| 1. |
- Anslan, Sten, et al.
(författare)
-
Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
- 2018
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 39, s. 29-40
-
Tidskriftsartikel (refereegranskat)abstract
- Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.
|
|
| 2. |
- Anslan, Sten, et al.
(författare)
-
Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests
- 2018
-
Ingår i: Soil Biology and Biochemistry. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0038-0717 .- 1879-3428. ; 116, s. 245-252
-
Tidskriftsartikel (refereegranskat)abstract
- Soil fauna mediate nutrient cycling through engineering physical properties and altering microbial commtmities in soil. Collembola is one of the most abundant groups of soil fauna, which regulates microbial communities by consumption and dispersal. The spatial structure of associations between Collembola and soil microbes have been described in several studies, but temporal variation of these associations remains unclear. Using high throughput sequencing, we studied the fungal communities on Collembola (Entomobiya nivalis, Orchesella flavescens, Pogonognathellus longicornis) body surface, gut and their immediate habitat (topsoil samples) in four seasons across three years. The soil samples were characterized by fairly uniform relative abundance of saprotrophic and mycorrhizal fungi, whereas collembolans were associated mostly with saprotrophs. The structure of fungal communities from all substrate types exhibited comparable patterns of temporal distance decay of shnilarity. Unlike in soil, fungal richness and composition in Collembola body and gut samples exhibited seasonal and annual variation, with a significant interaction term, indicating low predictability. These results reflect spatial and temporal plasticity of the fungal communities associated with epigeic Collembola, indicating the high adaptability of collembolans to available conditions. We found that the Collembola associations with fungi (including diet) did not vary among the studied epigeic Collembola species. The detected high diversity of fungi associated with Collembola suggests that dispersal by arthropod vectors may represent a powerful alternative to aerial dispersal of fungal propagules.
|
|
| 3. |
- Saitta, Alessandro, et al.
(författare)
-
Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem
- 2018
-
Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 28:1, s. 39-47
-
Tidskriftsartikel (refereegranskat)abstract
- Ecological and taxonomic knowledge is important for conservation and utilization of biodiversity. Biodiversity and ecology of fungi in Mediterranean ecosystems is poorly understood. Here, we examined the diversity and spatial distribution of fungi along an elevational gradient in a Mediterranean ecosystem, using DNA metabarcoding. This study provides novel information about diversity of all ecological and taxonomic groups of fungi along an elevational gradient in a Mediterranean ecosystem. Our analyses revealed that among all biotic and abiotic variables tested, host species identity is the main driver of the fungal richness and fungal community composition. Fungal richness was strongly associated with tree richness and peaked in Quercus-dominated habitats and Cistus-dominated habitats. The highest taxonomic richness of ectomycorrhizal fungi was observed under Quercus ilex, whereas the highest taxonomic richness of saprotrophs was found under Pinus. Our results suggest that the effect of plant diversity on fungal richness and community composition may override that of abiotic variables across environmental gradients.
|
|
