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首页> 美国卫生研究院文献>Genes >Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?
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Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

机译：单片段或大块土壤DNA元条形码：哪种方法能更好地表征表层土壤中用于样品分离的生物分类群？

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摘要

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina® MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.
机译：在法医地质案例中，样本量通常会限制使用批量方法对材料的常规表征。为了解决这个问题，生物分类单元的基于DNA的表征受到关注，因为存在的分类单元可用于样品间比较和来源归因。在我们最初的工作中，当从10种法医型表层土壤中分离的植物和昆虫片段中对Sanger进行DNA条形码测序时，捕获了低生物多样性。考虑到一些法医实验室现在可以使用大规模平行测序平台，我们评估了使用DNA元条形码可以更好地表征存在于同一表层土壤中的生物分类群。为此，在Illumina ® MiniSeq上扩增植物和动物条形码，并对三种不同的DNA样品类型（n = 50）进行测序：我们最初研究中使用的单个片段，以及250和100 mg散装土壤（来自最初研究中使用的10个地点）。总共572个独特的目标条形码序列通过了质量过滤，并用于下游统计分析：单个碎片分别为100 mg和250 mg散装土壤样品分别为54，321和285。植物条形码允许在非度量多维比例尺绘图中对样本位置进行一定的空间分离；从散装土壤制备的样品分离效果更好。这项研究证实，散装土壤DNA元条形码是一种更好的表征表层土壤中生物分类群的方法，它可以补充传统的地质检查方法。

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