Environmental DNA sequencing data from algal blooms in Lake Erie using Oxford Nanopore MinION
Koeppel, A. F.; Goodrum, W. J.; Steffen, M.; Wurch, L.; Turner, S. D.
Show abstract
Harmful Algal Blooms (HABs) pose a significant and increasing risk, both to human health and to the Blue Economy. Genomics approaches to early detection promise to help mitigate these risks. We have developed and prototyped HABSSED (HAB Surveillance by Sequencing of Environmental DNA), a portable, reliable, rapid, low-cost pipeline for detecting HABs in the field using 3rd generation sequencing with the Oxford Nanopore MinION device. We demonstrated the efficacy of our approach by sequencing existing samples collected from a National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory (GLERL) on Lake Erie. We sequenced environmental DNA (eDNA) from samples drawn before, during, and after a Microcystis bloom, and estimate the abundanced of HAB-associated taxa. While sequencing results showed some evidence of human and E. coli contamination, we find that the abundance of Mycrocystis and other HAB-associated orgnisms significantly differs between pre- and post-bloom environments. Here we describe the publicly available sequencing data that was generated as part of this research, which is available in the Sequence Read Archive (SRA) under accession number PRJNA812770.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams 95%
- eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot 94%
- Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates 94%
Similar papers in this journal
- eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake 97%
- Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis? 96%
- Water volume, biological and PCR replicates influence the characterization of deep-sea pelagic fish communities. 95%
Similar papers in this journal
- Sporadic Diurnal Fluctuations of Cyanobacterial Populations in Oligotrophic Temperate Systems Can Prevent Accurate Characterization of Change and Risk in Aquatic Systems 96%
- Microbiomes in drinking water treatment and distribution: a critical review and meta-analysis from source to tap 95%
- Impact of sulfamethoxazole on a riverine microbiome 94%
Similar papers in this journal
- In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day 95%
- Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-offs in Resource-Limited Settings 95%
- Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters 95%
Similar papers in this journal
- Considerations for metabarcoding-based port biological baseline surveys aimed at marine non-indigenous species monitoring and risk-assessments 95%
- Sampling The Zebrafish Gut Microbiota - A Genome Resolved Metagenomic Approach 94%
- Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range - A case study in Cyprus 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.