Fungal communities in decaying poplar pins in Northeastern USA discovered by MycoPins method
Citation
Shumskaya M, Lorusso N, Patel U, Leigh M, Somervuo P, Schigel D (2023). Fungal communities in decaying poplar pins in Northeastern USA discovered by MycoPins method. Version 1.9. Kean University. Sampling event dataset https://doi.org/10.15468/r7rxf6 accessed via GBIF.org on 2024-12-15.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.Sampling Description
Study Extent
The sampling event was performed from December 2020 to May 2021 in a suburban area of central New Jersey, Northeast of USA.Sampling
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.Quality Control
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.Method steps
- 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.
Taxonomic Coverages
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Fungirank: kingdom
Geographic Coverages
Central New Jersey, Northeastern USA
Bibliographic Citations
- 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
Contacts
Maria Shumskayaoriginator
position: Associate Professor
Kean University
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Nicholas Lorusso
originator
position: Assistant Professor
University of North Texas at Dallas
US
userId: http://orcid.org/0000-0002-3299-9205
Urvi Patel
originator
position: Student
Kean University
US
Madison Leigh
originator
position: Student
Kean University
US
Panu Somervuo
originator
position: Researcher
University of Helsinki
FI
userId: http://orcid.org/0000-0003-3121-4047
Dmitry Schigel
originator
position: Docent
FI
userId: http://orcid.org/0000-0002-2919-1168
Maria Shumskaya
metadata author
position: Associate Professor
Kean University
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Maria Shumskaya
author
position: Associate Professor
Kean University
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Maria Shumskaya
administrative point of contact
position: Associate Professor
Kean University
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X