Описание
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.
Записи данных
Данные этого occurrence ресурса были опубликованы в виде Darwin Core Archive (DwC-A), который является стандартным форматом для обмена данными о биоразнообразии в виде набора из одной или нескольких таблиц. Основная таблица данных содержит 9 101 записей.
Также в наличии 2 таблиц с данными расширений. Записи расширений содержат дополнительную информацию об основной записи. Число записей в каждой таблице данных расширения показано ниже.
Данный экземпляр IPT архивирует данные и таким образом служит хранилищем данных. Данные и метаданные ресурсов доступны для скачивания в разделе Загрузки. В таблице версий перечислены другие версии ресурса, которые были доступны публично, что позволяет отслеживать изменения, внесенные в ресурс с течением времени.
Версии
В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.
Как оформить ссылку
Исследователи должны дать ссылку на эту работу следующим образом:
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
Права
Исследователи должны соблюдать следующие права:
Публикующей организацией и владельцем прав на данную работу является United States Geological Survey. Насколько это возможно по закону, издатель отказался от всех прав на эти данные и посвятил их Public Domain (CC0 1.0). Пользователи могут без ограничений копировать, изменять, распространять и использовать работу, в том числе в коммерческих целях.
Регистрация в GBIF
Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 9d7baaac-57db-4852-9993-7f0e7f15635b. United States Geological Survey отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF-US.
Ключевые слова
Occurrence
Внешние данные
Ресурс также доступен в других форматах
| 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 |
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Контакты
- Metadata Provider ●
- Originator ●
- Point Of Contact
http://orcid.org/0000-0003-4879-3997
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Географический охват
The geographic coverage is part of the Miller Creek watershed including North Vogel Lake, Vogel Lake, and Miller Creek.
| Ограничивающие координаты | Юг Запад [60,984, -150,515], Север Восток [61,005, -150,41] |
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Таксономический охват
Annelida, Arthropoda, Mollusca
| Phylum | Annelida, Arthropoda, Mollusca |
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Временной охват
| Дата начала / Дата окончания | 2021-07-21 / 2022-08-29 |
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Данные проекта
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.
| Название | Inventory of Freshwater Invertebrates from the Miller Creek Watershed, Kenai Peninsula, Alaska, USA |
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| Идентификатор | https://ecos.fws.gov/ServCat/Reference/Profile/139305 |
| Описание района исследования | The study area included North Vogel Lake, Vogel Lake, and Miller Creek in the Miller Creek watershed, Kenai Peninsula, Alaska, USA. |
| Описание плана выполнения исследований | 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. |
Исполнители проекта:
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Методы сбора
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.
| Охват исследования | 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. |
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Описание этапа методики:
- 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.
Библиографические ссылки
- 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
- 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
- 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
- USGS Advanced Research Computing (2021) USGS Yeti Supercomputer. U.S. Geological Survey. https://doi.org/10.5066/F7D798MJ https://doi.org/10.5066/F7D798MJ
- 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
- 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
- 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
- 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
- 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
Дополнительные метаданные
| Альтернативные идентификаторы | 9d7baaac-57db-4852-9993-7f0e7f15635b |
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| https://doi.org/10.15468/49v6yh | |
| https://ipt.gbif.us/resource?r=knwr_miller_creek_2021 |