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Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases. [ABSTRACT FROM AUTHOR]

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]