Shrubs influence arbuscular mycorrhizal fungi communities in a semi-arid environment

Interactions between arbuscular mycorrhizal fungi (AMF) and plants are essential components of ecosystem functioning; however, they remain poorly known in dry ecosystems. We examined the relationship between seven shrub species and their associated AMF community in a semi-arid plant community in southern Spain. Soil characteristics and plant physiological status were measured and related to AMF community composition and genetic diversity by multivariate statistics. We found differences in AMF communities in soils under shrubs and in gaps among them, whereas no differences were detected among AMF communities colonizing roots. Soil nutrients content drove most of the spatial variations in the AMF community and genetic diversity. AMF communities were more heterogeneous in fertile islands with low nitrogen-to-phosphorus ratio and vice versa. AMF genetic diversity increased in soils limited by phosphorus and with high soil organic matter content, while AMF genetic diversity increased in roots growing in soil not limited by phosphorus. Overall, we could not find a clear link between plant performance and the associated AMF community. Our findings show that different shrub species generate islands of fertility which differ in nutrient content and, therefore, support different AMF communities, increasing AMF diversity at the landscape level.     

Evaluating the physical capture method of terminal restriction fragment length polymorphism for comparison of soil microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) is a popular method of comparative microbial community analysis which is normally accomplished by tagging terminal restriction fragments (T-RFs) with a fluorescent primer. Here, we evaluate an alternative method of T-RFLP where T-RFs are physically captured using a biotinylated primer and streptavidin-coated beads. This eliminates one of the primary criticisms of T-RFLP, namely that T-RFs cannot be identified by sequence analysis, and also represents an alternative method for collecting T-RFLP profiles. Microbial communities from forest, agricultural, and turf soils were investigated using several sets of primers specific for different microbial groups. The physical capture method of T-RFLP resulted in similar profiles to those generated by fluorescent T-RFLP. The relationships among ecosystem types captured by both methods and revealed by ordination were virtually identical. The total variance in the profiles that was attributed to ecosystem type was approximately equal, or greater, when generated by the physical capture method, depending on the primers used. However, physical capture T-RFLP resolved fewer T-RFs than fluorescent T-RFLP, and this may reduce the sensitivity to changes in non-dominant populations within the community. Direct cloning and sequencing of physical capture T-RFs revealed that most bands were not comprised of sequences related to those in the database that would generate T-RFs of similar size. T-RFs should therefore be identified by sequencing, rather than by comparing the sizes of T-RFs to computer digests of database sequences. Physical capture T-RFLP should be a useful tool to identify T-RFs by sequencing, and for laboratories without economical access to equipment required to perform fluorescent T-RFLP.     

No evidence that nitrogen enrichment affect fungal communities of Vaccinium roots in two contrasting boreal forest types

In boreal forests ericaceous shrubs often dominate the forest floor vegetation. Nitrogen enrichment has been shown to decrease shrub abundance and in this study we explored whether it also affects the root associated fungal communities. Fine roots of Vaccinium myrtillus were collected in a Norway spruce dominated forest and of Vaccinium vitis-idaea in a Scots pine dominated forest. In both forests, nitrogen enrichment was experimentally induced by adding 12.5 and 50 kg N ha⁻¹ yr⁻¹ for 12 (spruce forest) and four (pine forest) years. Based on terminal restriction fragment length polymorphisms, subcloning and sequencing analyses, the root associated fungal communities were examined. We found 93 fungal species including Asco-, Basidio- and Zygo-mycota. In general, the Rhizoscyphus ericae aggregate was the most dominant and this was followed by Herpotrichiellaceae and Sebacina. Ordination analysis revealed that nitrogen enrichment did not change species composition of the fungal communities in neither the spruce nor the pine forest, while fungal community structures were clearly discriminated between the dominant shrub species in each forest. Similarly, no fungal species showed a significant response to nitrogen enrichment. Therefore, nitrogen enrichment appears to have no effect on root associated fungi of understorey dwarf shrubs in boreal forests, while it is clear that spruce and pine forests harbor distinctive communities of these fungi.     

Woodland trees modulate soil resources and conserve fungal diversity in fragmented landscapes

Resource islands around woody plants are thought to define the structure and function of many semiarid and arid ecosystems, but their role in patterning of soil microbial communities remains largely unexamined in dry environments. This study examined soil resource distribution and associated fungal communities in two Allocasuarina luehmannii (buloke) remnants of semiarid north-western Victoria, Australia. These savannah-like woodlands are listed as endangered due to extensive clearing for agriculture. We used the DNA-based profiling technique T-RFLP and ordination-based statistical methods to compare fungal community compositions in surface soils from two remnants (located 1.6 km apart) and three sampling positions (beneath individual buloke canopies; grassy inter-canopy areas; and adjoining cleared paddocks). Resource island formation beneath buloke trees was clearly evident in soil physicochemical properties (e.g. threefold concentrations of total carbon and nitrogen in canopy versus non-canopy soils). This heterogeneity of resources was moderately correlated with soil fungal community compositions, which were distinct for each sampling position. We argue that fungal composition patterns reflected multiple roles of fungi in dryland ecosystems, namely: responses of saprotrophic fungi to tree organic matter inputs; specificity of ectomycorrhizal fungi to tree rooting zones; and fungal involvement in biological soil crusts that variably covered non-canopy soils. Our data did not indicate that buloke canopy areas were particular hotspots of soil fungal diversity, but that they increased landscape-level diversity by supporting a distinct suite of fungi. In addition, we provide evidence of phylogenetic differentiation of soil fungal communities between our two remnants, which adds to growing evidence of fungal genetic structure at localised scales. These findings highlight the importance of remnant trees in conserving both soil resources and microbial genetic diversity. In addition, evidence of differentiation of soil fungal phylogenetics between nearby but isolated remnants suggests that conserving soil fungal diversity requires conservation of host habitats over their entire (remaining) range, and indicates previously unseen consequences of tree loss from extensively cleared landscapes.