| 1. |
- Maillard, François, et al.
(författare)
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A cryptically diverse microbial community drives organic matter decomposition in forests
- 2024
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Ingår i: Applied Soil Ecology. - 0929-1393. ; 193
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Tidskriftsartikel (refereegranskat)abstract
- Despite the critical role of microorganisms in plant and fungal residue decomposition, our understanding of their full diversity remains limited. This is due largely to the rapid microbial succession during decomposition, a scarcity of studies including multiple sampling times, and the omission of a species richness index encompassing all decay stages. To address these gaps, we conducted a meta-analysis of 12 studies, each examining bacterial and fungal communities at multiple time points during decomposition. We aimed to determine the overall microbial diversity involved in decomposition processes by aggregating microbial richness at different time points. By comparing cumulative microbial OTU (operational taxonomic unit) richness with single time point microbial richness, we show that the cumulative richness was 2–5 times greater, indicating that a high yet frequently overlooked diversity of microorganisms is involved in the decomposition process. This pattern was consistent across different organic matter types (plant and fungal residues) for both major microbial domains (bacteria and fungi). Moreover, the appearance rate of novel OTUs generally decreased over time for most organic matter types, except for dead wood, which accumulated new fungal OTUs at a notable pace. Our results collectively emphasize the importance of considering various microbial domains, organic matter types, and time points to successfully characterize the diversity of microorganisms involved in decomposition. Further, given the hidden cumulative number of bacterial and fungal species held within plant and fungal residues across decay stages, we propose that these substrates are crucial microbial reservoirs to include to accurately assess global terrestrial microbial diversity.
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| 2. |
- Anslan, Sten, et al.
(författare)
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Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
- 2018
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 39, s. 29-40
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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.
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| 3. |
- Cantoran, Anahi, et al.
(författare)
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Defining a core microbial necrobiome associated with decomposing fungal necromass
- 2023
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Ingår i: FEMS Microbiology Ecology. - 0168-6496. ; 99:9
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Tidskriftsartikel (refereegranskat)abstract
- Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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| 4. |
- Jacobsen, Carsten Suhr, et al.
(författare)
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Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.
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| 5. |
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| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Forskningsöversikt (refereegranskat)abstract
- Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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