Scholarworks
ScholarWorks is an open access repository for the capture of the intellectual work of Montana State University (MSU) in support of its teaching, research and service missions. MSU ScholarWorks is a central point of discovery for accessing, collecting, sharing, preserving, and distributing knowledge to the Montana State University community and the world.
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MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data
(Springer Science and Business Media LLC, 2024-05) Lee, Kang Soo et al.; Hatzenpichler, Roland
Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘MicrobioRaman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository, residing within the BioStudies database1 — which is maintained by a public institution, the European Bioinformatics Institute — minimizes the risk of data loss or eventual abandonment, offering a long-term common reference for analysis with advantages in accessibility and transparency over commercial data analysis tools. We feel that MicrobioRaman will provide a foundation for this growing field by serving as an open-access repository for sharing microbiological Raman data and through the codification of a set of reporting standards.
Entropically driven aggregation of bacteria by host polymers promotes antibiotic tolerance in Pseudomonas aeruginosa
(Proceedings of the National Academy of Sciences, 2018-10) Secor, Patrick R.; Michaels, Lia A.; Ratjen, Anina; Jennings, Laura K.; Singh, Pradeep K.
Bacteria causing chronic infections are generally observed living in cell aggregates suspended in polymer-rich host secretions, and bacterial phenotypes induced by aggregated growth may be key factors in chronic infection pathogenesis. Bacterial aggregation is commonly thought of as a consequence of biofilm formation; however the mechanisms producing aggregation in vivo remain unclear. Here we show that polymers that are abundant at chronic infection sites cause bacteria to aggregate by the depletion aggregation mechanism, which does not require biofilm formation functions. Depletion aggregation is mediated by entropic forces between uncharged or like-charged polymers and particles (e.g., bacteria). Our experiments also indicate that depletion aggregation of bacteria induces marked antibiotic tolerance that was dependent on the SOS response, a stress response activated by genotoxic stress. These findings raise the possibility that targeting conditions that promote depletion aggregation or mechanisms of depletion-mediated tolerance could lead to new therapeutic approaches to combat chronic bacterial infections.
Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666
(American Society for Microbiology, 2009-06) Jennings, Laura; Chartrand, Michelle; Lacrampe-Couloume, Georges; Sherwood Lollar, Barbara; Spain, Jim C.; Gossett, James M.
Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from −17.4 to −22.4‰. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C═C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.
Coupon position does not affect Pseudomonas aeruginosa and Staphylococcus aureus biofilm densities in the CDC biofilm reactor
(Elsevier BV, 2024-08) Buckner, Elizabeth; Buckingham-Meyer, Kelli; Miller, Lindsey A.; Parker, Albert E.; Jones, Christopher J.; Goeres, Darla M.
The CDC Biofilm Reactor method is the standard biofilm growth protocol for the validation of US Environmental Protection Agency biofilm label claims. However, no studies have determined the effect of coupon orientation within the reactor on biofilm growth. If positional effects have a statistically significant impact on biofilm density, they should be accounted for in the experimental design. Here, we isolate and quantify biofilms from each possible coupon surface in the reactor to quantitatively determine the positional effects in the CDC Biofilm Reactor. The results showed no statistically significant differences in viable cell density across different orientations and vertical positions in the reactor. Pseudomonas aeruginosa log densities were statistically equivalent among all coupon heights and orientations. While the Staphylococcus aureus cell growth showed no statistically significant differences, the densities were not statistically equivalent among all coupon heights and orientations due to the variability in the data. Structural differences were observed between biofilms on the high-shear baffle side of the reactor compared to the lower shear glass side of the reactor. Further studies are required to determine whether biofilm susceptibility to antimicrobials differs based on structural differences attributed to orientation.
Biodegradability of unheated and laboratory heated dissolved organic matter
(Royal Society of Chemistry, 2024-01) Islam Promi, Saraf; Gardner, Courtney M.; Hohner, Amanda K.
Following wildfires, partially combusted biomass remains on the forest floor and erosion from the landscape can release dissolved pyrogenic organic matter (dPyOM) to surface waters. Therefore, post-fire alterations to dissolved organic matter (DOM) in aquatic systems may play a vital role in DOM stability and biogeochemical cycles. Dissolved PyOM biodegradation remains poorly understood and is expected to vary with combustion temperature and fuel source. In this study laboratory heating and leaching of forest floor materials (soil and litter) were used to compare the biodegradability of unheated, low (250 °C), and moderate (450 °C) temperature leachates. Inoculation experiments were performed with river microbes. Dissolved organic carbon (DOC) and nitrogen (DON), inorganic nitrogen, and DOM optical properties were monitored for 38 days. Inoculation experiments showed significantly greater DOC biodegradation of low and moderate temperature samples (64% and 71%, respectively) compared to unheated samples (32%). The greater DOC biodegradation may be explained by lower molecular weight DOM composition of heated leachates which was supported by higher initial E2/E3 ratios (absorbance at 250 nm/365 nm). Further, the observed decrease in the E2/E3 ratio after incubation suggests biodegradation of smaller compounds. This trend was greater for heated samples than unheated DOM. Specific ultraviolet absorbance increased after incubation, suggesting biodegradation of aliphatic compounds. Inoculated moderate temperature samples showed the greatest DON degradation (74%), followed by low temperature (58%) and unheated (51%) samples. Overall, results suggest that low and moderate temperature dPyOM was more biodegradable than unheated DOM, which may have implications for aquatic biogeochemical cycling, ecosystem function, and water quality in fire-impacted watersheds.