Biology subjects

Glassman, S.

Publications and source records attributed to Glassman, S..

3 recordsLinked to original sources

bioRxiv2024

Not All Is Lost: Resilience of Microbiome Samples to Freezer Failures and Long-term Storage

Advances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. In this study, we investigated the effects of an unforeseen short-term thaw event ([~]1 week) resulting from a freezer malfunction on soil samples stored at -80{degrees}C and extracted uncompromised DNA stored long-term at -20{degrees}C. We compared these samples against previously sequenced Illumina MiSeq data to assess whether the process of thawing soil or multi-year extracted DNA storage affected the resilience of bacterial or fungal richness or community composition, thereby impacting our ability to accurately determine treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at -80{degrees}C compared to storage of extracted DNA at -20{degrees}C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.

microbiology↗

bioRxiv2022

Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum

Arbuscular mycorrhizal fungi (AMF) remain understudied in perennial cropping systems. Citrus is a globally grown fruit tree and under threat by the pandemic Huanglongbing (HLB) disease. Here, we assessed in what capacity geographical location, management strategies and disease affect AMF citrus root communities. Root samples were collected from 88 trees in ten orchards located in the two major citrus producing states in the US. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. We used AMF-specific amplicon sequencing primers to capture community composition and diversity. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF references sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples with taxa belonging to six known (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and unknown Glomeraceae genera. Geographical location affected AMF community composition but not richness, whereas management practice and disease influenced both richness and composition. Our approach indicated that perennial agroecosystems share a set of AMF generalist and specialist taxa. Some taxa could improve environmental fitness and be exploited for agricultural purposes.

microbiology↗

bioRxiv2019

A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species

We have designed a simple, inexpensive system for the studying the response of soil microbes to fire. This system allows one to create post-fire environments in soil in reproducible and realistic ways. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near peak temperature for a significant time, and is accurately predicted by the log of soil depth and the mass charcoal burned. Flash fuels that left no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of postfire fungus, from uninoculated forest soil within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change significantly with the fire, although there is an overall reduction in richness and evenness. Extrapolating from the physical relationships we predict soil heating effects in wild fires are likely to be very patchy across the forest floor but the width of a survivable \"goldilocks zone\" will stay relatively constant across a range of fuel loads. We further predict that a necromass zone above it, which represents an open niche for pyrophilous microbes, increases in size rapidly with addition of fuel, and then remains nearly constant over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.

ecology↗