Figure 1.
Photograph of the flowerbed and agricultural field sites for soil sampling.
The unmanaged flowerbed framed by concrete walls (A) and the soybean-cultivated field (B) in the campus of Toyohashi University of Technology from autumn till winter in 2010.
Table 1.
Summary of SSU rDNA barcode analysis of nematodes isolated from flowerbed and agricultural field soils.
Figure 2.
Neighbor-joining tree of SSU rDNA barcode sequences of soil nematodes and reference nematode species.
SSU rDNA barcode sequences of 29 rOTUs from flowerbed and agricultural field soil nematodes (designated with K01rOTU and H01rOTU, and shown in red and blue, respectively) were analyzed with the corresponding SSU rDNA sequences of 107 reference nematodes (Table S1) and the resultant tree is displayed as a cladogram. Orders corresponding to the reference nematode species are indicated on the outside of the cladogram. The clade numbers (I–V) in the previous phylogenetic tree [21] were also indicated in parenthesis. Numbers on nodes are bootstrap values (>50%). Dilta littoralis (Arthropoda), Gordius aquaticus (Nematomorpha), Priapulus caudatus (Priapulida), Thulinia stephaniae (Tardigrada) were used as outgroup species.
Figure 3.
An unrooted phylogram of rOTUs from soil nematodes isolated from the flowerbed and agricultural field with predicted trophic types.
Twenty-nine SSU rDNA barcode sequences of K01rOTUs (flowerbed samples) and H01rOTUs (agricultural field samples) were aligned for preparing a phylogenetic tree. The numbers of soil nematodes belonging to each rOTU correspond to the numbers of open (flowerbed samples) and closed (agricultural field samples) squares at the right. Numbers on nodes are bootstrap values (>50%). Trophic types indicated in the rOTUs were derived from those of the nematode species with the highest homology in SSU rDNA barcode sequences (Table 1), and the feeding types for the rOTUs containing a large number of nematode members are shown in boldface. Bar: 0.1 substitutions per site.
Table 2.
Summary of SSU rDNA- and COI gene-barcode analyses using nematodes from the agricultural field soil.