Metabarcoding survey of Chironomids and Oligochaetes in Lake Maggiore

Registros

Los datos en este recurso de registros biológicos han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 427 registros.

Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es Consiglio Nazionale delle Ricerche - Istituto di Ricerca sulle Acque. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: c6686f13-e38d-4c24-bfd7-f1a8bd5f15b8.  Consiglio Nazionale delle Ricerche - Istituto di Ricerca sulle Acque publica este recurso y está registrado en GBIF como un publicador de datos avalado por Participant Node Managers Committee.

Palabras clave

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

Contactos

Cobertura geográfica

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.

Cobertura taxonómica

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.

Cobertura temporal

Métodos de muestreo

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).

Descripción de la metodología paso a paso:

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.

Referencias bibliográficas

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.

Metadatos adicionales