Descripción
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.
Registros
Los datos en este recurso de evento de muestreo 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 15 registros.
también existen 1 tablas de datos de extensiones. Un registro en una extensión provee información adicional sobre un registro en el core. El número de registros en cada tabla de datos de la extensión se ilustra a continuación.
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.
Derechos
Los usuarios deben respetar los siguientes derechos de uso:
El publicador y propietario de los derechos de este trabajo es Kean University. 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: 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48. Kean University publica este recurso y está registrado en GBIF como un publicador de datos avalado por GBIF-US.
Palabras clave
samplingEvent
Contactos
- Proveedor De Los Metadatos ●
- Autor ●
- Originador ●
- Punto De Contacto
- Associate Professor
http://orcid.org/0000-0001-7916-462X
- Originador
- Assistant Professor
- Originador
- Student
- Originador
- Student
Cobertura geográfica
Central New Jersey, Northeastern USA
| Coordenadas límite | Latitud Mínima Longitud Mínima [40,695, -74,271], Latitud Máxima Longitud Máxima [40,718, -74,234] |
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Cobertura taxonómica
No hay descripción disponible
| Reino | Fungi |
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Cobertura temporal
| Fecha Inicial / Fecha Final | 2020-11-23 / 2021-05-02 |
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Datos del proyecto
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.
| Título | MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris |
|---|---|
| Descripción del área de estudio | The study was concluded in a suburban area of central New Jersey, USA, from December 2020 to May 2021. |
Personas asociadas al proyecto:
- Autor
- Autor
Métodos de muestreo
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.
| Área de Estudio | The sampling event was performed from December 2020 to May 2021 in a suburban area of central New Jersey, Northeast of USA. |
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| Control de Calidad | 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. |
Descripción de la metodología paso a paso:
- 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.
Datos de la colección
| Nombre de la Colección | Kean University, Laboratory of Applied Genomics |
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| Métodos de preservación de los ejemplares | Congelado, Secado |
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Referencias bibliográficas
- 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
Metadatos adicionales
| Identificadores alternativos | 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48 |
|---|---|
| https://doi.org/10.15468/r7rxf6 | |
| https://ipt.gbif.us/resource?r=mycopins |