Metabarcoding reveals that rhizospheric microbiota of Quercus pyrenaica is composed by a relatively small number of bacterial taxa highly abundant

Abstract

Melojo oak (Quercus pyrenaica Willd.) is a key tree species of Mediterranean forests; however, these forests show an advanced stage of deterioration in the Iberian Peninsula. 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 oak-forest improvement. Here we reported, for the first time, the diversity of total (DNA-based) and potentially active (RNA-based) bacterial communities of different melojo-oak forest formations through pyrosequencing of 16S rRNA gene amplicons. We found that potentially active bacterial communities were as rich and diverse as total bacterial communities, but different in terms of relative abundance patterns in some of the studied areas. Both core 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 identifying major players for the development of bacterial bioinoculants.

Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

“…cDNA was obtained following the protocol described in Lasa et al [61]. cDNA and DNA yields and quality were checked both by electrophoresis in 0.8% (w/v) agarose gels stained with GelRed and visualized under UV light, and using a Qubit 3.0 fluorometer (Life Technologies, Grand Island, NY).…”

Characterization of the Belowground Microbial Community in a Poplar-Phytoremediation Strategy of a Multi-Contaminated Soil

“…The microbial community was analyzed through amplicon sequencing of the 16S rRNA gene and the 16S rRNA transcripts to directly compare the total and active microbial communities (Roesch et al, 2007;De Vrieze et al, 2018;Lasa et al, 2019a) and to better identify the microorganisms potentially involved in the soil decontamination processes. In total 3,995,841 raw reads were obtained from cDNA sequencing and after a trim and quality edit, 1,801,772 were retained: 48% of them derived from the Bulk Soil and 52% the Rhizosphere, respectively.…”

Characterization of the belowground microbial community in a poplar-assisted bioremediation strategy for restoring a multi-contaminated soil

“…The microbial community was analysed through amplicon sequencing of the 16S rRNA gene and the 16S rRNA transcripts to directly compare the total and active microbial communities [22,23,24] and to better identify the microorganisms potentially involved in the soil decontamination processes. In total 3,995,841 raw reads were obtained from cDNA sequencing and after a trim and quality edit, 1,801,772 were retained: 48% of them derived from the Bulk Soil and 52% the Rhizosphere, respectively.…”

“…Extraction of environmental RNA and DNA (eDNA) from each soil sample (Rhizo, Bulk and Control) was carried out using the RNA Power Soil Total RNA Isolation Kit and the DNA Elution Accessory kit (Qiagen), following the manufacturer's recommendations. In order to evaluate the putative active bacteria in Rhizosphere and Bulk Soil, the same soil samples were used for RNA extraction; the latter was extracted as reported above and ds-cDNA synthesized in accordance with [24]. Both eDNA and ds-cDNA were used as templates for MiSeq Illumina sequencing of the hypervariable V4-V5 of the 16S rRNA gene, using the U519F and U926R primers [55].…”