ArticlePloS one2015
Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Sampling Design and Sample Processing Affect Soil Biodiversity Assessments.Molecular ecology resources · 2026Article
- Article
- Habitat Disturbance Promotes Shifts in the Abundance of Major Fungal Phyla in the Roots of a Native Orchid,Plant-environment interactions (Hoboken, N.J.) · 2025Article
- Role of Fungi in Tumorigenesis: Promises and Challenges.Annual review of pathology · 2025Review
- Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.Scientific reports · 2024Article
- Multiple graphical views for automatically generating SQL for the MycoDiversity DB; making fungal biodiversity studies accessible.Biodiversity data journal · 2024Article
- Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan.Microbial ecology · 2023Article
- Article
- Mycobiome and Cancer: What Is the Evidence?Cancers · 2021Review
- Insufficient sampling constrains our characterization of plant microbiomes.Scientific reports · 2021Article
- The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks.PloS one · 2021Article
- New Insight into the Composition of Wheat Seed Microbiota.International journal of molecular sciences · 2020Article
- Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History.Applied and environmental microbiology · 2020Article
- Impacts of Sampling Design on Estimates of Microbial Community Diversity and Composition in Agricultural Soils.Microbial ecology · 2019Article
- Ectomycorrhizal fungal communities are dominated by mammalian dispersed truffle-like taxa in north-east Australian woodlands.Mycorrhiza · 2019Article
- Mycobiome diversity: high-throughput sequencing and identification of fungi.Nature reviews. Microbiology · 2019Review
- High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations.Molecular ecology resources · 2019Review
- Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient.PloS one · 2018Article
- Article
- Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.Applied and environmental microbiology · 2016Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.
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