Dataset Information

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil.

ABSTRACT: High-throughput amplicon sequencing technology has been widely used in soil microbiome studies. Here, we estimated the bias of amplicon sequencing data affected by DNA extraction methods in a saline soil, and a non-saline normal soil was used as a control. Compared with the normal soil, several unique points were observed in the saline soil. The soil washing pretreatment can improve not only DNA quantity and quality but also microbial diversities in the saline soil; therefore, we recommend the soil washing pretreatment for saline soils especially hypersaline soils that cannot be achieved with detectable DNA amounts without the pretreatment. Also, evenness indices were more easily affected by DNA extraction methods than richness indices in the saline soil. Moreover, proportions of Gram-positive bacteria had significant positive correlations with the achieved microbial diversities within replicates of the saline soil. Though DNA extraction methods can bias the microbial diversity or community and relative abundances of some phyla/classes can vary by a factor of more than five, soil types were still the most important factor of the whole community. We confirmed good comparability in the whole community, but more attention should be paid when concentrating on an exact diversity value or the exact relative abundance of a certain taxon. Our study can provide references for the DNA extraction from saline and non-saline soils and comparing sequencing data across studies who may employ different DNA extraction methods.

SUBMITTER: Xie K

PROVIDER: S-EPMC6088177 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil.

Xie Kehui K Deng Yong Y Zhang Xuze X Wang Xueting X Kang Guangbo G Bai Liang L Huang He H

Frontiers in microbiology 20180803

High-throughput amplicon sequencing technology has been widely used in soil microbiome studies. Here, we estimated the bias of amplicon sequencing data affected by DNA extraction methods in a saline soil, and a non-saline normal soil was used as a control. Compared with the normal soil, several unique points were observed in the saline soil. The soil washing pretreatment can improve not only DNA quantity and quality but also microbial diversities in the saline soil; therefore, we recommend the s ...[more]

PMID: 30127778

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Project description:Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

Dataset Information

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil.

Publications

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil.

Similar Datasets

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