Total and Active Core Microbiomes of Melojo Oak Are Composed by a Minority of Bacterial Taxa Highly Abundant

Abstract

Melojo oak (Quercus pyrenaica Willd.) is a key tree species of Mediterranean forests with high landscape value in the Iberian Peninsula. However, these forests exhibit an advanced stage of deterioration and their distribution area has been seriously reduced over the last decades. Plant-associated microorganisms play an essential role improving their host’s fitness, hence, a better understanding of oak rhizospheric microbiome, especially of those active members, could be the first step towards microbiome-based approaches for the improvement of the survival and growth of oak trees. Here we reported, for the first time, the diversity of total (DNA-based) and potentially active (RNA-based) bacterial communities of three types of Quercus pyrenaica Willd. forest formations through 454 pyrosequencing of 16S rDNA amplicons, and defined the rhizospheric core microbiome of Q. pyrenaica at Sierra Nevada National and Natural Park during spring season. In addition rRNA:rDNA ratio was calculated as a proxy of the contribution of each core taxon to the rhizosphere environment. We found that potentially active bacterial communities were as rich and diverse as DNA-based populations, but different in terms of relative abundance patterns in some of the studied areas. Both microbiomes were dominated by a relatively small percentage of OTUs, most of which showed positive correlation between both libraries. However, the uncoupling between abundance (rDNA) and potential activity (rRNA) for some taxa suggests that the most abundant taxa are not always the most active, and that low-abundance OTUs may have a strong influence on oak’s rhizospheric ecology. Thus, measurement of rRNA:rDNA ratio could be helpful in characterizing rhizospheric bacterial communities, their potential involvement in the functioning of the soil ecosystem and, therefore, in identifying major bacterial players for the development of microbiome-based strategies for future afforestation tasks.