title: Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas.
abstract: Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence.
authors.affiliation: McMaster University, Biology Department, Hamilton, ON, L8S 4K1, Canada.
authors.forename: Teresita M
authors.initials: TM
authors.lastname: Porter
authors.affiliation: Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
authors.forename: Shadi
authors.initials: S
authors.lastname: Shokralla
authors.affiliation: Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, E3B 6E1, Canada.
authors.forename: Donald
authors.initials: D
authors.lastname: Baird
authors.affiliation: McMaster University, Biology Department, Hamilton, ON, L8S 4K1, Canada.
authors.forename: G Brian
authors.initials: GB
authors.lastname: Golding
authors.affiliation: Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
authors.forename: Mehrdad
authors.initials: M
authors.lastname: Hajibabaei
mesh_terms: D000416:Alberta; D058448:Biota; D060365:Chloroplast Proteins / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic; D004271:DNA, Fungal / Q000032:analysis*; D018744:DNA, Plant / Q000032:analysis*; D004275:DNA, Ribosomal / Q000032:analysis*; D021903:DNA, Ribosomal Spacer / Q000032:analysis*; D005658:Fungi / Q000145:classification / Q000235:genetics; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics*; D018087:Plastids / Q000737:chemistry*; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology; D013045:Species Specificity; D053833:Wetlands
chemical_list: D060365:Chloroplast Proteins; D004271:DNA, Fungal; D018744:DNA, Plant; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers; D010940:Plant Proteins; D012987:Soil; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase