Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance
Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance
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DOI：
10.1016/j.soilbio.2022.108902
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发表时间：
2023-02
影响因子：
9.7
通讯作者：
Ting Li;Song Zhang;Jinming Hu;Haiyan Hou;Kexin Li;Qiuping Fan;Fang Wang;Linfeng Li;X. Cui;Dong Liu;Rongxiao Che
中科院分区：
文献类型：
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作者：
Ting Li;Song Zhang;Jinming Hu;Haiyan Hou;Kexin Li;Qiuping Fan;Fang Wang;Linfeng Li;X. Cui;Dong Liu;Rongxiao Che
作为大多数土壤微生物多样性和丰度研究的基石，土壤DNA提取受到土壤样品大小的内在影响，但其影响仍远未完全了解。本研究从荒漠、草甸、森林和农田生态系统采集土壤，研究土壤样品大小（0.01、0.025、0.25、0.50和1.00 g）对原核生物和真菌群落分析的影响。通过实时荧光定量PCR和NovaSeq高通量测序分析土壤微生物丰度和多样性。我们发现用于DNA提取的土壤样品大小通常不影响微生物丰度的测定。相反，微生物丰富度、群落组成和共生模式随土壤样品大小而变化。在大多数生态系统中，0.01 ~ 0.025 g土壤的微生物丰富度和共生频率低于0.25 ~ 1.00 g土壤的微生物丰富度和共生频率。当土壤样品粒径小于等于0.50 g时，微生物群落组成也受土壤样品粒径的影响。特别是，用于DNA提取的小土壤样品尺寸（即≤0.025 g）揭示了土壤微生境中微生物群落分布的巨大差异。总的来说，在大多数生态系统中，至少应使用0.25克土壤来确定微生物的总体多样性。对于微生物细胞密度较低的土壤，应从0.50 g甚至更多的土壤中提取DNA。因此，土壤微生物多样性和共生模式的分析，而不是丰度，本质上受DNA提取土壤样品尺寸的影响，而最佳土壤样品尺寸的选择取决于土壤类型和研究目的。
As the cornerstone of most soil microbial diversity and abundance research, soil DNA extraction is inherently influenced by soil sample sizes, yet the effects remain far from fully understood. In this study, soils were collected from desert, meadow, forest, and cropland ecosystems to examine the effects of soil sample sizes (i.e., 0.01, 0.025, 0.25, 0.50, and 1.00 g) on prokaryotic and fungal community analysis. Soil microbial abundance and diversity were analyzed through real-time PCR and NovaSeq high-throughput sequencing, respectively. We found that soil sample sizes for DNA extraction generally did not affect microbial abundance determination. In contrast, microbial richness, community composition, and co-occurrence patterns varied with different soil sample sizes. The microbial richness and co-occurrence frequency obtained from 0.01 to 0.025 g of soils were lower than those determined based on 0.25–1.00 g of soils in most ecosystems. Microbial community composition was also affected by the soil sample sizes when they were 0.50 g or less. In particular, small soil sample sizes for DNA extraction (i.e.,≤ 0.025 g) revealed dramatic variations in microbial community profiles among soil microhabitats. Collectively, in most ecosystems, at least 0.25 g of soils should be used to determine the overall diversity of microbes. As for the soils with low microbial cellular density, DNA should be extracted from 0.50 g or even more soils. Thus, the analysis of soil microbial diversity and co-occurrence patterns rather than abundance are substantially affected by the soil sample sizes for DNA extraction, and the choice of optimum soil sample sizes depends on soil types and research purposes.