Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches

Authors: TREONIS, AMY - University Of Richmond; UNANGST, SAMMI - University Of Richmond; Kepler, Ryan; Buyer, Jeffrey; Cavigelli, Michel; Mirsky, Steven; Maul, Jude

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/17/2018
Publication Date: 1/31/2018
Citation: Treonis, A.M., Unangst, S., Kepler, R.M., Buyer, J.S., Cavigelli, M.A., Mirsky, S.B., Maul, J.E. 2018. Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches. Scientific Reports. 8:2004. https://doi.org/10.1038/s41598-018-20366-5.
DOI: https://doi.org/10.1038/s41598-018-20366-5

Interpretive Summary: Soil ecosystems are complex environments harboring diverse assemblages of prokaryotic and eukaryotic organisms. These organisms play vital roles in ecosystem functions, including decomposition and nutrient generation. Soil biota have shown sensitivity to agricultural management strategies (e.g., tillage, herbicide and pesticide application, organic amendment), but our understanding of how soil biodiversity is affected by land use change lags behind above-ground habitats. Nematode species have diverse roles in soils as fungal-feeders, bacterial-feeders, omnivore/predators, or plant-parasites, making them an ideal indicator group for assessment of soil biota health. Different cropping systems have been shown to have variable effects on nematode communities, and the responses of nematode trophic groups can provide insight into the functioning of the soil food web. Using both molecular and morphological approaches, we compared nematode communities in soils from field plots that were in a corn, soybean and wheat rotation, and were managed: 1) conventionally with chisel tillage, 2) conventionally without tillage, and 3) under organic standards with chisel tillage. Some free-living taxa, such as Tylenchidae and Cephalobidae, showed positive correlations to soil organic carbon and nitrogen content, which were enhanced in organic soils. The density of omnivore/predator nematode taxa was reduced in no-till soils at the 0-5 cm depth as compared to conventional, while some plant-parasitic taxa increased in abundance at the same depth. In contrast, organic soils showed an increase in fungal-feeding nematodes at the 5-20 cm depth, and overall nematode abundance was higher in organic soils than in no-till. Results from this study show that farming systems that differ in their tillage, crop rotation and fertilizer regime can impact the structure, and by extension, the function of the soil nematode community. Organically managed systems showed the highest degree of food web stability, and higher concentration of beneficial nematodes than the conventional systems at all depths. In addition, this study shows that molecular techniques focusing on sequencing of rRNA genes can be used with the same fidelity as the time consuming morphological technique. These results are the first side-by-side comparison of sequencing and morphological techniques for nematode community assessment, and the consistency among techniques suggests molecular ecologists, who do not have expertise in nematology, can use standard high throughput sequencing techniques to assess the community structure of this critical group of soil dwelling organisms. This work will be useful to scientists studying nematode populations in soil environments.

Technical Abstract: Communities of soil nematodes impact ecosystem functions, including plant growth, decomposition, and nutrient cycling, all of which are vital processes in agriculture. We used complementary morphological and DNA metabarcoding analyses to characterize soil nematode communities in three cropping systems (conventional, no-till, and organic) from a long-term field experiment. The soils at this field site contained diverse nematode communities, with metabarcoding revealing the presence of OTUs corresponding to taxa that were not detected morphologically. According to both metabarcoding and morphological analyses, the diversity and abundance of nematodes differed among the cropping systems and with depth in the soil profile. Some free-living taxa, such as Tylenchidae and Cephalobidae, showed positive correlations to soil organic carbon and nitrogen content, which were enhanced in organic soils. The density of omnivore/predator nematode taxa was reduced in no-till soils at the 0-5 cm depth as compared to conventional, while some plant-parasitic taxa increased in abundance at the same depth. Bacterial-feeder abundance was lower at 5-20 cm in no-till soils. In contrast, organic soils showed an increase in fungal-feeding nematodes at the 5-20 cm depth, and overall nematode abundance was higher in organic soils than in no-till. The Bongers Maturity Index was higher in organic soils than in conventional or no-till at the 5-25 cm depth and higher than no-till at 0-5 cm. Taxonomic richness at the family level did not vary among the cropping systems, but both the Shannon and Simpson indices were significantly lower in organic soils than in no-till. However, metabarcoding revealed within-family differences in diversity, including reduced richness of both Rhabditidae and Cephalobidae in organic plots. These results support the value of metabarcoding and OTU-level analyses in order to provide a deeper understanding of how cropping systems mold nematode communities. Overall, nematode communities in this field experiment do not reflect any biological benefits of no-till practices, and the potential reduction in biological control of plant-parasitic species by omnivore/predator taxa in no-till soils could be problematic. In contrast, the organic system showed improvements in soil properties and contained nematode communities associated with increased soil total carbon and nitrogen as well as increased soil particulate organic matter.