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Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils
- Source :
- Applied and Environmental Microbiology. 83
- Publication Year :
- 2017
- Publisher :
- American Society for Microbiology, 2017.
-
Abstract
- The nodule-forming actinobacterial genus Frankia can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of Frankia strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these Frankia clusters by either Sybr Green- or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 × 10 5 to 15 × 10 5 cells (g soil) −1 depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under Alnus glutinosa , a host plant for cluster 1 frankiae, or Betula nigra , a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees. IMPORTANCE Root nodule formation by the actinobacterium Frankia is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on Frankia have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus Frankia . Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.
- Subjects :
- DNA, Bacterial
0301 basic medicine
Root nodule
030106 microbiology
Frankia
Alnus
Real-Time Polymerase Chain Reaction
Plant Roots
Applied Microbiology and Biotechnology
Trees
Soil
03 medical and health sciences
23S ribosomal RNA
Botany
Methods
TaqMan
Symbiosis
Betula
Phylogeny
Soil Microbiology
DNA Primers
Ecology
biology
Host (biology)
fungi
Genetic Variation
Species diversity
Ribosomal RNA
biology.organism_classification
RNA, Ribosomal, 23S
Alnus glutinosa
Genes, Bacterial
Multigene Family
DNA Probes
Root Nodules, Plant
Sequence Alignment
Sequence Analysis
Food Science
Biotechnology
Subjects
Details
- ISSN :
- 10985336 and 00992240
- Volume :
- 83
- Database :
- OpenAIRE
- Journal :
- Applied and Environmental Microbiology
- Accession number :
- edsair.doi.dedup.....4bdc30299de79718962a20876b868cb1