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Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape
Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Örebro University, School of Science and Technology.ORCID iD: 0000-0003-4384-5014
Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2017 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 22, article id e01938-17Article in journal (Refereed) Published
Abstract [en]

RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following (13)CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the (13)C- and (12)C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in (13)C in rhizosphere soil. Olpidium and Dendryphion were abundant in the (12)C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily (13)C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was (13)C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napusIMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following (13)CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

Place, publisher, year, edition, pages
American Society for Microbiology , 2017. Vol. 83, no 22, article id e01938-17
Keywords [en]
Brassica napus, bacteria, carbon allocation, fungi, high-throughput sequencing, rhizosphere microbiome, root microbiome
National Category
Microbiology
Identifiers
URN: urn:nbn:se:oru:diva-62486DOI: 10.1128/AEM.01938-17ISI: 000414001000020PubMedID: 28887416Scopus ID: 2-s2.0-85032669754OAI: oai:DiVA.org:oru-62486DiVA, id: diva2:1160527
Funder
Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 2011-1211Available from: 2017-11-27 Created: 2017-11-27 Last updated: 2017-11-27Bibliographically approved

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