Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

• Published in: Applied and environmental microbiology 2017-11, Vol.83 (22), p.1
• Main Authors: Gkarmiri, Konstantia, Mahmood, Shahid, Ekblad, Alf, Alström, Sadhna, Högberg, Nils, Finlay, Roger
• Format: Article
• Language: English
• Subjects: Acidobacteria; Actinobacteria; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - growth & development; Bacteria - isolation & purification; Bacteroidetes; Brassica; Brassica napus; Brassica rapa - growth & development; Brassica rapa - microbiology; Carbon; carbon allocation; Chloroflexi; Clonostachys; Colonization; Cryptococcus; Deoxyribonucleic acid; DNA; Enrichment; Flavobacterium; Fungi; Fungi - classification; Fungi - genetics; Fungi - growth & development; Fungi - isolation & purification; Gemmatimonadetes; Gene sequencing; high-throughput sequencing; Isotopes; Microbiology; Microbiomes; Microbiota; Mikrobiologi; Next-generation sequencing; Nitrososphaera; Phylogeny; Planctomycetes; Plant Microbiology; Plant Roots - microbiology; Plants; Proteobacteria; Rape plants; Rapeseed; Rhizobium; Rhizosphere; rhizosphere microbiome; Rhodoplanes; Ribonucleic acid; RNA; root microbiome; Roots; Soil Microbiology; Soil microorganisms; Soils; Sphingomonas; Streptomyces; Taxa; Verrucomicrobia
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/AEM.01938-17

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 CO 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. , , , , , , and were the most active bacterial phyla in the rhizosphere soil. were more active in roots. The most abundant bacterial genera were well represented in both the C- and C-RNA fractions, while the fungal taxa were more differentiated. , , and were dominant in roots, whereas and ( ) were dominant in rhizosphere soil. " Nitrososphaera" was enriched in C in rhizosphere soil. and were abundant in the C-RNA fraction of roots; was abundant in both roots and rhizosphere soil and heavily C enriched. was dominant in rhizosphere soil and less abundant, but was 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 This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following CO labeling and compares these with other less active groups not incorporating a plant assimilate. 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.