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Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes

Collected bulk and rhizosphere samples in two different growth stages of Pisum sativum in the Netherlands, with different types of soil management. This run contains only bacteria sequences. Variable ribosomal DNA regions were selected for the characterization of each of the four organismal groups., Collected bulk and rhizosphere samples in two different growth stages of Pisum sativum in the Netherlands, with different types of soil management. This run contains only bacteria sequences. Variable ribosomal DNA regions were selected for the characterization of each of the four organismal groups.

Collected bulk and rhizosphere samples in two different growth stages of Pisum sativum in the Netherlands, with different types of soil management. Three major organismal groups were assessed: fungi, protists and metazoa. Variable ribosomal DNA regions were selected for the characterization of each of the four organismal groups., Collected bulk and rhizosphere samples in two different growth stages of Pisum sativum in the Netherlands, with different types of soil management. Three major organismal groups were assessed: fungi, protists and metazoa. Variable ribosomal DNA regions were selected for the characterization of each of the four organismal groups.