The objective of this study was to test whether soil types can be characterized by their arbuscular mycorrhizal fungal (AMF) communities. To answer this question, a well-defined study area in the temperate climatic zone of Central Europe was chosen with a large spectrum of soils and parent materials. Representative soil samples were taken from three soil types (Cambisol, Fluvisol and Leptosol) at in total 16 sites differing in agricultural land use intensity (9 grasslands and 7 arable lands). AMF spores were isolated and morphologically identified directly from field soils and after reproduction in trap cultures. AMF diversity and community composition strongly depended on soil type and land use intensity, and several AMF species were characteristic for a specific soil type or a specific land use type and hence had a specific niche. In contrast, other AM fungi could be considered as ‘generalists’ as they were present in each soil type investigated, irrespective of land use intensity. An estimated 53% of the 61 observed AMF species could be classified as ‘specialists’ as (almost) exclusively found in specific soil types and/or under specific land use intensities; 28% appeared to be ‘generalists’ and 19% could not be classified. Plant species compositions (either natural or planted) had only a subordinate influence on the AMF communities. In conclusion, land use intensity and soil type strongly affected AMF community composition as well as the presence and prevalence of many AM fungi. Future work should examine how the differences in AMF species compositions affect important ecosystem processes in different soils and to which extent the loss of specific groups of AM fungi affect soil quality.

Soil type and land use intensity determine the composition of arbuscular mycorrhizal fungal communities

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects’) was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

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The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

Plant beneficial microorganisms, such as arbuscular mycorrhiza fungi (AMF), increasingly attract
scientific and agronomic attention due to their capacity to increase nutrient accessibility for plants
and to reduce inorganic fertilizer requirements. AMF are thought to form symbioses with most land
plants, obtaining carbon from the autotrophic host whilst enhancing uptake of poorly available
nutrients.
The species of AMF are mainly identified by spore morphology, which is time consuming, requires
expertise and is rarely applicable to AMF identification in roots. Molecular tools such as analysis of
standardized DNA fragment sequences may allow the recognition of species through a ‘DNA
barcode’, which may partly overcome this problem. The focus of this study was to evaluate
different regions of widely used rDNA repeats for their use as DNA barcodes for AMF including the
small subunit rRNA gene (SSU), the internal transcribed spacer (ITS) and the large subunit rRNA
gene (LSU). Closely related species in the genus Ambispora, members of which have dimorphic
spores, could not be separated by analysis of the SSU region, but of the ITS region. Consequently,
the SSU was not used for subsequent analysis, but a DNA fragment covering a small part of the
SSU, the entire ITS region and about 800 bp of the LSU (SSUmCf-LSUmBr fragment) was
analysed, providing phylogenetic resolution to species. New AMF specific primers for these
potential barcoding regions were developed and can be applied, without amplification of non-target
organisms, for AMF species determination, including identification from field and root samples.
Analyses based on the application of the SSUmCf-LSUmBr fragment showed that the widely used
AMF model organism Glomus sp. DAOM197198 (formerly called Glomus intraradices) is not
conspecific with Gl. intraradices. The SSUmCf-LSUmBr fragment clearly provides a much higher
species resolution capacity when compared with the formerly preferred ITS and LSU regions.
Further study of several groups of AMF species using different regions of the SSUmCf-LSUmBr
fragment revealed that only the complete SSUmCf-LSUmBr fragment allowed separation of all
analysed species. Based on these results, an extended DNA barcode covering the ITS region and
parts of the LSU region is suggested as a DNA barcode for AMF. The complete SSUmCf-LSUmBr
fragment sequences can serve as a database backbone for also using smaller rDNA fragments as
barcodes. Although the smallest fragment (approximately 400 bp) analysed in this study was not
able to discriminate among AMF species completely, such short regions covering the ITS2 or LSU
D2 regions, respectively, would most likely be suitable for community analyses with 454 GS-FLX
Titanium sequencing, providing that the analyses is based on the longer DNA sequences.

/pdf/dna-barcoding-of-arbuscular-mycorrhizal-fungi-3j9v2goz0g.pdf

DNA barcoding of arbuscular mycorrhizal fungi

Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here, we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize vs. potato), soil type (sand vs. clay-textured soils) and habitat (plant root vs. bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species-poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive ‘loss’ from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass-cropping history together explained 32% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a ‘bottleneck effect’ on AMF communities through increased stochastic effects under environmental stress.

Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

The community composition of arbuscular mycorrhizal fungi (AMF) was investigated in roots of four different plant species (Inula salicina, Medicago sativa, Origanum vulgare, and Bromus erectus) sampled in (1) a plant species-rich calcareous grassland, (2) a bait plant bioassay conducted directly in that grassland, and (3) a greenhouse trap experiment using soil and a transplanted whole plant from that grassland as inoculum. Roots were analyzed by AMF-specific nested polymerase chain reaction, restriction fragment length polymorphism screening, and sequence analyses of rDNA small subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic phylotypes. Overall, 16 phylotypes from several lineages of AMF were detected. The community composition was strongly influenced by the experimental approach, with additional influence of cultivation duration, substrate, and host plant species in some experiments. Some fungal phylotypes, e.g., GLOM-A3 (Glomus mosseae) and several members of Glomus group B, appeared predominantly in the greenhouse experiment or in bait plants. Thus, these phylotypes can be considered r strategists, rapidly colonizing uncolonized ruderal habitats in early successional stages of the fungal community. In the greenhouse experiment, for instance, G. mosseae was abundant after 3 months, but could not be detected anymore after 10 months. In contrast, other phylotypes as GLOM-A17 (G. badium) and GLOM-A16 were detected almost exclusively in roots sampled from plants naturally growing in the grassland or from bait plants exposed in the field, indicating that they preferentially occur in late successional stages of fungal communities and thus represent the K strategy. The only phylotype found with high frequency in all three experimental approaches was GLOM A-1 (G. intraradices), which is known to be a generalist. These results indicate that, in greenhouse trap experiments, it is difficult to establish a root-colonizing AMF community reflecting the diversity of these fungi in the field roots because fungal succession in such artificial systems may bias the results. However, the field bait plant approach might be a convenient way to study the influence of different environmental factors on AMF community composition directly under the field conditions. For a better understanding of the dynamics of AMF communities, it will be necessary to classify AMF phylotypes and species according to their life history strategies.

/pdf/the-cultivation-bias-different-communities-of-arbuscular-l1gkm7u82y.pdf

The cultivation bias: different communities of arbuscular mycorrhizal fungi detected in roots from the field, from bait plants transplanted to the field, and from a greenhouse trap experiment

The community composition of arbuscular mycorrhizal fungi (AMF) was analyzed in roots of Gentiana verna, Gentiana acaulis, and accompanying plant species from two species-rich Swiss alpine meadows located in the same area. The aim of the study was to elucidate the impact of host preference or host specificity on the AMF community in the roots. The roots were analyzed by nested PCR, restriction fragment length polymorphism screening, and sequencing of ribosomal DNA small-subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic sequence types. The AMF community composition was strongly influenced by the host plant species, but compositions did not significantly differ between the two sites. Detailed analyses of the two cooccurring gentian species G. verna and G. acaulis, as well as of neighboring Trifolium spp., revealed that their AMF communities differed significantly. All three host plant taxa harbored AMF communities comprising multiple phylotypes from different fungal lineages. A frequent fungal phylotype from Glomus group B was almost exclusively found in Trifolium spp., suggesting some degree of host preference for this fungus in this habitat. In conclusion, the results indicate that within a relatively small area with similar soil and climatic conditions, the host plant species can have a major influence on the AMF communities within the roots. No evidence was found for a narrowing of the mycosymbiont spectrum in the two green gentians, in contrast to previous findings with their achlorophyllous relatives.

Cooccurring Gentiana verna and Gentiana acaulis and their neighboring plants in two Swiss upper montane meadows harbor distinct arbuscular mycorrhizal fungal communities.

Zuzana Sykorová

Papers

Cooccurring Gentiana verna and Gentiana acaulis and their neighboring plants in two Swiss upper montane meadows harbor distinct arbuscular mycorrhizal fungal communities.