Biology subjects

Randolph, J. W. J.

Publications and source records attributed to Randolph, J. W. J..

2 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↗

bioRxiv2021

Bacterial and fungal communities experience rapid succession during the first year following a wildfire in a California chaparral.

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

microbiology↗