Distinct Ectomycorrhizospheres Share Similar Bacterial Communities as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

Abstract

Analysis of the 16S rRNA gene sequences generated from Xerocomus pruinatus and Scleroderma citrinum ectomycorrhizospheres revealed that similar bacterial communities inhabited the two ectomycorrhizospheres in terms of phyla and genera, with an enrichment of the Burkholderia genus. Compared to the bulk soil habitat, ectomycorrhizospheres hosted significantly more Alpha-, Beta-, and Gammaproteobacteria. E ctomycorrhizal fungi are important actors of nutrient cycling in the forest ecosystems. They enhance the nutrient uptake capacity of plants due to their ability to mobilize carbon from organic matter and access chemical elements with low mobility in the soil, such as nutritive cations, phosphorus, and nitrogen (5,15,32). They also connect tree roots to the surrounding soil and form a very specific ecological environment, the ectomycorrhizosphere (19). Apart from its physical and chemical characteristics, which differ from those of the rhizosphere (26, 28), the ectomycorrhizosphere is characterized by diverse fungal and bacterial communities that inhabit the same environment. Consequently, the functioning of the ectomycorrhizal symbiosis is influenced by each partner of the ectomycorrhizal (ECM) complex (6,8, 9).Cultivation-dependent and -independent studies have demonstrated the structuring effect of the mycorrhizal fungi on the soil bacterial communities. They revealed that the bacterial communities colonizing the ectomycorrhizal roots differed from those of uncolonized roots and that the ectomycorrhizal species differentially impacted the structure of ectomycorrhizosphere bacterial communities (2,11,12,22,35,37). One mycorrhizal species could be colonized by either very similar or contrastingly different bacterial communities (2,11,13). Certain ectomycorrhizal species associated with Betula pubescens, such as Piloderma fallax or Pseudotomentella tristis, were colonized by distinct bacterial communities, whereas the bacterial communities colonizing the ectomycorrhizosphere of Tomentellopsis submollis or Lactarius torminosus were more similar (13), thus suggesting that the taxonomic classification of the host mycorrhizal fungi was not always the main structuring parameter of the bacterial communities. Within this context, a comprehensive description of the ectomycorrhizosphere bacterial communities using a pyrosequencing-based approach would detail the structure and diversity of the bacterial communities coexisting in this specific ecological habitat as well as impart access to the rare taxonomic groups.In a recent study, Uroz et al. (36) used pyrosequencing of 16S rRNA fragments to compare the composition of bacterial communities inhabiting the oak (Quercus petraea) rhizosphere and surrounding bulk soil. In the study presented here, we investigated in the same soil core the composition and structure of bacterial communities inhabiting the ectomycorrhizosphere, which is a specific subhabitat of the rhizosphere. Pyrosequencing tags spanning the V5 to V6 hypervariable regions of the 16S rRNA gene were used to compa...

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

“…For Acidobacteria and Verrucomicrobia, two phyla containing OTUs that showed high co-occurrence with fungi, low pH dependency has been demonstrated but to our knowledge there is no evidence for beneficial interactions between members of those phyla and fungi. In contrast, while the genus Burkholderia also shows strong preference for acidic soils (Stopnisek et al, 2014), mounting evidence suggests that many Burkholderia species establish direct associations with fungi and may often live directly on or inside fungal cells (Warmink et al, 2011;Nazir et al, 2012;Uroz et al, 2012). Thus, we speculate that the strong co-occurrence of Burkholderia and fungi indicates that the two organisms interact with each other in the soil, rather than just reflecting shared niche preferences.…”

“…Burkholderia are particularly abundant in soil where they can be associated with a wide range of plants (Elliott et al, 2009;Carlier and Eberl, 2012), invertebrates (Kikuchi et al, 2005) and fungi (Warmink et al, 2009;Uroz et al, 2012;Scherlach et al, 2013). Since Burkholderia are mostly found in acidic soils (Stopnisek et al, 2014), interactions with fungi might be of particular relevance as fungi also favour acidic environments.…”

Bacterial community diversity in municipal waste landfill sites

“…Bacterial amplicon libraries were constructed for 454 pyrosequencing using the primers 341F (5′-CCTACGGG AGGCAGCAG-3′) and 1073R (5′-ACGAGCTGACGACA RCCATG-3′) for the V3-V6 regions of the 16S rRNA gene (Uroz et al 2012). Barcodes of ten nucleotides in length were designed for the bacterial sequencing for the sorting of multiple samples within a single 454 GS-FLX run.…”

Correlation of the Abundance of Betaproteobacteria on Mineral Surfaces with Mineral Weathering in Forest Soils

“…Genomic DNA (gDNA) was extracted from 250 mg of apatite particles or from the surrounding bulk soil using the PowerSoil DNA kit (MO BIO Laboratories, Inc.). Amplicon libraries targeting the V5-V6 hypervariable regions of the 16S rRNA gene were generated as described by Uroz et al (52,55). Pyrosequencing resulted in ca 230,000 reads which passed the length and quality criteria (16).…”