Abstract
The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.
Highlights
Several studies have investigated the main biotic and abiotic factors determining the structure and functioning of soil microbial communities
A significantly lower pH was measured in the Norway spruce rhizosphere compared to the bulk soil samples, though no difference in pH was observed for the beech bulk and rhizosphere soils
More exchangeable potassium was measured in the Norway spruce (p = 0.007) and beech (p = 0.02) rhizospheres than in their corresponding bulk soil samples, and significantly more Fe3+ was observed in the Norway spruce rhizosphere compared to the bulk soil samples (p = 0.02)
Summary
Several studies have investigated the main biotic and abiotic factors determining the structure and functioning of soil microbial communities. Cultivation-independent studies have shown an increase in the relative abundance of specific functional genes related to nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance in the rhizosphere[21,23] These results suggest that plants enrich nutritional helper microbial communities within the vicinity of their roots. Urbanova et al.[36] analyzed the soil stratification of both fungal and bacterial communities using high-throughput sequencing technology, determining how these two communities (archaeal communities were not considered) were distributed and whether this distribution varied for different tree species None of these studies assessed differences in rhizosphere and bulk soil microbial communities in terms of structure, diversity and composition. The same soil samples were used for quantitative PCR to quantify the archaeal, bacterial and fungal community abundance as well as that of specific bacterial genera such as Burkholderia and Collimonas known for their efficacy in weathering minerals at this experimental site[15,18,38]
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