Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity
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 <i>Dactylis...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
|
| Series: | Diversity |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1424-2818/12/10/392 |
| _version_ | 1797551236422041600 |
|---|---|
| author | Jennifer Estendorfer Barbara Stempfhuber Gisle Vestergaard Stefanie Schulz Matthias C. Rillig Jasmin Joshi Peter Schröder Michael Schloter |
| author_facet | Jennifer Estendorfer Barbara Stempfhuber Gisle Vestergaard Stefanie Schulz Matthias C. Rillig Jasmin Joshi Peter Schröder Michael Schloter |
| author_sort | Jennifer Estendorfer |
| collection | DOAJ |
| description | 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 <i>Dactylis glomerata</i> L. and to assess the part that is most sensitive to land management. <i>Dactylis glomerata</i> 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. <i>Pseudomonas</i>, <i>Rhizobium</i> and <i>Bradyrhizobium</i> were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were <i>Rhodoplanes</i>, <i>Methylibium</i>, <i>Kaistobacter</i> and <i>Bradyrhizobium</i>. 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. |
| first_indexed | 2024-03-10T15:41:42Z |
| format | Article |
| id | doaj.art-ad6851f8587f420a88d4f62bd70120e4 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T15:41:42Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-ad6851f8587f420a88d4f62bd70120e42023-11-20T16:49:37ZengMDPI AGDiversity1424-28182020-10-01121039210.3390/d12100392Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use IntensityJennifer Estendorfer0Barbara Stempfhuber1Gisle Vestergaard2Stefanie Schulz3Matthias C. Rillig4Jasmin Joshi5Peter Schröder6Michael Schloter7Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyResearch Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyResearch Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyResearch Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyInstitute for Biology, Freie Universität Berlin, 14195 Berlin, GermanyEastern Switzerland University of Applied Sciences, ILF Institute for Landscape and Open Space—Landscape Ecology, 8640 Rapperswil, SwitzerlandResearch Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyResearch Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg, GermanyPlant-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 <i>Dactylis glomerata</i> L. and to assess the part that is most sensitive to land management. <i>Dactylis glomerata</i> 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. <i>Pseudomonas</i>, <i>Rhizobium</i> and <i>Bradyrhizobium</i> were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were <i>Rhodoplanes</i>, <i>Methylibium</i>, <i>Kaistobacter</i> and <i>Bradyrhizobium</i>. 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.https://www.mdpi.com/1424-2818/12/10/392land use intensityplant-associated microbiomeendophytesrhizospherebiodiversitybacteria |
| spellingShingle | Jennifer Estendorfer Barbara Stempfhuber Gisle Vestergaard Stefanie Schulz Matthias C. Rillig Jasmin Joshi Peter Schröder Michael Schloter Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity Diversity land use intensity plant-associated microbiome endophytes rhizosphere biodiversity bacteria |
| title | Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity |
| title_full | Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity |
| title_fullStr | Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity |
| title_full_unstemmed | Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity |
| title_short | Definition of Core Bacterial Taxa in Different Root Compartments of <em>Dactylis glomerata</em>, Grown in Soil under Different Levels of Land Use Intensity |
| title_sort | definition of core bacterial taxa in different root compartments of em dactylis glomerata em grown in soil under different levels of land use intensity |
| topic | land use intensity plant-associated microbiome endophytes rhizosphere biodiversity bacteria |
| url | https://www.mdpi.com/1424-2818/12/10/392 |
| work_keys_str_mv | AT jenniferestendorfer definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT barbarastempfhuber definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT gislevestergaard definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT stefanieschulz definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT matthiascrillig definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT jasminjoshi definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT peterschroder definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity AT michaelschloter definitionofcorebacterialtaxaindifferentrootcompartmentsofemdactylisglomerataemgrowninsoilunderdifferentlevelsoflanduseintensity |