ArticleFrontiers in microbiology2016
Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Desiccation to DNA: Bulk DNA Metabarcoding of Macroinvertebrate Egg Banks via Sugar-Flotation Enhances Biodiversity Surveys of Dry Salt Lakes.Ecology and evolution · 2026Article
- Soil Bacterial Community Structure and Functional Potential in the Caspian Drylands of Western Kazakhstan.Biology · 2026Article
- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- So far but so close: the biogeography of soil and plant-associated fungi in one of the most remote landmasses on Earth.ISME communications · 2026Article
- Decoding the rhizosphere microbiome againstFrontiers in microbiomes · 2026Review
- Cost-effective DNA extraction method optimized for high yield and long fragments from coastal sediments.PloS one · 2026Article
- Green synthesis of silver nanoparticles using Sudanese Candida parapsilosis: a sustainable approach to combat antimicrobial resistance.BMC microbiology · 2025Article
- Effects of Filtration Volumes on Bacterial Diversity and Community Structure in Freshwater Lakes.Ecology and evolution · 2025Article
- Measurement of the effectiveness of Clonostachys rosea in reducing Fusarium biomass on wheat straw.Journal of applied genetics · 2024Article
- Review
- Effects of Different Heavy Metal Stressors on the Endophytic Community Composition and Diversity ofMicroorganisms · 2024Article
- Variations in microbial community compositions and processes imposed under contrast geochemical contexts in Sicilian mud volcanoes, Italy.Frontiers in microbiology · 2024Article
- Plant and soil microbial composition legacies following indaziflam herbicide treatment.Frontiers in microbiology · 2024Article
- A cryopreservation method to recover laboratory- and field-derived bacterial communities from mosquito larval habitats.PLoS neglected tropical diseases · 2023Article
- The community ecology perspective of omics data.Microbiome · 2022Article
- A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.Microorganisms · 2022Article
- Analysis of endophyte diversity of two Gentiana plants species and the association with secondary metabolite.BMC microbiology · 2022Article
- Seed quantity affects the fungal community composition detected using metabarcoding.Scientific reports · 2022Article
- Analysis of endophyte diversity ofPeerJ · 2022Article
- Analysis of Endophyte Diversity ofMicroorganisms · 2021Article
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4 authors.
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Abstract
We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.
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