high-throughput belowground plant diversity assay using next-generation sequencing of the trnL intron

high-throughput belowground plant diversity assay using next-generation sequencing of the trnL intron

AIMS: We refine and test a next-generation sequencing assay for the molecular identification and quantification of plant roots from mixed-species samples. METHODS: We modified primers targeting the trnL intron to provide greater taxonomic resolution and developed an improved bioinformatics pipeline...

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Bibliographic Details
Published in:Plant and soil Vol. 404; no. 1-2; pp. 361 - 372
Main Authors: Lamb, E. G, T. Winsley, C. L. Piper, S. A. Freidrich, S. D. Siciliano
Format: Journal Article
Language:English
Published: Cham Springer International Publishing 01-07-2016
Springer
Springer Nature B.V
Subjects:
Bioassays
Biodiversity
Bioinformatics
Biological taxonomies
Biomedical and Life Sciences
Community structure
DNA sequencing
Ecology
Flowers & plants
Genetic aspects
Grassland soils
Grasslands
high-throughput nucleotide sequencing
Introns
Life Sciences
Methods
Nucleotide sequences
Observations
Pipelines
Plant communities
Plant diversity
Plant Physiology
Plant roots
Plant Sciences
Plant-soil relationships
Plants
Regular Article
rooting
Roots
Soil Science & Conservation
Species diversity
Species richness
Taiga & tundra
Tundra
Arctic region
PN, Arctic
High Arctic tundra
Plant root identification
Next-generation sequencing
Plant root diversity
Fescue grassland
L
Illumina
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Description
Summary:AIMS: We refine and test a next-generation sequencing assay for the molecular identification and quantification of plant roots from mixed-species samples. METHODS: We modified primers targeting the trnL intron to provide greater taxonomic resolution and developed an improved bioinformatics pipeline that can identify roots based on global, site-, and plot-specific taxon lists. We tested our primers and pipeline on mock plant communities of known composition and mixed-species samples of roots collected from temperate grassland and high Arctic tundra communities. RESULTS: We retrieved a high correlation (0.72) between observed and expected community dissimilarities. We found positive linear relationships between aboveground and belowground species richness in the grassland community, with higher correlations for plot-specific reference databases (R = 0.70) than a global reference database (R = 0.48). This highlights the importance of local reference databases within the bioinformatics pipeline. Lower root than aboveground richness suggests that typical root lateral spread in this grassland is less than 25 cm. We observed lateral rooting extents of up to 40 cm and rooting depths of up to 30 cm for six high Arctic species. CONCLUSIONS: Testing on mock community, grassland, and tundra samples demonstrated that next-generation sequencing using our improved trnL primers and pipeline can successfully recover plant root community structure.
Bibliography:http://dx.doi.org/10.1007/s11104-016-2852-y
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0032-079X
1573-5036
DOI:10.1007/s11104-016-2852-y