454‐sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities

Abstract

Summary 1.Disturbance is assumed to be a major driver of plant community composition, but whether similar processes operate on associated soil microbial communities is less known. Based on the assumed trade-off between disturbance tolerance and competiveness, we hypothesize that a severe disturbance applied within a semi-natural grassland would shift the arbuscular mycorrhizal (AM) fungal community towards disturbance-tolerant fungi that are rare in undisturbed soils. 2. We used 454-sequencing of the large subunit rDNA region to characterize AM fungal communities in Plantago lanceolata roots grown in the field for 4 months and exposed either to no disturbance or to severe disturbance where fungi from undisturbed soil were either permitted or prevented from re-colonizing the disturbed area. This allowed for a distinction between AM fungi that survived the disturbance and those that quickly re-colonized after a disturbance. To identify AM fungi that could potentially colonize the experimental plants, we also analysed roots from adjacent, undisturbed vegetation. 3. We found 32 fungal operational taxonomic units (OTUs) distributed across five known AM fungal families. Contrary to our expectations, disturbance did not significantly alter the community composition and OTU richness. Instead, OTU abundances were positively correlated across treatments; i.e., common OTUs in undisturbed soil were also common after the severe disturbance. However, the distribution of OTUs within and between plots was largely unpredictable, with approximately 40% of all sequences within a sample belonging to a single OTU of varying identity. The distribution of two plant species that are often poorly colonized by AM fungi (Dianthus deltoides and Carex arenaria) correlated significantly with the OTU composition, which may indicate that host quality could be an additional driver of fungal communities. 4. Synthesis. Our results suggest that factors other than disturbance drive the relative abundance of OTUs in this grassland and question the long-held assumption that communities shift in a predictable manner after a disturbance event. The reassembly of this fungal community indicates a high community resilience, but substantial local stochasticity and dominance by single OTUs, which could be due to priority effects among abundant AM fungi possessing a similar -and high -degree of disturbance tolerance.

Loss in microbial diversity affects nitrogen cycling in soil

“…While this prediction did not hold true in the original work of Franklin et al (2001), other studies using a similar dilution approach also reported greater differences between fingerprints obtained from the samples inoculated with the highest dilution (Griffiths et al, 2001;Wertz et al, 2006). This higher variability could be attributed to the stochastic removal of some species, lower interspecific competition or to priority effects with the establishment of some OTU influencing subsequent colonization by others, all leading to increased stochastic reassembly in the most diluted treatment during soil re-colonization (Lekberg et al, 2012).…”

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

“…Thus, until now, a robust tracing of AMF at the species level has not been possible with 454 sequencing, but data regarding basic AMF community patterns and the putative factors driving such communities have been obtained (Öpik et al 2009;Dumbrell et al 2011;Davison et al 2012;Lekberg et al 2012;Öpik et al 2013). Most of the earlier 454 sequencing based AMF community studies analyzed data by clustering reads into 97 %-OTUs and matching them using BLAST.…”

“…Other studies using 454 sequencing have reported 70 AMF OTUs in an area of approximately 7 m 2 , analyzing samples at summer and winter seasons (Dumbrell et al 2011), 32 AMF OTUs in grassland plots (Lekberg et al 2012), and 37 (Davison et al 2012) and 48 (Öpik et al 2009) AMF OTUs in forest plots. However, interpreting and comparing richness and species diversity is difficult from afore mentioned studies, for example because the number of OTUs is strongly dependent on the variability of the marker region and the threshold value used.…”

The molecular diversity of arbuscular mycorrhizal fungi in the arsenic mining impacted sites in Hunan Province of China

“…The data was processed in accordance with the method of Lekberg et al (2012) and Xiang et al (2014). Sorting and trimming of sequences based on size (>450 bp) and quality (>5 sequences) were performed by using the Mothur software (version 1.32.1, http://www.mothur.org).…”