Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land‐use gradient using a pyrosequencing approach

Abstract

SummaryThe biodiversity of arbuscular mycorrhizal fungi (AMF) communities present in five Sardinian soils (Italy) subjected to different land-use (tilled vineyard, covered vineyard, pasture, managed meadow and cork-oak formation) was analysed using a pyrosequencing-based approach for the first time. Two regions of the 18S ribosomal RNA gene were considered as molecular target. The pyrosequencing produced a total of 10924 sequences: 6799 from the first and 4125 from the second target region. Among these sequences, 3189 and 1003 were selected to generate operational taxonomic units (OTUs) and to evaluate the AMF community richness and similarity: 117 (37 of which were singletons) and 28 (nine of which were singletons) unique AMF OTUs were detected respectively. Within the Glomeromycota OTUs, those belonging to the Glomerales order were dominant in all the soils. Diversisporales OTUs were always detected, even though less frequently, while Archaeosporales and Paraglomerales OTUs were exclusive of the pasture soil. Eleven OTUs were shared by all the soils, but each of the five AMF communities showed particular features, suggesting a meaningful dissimilarity among the Glomeromycota populations. The environments with low inputs (pasture and covered vineyard) showed a higher AMF biodiversity than those subjected to human input (managed meadow and tilled vineyard). A reduction in AMF was found in the cork-oak formation because other mycorrhizal fungal species, more likely associated to trees and shrubs, were detected. These findings reinforce the view that AMF biodiversity is influenced by both human input and ecological traits, illustrating a gradient of AMF communities which mirror the land-use gradient. The high number of sequences obtained by the pyrosequencing strategy has provided detailed information on the soil AMF assemblages, thus offering a source of light to shine on this crucial soil microbial group.

Changes in Land Use System and Environmental Factors Affect Arbuscular Mycorrhizal Fungal Density and Diversity, and Enzyme Activities in Rhizospheric Soils of Acacia senegal (L.) Willd.

“…Klironomos and Hart [42] described large between-and within-site variations in the composition of AMF communities. Physical and chemical properties of soil and climatic factors such as soil moisture might explain differences observed between Dahra and Goudiry sites [43,44]. The effect of land uses (plantation versus natural population) on the diversity of AMF was noticed in the site of Dahra, but not in that of Goudiry.…”

Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brûlé

“…Their presence in the May samplings can be explained by the preferential early season activity of this family ( Hijri et al 2006). On the other hand, the finding of Archaeospora trappei (VTX00245) in the soil was not expected, since Archaeospora species are not found easily in either soil or in field roots ( Hijri et al 2006), although more sequences belonging to Archaeospora have recently been discovered by means of next generation sequencing ( Lumini et al, 2010 andÖpik et al, 2010).…”

“…A threshold of 97 % identity, corresponding to 0.03 dissimilarity, was used to define the OTUs. Although this distance cut-off is arbitrary, and can be considered controversial, it was chosen on the basis of previous studies on AMF biodiversity (Lumini et al, 2010 andBorriello et al, 2012). Two reorganizations of the Glomeromycota classification have recently been published (Oehl et al, 2011 andKrüger et al, 2012).…”

Interactions of fungi with other organisms

“…Thus, AM fungi may influence the structure and composition of vascular plant communities (Klironomos 2003). The recent use of new metabarcoding approaches based on high-throughput sequencing is providing detailed information on the AM fungal assemblages (Ö pik et al 2009;Lumini et al 2010;Dumbrell et al 2011;Becklin et al 2012;Lin et al 2012), thus increasing our understanding on the diversity of AM fungal communities in natural and agricultural soils.…”