Survey of Saproxylic Fungi Communities from Franklin Parker Preserve, New Jersey, USA, via metabarcoding
Citation
Shumskaya M, Zambell C, Annuzzi J, Berisha K, Benjamin S, Emezua J, Gardner Z, Huerta-Aguilar S, Laboy A, Shaikh S, Blue S, Hylton N (2020). Survey of Saproxylic Fungi Communities from Franklin Parker Preserve, New Jersey, USA, via metabarcoding. Version 1.3. Kean University. Occurrence dataset https://doi.org/10.15468/44bgnt accessed via GBIF.org on 2024-12-14.Description
The focus of this survey is fungi from Franklin Parker Reserve, NJ, that inhabit dead wood. In order to survey the communities of dead wood fungi, in June 2018, 7 drills were made in 10 logs, each drill was separated by 1 meter. Sawdust from each log was pooled. Logs included various stages of decay, also some were standing dead wood. Samples were collected for DNA to be extracted and for fungi to be identified. In order to do it, metabarcoding of sawdust samples is performed. The analysis includes DNA isolation from dead wood, PCR of ITS2 regions unique to fungi using tagged primers, and next generation sequencing (NGS). Results from NGS were analyzed via SCATA bioinformatics pipeline to identify the fungal samples in the sawdust. The work was performed by students of Kean University, NJ, in order to practice saproxylic biodiversity assessment, metabarcoding, and GBIF publication.Sampling Description
Study Extent
10 dead wood logs were drilled, 7 drills per log (distance 1 m between the drills). Logs were randomly chosen while moving around the Franklin Parker Preserve.Sampling
For each of the log, 7 drills were performed and pooled, homogenized frozen at -80C.Method steps
- DNA was extracted from each of the samples with protocol based on PowerMax soil kit (MoBio, now Qiagen).
- For each DNA extract 1 µl, the ITS2 region was amplified in triplicates with the primers gITS7 and ITS4, using Phusion DNA Polymerse (Fisher Scientific).
- All PCR reactions were tagged with unique 8-9 bp tags. All PCR reactions were mixed in one multiplex sample in equal concentrations and then sent to sequencing with the Illumina MiSeq platform using 2X 250 bp paired end seqencensing.
- Data from two sequencing runs were pooled. Paired reads were demultiplexed and analysed with SCATA online platform https://scata.mykopat.slu.se/. Sequences were annotated by comparison with the UNITE database, as well as BLASTed manually. We used 98- 70% sequence identity as for assigning OTUs to species, genus, family, order, or class and kingdom respectively.
Taxonomic Coverages
Fungi
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Fungirank: kingdom
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Plantaerank: kingdom
Geographic Coverages
Franklin Parker Reserve in New Jersey, USA
Bibliographic Citations
Contacts
Maria Shumskayaoriginator
1000 Morris Ave
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Christopher Zambell
originator
position: Lecturer
Kean University
US
userId: http://orcid.org/0000-0003-4697-5885
Julia Annuzzi
originator
position: Student
Kean University
US
Keid Berisha
originator
position: student
Kean University
US
Shakira Benjamin
originator
position: student
Kean University
US
Jacob Emezua
originator
position: student
Kean University
US
Zachary Gardner
originator
position: student
Kean University
US
Steven Huerta-Aguilar
originator
position: student
Kean University
US
Alyssa Laboy
originator
position: student
Kean University
US
Shirin Shaikh
originator
position: student
Kean University
US
Shazneka Blue
originator
position: student
Kean University
US
Njemile Hylton
originator
position: student
Union County College
US
Maria Shumskaya
metadata author
1000 Morris Ave
Union
07083
New Jersey
US
Telephone: 73695
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Maria Shumskaya
author
1000 Morris Ave
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X
Maria Shumskaya
administrative point of contact
1000 Morris Ave
Union
07083
New Jersey
US
email: mshumska@kean.edu
userId: http://orcid.org/0000-0001-7916-462X