Metabarcoding survey of Chironomids and Oligochaetes in Lake Maggiore
Citation
Zaupa S, Fontaneto D, Sabatino R, Boggero A (2023). Metabarcoding survey of Chironomids and Oligochaetes in Lake Maggiore. Version 1.7. Consiglio Nazionale delle Ricerche - Istituto di Ricerca sulle Acque. Occurrence dataset https://doi.org/10.15468/8wbqfc accessed via GBIF.org on 2024-08-20.Description
This data set includes the identified chironomids and oligochaetes in Lake Maggiore and their respective GenBank accession number (AccNumGenBank=the unique identifier for a sequence record). Each row contains a record of a macroinvertebrate taxon from a sample from Lake Maggiore that were proceeded for DNA extraction. All sequences were checked in GenBank through Blast searches to check their identity at the high taxonomic level and confirm that they indeed were from chironomids and oligochaetes. Tha data sheet includes columns with the following labels:1) eventide, occurrenceID, eventDate, scientificName, taxonRank, kingdom, phylum, subphylum, class, order, family, family, subfamily, tribe, genus, species, decimalLatitude, decimalLongitude, geodeticDatum, countryCode, organismQuantity, organismQuantityType, DNA_sequence (=AccNumGenBank), preparations, target_gene.
Sampling Description
Study Extent
The dataset contains information on 428 occurrences for 55 taxa. The occurrences were recorded during the years 2019-2022. The study area is 212.5 km^2.Sampling
For each sampling station, sediment samples were collected using a spatula. Aliquots of sediment were collected in plastic jars and kept at controlled temperatures between 4 and 7 °C to preserve live animals. Sediment samples were then sorted at the stereomicroscope (Leica M125, 80x magnification) to isolate chironomid larvae and oligochaetes. Single animals were isolated: each animal was cut in two pieces, one piece to be used for morphological identification and one piece for DNA extraction (Zaupa et al., 2022). Species identification was performed by preparing Faure slides mounts of head for chironomid larvae and front end with chaetae distribution and genital apparatus for oligochaetes (Andersen et al., 2013; Timm, 2009). DNA extraction was performed, using PureLink® Genomic DNAKit (Invitrogen by Life Technologies, Thermo Fisher Scientific, Monza (MB), Italy), following manufacturer's instructions, for chironomid larvae; for oligochaetes, 40 µl of Chelex (BioRad, Segrate (MI), Italy) + 1 µl Proteinase K (PanReac AppliChem, Monza (MB), Italy. DNA was amplified with PCR to obtain the barcoding Folmer fragment of the cytochrome c oxidase subunit I (COI), with primers HCO2198 and LCO1490 (Folmer et al., 1994; Hebert et al., 2003).Quality Control
All sequences were checked in GenBank.Method steps
- Sediment samples were sorted at the stereomicroscope and single animals were cut in two pieces, one piece to be used for morphological identification and one piece for DNA extraction. Identification was performed to species level whenever possible, using relevant taxonomic keys (e.g. Andersen et al., 2013; Timm, 2009). DNA was amplified with PCR to obtain the barcoding Folmer fragment of the cytochrome c oxidase subunit I (COI), with primers HCO2198 and LCO1490 (Folmer et al., 1994; Hebert et al., 2003). Amplicons were sequenced (Sanger sequensing) at Macrogen Europe (Amsterdam (BA), The Netherlands; https://www.macrogen-europe.com/); chromatograms were checked in FinchTV 1.5.0 (https://digitalworldbiology.com/FinchTV), with forward and reverse sequences merged using Mesquite 3.6 (https://www.mesquiteproject.org/). Sequences were aligned with MAFFT 7 (Katoh et al., 2013). All sequences were checked in GenBank through Blast searches to check their identity at the high taxonomic level and confirm that they indeed were from chironomids and oligochaetes. Then, we reported the best hits in GenBank, saving their accession numbers, species names, and geographic origin. We then followed the accepted threshold of 3% as a cutoff value for DNA barcoding in COI in invertebrates (Hebert et al., 2003) to confirm species identity. For species where a molecular match was found, the dataset includes the identified species and Genbak accession number.
Taxonomic Coverages
The data set covers organisms of the Phyla Anellida and Arthropoda.
Data from species, genus, family, order and class rank were included in the dataset.
Data from species, genus, family, order and class rank were included in the dataset.
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Annelidarank: phylum
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Arthropodarank: phylum
Geographic Coverages
Lake Maggiore, the sampling were collected in the littoral areas, from the shores, and covered natural and human-modified habitats, mostly sandy sediments in natural habitats and pebbles/rocks for human-modified habitats. Data are georeferenced according to WGS 84 datum.
Bibliographic Citations
- Andersen T, Cranston PS, Epler JH (eds), 2013. Chironomidae of the Holarctic Region: Keys and diagnoses. Part 1 - Larvae. Insect Systematics and Evolution Supplements (formerly Entomologica Scandinavica Supplement) 66, 573 pp. -
- Boggero A, Zaupa S, Borgomaneiro G, Eckert E, Gariboldi L, Marchetto A, Musazzi S, Sabatino R, Paganelli D, Fontaneto D, (2021) (in press). Ricerca ed innovazione sul Lago Maggiore: indicatori di qualità nel continuum acqua - rive. Rapporto finale 2019-2021. Commissione Internazionale per la Protezione delle Acque Italo-Svizzere (Ed.): 220 pp. -
- Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3(5):294-9. -
- Hebert PD, Cywinska A, Ball SL, DeWaard JR, 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences 270(1512):313-321. -
- Katoh K, Standley DM, 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772-780. Timm T, 2009. A guide to the freshwater Oligochaeta and Polychaeta of Northern and Central Europe. Lauterbornia 66:235 pp. -
- Zaupa S, Fontaneto D, Sabatino R, Boggero A, (2022) (submitted). Building a local reference library for metabarcoding survey of lake macrobenthos: oligochaetes and chironomids from Lake Maggiore. Advances in Oceanography and Limnology. -
Contacts
Silvia Zaupaoriginator
position: PostDoc
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbania
IT
email: silvia.zaupa@gmail.com
userId: https://orcid.org/0000-0001-7379-6087
Diego Fontaneto
originator
position: Researcher
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbania
IT
email: diego.fontaneto@cnr.it
userId: https://orcid.org/0000-0002-5770-0353
Raffaella Sabatino
originator
position: PostDoc
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbano-Cusio-Ossola
IT
email: raffaella.sabatino@irsa.cnr.it
userId: https://orcid.org/0000-0003-0093-7808
Angela Boggero
originator
position: Resarcher
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbano-Cusio-Ossola
IT
email: angela.boggero@cnr.it
userId: https://orcid.org/0000-0002-7534-3126
Silvia Zaupa
metadata author
position: PostDoc
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbania
IT
email: silvia.zaupa@gmail.com
Lyudmila Kamburska
point of contact
Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca sulle Acque (IRSA); National Biodiversity Future Center (NBFC)
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbania
IT
Telephone: 3468473975
email: lyudmila.kamburska@irsa.cnr.it
Silvia Zaupa
administrative point of contact
position: PostDoc
CNR-IRSA
Largo Vittorio Tonolli 50 CNR-IRSA
Verbania
28922
Verbano-Cusio-Ossola
IT
email: silvia.zaupa@gmail.com