Search

Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.

Despite being well adapted to the long seasonal droughts of the Mediterranean Basin, the holm oak (Quercus ilex L. subsp. ballota (Desf.) Samp.) has undergone a gradual decline during the last decades. The reasons of this decline are not fully understood, but evidence suggests that the quality and quantity of the interactions of holm oaks with the soil microbiota are playing a central role in the resilience of this species. With the aim to test the previous statement as our hypothesis, 9 oak savannah sites (called dehesas from here on) were sampled, in which asymptomatic (healthy) and symptomatic (early stage of decline) trees were interspersed. Using high throughput amplicon sequencing, soil bacterial and fungal biota (called soil microbiota from here on) were sequenced. Our results showed that soil fungal community composition differed between healthy and declining trees whereas bacterial communities did not show significant differences. Specifically, the degree of holm-oak defoliation was negatively correlated to the relative abundance of ectomycorrhizal (ECM) fungi and fungal endophytes, suggesting a relation between trees' health and soil fungal symbionts. Although our observational study cannot give a final answer to the directionality of the relationships observed, our results support the idea that small changes in symbiont abundance might be causing holm oaks to lose their ability to withstand the strong environmental pressures. • Microbial soil diversity correlates with tree health status. • Fungal diversity is more related to tree health than bacterial diversity. • The abundance of ectomycorrhiza (ECM) and fungal endophytes is related to tree resilience. • Small spatial variability in plant-fungal symbiotic relations influences tree health. [ABSTRACT FROM AUTHOR]