Profiling Nematode Communities in Unmanaged Flowerbed and Agricultural Field Soils in Japan by DNA Barcode Sequencing

• Published in: PloS one Vol. 7; no. 12; p. e51785
• Main Authors: Morise, Hisashi, Miyazaki, Erika, Yoshimitsu, Shoko, Eki, Toshihiko
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20.12.2012; Public Library of Science (PLoS)
• Subjects: Agricultural industry; Agricultural land; Agricultural practices; Agriculture; Analysis; Animals; Bacteria; Bar codes; Biology; Biotechnology; COI protein; Communities; Cytochrome; Deoxyribonucleic acid; DNA; DNA barcoding; DNA Barcoding, Taxonomic; DNA sequencing; DNA, Helminth - genetics; DNA, Plant - genetics; DNA, Ribosomal - genetics; Ecosystems; Electron Transport Complex IV - genetics; Feeders; Flotation; Flowers - genetics; Flowers - parasitology; Food chains; Food plants; Food webs; Gene sequencing; Genes; Japan; Laboratories; Life sciences; Longidoridae; Methods; Mitochondria; Morphology; Mylonchulus; Nematoda; Nematoda - classification; Nematoda - genetics; Nematoda - growth & development; Nematodes; Nucleotide sequence; Oxidases; Parasites; Phylogenetics; Phylogeny; Plant growth; Polymerase Chain Reaction; Predators; Roundworms; Securities; Sequence Analysis, DNA; Soil - parasitology; Soil analysis; Soil ecology; Soil environment; Soils; Soybeans; Studies; Taxonomy; Xiphinema; Japan
• DOI: 10.1371/journal.pone.0051785
• ISSN: 1932-6203

Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis.