| Zdroj: |
Donhauser, J, Briones, M J I, Mikola, J, Jones, D, Eder, R, Filser, J, Frossard, A, Krogh, P H, Sousa, P, Cortet, J, Desie, E, Domene, X, Djuric, S, Hackenberger, D, Jiménez, J, Iamandei, M, Rissmann, C, Schmidt, O, Shanskiy, M, Silfver, T, Vancampenhout, K, Vasutova, M, Velizarova, E & Frey, B 2022, ' Extracting DNA from soil or directly from isolated nematodes indicate dissimilar community structure for Europe-wide forest soils ', Soil Biology & Biochemistry . |
| Popis: |
Nematodes are globally the most abundant soil animals and play a crucial role in soil food-webs. DNA metabarcoding offers a time-effective alternative to morphology-based assessments of nematode diversity. However, it is unclear how different DNA extraction methods prior to metabarcoding could affect community analysis. We used forest soils from a European latitudinal gradient (39 to 79°N, ~4500 km, covering six biomes) to systematically evaluate the effect of two sources of nematode DNA either directly extracted from soils vs. extracted from nematodes previously isolated from soils hypothesizing that the DNA source material may produce different diversities, community structure and feeding type. Nematode-sample DNA exhibited a higher richness, while no difference in Shannon diversity was found between the approaches. The DNA sources also created significantly different community structure, with greater differences observed across soil-extracted DNA than nematode- sample DNA. Communities that were identified using soil-extracted DNA correlated more strongly with environmental factors. The most overrepresented species in nematode-sample DNA were Heterocephalobus elongatus, Eucephalobus striatus and Hexatylus sp., whereas Phasmarhabditis sp. and Eumonhystera filiformis were overrepresented in soil-extracted DNA. Read abundances of feeding types significantly differed between the DNA sources and across sites, with a significant effect of biome on both ecto- and endoparasitic herbivores in soil-extracted DNA and for ectoparasitic herbivores only in nematode-sample DNA. Collectively, our data suggest that caution is required when interpreting metabarcoding results as different sample sizes and extraction methods introduce experimental bias reducing differences in nematode communities across sites and obscuring the relationships between community structure and environmental drivers. This is particularly relevant for future meta-analyses. |
