Table 1.
Primer pairs used in this study.
Fig 1.
Mean relative abundance of nematode sequence reads amplified using different primer sets and DNA sources at phylum rank.
NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b. SE.10 = Soil DNA extraction using 10 g of dry soil, and SE.1.25 = Soil DNA extraction using 1.25 g of dry soil.
Fig 2.
Venn diagrams showing the number of nematode taxa detected using different primers and DNA sources.
(A) Identification at the genus level, and (B) Identification at the species level. NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b. SE.10 = Soil DNA extraction using 10 g of dry soil and SE.1.25 = Soil DNA extraction using 1.25 g of dry soil.
Fig 3.
Hierarchical clustering heat map based on the relative abundance of the 20 most abundant nematode taxa.
Columns represent DNA extraction method and rows correspond to nematodes OTUs assigned at the genus and species levels. Dendrograms of hierarchical cluster analysis, grouping nematode genera and DNA extraction methods, are displayed on the left and top, respectively. Colors indicate standardized abundance values, with warmer colors representing higher relative abundance. NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b. SE.10 = Soil DNA extraction using 10 g of dry soil, and SE.1.25 = Soil DNA extraction using 1.25 g of dry soil.
Fig 4.
Non-metric multidimensional scaling (NMDS) ordination plot illustrating differences among DNA sources plotted in species space across primer sets (NF1, NemF, and NemFopt).
The circles surrounding the clusters represent 90% confidence intervals. Each point represents a sample, and colors indicate extraction method. NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b. SE.10 = Soil DNA extraction using 10 g of dry soil, and SE.1.25 = Soil DNA extraction using 1.25 g of dry soil.
Fig 5.
Principal coordinates analysis (PCoA) of nematode community composition based on NF1, NemF, and NemFopt primers across soil types.
Points represent individual samples, colored by primer and shaped by soil type (clay vs. sand). Ellipses indicate 95% confidence intervals around primer-specific centroids. Axis percentages denote the proportion of variance explained by each principal coordinate.
Table 2.
Summary of analyses of variance (F value) for the effects of soil type (Soil), DNA extraction method (Extraction), and their interaction (Soil × Extraction) on nematode variables, as determined by each primer pair. Two soil types (clay and sandy), and three DNA sources (NE, SE.1.25 and SE.10) were compared across the primers NF1, NemF, and NemFopt.
Fig 6.
Relative abundance of nematode communities.
(A) Relative abundance of feeding groups across different DNA sources using the three primer sets, (B) Relative abundance of feeding groups in different agricultural soils, and (C) Relative abundance of nematode colonizer-persister (c-p) classification, pp is used to differentiate plant-parasitic nematodes from free-living nematodes. NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b.
Fig 7.
Nematode indices using different primer sets and DNA sources.
Differences among extraction methods and primer sets were assessed using linear mixed-effects models with subplot as a random effect. MI = maturity index, EI = enrichment index, SI = structure index. NE = Nematodes DNA extraction, SE = Soil DNA extraction, NemFopt = NemFopt–18Sr2bRopt, NemF = NemF–18Sr2b, and NF1 = NF1–18Sr2b. P = Primer set, M = Method of extraction and their interactions. ANOVA results: ***P < 0.001, **P < 0.01, *P < 0.05, n. s. = not significant.