Fungal communities in decaying poplar pins in Northeastern USA discovered by MycoPins method

Sampling event
Latest version published by Kean University on Mar 22, 2023 Kean University
Publication date:
22 March 2023
Published by:
Kean University
License:
CC-BY 4.0

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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.

Data Records

The data in this sampling event 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 15 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Event (core)
15
Occurrence 
1380

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

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Rights

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The publisher and rights holder of this work is Kean University. 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: 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48.  Kean University publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.

Keywords

samplingEvent

Contacts

Maria Shumskaya
  • Metadata Provider
  • Author
  • Originator
  • Point Of Contact
Associate Professor
Kean University
07083 Union
New Jersey
US
Nicholas Lorusso
  • Originator
Assistant Professor
University of North Texas at Dallas
US
Urvi Patel
  • Originator
Student
Kean University
US
Madison Leigh
  • Originator
Student
Kean University
US
Panu Somervuo
  • Originator
Researcher
University of Helsinki
FI
Dmitry Schigel

Geographic Coverage

Central New Jersey, Northeastern USA

Bounding Coordinates South West [40.695, -74.271], North East [40.718, -74.234]

Taxonomic Coverage

No Description available

Kingdom Fungi

Temporal Coverage

Start Date / End Date 2020-11-23 / 2021-05-02

Project Data

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.

Title MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris
Study Area Description The study was concluded in a suburban area of central New Jersey, USA, from December 2020 to May 2021.

The personnel involved in the project:

Maria Shumskaya
Urvi Patel
  • Author
Madison Leigh
  • Author

Sampling Methods

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.

Study Extent The sampling event was performed from December 2020 to May 2021 in a suburban area of central New Jersey, Northeast of USA.
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 step description:

  1. 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.

Collection Data

Collection Name Kean University, Laboratory of Applied Genomics
Specimen preservation methods Deep frozen,  Dried

Bibliographic Citations

  1. 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
  2. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 17: 10-12. doi:10.14806/ej.17.1.200
  3. 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
  4. 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
  5. 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
  6. 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

Additional Metadata

Alternative Identifiers 94d0f0a0-183f-49ae-aa8c-1bc4e930ec48
https://doi.org/10.15468/r7rxf6
https://ipt.gbif.us/resource?r=mycopins