Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities

DNA metabarcoding is an emerging technique for enhancing microbial community monitoring programs that assess water quality and environmental health. However, comparability between studies is limited by a lack of standardized laboratory protocols. To contribute to protocol optimization and decision making, we compare seven commercially available DNA extraction kits and evaluate their impact on DNA yield, PCR inhibitor removal, and taxonomic resolution of microplankton, microalgae, and particle-associated bacterial communities using 18S V9 and 16S V3-V4 amplicon sequencing of samples from two contrasting estuarine environments varying in salinity and productivity. We observed greater DNA yields and detected PCR inhibition at the higher productivity, lower salinity site. The Qiagen DNeasy PowerSoil Pro and Omega E.Z.N.A. Tissue DNA kits both yielded greater amounts of DNA, but only the soil- and plant-specific kits effectively removed PCR inhibitors. Notably, differences in taxonomic richn..., DNA was extracted from filtered surface water samples at two sites using seven commercially available DNA extraction methods: Omega E.Z.N.A. Tissue DNA Kit, Omega E.Z.N.A. Tissue DNA Kit+ Bead-Beating, Qiagen DNeasy Blood & Tissue Kit, Omega E.Z.N.A. Soil DNA Kit, Qiagen DNeasy Blood & Tissue Kit+ Bead-Beating, Qiagen DNeasy Plant Pro Kit, and Qiagen DNeasy PowerSoil Pro Kit.
Extracted DNA was amplified using a two-step PCR method and sequenced using an Illumina MiSeq. Reads were demultiplexed using the Illumina MiSeq Software and quality control was performed using fastp. Primer trimming, denoising, ASV generation, and taxonomic assignments were performed using QIIME2., # Data from: Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities

Dataset DOI: [10.5061/dryad.98sf7m0w3](10.5061/dryad.98sf7m0w3)

## Description of the data and file structure

### Files and variables

#### File: feature-table-16S.tsv

**Description:** ASV counts for the 16S dataset

##### Variables

* OTU ID = ASV ID
* Sample Number

#### File: silva-taxonomy-16S.tsv

**Description:** Taxonomic assignments for each ASV from the 16S dataset

##### Variables

* Feature ID: ASV ID
* Taxon: Taxonomic lineage
* Consensus: VSearch consensus

#### File: pr2-taxonomy-18S.tsv

**Description:** Taxonomic assignments for each ASV from the 18S dataset

##### Variables

* Feature ID: ASV ID
* Taxon: Taxonomic lineage
* Consensus: VSearch consensus

#### File: feature-table-18S.tsv

**Description:** ASV counts for the 18S dataset

##### Variables

* OTU ID = ASV ID
* Sample Number

#### File: dna-sequences_18S.fasta

**Description:** Sequences f..., ,