A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes

Abstract

Plant-symbiotic arbuscular mycorrhizal fungi (AMF) are of high global ecological and economic importance, but describing environmental communities of AMF at the species level remains a challenge, despite the need to understand AMF-plant preferences and to apply AMF in sustainable agriculture. Here, the potato-associated AMF species community composition was assessed for three Andean countries along an altitudinal gradient and at different plant stages, by using 454 GS-FLX+ sequencing of a 760 bp LSU rRNA gene PCR amplicon. Two methods were compared: defining OTUs based on a simple sequence similarity threshold, or affiliating reference sequences to species based on a high throughput phylogenetic annotation approach using an evolutionary placement algorithm (EPA). The EPA-based approach was not only more precise, but also fundamental to robustly unveil the AMF species community composition. The principal advantage of this approach was also demonstrated by using artificially constructed datasets based on validated public database sequences. The affiliation of sequence reads to species using phylogenetic annotation revealed a surprisingly conserved AMF core-species community structure in Andean potatoes, regardless of different plant stages and environmental factors. In total, 41 species were detected and in some cases more than 25 species were found colonizing an individual root system. Acaulospora species were identified as dominant colonizers, co-occurring with Cetraspora nodosa and certain Claroideoglomus and Rhizophagus species in most potato root samples.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

“…2D), sequences from the same species were commonly split into multiple OTUs (Fig. 4G to J), a finding similar to the findings of another recent study (34). In contrast, for genera with little between-isolate variation, sequences from isolates of different species could be lumped into the same OTU.…”

“…Direct assessments that use sequences from individual AM fungal species to evaluate the performance of sequence-based methods of species identification are generally lacking for AM fungi. However, one such direct assessment using sequences from isolates of the genus Rhizoglomus found multiple OTUs per species and a mismatch between OTUs and clades of the gene tree (34). Given the large amount of withinspecies sequence variation that occurs in AM fungi, it is possible that this pattern of multiple OTUs per species of Rhizoglomus is not unique among AM fungal groups, and therefore the key assumption that each OTU corresponds to a species-level group of sequences may not hold for AM fungi in general.…”

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition

“…Prior to our PCoA analyses, OTUs represented by fewer than 5 reads were removed, as rare OTUs have a marginal effect on subsequent multivariate statistical analyses (Lindahl et al, 2013; Tedersoo et al, 2014). Raw read counts were then normalized using the package DESeq2 in R (Senés-Guerrero and Schüßler, 2016) and relative abundance of matrix was obtained for calculation of Bray–Curtis distances. The influences of latitude, sea region and habitat type on the difference of fungal beta-diversity were explored with adonis functions with permutations = 200.…”

Soil conservation practices for insect pest management in highly disturbed agroecosystems – a review

“…In its center of origin, potato is associated with at least 41 species of symbiotic fungi (Sen es-Guerrero & Sch€ ußler, 2016). Although responses may vary depending on specific conditions (Duffy & Cassells, 2000;Douds et al, 2007), arbuscular mycorrhizae are generally known to promote potato growth and yield.…”