Biology subjects

Pulido-Chavez, M. F.

Publications and source records attributed to Pulido-Chavez, M. F..

4 recordsLinked to original sources

bioRxiv2024

Chaparral wildfire shifts the functional potential for soil pyrogenic organic matter and nitrogen cycling

Wildfires reshape soil microbiomes and chemistry, enhancing nitrogen availability and leaving behind pyrogenic organic matter (PyOM), a difficult to degrade carbon substrate potentially used by pyrophilous or "fire-loving" microbes. Understanding whether pyrophilous bacteria can metabolize post-fire resources is critical for predicting the fate of both carbon and nitrogen. We explored how secondary succession of pyrophilous bacteria align with changes in functional gene composition, particularly genes related to PyOM degradation and microbial nitrogen metabolism using shotgun metagenomics on 30 burned and unburned soils collected at 17, 25, 34, 131, and 376 days after a high-severity wildfire in a fire-adapted chaparral in Southern California. In burned soils, genes for PyOM degradation increased over time by 167% and for inorganic nitrogen cycling by 117%, while unburned soils showed no significant changes. Genes encoding catechol and protocatechuate, intermediates in the PyOM degradation pathway, indicate that the easier-to-degrade ortho-cleavage pathways consistently dominated the burned plots. These pathways co-occurred with genes for nitrification and nitrogen retention, including assimilatory and dissimilatory nitrate reduction to ammonia (DNRA). We also identified 446 bacterial metagenome-assembled genomes (MAGs) and linked gene profiles to dominant taxa and found that increases in genes for PyOM and nitrogen cycling paralleled the dominance of pyrophilous Massilia and Noviherbaspirillum, which encoded distinct pathways for PyOM and inorganic nitrogen use over time. Together, these findings reveal previously unrecognized functional shifts in bacterial communities over a high-resolution successional timeline, providing insights into the long-term impact of fire on microbial-mediated ecosystem processes that shape soil carbon and nitrogen dynamics.

microbiology↗

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↗

bioRxiv2021

Prescribed versus wildfire impacts on exotic plants and soil microbes in California grasslands

O_LIPrescribed fire is often used as a management tool to decrease exotic plant cover and increase native plant cover in grasslands. These changes may also be mediated by fire impacts on soil microbial communities, which drive plant productivity and function. Yet, the ecological effects of prescribed burns compared to wildfires on either plant or soil microbial composition remain unclear. C_LIO_LIHere, we investigated the impacts of a spring prescribed fire versus a fall wildfire on plant cover and community composition and bacterial and fungal richness, abundance, and composition in a California grassland. We used qPCR of 16S and 18S to assess impacts on bacterial and fungal abundance and Illumina MiSeq of 16S and ITS2 to assess impacts on bacterial and fungal richness and composition. C_LIO_LIWildfire had stronger impacts than prescribed fire on microbial communities and both fires had similar impacts on plants with both prescribed and wildfire reducing exotic plant cover but neither reducing exotic plant richness. Fungal richness declined after the wildfire but not prescribed fire, but bacterial richness was unaffected by either. Yet increasing char levels in both fire types resulted in reduced bacterial and fungal biomass, and both fire types slightly altered bacterial and fungal composition. C_LIO_LIExotic and native plant diversity differentially affected soil microbial diversity, with native plant diversity leading to increased arbuscular mycorrhizal fungal richness while exotic plant diversity better predicted bacterial richness. However, the remainder of the soil microbial communities were more related to aspects of soil chemistry including cation exchange capacity, organic matter, pH and phosphorous. C_LIO_LISynthesis and applications. Understanding the different ecological effects of prescribed fires and wildfires on plant and soil communities are key to enhancing a prevalent management action and to guide potential management opportunities post wildfires. Our coupled plant and soil community sampling allowed us to capture the sensitivity of the fungal community to fire and highlights the importance of potentially incorporating management actions such as soil or fungal amendments to promote this critical community that mediates native plant performance. C_LI

ecology↗