Description
The MycoPins method is a protocol to monitor early colonization events in communities of wood-inhabiting fungi in fine woody debris. The sampling dataset presented here is based on fieldwork from a time series experiment on standard sterilized poplar pins (furniture wooden dowels 1 cm diameter, 3 cm length) that were placed in soil to decay, then collected and subjected to DNA metabarcoding analysis and automated molecular identification of species. The list of species for each sampling point during the duration of the experiment was produced by a taxonomic classifier PROTAX (Abarenkov, 2018). PROTAX analyses the DNA sequences and provides with a table of reliably identified (probability >0.9) species, which is about 10% of the overall sequences from our experiment. The list of published species is limited to only 10% because while identifying the species, PROTAX takes into the account the uncertainty and mislabelings in the UNITE database that was used as a reference.
Enregistrements de données
Les données de cette ressource données d'échantillonnage ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 15 enregistrements.
1 tableurs de données d'extension existent également. Un enregistrement d'extension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre d'enregistrements dans chaque tableur de données d'extension est illustré ci-dessous.
Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.
Versions
Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est Kean University. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48. Kean University publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF-US.
Mots-clé
samplingEvent
Contacts
- Fournisseur Des Métadonnées ●
- Auteur ●
- Créateur ●
- Personne De Contact
http://orcid.org/0000-0001-7916-462X
- Créateur
- Créateur
- Créateur
Couverture géographique
Central New Jersey, Northeastern USA
| Enveloppe géographique | Sud Ouest [40,695, -74,271], Nord Est [40,718, -74,234] |
|---|
Couverture taxonomique
Pas de description disponible
| Kingdom | Fungi |
|---|
Couverture temporelle
| Date de début / Date de fin | 2020-11-23 / 2021-05-02 |
|---|
Données sur le projet
MycoPins is a straightforward method for studying and monitoring dead wood colonization by fungi. The method combines standardized fieldwork sampling that includes experimental exposure of wooden pins to lignicolous fungi in the environment, followed by subsequent metabarcoding analysis of fungal DNA from the colonized pins.
| Titre | MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris |
|---|---|
| Description du domaine d'étude / de recherche | The study was concluded in a suburban area of central New Jersey, USA, from December 2020 to May 2021. |
Les personnes impliquées dans le projet:
- Auteur
- Auteur
Méthodes d'échantillonnage
Sterilized poplar pins (wooden dowels) 1 cm in diameter and 3 cm long were placed in triplicates on November 23rd, 2020 in soil 2 cm from the surface, covered with debris and allowed to decay. Pins were extracted after 14, 28, 42, 77 and 160 days. Each pin was saved as an event, with parent events assigned to each date of extraction. Upon extraction, two pins for each triplicate were wrapped in brown paper and dried for 5 hours at 45°C in a conventional food dehydrator, and one pin was frozen at -80°C. Two sterile negative control pins were exposed to air in the field for 30 min and then one was dried and one frozen using the same methods used to store sample pins.The interior of each pin was drilled by a 2 mm fire-sterilized drill bit, DNA was isolated and PCR for the ITS2 gene region from the extracted DNA was carried out with the primers fITS7 forward (F), 5’-GTGARTCATCGAATCTTTG, and ITS4 reverse (R), 5’-TCCTCCGCTTATTGATATGC (Clemmensen, 2016). PCR amplicons were sequenced using an Illumina 2x 250 paired-end (PE) configuration.
| Etendue de l'étude | The sampling event was performed from December 2020 to May 2021 in a suburban area of central New Jersey, Northeast of USA. |
|---|---|
| Contrôle qualité | During pre-processing of the sequencing data, raw pair-end sequences were merged using PEAR (Zhang et al, 2014), cutadapt (Martin 2011) was used for trimming and removing adapter/tag sequencing, and sequences were clustered using VSEARCH (Rognes et al, 2016) with 99% sequence similarity threshold. The resulting centroid sequences were processed with PROTAX (Abarenkov et al, 2018). Identification of species was performed using UNITE v 7.1 database. When calculating abundances of different taxa, the cluster sizes were taken into account. A sample-taxon table was produced as an output where the abundances were counted as the number of sequences whose taxon membership probability exceeded a 0.9 threshold (reliable identification). The resultant lists of species for each event (species in each pin) are shared in this dataset publication. |
Description des étapes de la méthode:
- For the detailed step-by-step description, please see our recent paper: Shumskaya M., Lorusso N., Patel U., Leigh M., Somervuo P., Schigel D. (2023) "MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris". MycoKeys 96:77-95.
Données de collection
| Nom de la collection | Kean University, Laboratory of Applied Genomics |
|---|
| Méthode de conservation des spécimens | Deep frozen, Dried |
|---|
Citations bibliographiques
- Clemmensen KE, Ihrmark K, Durling MB, Lindahl BD (2016) Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons. Methods in molecular biology (Clifton, NJ) 1399: 61-88. doi:10.1007/978-1-4939-3369-3_4
- Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 17: 10-12. doi:10.14806/ej.17.1.200
- Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: a versatile open source tool for metagenomics. Peerj 4. doi:10.7717/peerj.2584
- Zhang JJ, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30: 614-620. doi:10.1093/bioinformatics/btt593
- Abarenkov K, Somervuo P, Nilsson RH, Kirk PM, Huotari T, Abrego N, Ovaskainen O (2018) PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences. New Phytologist 220: 517-525 doi:10.1111/nph.15301
- Shumskaya M, Lorusso N, Patel U, Leigh M, Somervuo P, Schigel D. (2023) MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris. doi: 10.3897/mycokeys.96.101033
Métadonnées additionnelles
| Identifiants alternatifs | 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48 |
|---|---|
| https://doi.org/10.15468/r7rxf6 | |
| https://ipt.gbif.us/resource?r=mycopins |