In order to understand fine scale effects of nutrient availability through fertilization treatments on the soil eukaryotic microbial community, a multiple barcoding approach was applied on soil from four different treatments of the Bad Lauchstädt Long Term Static Fertilization Experiment (Germany). Eukaryotic microbial communities were PCR amplified from soil genomic DNA templates using a universal eukaryotic 18S rRNA primer pair as well as five specific primer pairs for different protist groups (18S rRNA; Cercozoa, Chrysophyceae-Synurophyceae, Kinetoplastida), Fungi (internal transcribed spacer) and algae (universal plastid amplicon). Amplicons were pyrosequenced and a total of 88,706 quality filtered reads were clustered in to 1,232 OTUs among the 6 marker datasets. Comparison of the taxonomic coverage of the different algal, fungal and protist groups by the universal eukaryotic barcode with the specific primer pairs based on overlapping OTUs assignment first revealed that half of the eukaryotic taxa disclosed in this study were missed by the universal eukaryotic marker. Low variations in OTU richness were observed between organic (farmyard manure), mineral (NPK) and non-fertilized soils, which was partially explained by an high proportion of core microbiome. However, eukaryotic microbial community compositions appeared highly structured in response to organic fertilization in all datasets (PERMANOVA p.value < 0.05) but not in the universal eukaryotic 18S dataset, whereas mineral fertilization only played a minor role. Nevertheless, by splitting the eukaryotic dataset among the different phyla, significant effect of organic fertilization on community composition of Ciliophora, Cercozoa and Fungi was observed. A co-occurrence network analysis based on non-random co-occurrence and exclusion revealed a complex assembly patterns between OTUs derived from different trophic levels. Our results showed that eukaryotic microbial community significantly changed at all trophic levels due to an increase in organic nutrients availability. We also observed that such a long term environmental shaping of eukaryotic microbial community composition can be better assessed using a multiple barcoding approach.
| Accession | PRJEB5170 |
| Scope | Monoisolate |
| Publications | Lentendu G et al., "Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach.", Mol Ecol, 2014 Jul;23(13):3341-55 |
| Submission | Registration date: 4-Mar-2014
UFZ - Helmholtz Centre |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 71 |
| Publications |
| PubMed | 1 |
| Other datasets |
| BioSample | 71 |