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Optimizing DNA Extraction from Cave Microorganisms
Author(s) -
Warming Allison,
Peters Justin
Publication year - 2021
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2021.35.s1.02063
Subject(s) - cave , microorganism , dna extraction , biology , isolation (microbiology) , bacteria , dna , internal transcribed spacer , ribosomal rna , 16s ribosomal rna , computational biology , polymerase chain reaction , microbiology and biotechnology , genetics , ecology , gene
Wind Cave near Hot Springs, South Dakota has over 150 miles of surveyed area and is yet to be completely mapped. Identifying the types of microorganisms living in the cave will provide insights into understanding what types of organisms could be found in other extreme environments. The main question to be answered in this work is which commercial DNA isolation kits provide the best yield of purified DNA from microorganisms collected at Wind Cave. Samples from the cave were collected and grown on culture media. Taking an unbiased approach, seven commercially available DNA isolation kits were evaluated using the manufacturers’ recommended protocols. Kits from Omega Bio‐tek and Qiagen exhibited optimal performance and were most effective at isolating DNA from the samples collected in Wind Cave. The DNA obtained from the samples will be used to perform PCR‐based sequencing analysis using primers targeting either a specific region of the 16S small ribosomal subunit of prokaryotes for bacteria and archaea or an internal transcribed spacer (ITS) for identifying fungal microbial eukaryotic lineages.