Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Arbuscular Mycorrhizal Fungi Assemblages in Chernozems

  • Chantal HamelEmail author
  • Luke D. Bainard
  • Mulan Dai
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_116-1


Arbuscular Mycorrhizal Fungal Community Operational Taxonomic Unit Fungal Endophyte Black Soil 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Diversity, arbuscular mycorrhizal fungi, Canadian Prairie, Chernozem, land use.


AM fungi are obligate plant symbionts that form the phylum Glomeromycota. These fungi contribute to plant nutrient uptake, influence soil biotic and abiotic environments, and provide important ecosystem services. 454-pyrosequencing of amplicons from metagenomic DNA revealed the distribution of AM fungi in major Canadian Chernozem great groups as influenced by land use and crop management.


AM fungi form a mycorrhizal symbiosis with the roots of the majority of land plants. They have coevolved with plants over 450 Ma to produce today’s mycorrhiza, which is an organ specialized in the extraction of soil nutrients. As such, AM fungi are seen as a key stone of agricultural sustainability (Garg and Chandel 2010).

World grain, pulse, and biofuel crop production mainly occurs on deep (typically >18–25 cm) warm-colored soils rich in humus (>0.6 % organic carbon) and weatherable minerals, with high levels of base saturation (>50 %) and calcium as the main exchangeable cation (Durán et al. 2011). These soils have similar properties but have different names in other soil classification systems. They are Chernozems in Canada, Ukraine, and Russia; Mollisols in the USA and South America; Isohumosols or Black Soils in China; and Chernozems, Kastanozems, and Phaeozems according to the FAO (Liu et al. 2012). These soils have typically developed under condition of moisture deficit and grassland vegetation in temperate regions around the globe. They mainly occur in a band across Eastern Europe and Central Asia, in northeast China, from south-central Canada down to the Gulf of Mexico, and over most of Uruguay and part of Argentina.

Tackling the Complexity of Soil Biodiversity

Soil hosts an extremely high level of microbial diversity (Young and Crawford 2004). However, high-throughput next-generation sequencing now allows generation of the massive sequence data required to characterize soil microbial diversity.

Amplicon sequencing is preferred over whole genome sequencing for the study of the taxonomic diversity of targeted microbial groups. The 454 FLX and 454 FLX + technologies allow the sequencing of DNA amplicons up to 400 and 800 bp in length, respectively. Such long sequences contain sufficient taxonomic information for the characterization of microbial communities and their use conveniently eliminates the need for sequence assembly.

Pyrosequencing of amplicons and bioinformatic analysis of sequence data yield the profile of operational taxonomic units (OTU) of the target microbial group in a soil sample. The concept of an OTU is useful in soil microbiology as the majority of microbial species are still undescribed. OTUs serve as a proxy for species making it possible to measure and describe soil microbial diversity. In addition, OTUs can be identified by comparison with known sequences in public databases such as GenBank and MaarjAM. AM fungi have been difficult to study due to their obligate biotrophy and inability to grow in pure culture. However, polymerase chain reaction (PCR) made possible the amplification of DNA from their spores and enabled the molecular characterization and classification of taxa within the Glomeromycota (Schuessler 2013).

Fungal diversity is commonly assessed based on the internal transcribed spacer (ITS) of the ribosomal RNA gene. However, abundant SSU rRNA gene sequences of AM fungi are found in databases due to the traditional use of this region for the Glomeromycota. Several primers sets producing taxonomically informative amplicons short enough for use with first- and next-generation molecular techniques have been used in ecological studies of AM fungi.

The AM fungi have a patchy distribution in soil (Hart and Klironomos 2003). Thus in order to capture their diversity, multiple samples must be taken at a study site. A composite sample is usually made by pooling and homogenizing all the samples from a sampling site. The distribution of organisms varies with soil depth, thus sampling depth also matters. The AM fungi are normally found within the rooting depth.

Arbuscular Mycorrhizal Fungi in the Canadian Chernozems

AM fungal communities in the Canadian Prairie Chernozem soils are composed of a few dominant and a large number of subordinate taxa. Less than 6 % of the AM fungal OTUs accounted for half of all AM fungal reads (Dai et al. 2013). Across the Canadian prairie landscape, the Glomeraceae were the most abundant family, accounting for 65 % of all AM fungal OTUs and 54 % of the AM fungal reads. The Claroideoglomeraceae is second in abundance with 25 % of all AM fungal OTUs and 39 % of the AM fungal reads. Diversisporaceae accounted for 8 % of the OTUs and 7 % of the AM fungal reads. Paraglomaceae, Gigasporaceae, and Archeosporaceae are poorly distributed across the prairie landscape, and Gigasporaceae and Archeosporaceae are rare.

In other regions, spore counts in grazed Kastanozems of Inner Mongolia revealed that the AM fungal communities resembled those observed in Canadian Chernozems (Tian et al. 2009). The Gigasporaceae are susceptible to disturbance and largely absent in croplands, which explains their greater abundance in the Kastanozems than in the Canadian Prairie Chernozems (Dai et al. 2012, 2013). Poorer AM fungal diversity is reported from American spore-based surveys of Mollisols under tallgrass prairie cover where Paraglomaceae and Archeosporaceae were undetected (Eom et al. 2001; Bentivenga and Hetrick 1992). Tallgrass prairies managed with fire were found to be very highly dominated by the Glomeraceae (Bentivenga and Hetrick 1992), underlining the importance of land use in the structuring of AM fungal communities.

AM fungi share root occupation with fungal endophytes belonging to different taxonomic groups. Non-AM fungal endophytes are particularly abundant in temperate grasslands (Porras-Alfaro et al. 2011). This observation triggered the question as to whether AM fungi are at the end of their range in dry areas.

This hypothesis was explored in the Canadian Prairie using primers Glo1/NS31, which produced 18S rDNA amplicons of about 230 bp (Yang et al. 2010). A succession of AM fungi was detected as the soil dried from early to late summer, suggesting that the adaptation of AM fungi to soil moisture availability varies with species. Glomus viscosum, Funneliformis mosseae, and Glomus hoi were dominant in early summer, under conditions of moisture sufficiency, whereas the dominant AM fungal OTUs in late season conditions (i.e., dry soil) belonged to Glomus iranicum and Glomus macrocarpum. This concurs with the previous observation of differences in the seasonal pattern of sporulation of different AM fungal species (Dhillion and Anderson 1993). Seasonal variation of AM fungi in the North American Great Plains was also described as the replacement of the fungi of the order Helotiales by AM fungi as the season unfolds in the North American Great Plains (Jumpponen 2011).

The Chernozem great groups are distributed along a gradient of precipitation radiating outward from the US border in eastern Alberta, i.e., from the Brown soil zone through Dark Brown and Black soils up to the Gray soil zone at the fringe of the boreal forest. The lowest abundance, richness, and diversity of AM fungi were observed in the driest soil zone (Brown Chernozem), which supported a negative impact of moisture deficit on these fungi.

Soil moisture appears to be just one of several factors that influence the composition of AM fungal communities in Chernozem soils. Despite the highest levels of precipitation in the Gray soil zone, the highly productive Black soils harbor the most abundant and diverse AM fungal communities (Dai et al. 2012). Black, Gray, Dark Brown, and Brown soils had an average of 10.2, 7.1, 7.0, and 6.2 AM fungal OTUs, respectively, and the Shannon diversity index of these soil groups follows a similar trend. AM fungal communities in Brown soils are characterized by a reduced relative abundance of Claroideoglomeraceae compared to Black and Dark Brown soils. Other important factors that influenced the abundance of AM fungal OTUs were A horizon thickness and physicochemical properties of the soils, such as bulk density, Zn level, pH, electrical conductivity, and sulfur level.

Soils are classified based on their physical and chemical properties. A soil type represents a living environment inhabited by different AM fungal communities. American Mollisols and Alfisols contain distinct AM fungal spore assemblages (Ji et al. 2012). Similarly, Canadian Chernozems and Podzols and even different great groups of Chernozems contained distinct assemblages of AM fungal rRNA gene sequences (Dai et al. 2013).

Land use modifies the conditions of the soil environment and the impact of land use on the structure of AM fungal communities exceeds that of soil type. In the Canadian Prairie, roadsides host a higher level of AM fungal diversity than cropland or natural areas (Dai et al. 2013). Roadsides have higher soil moisture levels than cropland and most natural areas, further indicating that water availability is an important determinant of the abundance and structure of AM fungal communities. Seven percent of the AM fungal OTUs found across the prairie soil zones are unique to croplands, whereas 14 % of the AM fungal OTUs are specific to roadsides. Roadsides and natural areas are dominated by an OTU closely related to Claroideoglomus lamellosum, C. etunicatum, and C. claroideum, which account for 14 % and 19 % of all AM fungal reads. In cropland, an OTU closely related to Funneliformis mosseae accounted for as much as 17 % of all AM fungal reads. The dominance of F. mosseae in croplands of the Canadian prairie is supported by studies based on metagenomic methods (Ma et al. 2005; Sheng et al. 2012; Dai et al. 2012, 2013) and on spore counts (Talukdar and Germida 1993).

Crop management systems also have a strong influence on the composition of AM fungal communities in Chernozem soils. Organic systems have been shown to support more abundant and diverse AM fungal communities compared to conventional systems (Dai et al. 2014). Organic systems also promote greater proliferation of Claroideoglomus and of incertae sedis taxa of the Glomeraceae, currently referred to as Glomus iranicum and Glomus indicum. However, these Glomeraceae incertae sedis are seemingly parasitic as they were associated with reduced crop growth and N and P uptake efficiency.


Metagenomic studies on the distribution of AM fungi in Chernozems are extremely useful to understand how the living soil provides ecological services and supports the production of food and bioproducts. Brown Chernozems are relatively poor in symbiotic AM fungi and are less hospitable to the Claroideoglomus than other Chernozems, whereas Black Chernozems are rich in AM fungal resources. The influence of soil type on the composition of AM fungal communities is relatively small compared to that of land use type. Funneliformis have a competitive edge and proliferate in conventional crop production systems, whereas Claroideoglomus and Glomeraceae incertae sedis are favored in organic production systems. These Glomeraceae incertae sedis, currently known as the G. iranicum/G. indicum group, are associated with reduced crop productivity and nutrient uptake.


  1. Bentivenga SP, Hetrick BAD. The effect of prairie management practices on mycorrhizal symbiosis. Mycologia. 1992;84:522–7.CrossRefGoogle Scholar
  2. Dai M, Bainard LD, Hamel C, Gan Y, Lynch D. Impact of land use on arbuscular mycorrhizal fungal communities in rural Canada. Appl Environ Microbiol. 2013;79:6719–29. doi:10.1128/aem.01333-13.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Dai M, Hamel C, Bainard LD, St. Arnaud M, Grant CA, Lupwayi NZ, Malhi SS, Lemke R. Negative and positive contributions of arbuscular mycorrhizal fungal taxa to wheat production and nutrient uptake efficiency inorganic and conventional system in the canadian prairie. Soil Biol Biochem. 2014;74:156–166.Google Scholar
  4. Dai M, Hamel C, St. Arnaud M, He Y, Grant C, Lupwayi N, Janzen H, Malhi SS, Yang X, Zhou Z. Arbuscular mycorrhizal fungi assemblages in chernozem great groups revealed by massively parallel pyrosequencing. Can J Microbiol. 2012;58:81–92.PubMedCrossRefGoogle Scholar
  5. Dhillion SS, Anderson RC. Seasonal dynamics of dominant species of arbuscular mycorrhizae in burned and unburned sand prairies. Can J Bot. 1993;71:1625–30.CrossRefGoogle Scholar
  6. Durán A, Morrás H, Studdert G, Xiaobing L. Distribution, properties, land use and management of Mollisols in South America. Chin Geogr Sci. 2011;21:511–30.CrossRefGoogle Scholar
  7. Eom AH, Wilson GWT, Hartnett DC. Effects of ungulate grazers on arbuscular mycorrhizal symbiosis and fungal community structure in tallgrass prairie. Mycologia. 2001;93:233–42.CrossRefGoogle Scholar
  8. Garg N, Chandel S. Arbuscular mycorrhizal networks: process and functions. A review. Agron Sustain Dev. 2010;30:581–99.CrossRefGoogle Scholar
  9. Hart MM, Klironomos JN. Diversity of arbuscular mycorrhizal fungi and ecosystem functioning. In: van der Heijden MGA, editor. Mycorrhizal ecology, Ecological studies, vol. 157. Berlin: Springer; 2003. p. 225–42.CrossRefGoogle Scholar
  10. Ji B, Bentivenga SP, Casper BB. Comparisons of AM fungal spore communities with the same hosts but different soil chemistries over local and geographic scales. Oecologia. 2012;168:187–97.PubMedCrossRefGoogle Scholar
  11. Jumpponen A. Analysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots. Mycorrhiza. 2011;21:453–64.PubMedCrossRefGoogle Scholar
  12. Liu X, Lee Burras C, Kravchenko YS, Duran A, Huffman T, Morras H, Studdert G, Zhang X, Cruse RM, Yuan X. Overview of Mollisols in the world: distribution, land use and management. Can J Soil Sci. 2012;92:383–402.CrossRefGoogle Scholar
  13. Ma WK, Siciliano SD, Germida JJ. A PCR-DGGE method for detecting arbuscular mycorrhizal fungi in cultivated soils. Soil Biol Biochem. 2005;37:1589–97.CrossRefGoogle Scholar
  14. Porras-Alfaro A, Herrera J, Natvig DO, Lipinski K, Sinsabaugh RL. Diversity and distribution of soil fungal communities in a semiarid grassland. Mycologia. 2011;103:10–21.PubMedCrossRefGoogle Scholar
  15. Schuessler A. Glomeromycota. Taxonomy. 2013. Accessed 6 Nov 2013. http://schussler.userweb.mwn.de/amphylo/
  16. Sheng M, Hamel C, Fernandez MR. Cropping practices modulate the impact of glyphosate on arbuscular mycorrhizal fungi and rhizosphere bacteria in agroecosystems of the semiarid prairie. Can J Microbiol. 2012;58:990–1001.PubMedCrossRefGoogle Scholar
  17. Talukdar NC, Germida JJ. Occurrence and isolation of vesicular-arbuscular mycorrhizae in cropped field soils of Saskatchewan, Canada. Can J Microbiol. 1993;39:567–75.CrossRefGoogle Scholar
  18. Tian H, Gai JP, Zhang JL, Christie P, Li L. Arbuscular mycorrhizal fungi in degraded typical steppe of Inner Mongolia. Land degrad dev. 2009;20:41–54.CrossRefGoogle Scholar
  19. Yang C, Hamel C, Schellenberg MP, Perez JC, Berbara RL. Diversity and functionality of arbuscular mycorrhizal fungi in three plant communities in semiarid Grasslands National Park. Can Microb Ecol. 2010;59:724–33.CrossRefGoogle Scholar
  20. Young IM, Crawford JW. Interactions and self-organization in the soil-microbe complex. Science. 2004;304:1634–7.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food CanadaSwift CurrentCanada