Biology subjects

Bean, H. D.

Publications and source records attributed to Bean, H. D..

5 recordsLinked to original sources

bioRxiv2026

Signaling metabolites spatially organize a multispecies mutualism in the soil microbiome

A plant-independent avenue for N2-fixation takes place in desert topsoils through a "C-for-N" mutualism between heterodiazotrophs and the cyanobacterium Microcoleus vaginatus. These partners come together within a diverse soil microbiome under conditions of N-limitation for the phototroph and C limitation for the heterotrophs. We hypothesized that extracellular chemical signaling might enable partner selection and collocation, though infomolecules shaping inter-microbial architecture were unknown. We show that the complex chemical composition of M. vaginatus exometabolome depends on its N-limitation status, thus potentially offering information to mutualists. In chemotactic assays, the exometabolome effectively repelled most native soil bacteria, particularly intensely when under N-limitation. Bacterial assemblages circumventing the repulsion were enriched in species that are rare in the soil microbiome, and that functionally resemble mutualistic cyanospheres (showing high N2-fixation potential, secretion of urea, and copiotrophy), setting the stage for a working symbiosis. Further, we could reproduce the enrichment of copiotrophs and nitrogen-fixers using mixtures of N-acetylglutamic acid, N-acetylmethionine, indole-3-acetic acid, and 5'-methylthioadenosine, all preferentially released by M. vaginatus under N-limitation. These signaling molecules did not result in an enrichment of urea producers, however. The results demonstrate that trans-species communication through specific infochemicals, together with already known quorum-sensing-like intraspecific communication in M. vaginatus, act as a tool to organize microbiomes spatially and to attain mutualistic partner specificity in an open, crowded background.

microbiology↗

bioRxiv2026

The Chromobacterium Volatilome is Strongly Influenced by Growth on Liquid versus Solid Media

The study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture conditions. To test this idea, we characterized the volatilomes of Chromobacterium violaceum (strain ATCC(R) 12472) and C. vaccinii (strain MWU328), and those of their isogenic cviR- quorum sensing mutants cultured on solid versus liquid Kings Medium B media. VOCs were sampled using thin-film solid-phase microextraction (TF-SPME) and analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GCxGC-TOFMS). Of the three variables examined - Chromobacterium species, media type, and quorum sensing ability - growth on liquid versus solid media caused the most significant differences in the volatilomes. Bacterial species and quorum sensing ability were also influential, but to a lesser degree. Our findings indicate the importance of growth conditions in microbial volatilomics, and therefore, more consideration should be given to how microorganisms are cultured for volatilome analyses. ImportanceThe purpose of this work is to elucidate the differences in the volatile metabolic profiles of Chromobacterium spp. by exploring them through the lens of three variables: growth conditions, species, and the ability to quorum sense. Work on organismal metabolic differences stemming from factors such as liquid versus solid media types remains broadly overlooked. Understanding these effects will allow future researchers to design more robust experiments that better translate to native microbial ecosystems such as rhizosphere and phyllosphere, where volatile compounds may influence plant-pathogen or plant-saprobe interactions.

microbiology↗

bioRxiv2022

Volatile metabolites in lavage fluid are correlated to Valley fever disease severity in murine model lung infections

Coccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections, to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host-pathogen interactions, we infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira via intranasal inoculation. We measured fungal dissemination and collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid phase microextraction (SPME) and two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated to cytokine abundances and clustered mice by disease severity. These 36 VOCs were also able to separate mice with a moderate to high disease severity by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect Coccidioidal infection and provide clinically relevant information on disease severity. IMPORTANCECoccidioidomycosis, or Valley fever, is a fungal disease endemic to the North and South American arid regions. Forty percent of individuals infected with Valley fever will exhibit symptoms consistent with community-acquired pneumonia. However, misdiagnosis frequently occurs in these cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in receiving an accurate diagnosis. Herein, we used a murine lung infection model as a step towards developing a breath-based diagnostic for Valley fever. We infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira and collected bronchoalveolar lavage fluid for untargeted volatile metabolomics. We observed that volatile metabolites in the bronchoalveolar lavage fluid of Cocci-inoculated mice were significantly correlated to disease severity, as measured by immune response. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test.

microbiology↗

bioRxiv2021

Lifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp.

Valley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North and South American deserts. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore new diagnostic tools are needed. We are working toward the development of a breath-based diagnostic for coccidioidomycosis, and in this initial study we characterized the volatile metabolomes (or volatilomes) of in vitro cultures of Coccidioides. Using solid-phase microextraction and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOFMS), we characterized the VOCs produced by six strains of each species during mycelial or spherule growth. We detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on growth phase (spherule versus mycelia) than on the species. The volatile profiles of C. immitis and C. posadasii have strong similarities, indicating that a single suite of Valley fever breath biomarkers can be developed to detect both species. IMPORTANCECoccidioidomycosis, or Valley fever, causes up to 30% of community-acquired pneumonias in endemic and highly populated areas of the US desert southwest. The infection is difficult to diagnose by standard serological and histopathological methods, which delays an appropriate treatment. Therefore, we are working toward the development of breath-based diagnostics for Valley fever. In this study, we characterized the volatile metabolomes of six strains each of Coccidioides immitis and C. posadasii, the dimorphic fungal species that cause Valley fever. By analyzing the volatilomes during the two modes of growth for the fungus--mycelia and spherules--we observed that the lifecycle plays a significant role in the volatiles produced by Coccidioides. In contrast, we observed no significant differences in the C. immitis versus C. posadasii volatilomes. These data suggest that lifecycle, rather than species, should guide the selection of putative biomarkers for a Valley fever breath test.

microbiology↗

bioRxiv2020

PSEUDOMONAS AERUGINOSA VOLATILOME CHARACTERISTICS AND ADAPTATIONS IN CHRONIC CYSTIC FIBROSIS LUNG INFECTIONS

Pseudomonas aeruginosa chronic lung infections in individuals with cystic fibrosis (CF) significantly reduce quality of life and increase morbidity and mortality. Tracking these infections is critical for monitoring patient health and informing treatments. We are working toward the development of novel breath-based biomarkers to track chronic P. aeruginosa lung infections in situ. Using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOFMS), we characterized the in vitro volatile metabolomes (or volatilomes) of 81 P. aeruginosa isolates collected from 17 CF patients over at least a five-year period of their chronic lung infections. We detected 539 volatiles produced by the P. aeruginosa isolates, 69 of which were core volatiles that were highly conserved. We found that each early infection isolate has a unique volatilome, and as infection progresses, the volatilomes of isolates from the same patient become increasingly dissimilar, to the point that these intra-patient isolates are no more similar to one another than to isolates from other patients. We observed that the size and chemical diversity of P. aeruginosa volatilomes do not change over the course of chronic infections; however, the relative abundances of core hydrocarbons, alcohols, and aldehydes do change, and are correlated to changes in phenotypes associated with chronic infections. This study indicates that it may be feasible to track P. aeruginosa chronic lung infections by measuring changes to the infection volatilome, and lays the groundwork for exploring the translatability of this approach to direct measurement using patient breath. IMPORTANCEPseudomonas aeruginosa is a leading cause of chronic lung infections in cystic fibrosis (CF), and are correlated with lung function declines. Significant clinical efforts are, therefore, aimed at detecting infections and tracking them for phenotypic changes, such as mucoidy and antibiotic resistance. Both the detection and tracking of lung infections relies on sputum cultures, but due to improvements in CF therapies, sputum production is declining though risks for lung infections persist. Therefore, we are working toward the development of breath-based diagnostics for CF lung infections. In this study we characterized of the volatile metabolomes of 81 P. aeruginosa clinical isolates collected from 17 CF patients over a duration of at least five years of a chronic lung infection. We found that the volatilome of P. aeruginosa adapts over time, and correlates to infection phenotype changes, suggesting it may be possible to track chronic CF lung infections with a breath test.

microbiology↗