Metabarcoding Data from an Inventory of Freshwater Invertebrates from the Miller Creek Watershed, Kenai Peninsula, Alaska, USA

Occurrence
Latest version published by United States Geological Survey on Mar 31, 2023 United States Geological Survey
Publication date:
31 March 2023
License:
CC0 1.0

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

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Description

Because benthic macroinvertebrates and zooplankton are susceptible to the pesticide rotenone, we surveyed freshwater macroinvertebrates in the Miller Creek Watershed, Kenai Peninsula, Alaska ahead of a rotenone treatment in fall 2021 to eradicate a population of invasive northern pike (Esox lucius Linnaeus, 1758). We collected 32 samples in 2021 and another 32 post-treatment invertebrate samples in 2022 at the same places and during the same time of year to enable comparison of pre- and post-treatment freshwater invertebrate communities.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 9,101 records.

2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)
9101
Identification 
9140
dnaDerivedData 
9101

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Bowser M L, Artaiz S I, Danner J M, Dent K K, Meyer B, Watts D, Wyrick W R (2022): Metabarcoding Data from an Inventory of Freshwater Invertebrates from the Miller Creek Watershed, Kenai Peninsula, Alaska, USA. v1.3. United States Geological Survey. Dataset/Occurrence. https://bison.usgs.gov/ipt/resource?r=knwr_miller_creek_2021&v=1.3

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 9d7baaac-57db-4852-9993-7f0e7f15635b.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.

Keywords

Occurrence

External data

The resource data is also available in other formats

Miller Creek Watershed aquatic invertebrate inventory, raw metabarcoding data from the 2021 field season https://ecos.fws.gov/ServCat/Reference/Profile/139306 UTF-8 FASTQ

Contacts

Matthew L. Bowser
  • Metadata Provider
  • Originator
  • Point Of Contact
Fish and Wildlife Biologist
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
PO Box 2139
99669 Soldotna
AK
US
Samuel I. Artaiz
  • Originator
Biological Technician
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
US
Jake M. Danner
  • Originator
Biological Technician
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
US
Kris K. Dent
  • Originator
Biologist
Alaska Department of Fish and Game
Soldotna
Alaska
US
Benjamin Meyer
  • Originator
Environmental Scientist
Kenai Watershed Forum
Soldotna
Alaska
US
Dom Watts
  • Originator
Pilot/Biologist
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
Soldotna
Alaska
US
Warren R. Wyrick
  • Originator
Biologist
Alaska Department of Fish and Game
Soldotna
Alaska
US
Anya Bronowski
  • Originator
Biological Technician
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
Soldotna
Alaska
US
Jackie Morton
  • Originator
Biological Technician
U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge
Soldotna
Alaska
US
Benyamin Wishnek
  • Originator
South Region Early Detection Rapid Response Project Manager
U.S. Fish and Wildlife Service, Alaska Region
Soldotna
Alaska
US

Geographic Coverage

The geographic coverage is part of the Miller Creek watershed including North Vogel Lake, Vogel Lake, and Miller Creek.

Bounding Coordinates South West [60.984, -150.515], North East [61.005, -150.41]

Taxonomic Coverage

Annelida, Arthropoda, Mollusca

Phylum Annelida, Arthropoda, Mollusca

Temporal Coverage

Start Date / End Date 2021-07-21 / 2022-08-29

Project Data

Because benthic macroinvertebrates and zooplankton are susceptible to the pesticide rotenone, surveys of freshwater macroinvertebrates were conducted in the Miller Creek Watershed, Kenai Peninsula, Alaska ahead of a planned rotenone treatment in fall 2021. Currently, 32 of 32 planned samples have been collected in 2021. Another 32 post-treatment invertebrate samples are planned in 2022 to enable comparison of pre- and post-treatment freshwater invertebrate communities.

Title Inventory of Freshwater Invertebrates from the Miller Creek Watershed, Kenai Peninsula, Alaska, USA
Identifier https://ecos.fws.gov/ServCat/Reference/Profile/139305
Study Area Description The study area included North Vogel Lake, Vogel Lake, and Miller Creek in the Miller Creek watershed, Kenai Peninsula, Alaska, USA.
Design Description At each of two visits per year we planned to collect 3 D-net samples, 3 Ekman dredge samples, and 2 Wisconsin net samples in Vogel Lake; 2 D-net samples, 2 Ekman dredge samples, and 1 Wisconsin net sample in North Vogel Lake; and 3 D-net samples in Miller Creek, a total of 16 invertebrate samples per visit, 32 samples per year, and 64 samples over the two year project. At North Vogel Lake, Vogel Lake, and upper Miller Creek we sampled twice in 2021: first on July 20--23 and second on August 28. We sampled at 15 sites using three methods. We failed to make it out to the mouth of Miller Creek in July and August, collecting samples there only on September 13, 2021.

The personnel involved in the project:

Matthew Bowser
Samuel Artaiz
  • Author
Jake Danner
  • Author
Kris Dent
  • Author
Robert Massengill
Benjamin Meyer
  • Author
Dom Watts
  • Author
Warren Wyrick
  • Author

Sampling Methods

Field methods generally followed the methods of Massengill (2014, 2017). We took vertical plankton tows in the deepest parts of the lakes using an Aquatic Research Instruments Wisconsin net. We sampled littoral areas using with D-nets. We obtained benthic samples using either an AMS Incorporated model 445.11 Ekman dredge or an AMS Incorporated model 445.60 stainless steel dredge. Most benthic samples were sorted using a series of sieves.

Study Extent The study extent included 3 D-net samples, 3 Ekman dredge samples, and 2 Wisconsin net samples in Vogel Lake; 2 D-net samples, 2 Ekman dredge samples, and 1 Wisconsin net sample in North Vogel Lake; and 3 D-net samples in Miller Creek, a total of 16 invertebrate samples per visit, sampled twice per year for a total of 32 samples per year.

Method step description:

  1. Metabarcoding samples were stored in a -23 °C freezer exept when samples were being processed. Invertebrates were separated from debris by hand under a dissecting microscope. Care was taken to reduce possible crosscontamination of DNA among samples. Samples were shipped out on ice on September 29, 2021, arriving the next day at MR DNA (Shallowater, Texas, http://www. mrdnalab.com). We chose to use the mlCOIintF/jgHCO2198 primer set of Leray et al. (2013) for PCR, targeting a 313 bp region of the COI DNA barcoding region. The mlCOIintF/jgHCO2198 primer pair was used with barcode on the forward primer in a 30–35 PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94 °C for 3 minutes, followed by 30– 35 cycles of 94 °C for 30 s, 53 °C for 40 seconds and 72 °C for 1 minute, after which a final elongation step at 72 °C for 5 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads. The pooled and purified PCR product was used to prepare an illumina DNA library. Sequencing was performed at MR DNA on a MiSeq following the manufacturer’s guidelines. We processed the raw sequence data on the USGS Yeti supercomputer (USGS Advanced Research Computing, 2021) using R, version 4.1.1 for manipulating data and Je, version 2.0.RC (Girardot et al., 2016) for demultiplexing. The raw data included reads in alternating directions with the sample barcodes only on one read. Accordingly, we exectued the je demultiplex command, accepting the defaults that only require one of the two reads to contain a sample barcode. Raw read data were processed using MetaWorks, version 1.9.5 (Porter and Hajibabaei, 2020), running the default analysis options for metazoan COI DNA barcode sequences. Sequences were identified using the RDP classifier, version 2.13 (Wang et al., 2007) and the CO1 Classifier, version 4.0.1 reference library (Porter, 2017; Porter and Hajibabaei, 2018). Finally, we also compared the sequences to libraries we had obtained in previous metabarcoding projects on the Kenai Peninsula.

Bibliographic Citations

  1. Massengill R (2014) Control Efforts for Invasive Northern Pike on the Kenai Peninsula, 2009. Special Publication 14-11. URL http://www.adfg.alaska.gov/FedAidPDFs/SP14-11.pdf http://www.adfg.alaska.gov/FedAidPDFs/SP14-11.pdf
  2. Massengill R (2017) Stormy Lake Restoration: Invasive Northern Pike Eradication, 2012. Special Publication 17-18, Alaska Department of Fish and Game, Divisions of Sport Fish and Commercial Fisheries. http://www.adfg.alaska.gov/FedAidPDFs/SP17-18.pdf http://www.adfg.alaska.gov/FedAidPDFs/SP17-18.pdf
  3. Leray M, Yang Y J, Meyer C P, Mills S C, Agudelo N, Ranwez V, Boehm J T, Machida R J (2013) A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology https://doi.org/10.1186/1742-9994-10-34 https://doi.org/10.1186/1742-9994-10-34
  4. USGS Advanced Research Computing (2021) USGS Yeti Supercomputer. U.S. Geological Survey. https://doi.org/10.5066/F7D798MJ https://doi.org/10.5066/F7D798MJ
  5. Girardot C, Scholtalbers J, Sauer S, Su S-Y, Furlong E E (2016) Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics 17:419. https://doi.org/10.1186/s12859-016-1284-2 https://doi.org/10.1186/s12859-016-1284-2
  6. Porter T M, Hajibabaei M (2020). METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments. BioRxiv, 2020.07.14.202960. https://doi.org/10.1101/2020.07.14.202960 https://doi.org/10.1101/2020.07.14.202960
  7. Wang Q,Garrity G M, Tiedje J M, Cole J R (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73:5261. https://doi.org/10.1128/AEM.00062-07 https://doi.org/10.1128/AEM.00062-07
  8. Porter T M (2017) Eukaryote CO1 Reference Set For The RDP Classifier. https://doi.org/10.5281/zenodo.4741447 https://doi.org/10.5281/zenodo.4741447
  9. Porter T M, Hajibabaei M (2018) Automated high throughput animal CO1 metabarcode classification. Scientific Reports 8:4226. https://doi.org/10.1038/s41598-018-22505-4 https://doi.org/10.1038/s41598-018-22505-4

Additional Metadata

Alternative Identifiers 9d7baaac-57db-4852-9993-7f0e7f15635b
https://doi.org/10.15468/49v6yh
https://ipt.gbif.us/resource?r=knwr_miller_creek_2021