Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil
Marie Uksa
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
Search for more papers by this authorFranz Buegger
Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorSilvia Gschwendtner
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorTillmann Lueders
Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorSusanne Kublik
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorTimo Kautz
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorMiriam Athmann
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorUlrich Köpke
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorJean Charles Munch
Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
Search for more papers by this authorCorresponding Author
Michael Schloter
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
For correspondence. E-mail [email protected]; Tel. (+49) 89 3187 2304; Fax (+49) 89 3187 3376.Search for more papers by this authorDoreen Fischer
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorMarie Uksa
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
Search for more papers by this authorFranz Buegger
Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorSilvia Gschwendtner
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorTillmann Lueders
Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorSusanne Kublik
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorTimo Kautz
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorMiriam Athmann
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorUlrich Köpke
Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
Search for more papers by this authorJean Charles Munch
Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
Search for more papers by this authorCorresponding Author
Michael Schloter
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
For correspondence. E-mail [email protected]; Tel. (+49) 89 3187 2304; Fax (+49) 89 3187 3376.Search for more papers by this authorDoreen Fischer
Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
Search for more papers by this authorSummary
Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
Supporting Information
Additional Supporting Information may be found in the online version of this article at the publisher's web-site:
| Filename | Description |
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| emi412588-sup-0001-suppinfo1.pdf264.7 KB |
Fig. S1. Root biomass along soil depth (A) and 13C enrichment in the plant shoot (B), rhizosphere (C) and bulk soil (D). Different letters indicate significant differences (P ≤ 0.05). Topsoil (0-20 cm); Subsoil U (upper subsoil, 20-50 cm); Subsoil L (lower subsoil, 50-80 cm). Fig. S2. Relative abundance of bacterial phyla in different soil depths. Data are obtained from Table S1. Topsoil (0-20 cm); Subsoil U (upper subsoil, 20-50 cm); Subsoil L (lower subsoil, 50-80 cm). Fig. S3. 16S rRNA gene T-RFLP fingerprint of rhizosphere and bulk soil DNA samples before density fractionation. In the heatmap, TRFs with a minimum relative abundance of 1.5% in at least one sample are ordered from top to bottom according to their mean relative abundance. Top – Topsoil (0-20 cm); Sub U – Upper Subsoil (20-50 cm); Sub L – Lower Subsoil (50-80 cm); 13C-lab – plants were labelled with 13C-CO2; control – no labelling. The TRF number indicates the length of the restriction fragment in bp. Fig. S4. Internal calibration of buoyant density and genomic GC content. The weighted mean densities of classifiable genera in the control samples (n = 234) are set into relation of genomic GC content information of the same taxa from NCBI genome database. The colour of each dot represents the phylum affiliation of the genus. Table S1: Relative abundance of bacterial phyla in different soil depths. Topsoil (0-20 cm); Subsoil U (upper subsoil, 20-50 cm); Subsoil L (lower subsoil, 50-80 cm). Significant differences between soil depths were calculated with univariate ANOVA (P < 0.05) followed by HSD post hoc test. |
| emi412588-sup-0002-suppinfo2.docx65.9 KB | Supplementary Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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