Browsing by Subject "16S rRNA gene"

Now showing 1 - 2 of 2

Effect of long-term agricultural management on the soil microbiota influenced by the time of soil sampling
(2022) Fernandez-Gnecco, Gabriela; Covacevich, Fernanda; Consolo, Veronica F.; Behr, Jan H.; Sommermann, Loreen; Moradtalab, Narges; Maccario, Lorrie; Sørensen, Søren J.; Deubel, Annette; Schellenberg, Ingo; Geistlinger, Joerg; Neumann, Günter; Grosch, Rita; Smalla, Kornelia; Babin, Doreen
Application of agrochemicals and mechanization enabled increasing agricultural productivity yet caused various environmental and soil health-related problems. Agricultural practices affect soil microorganisms, which are the key players of many ecosystem processes. However, less is known about whether this effect differs between time points. Therefore, soil was sampled in winter (without crop) and in summer (in the presence of maize) from a long-term field experiment (LTE) in Bernburg (Germany) managed either under cultivator tillage (CT) or moldboard plow (MP) in combination with either intensive nitrogen (N)-fertilization and pesticides (Int) or extensive reduced N-fertilization without fungicides (Ext), respectively. High-throughput sequencing of 16S rRNA gene and fungal ITS2 amplicons showed that changes in the microbial community composition were correlated to differences in soil chemical properties caused by tillage practice. Microbial communities of soils sampled in winter differed only depending on the tillage practice while, in summer, also a strong effect of the fertilization intensity was observed. A small proportion of microbial taxa was shared between soils from the two sampling times, suggesting the existence of a stable core microbiota at the LTE. In general, taxa associated with organic matter decomposition (such as Actinobacteria, Bacteroidetes, Rhizopus, and Exophiala) had a higher relative abundance under CT. Among the taxa with significant changes in relative abundances due to different long-term agricultural practices were putative pathogenic (e.g., Gibellulopsis and Gibberella) and beneficial microbial genera (e.g., Chitinophagaceae, Ferruginibacter, and Minimedusa). In summary, this study suggests that the effects of long-term agricultural management practices on the soil microbiota are influenced by the soil sampling time, and this needs to be kept in mind in future studies for the interpretation of field data.
Long-term fertilization strategy impacts rhizoctonia solani-microbe interactions in soil and rhizosphere and defense responses in lettuce
(2022) Sommermann, Loreen; Babin, Doreen; Behr, Jan Helge; Chowdhury, Soumitra Paul; Sandmann, Martin; Windisch, Saskia; Neumann, Günter; Nesme, Joseph; Sørensen, Søren J.; Schellenberg, Ingo; Rothballer, Michael; Geistlinger, Joerg; Smalla, Kornelia; Grosch, Rita
The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).