title: Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.
abstract: Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers.
authors.affiliation: Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
authors.forename: Kevin V
authors.initials: KV
authors.lastname: Solomon
authors.affiliation: Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
authors.forename: John K
authors.initials: JK
authors.lastname: Henske
authors.affiliation: Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, United Kingdom.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Theodorou
authors.affiliation: Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA. Electronic address: momalley@engineering.ucsb.edu.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: O'Malley
mesh_terms: D015925:Cryopreservation / Q000379:methods*; D004271:DNA, Fungal / Q000302:isolation & purification*; D005658:Fungi; D000069196:Gastrointestinal Microbiome; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal
keywords: Anaerobic fungi; Cryopreservation; Genome isolation; Genome sequencing; Gut fungi; Microbiome; Next generation sequencing; Non-model microbes