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Open AccessFeature PaperArticle

Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity

1
Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, Germany
2
Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
3
Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
4
Eastern Switzerland University of Applied Sciences, ILF Institute for Landscape and Open Space—Landscape Ecology, 8640 Rapperswil, Switzerland
5
Chair for Soil Sciences, Technical University Munich, 85354 Freising, Germany
*
Author to whom correspondence should be addressed.
Diversity 2020, 12(10), 392; https://doi.org/10.3390/d12100392
Received: 17 August 2020 / Revised: 29 September 2020 / Accepted: 2 October 2020 / Published: 13 October 2020
(This article belongs to the Special Issue Plant-Soil Interactions)
Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity. View Full-Text
Keywords: land use intensity; plant-associated microbiome; endophytes; rhizosphere; biodiversity; bacteria; core microbiome; Pseudomonas land use intensity; plant-associated microbiome; endophytes; rhizosphere; biodiversity; bacteria; core microbiome; Pseudomonas
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Estendorfer, J.; Stempfhuber, B.; Vestergaard, G.; Schulz, S.; Rillig, M.C.; Joshi, J.; Schröder, P.; Schloter, M. Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity. Diversity 2020, 12, 392.

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