Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone...

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Bibliographic Details
Published in:PloS one 2016-01, Vol.11 (1), p.e0146558
Main Authors: Pascual, Javier, Blanco, Silvia, García-López, Marina, García-Salamanca, Adela, Bursakov, Sergey A, Genilloud, Olga, Bills, Gerald F, Ramos, Juan L, van Dillewijn, Pieter
Format: Article
Language:English
Subjects:
Acidobacteria
Actinobacteria
Alphaproteobacteria
Analysis
Bacteria
Betaproteobacteria
Biogeochemical cycles
Communities
Councils
Cultivation
Datasets
Gemmatimonadetes
Genetic Variation
Laboratories
Microbiomes
Microbiota - genetics
Microorganisms
Molecular Typing
National parks
Nitrogen
Nutrients
Oils & fats
Parks, Recreational
Plant hormones
Plant roots
Plant Roots - microbiology
Proteobacteria
Rhizosphere
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
rRNA 16S
Salinity
Sequence Analysis, RNA
Soil Microbiology
Spain
State budgets
Thyme
Thyme (Plant)
Thymus Plant - microbiology
Thymus zygis
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Summary:Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0146558