.14753 DOI

Delavaux CS, Smith-Ramesh LM, Kuebbing SE (2017) Beyond nutrients: a meta‐analysis of the diverse effects of arbuscular mycorrhizal fungi on plants and soils. Ecology 98(8):2111–2119. https://doi.org/10.1002/ecy.1892 PubMed DOI

Delgado-Baquerizo M, Reich PB, Trivedi C et al (2020) Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol 4(2):210–220. https://doi.org/10.1038/s41559-019-1084-y PubMed DOI

Druille M, Cabello MN, Omacini M, Golluscio RA (2013a) Glyphosate reduces spore viability and root colonization of arbuscular mycorrhizal fungi. Appl Soil Ecol 64:99–103. https://doi.org/10.1016/j.apsoil.2012.10.007 DOI

Druille M, Omacini M, Golluscio RA, Cabello MN (2013b) Arbuscular mycorrhizal fungi are directly and indirectly affected by glyphosate application. Appl Soil Ecol 72:143–149. https://doi.org/10.1016/j.apsoil.2013.06.011 DOI

Fadiji AE, Babalola OO (2020) Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods 170:105860. https://doi.org/10.1016/j.mimet.2020.105860 PubMed DOI

Faggioli VS, Cabello MN, Grilli G, Vasar M, Covacevich F, Öpik M (2019) Root colonizing and soil borne communities of arbuscular mycorrhizal fungi differ among soybean fields with contrasting historical land use. Agr Ecosyst Environ 269:174–182. https://doi.org/10.1016/j.agee.2018.10.002 DOI

Faggioli VS, Covacevich F, Grilli G et al (2022) Environmental response of arbuscular mycorrhizal fungi under soybean cultivation at a regional scale. Mycorrhiza 32:425–438. https://doi.org/10.1007/s00572-022-01093-2 PubMed DOI

Gerdemann JW, Nicolson TH (1963) Spores of mycorrhizal Endogone species extracted from soil by wet Sieving and decanting. T Brit Mycol Soc 46(2):235–244. https://doi.org/10.1016/S0007-1536(63)80079-0 DOI

Grilli G, Cofré N, Marro N, Videla M, Urcelay C (2023) Shifts from conventional horticulture to agroecology impacts soil fungal diversity in central Argentina. Micol Prog. https://doi.org/10.1007/s11557-023-01872-x

Hart MM, Klironomos JN (2003) Diversity of arbuscular mycorrhizal fungi and ecosystem functioning. Mycorrhizal ecology. Springer, Berlin, Heidelberg, pp 225–242. DOI: https://doi.org/10.1007/978-3-540-38364-2_9 DOI

Hart MM, Aleklett K, Chagnon PL et al (2015) Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. New Phytol 207(1):235–247. https://doi.org/10.1111/nph.13340 PubMed DOI

Hoeksema JD, Chaudhary VB, Gehring CA, Johnson NC, Karst J, Koide RT, Pringle A, Zabinski C, Bever JD, Moore JC, Wilson GWT, Klironomos JN, Umbanhowar J (2010) A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi. Ecol Lett 13:394–407. https://doi.org/10.1111/j.1461-0248.2009.01430.x PubMed DOI

Jiao H, Chen Y, Lin X, Liu R (2011) Diversity of arbuscular mycorrhizal fungi in greenhouse soils continuously planted to watermelon in North China. Mycorrhiza 21:681–688. https://doi.org/10.1007/s00572-011-0377-z PubMed DOI

Johnson NC, Angelard C, Sanders IR, Kiers ET (2013) Predicting community and ecosystem outcomes of mycorrhizal responses to global change. Ecol Lett 16:140–153. https://doi.org/10.1111/ele.12085 PubMed DOI

Karst J, Piculell B, Brigham C, Booth M, Hoeksema JD (2013) Fungal communities in soils along a vegetative ecotone. Mycologia 105(1):61–70. https://doi.org/10.3852/12-042 PubMed DOI

Kemmelmeier K, dos Santos DA, Grittz GS et al (2022) Composition and seasonal variation of the arbuscular mycorrhizal fungi spore community in litter, root mat, and soil from a subtropical rain forest. Mycorrhiza 32:409–423. https://doi.org/10.1007/s00572-022-01084-3 PubMed DOI

Kokkoris V, Hart MM (2019) The role of in vitro cultivation on symbiotic trait and function variation in a single species of arbuscular mycorrhizal fungus. Fungal Biol 123:732–744. https://doi.org/10.1016/j.funbio.2019.06.009 PubMed DOI

Kokkoris V, Banchini C, Paré L et al (2024) Rhizophagus irregularis, the model fungus in arbuscular mycorrhiza research, forms dimorphic spores. New Phytol 242(4):1771–1784. https://doi.org/10.1111/nph.19121 PubMed DOI

Kolaříková Z, Slavikova R, Krüger C, Krüger M, Kohout P (2021) PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi. New Phytol 231(1):490–499. https://doi.org/10.1111/nph.17372 PubMed DOI

Lanfranco L, Bonfante P, Genre A (2016) The mutualistic interaction between plants and arbuscular mycorrhizal fungi. Microbiol Spectr 4(6):4–6. https://doi.org/10.1128/microbiolspec.funk-0012-2016 DOI

Lange V, Böhme I, Hofmann J et al (2014) Cost-efficient high-throughput HLA typing by miseq amplicon sequencing. BMC Genomics 15:1–11. https://doi.org/10.1186/1471-2164-15-63 DOI

Lee SJ, Risse E, Mateus ID, Sanders IR (2024) Evolution of unexpected diversity in a putative mating type locus and its correlation with genome variability reveals likely asexuality in the model mycorrhizal fungus Rhizophagus irregularis. BMC Genomics 25(1):888. https://doi.org/10.1186/s12864-024-10770-9 PubMed DOI PMC

Lekberg Y, Vasar M, Bullington LS et al (2018) More Bang for the Buck?? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? New Phytol 220(4):971–976. https://www.jstor.org/stable/90026163 PubMed DOI

Li S, Deng Y, Wang Z et al (2020) Exploring the accuracy of amplicon-based internal transcribed spacer markers for a fungal community. Mol Ecol Resour. 2020; 20: 170–184. https://doi.org/10.1111/1755-0998.13097

Manoharan L, Rosenstock NP, Williams A, Hedlund K (2017) Agricultural management practices infuence AMF diversity and community composition with cascading efects on plant productivity. Appl Soil Ecol 115:53–59. https://doi.org/10.1016/j.apsoil.2017 03.012 DOI

Marro N, Grilli G, Soteras F, Caccia M, Longo S, Cofré N, Borda V, Burni M, Janoušková M, Urcelay C (2022) The effects of arbuscular mycorrhizal fungal species and taxonomic groups on stressed and unstressed plants: a global meta-analysis. New Phytol 235:320–332. https://doi.org/10.1111/nph.18102 PubMed DOI

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. https://doi.org/10.14806/ej.17.1.200 DOI

Oksanen J, Blanchet FG, Kindt R, Legendre P, O’hara RB, Simpson GL et al (2011) Vegan: community ecology package. Version 1.17–9. R Project for Statistical Computing, Vienna

Oliveira J, Yildirir G, Corradi N (2024) From Chaos comes order: genetics and genome biology of arbuscular mycorrhizal Fungi. Annu Rev Microbiol 78. https://doi.org/10.1146/annurev-micro-041522-105143

Omar M, Bolland L, Heather W (1979) A permanent mounting medium for fungi. Bull Brit Mycol Soc 13:31–32 DOI

Ontivero RE, Voyron S, Allione LVR et al (2020) Impact of land use history on the arbuscular mycorrhizal fungal diversity in arid soils of Argentinean farming fields. FEMS Microbiol Lett 367(14):fnaa114. https://doi.org/10.1093/femsle/fnaa114 PubMed DOI

Öpik M, Davison J (2016) Uniting species-and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity. Fungal Ecol 24:106–113. https://doi.org/10.1016/j.funeco.2016.07.005 DOI

Öpik M, Vanatoa A, Vanatoa E et al (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol 188(1):223–241. https://doi.org/10.1111/j.1469-8137.2010.03334.x PubMed DOI

Öpik M, Davison J, Moora M, Zobel M (2014) DNA-based detection and identification of glomeromycota: the virtual taxonomy of environmental sequences. Botany 92(2):135–147. https://doi.org/10.1139/cjb-2013-0110 DOI

Pacheco Flores de Valgaz A, Naranjo-Morán J, Reyes Román G, Oviedo-Anchundia J, Ratti Torres M, Barcos-Arias M (2022) Discovering the diversity of arbuscular mycorrhizal Fungi associated with two cultivation practices of Theobroma cacao. Diversity 14(8):651. https://doi.org/10.3390/d14080648 DOI

Prates Júnior P, Moreira BC, da Silva MDCS et al (2019) Agroecological coffee management increases arbuscular mycorrhizal fungi diversity. PLoS ONE 14(1):e0209093. https://doi.org/10.1371/journal.pone.0209093 PubMed DOI PMC

R Core Team (2024) R: a Language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

Rillig MC, Mummey DL (2006) Mycorrhizas and soil structure. New Phytol 171(1):4153. https://doi.org/10.1111/j.1469-8137.2006.01750.x DOI

Rosendahl S, Matzen HB (2008) Genetic structure of arbuscular mycorrhizal populations in fallow and cultivated soils. New Phytol 179(4):1154–1161. https://doi.org/10.1111/j.1469-8137.2008.02535.x PubMed DOI

Sanders IR (2004) Plant and arbuscular mycorrhizal fungal diversity: are we looking at the relevant levels of diversity and are we using the right techniques? New Phytol 415–418. https://www.jstor.org/stable/1514749

Schoch CL, Seifert KA, Huhndorf S et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci 109(16):6241–6246. https://doi.org/10.1073/pnas.1117018109 DOI

Sieverding E (1991) Vesicular-arbuscular mycorrizal in Tropical Agrosystems. Federal Republic of Germany: Deutsche Gesellssachoff fur Techniische Zusam menarbeit (Gtz) GMBH, 371 pp

Silvani VA, Colombo RP, Scorza MV et al (2017) Arbuscular mycorrhizal fungal diversity in high-altitude hypersaline Andean wetlands studied by 454-sequencing and morphological approaches. Symbiosis 72:143–152. https://doi.org/10.1007/s13199-016-0454-3 DOI

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

Stevens BM, Propster JR, Öpik M et al (2020) Arbuscular mycorrhizal fungi in roots and soil respond differently to biotic and abiotic factors in the Serengeti. Mycorrhiza 30:79–95. https://doi.org/10.1007/s00572-020-00931-5 PubMed DOI

Thiéry O, Moora M, Vasar M, Zobel M, Öpik M (2012) Inter-and intrasporal nuclear ribosomal gene sequence variation within one isolate of arbuscular mycorrhizal fungus, Diversispora Sp. Symbiosis 58(1):135–147. https://doi.org/10.1007/s13199-012-0212-0 DOI

Toju H, Tanabe AS, Yamamoto S et al (2012) High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS ONE 7(7):e40863. https://doi.org/10.1371/journal.pone.0040863 PubMed DOI PMC

van der Heijden MG, Scheublin TR (2007) Functional traits in mycorrhizal ecology: their use for predicting the impact of arbuscular mycorrhizal fungal communities on plant growth and ecosystem functioning. New Phytol 174(2):244–250. http://www.jstor.org/stable/30149330 PubMed DOI

van der Heijden MG, Boller T, Wiemken A, Sanders IR (1998) Different arbuscular mycorrhizal fungal species are potential determinants of plant community structure. Ecology 79(6):2082–2091. https://doi.org/10.1890/0012-9658 DOI

Větrovský T, Kolaříková Z, Lepinay C et al (2023) GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies. New Phytol 240:2151–2163. https://doi.org/10.1111/nph.19283 PubMed DOI

Vieira CK, Marascalchi MN, Rodrigues AV, de Armas RD, Stürmer SL (2018) Morphological and molecular diversity of arbuscular mycorrhizal fungi in revegetated iron-mining site has the same magnitude of adjacent pristine ecosystems. J Environ Sci 67:330–343. https://doi.org/10.1016/j.jes.2017.08.019 DOI

Vieira LC, Silva DKAD, Escobar IEC, Silva JMD, Moura IAD, Oehl F, Silva GAD (2020) Changes in an arbuscular mycorrhizal fungi community along an environmental gradient. Plants 9(1):52. https://doi.org/10.3390/plants9010052 PubMed DOI PMC

Wetzel K, Silva G, Matczinski U, Oehl F, Fester T (2014) Superior differentiation of arbuscular mycorrhizal fungal communities from till and no-till plots by morphological spore identification when compared to T-RFLP. Soil Biol Biochem 72:88–96. https://doi.org/10.1016/j.soilbio.2014.01.033 DOI

Xiang D, Verbruggen E, Hu Y, Veresoglou SD et al (2014) Land use influences arbuscular mycorrhizal fungal communities in the farming–pastoral ecotone of Northern China. New Phytol 204(4):968–978. https://doi.org/10.1111/nph.12961 PubMed DOI