Metabarcoding survey of Chironomids and Oligochaetes in Lake Maggiore

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 427 records.

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:

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://cloud.gbif.org/eca/resource?r=lake_maggiore_cipais&v=1.7

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Consiglio Nazionale delle Ricerche - Istituto di Ricerca sulle Acque. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: c6686f13-e38d-4c24-bfd7-f1a8bd5f15b8.  Consiglio Nazionale delle Ricerche - Istituto di Ricerca sulle Acque publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Participant Node Managers Committee.

Keywords

Occurrence; DNA Barcode; Macroinvertebrates; Lentic waters; Midges; Freshwater annelid

Contacts

Geographic Coverage

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.

Taxonomic Coverage

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.

Temporal Coverage

Sampling Methods

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).

Method step description:

1. 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.

Bibliographic Citations

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.

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