Biology subjects

Brumfield, K. D.

Publications and source records attributed to Brumfield, K. D..

3 recordsLinked to original sources

bioRxiv2026

Microbial Community Multi-omic Analysis of Marsh Sediment post Crustacean Shell Compost Enrichment: pathogen emergence and community response

Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA), which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.

microbiology↗

bioRxiv2025

A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes

Advances in next generation sequencing have made it possible to explore microbial community dynamics and regulation of functionally important genes through metagenomics and metatranscriptomics. However, the use of meta-omics to link enzyme function directly with complex, community-level phenotypes remain largely unexplored. To overcome this gap, we developed a novel framework that integrates ecological concepts by microbial community perturbation with association analysis to a targeted phenotype. Specifically, we introduce a hypothesis-free "bait and switch" strategy demonstrated through salt marsh soil microcosm pulse experiments to detect and characterize novel enzymes responsible for chitin degradation. Soil microbial communities were "baited" with shell compost, a chitin-rich substrate, to trigger community succession toward chitin degraders and gene upregulation of chitinases. A "switch" was then employed, by addition of glucose, inducing rapid downregulation of genes putatively responsible for chitin degradation. Results demonstrate the feasibility of this approach to identify functionally important enzymes, in this example, 48 hours after chitin addition. The bait and switch community perturbation provides a framework for discovery of polymer degrading enzymes present in complex microbial communities and serves as a proof of concept applicable for linking enzyme function with emergent community level phenotypes.

microbiology↗

bioRxiv2023

Environmental Factors Associated with Incidence and Distribution of V. parahaemolyticus and V. vulnificus in Chesapeake Bay, Maryland, USA: A three-year case study

Members of the genus Vibrio are ecologically significant bacteria native to aquatic ecosystems globally, and a few can cause diseases in humans. Vibrio-related illnesses have increased in recent years, primarily attributed to changing environmental conditions. Therefore, understanding the role of environmental factors in the occurrence and growth of pathogenic strains is crucial for public health. Water, oyster, and sediment samples were collected between 2009 and 2012 from Chester River and Tangier Sound sites in Chesapeake Bay, Maryland, USA, to investigate the relationship between water temperature, salinity, and chlorophyll with the incidence and distribution of Vibrio parahaemolyticus (VP) and Vibrio vulnificus (VV). Odds ratio analysis was used to determine association between the likelihood of VP and VV presence and these environmental variables. Results suggested that water temperature threshold of 20{degrees}C or higher was associated with an increased risk, favoring the incidence of Vibrio spp. A significant difference in salinity was observed between the two sampling sites, with distinct ranges showing high odds ratio for Vibrio incidence, especially in water and sediment, emphasizing the impact of salinity on VP and VV incidence and distribution. Notably, salinity between 9-20 PPT consistently favored the Vibrio incidence across all samples. Relationship between chlorophyll concentrations and VP and VV incidence varied depending on sample type. However, chlorophyll range of 0-10 {micro}g/L was identified as critical in oyster samples for both vibrios. Analysis of odds ratios for water samples demonstrated consistent outcomes across all environmental parameters, indicating water samples offer a more reliable indicator of Vibrio spp. incidence. ImportanceUnderstanding the role of environmental parameters in the occurrence of Vibrio species posing significant public health risks and economic burdens such as Vibrio parahaemolyticus and Vibrio vulnificus are of paramount importance. These aquatic bacteria are responsible for various human diseases, including gastroenteritis and wound infections, which can be severe and sometimes fatal. Recent observations suggest that certain environmental conditions may favor the growth of Vibrio, leading to more severe disease outcomes. By investigating the environmental factors that influence the occurrence of Vibrio parahaemolyticus and Vibrio vulnificus, the need to gain insights into the favorable ranges of environmental variables is apparent. The significance of this research is in identifying the favorable ranges of environmental and ecological factors, which holds the potential to provide an aid in the intervention and mitigation strategies through the development of predictive models, ultimately enhancing our ability to manage and control diseases caused by these pathogens.

ecology↗