Biology subjects

DeBruyn, J. M.

Publications and source records attributed to DeBruyn, J. M..

3 recordsLinked to original sources

bioRxiv2025

Seasonal Enhancement of the Viral Shunt Catalyzes a Subsurface Oxygen Maximum in the Sargasso Sea

Subsurface oxygen maxima (SOMs) occur directly beneath the mixed layer of stratified water columns across oligotrophic open ocean basins. SOMs occur seasonally and are hypothesized to result from elevated microbial net primary productivity (NPP). Here, we set out to identify mechanistic drivers of the SOM near the Bermuda Atlantic Time Series (BATS) site in the Sargasso Sea in October 2019. Coupled time-series analysis of metatranscriptomics, flow cytometry, and family-specific cyanophage quantification revealed elevated Prochlorococcus abundances, cyanophage abundances, and cyanophage-specific transcriptional activity in the SOM. These findings spurred us to analyze historical oxygen saturation profiles at BATS - identifying a repeated, seasonal cycle in SOM emergence associated with elevated virus-like particles and Prochlorococcus numbers. Returning to the 2019 study site, we found that transcriptional markers for increased dissolved organic matter uptake by copiotrophic bacteria were enriched in the SOM, consistent with enhanced catabolic activity due to the viral shunt. In addition, Prochlorococcus exhibited enrichment in ammonium transport transcripts at the SOM, consistent with increased responsiveness to remineralization activity by heterotrophs. Altogether, these findings suggest that enhanced viral lysis leads to locally elevated nutrient recycling and oxygen production, further reinforcing hypotheses that viruses may play a critical role in the emergence of SOMs in the oligotrophic ocean.

ecology↗

bioRxiv2019

Patterns of microbial colonization of human bone from surface-decomposed remains

Microbial colonization of bone is an important mechanism of post-mortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain patterns of human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria (36%), Actinobacteria (23%), Firmicutes (13%), Bacteroidetes (12%), and Planctomycetes (4.4%). Eukaryotic bone colonizers were from Ascomycota (40%), Apicomplexa (21%), Annelida (19%), Basidiomycota (17%), and Ciliophora (14%). Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to patterns of DNA preservation, complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing human bone and contributing to human skeletal DNA degradation.

microbiology↗

bioRxiv2019

Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems

Polyethylene (PE) plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to PE-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However inadequate research regarding the impacts of repeated incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA. Treatments included four plastic BDMs, a completely biodegradable cellulose mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA amplicon sequencing revealed significant differences by location and season. Differences in bacterial communities by mulch treatment were not significant for any season in either location, except for Fall 2015 in WA where differences were observed between BDMs and no-mulch plots. Extracellular enzyme rate assays were used to characterize communities functionally, revealing significant differences by location and sampling season in both TN and WA but minimal differences between BDMs and PE treatments. Limited effects of BDM incorporation on soil bacterial community structure and soil enzyme activities when compared to PE suggest that BDMs have comparable influences on soil microbial communities, and therefore could be considered an alternative to PE.\n\nImportancePlastic film mulches increase crop yields and improve fruit quality. Most plastic mulches are made of polyethylene (PE), which is poorly degradable, resulting in undesirable end-of-life outcomes. Biodegradable mulches (BDMs) may be a sustainable alternative to PE. BDMs are made of polymers which can be degraded by soil microbial enzymes, and are meant to be tilled into soil after use. However, uncertainty about impacts of tilled-in BDMs on soil health has restricted adoption of BDMs. Our previous research showed BDMs did not have a major effect on a wide range of soil quality indicators (Sintim et al. 2019); here we focus on soil microbial communities, showing that BDMs do not have detectable effects on soil microbial communities and their functions, at least over the short term. This informs growers and regulators about use of BDMs in crop production, paving a way for an agricultural practice that reduces environmental plastic pollution.

microbiology↗