Scholarly Work - Chemical & Biological Engineering
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/8718
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Item Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream(2019-10) Dieser, Markus; Smith, Heidi J.; Ramaraj, Thiruvarangan; Foreman, Christine M.As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.Item Quorum sensing inhibition as a promising method to control biofilm growth in metalworking fluids(2019-04) Ozcan, Safiye S.; Dieser, Markus; Parker, Albert E.; Balasubramanian, Narayanaganesh; Foreman, Christine M.Microbial contamination in metalworking systems is a critical problem. This study determined the microbial communities in metalworking fluids (MWFs) from two machining shops and investigated the effect of quorum sensing inhibition (QSI) on biofilm growth. In both operations, biofilm-associated and planktonic microbial communities were dominated by Pseudomonadales (60.2–99.7%). Rapid recolonization was observed even after dumping spent MWFs and meticulous cleaning. Using Pseudomonas aeruginosa PAO1 as a model biofilm organism, patulin (40 µM) and furanone C-30 (75 µM) were identified as effective QSI agents. Both agents had a substantially higher efficacy compared to α-amylase (extracellular polymeric substance degrading enzyme) and reduced biofilm formation by 63% and 76%, respectively, in MWF when compared to untreated controls. Reduced production of putatively identified homoserine lactones and quinoline in MWF treated with QS inhibitors support the effect of QSI on biofilm formation. The results highlight the effectiveness of QSI as a potential strategy to eradicate biofilms in MWFs.Item Dynamic processing of DOM: Insight from exometabolomics, fluorescence spectroscopy, and mass spectrometry(2018-06) Smith, Heidi J.; Tigges, Michelle M.; D'Andrilli, Juliana; Parker, Albert E.; Bothner, Brian; Foreman, Christine M.Dissolved organic matter (DOM) in freshwater environments is an important source of organic carbon, supporting bacterial respiration. Frozen environments cover vast expanses of our planet, with glaciers and ice-sheets storing upwards of 6 petagrams of organic carbon. It is generally believed that DOM liberated from ice stimulates downstream environments. If true, glacial DOM is an important component of global carbon cycling. However, coupling the release of DOM to microbial activity is challenging due to the molecular complexity of DOM and the metabolic connectivity within microbial communities. Using a single environmentally relevant organism, we demonstrate that processing of compositionally diverse DOM occurs, but, even though glacially derived DOM is chemically labile, it is unable to support sustained respiration. In view of projected changes in glacier DOM export, these findings imply that biogeochemical impacts on downstream environments will depend on the reactivity and heterogeneity of liberated DOM, as well as the timescale.Item A 21 000-year record of fluorescent organic matter markers in the WAIS Divide ice core(2017-05) D'Andrilli, Juliana; Foreman, Christine M.; Sigl, Michael; Priscu, John C.; McConnell, Joseph R.Englacial ice contains a significant reservoir of organic material (OM), preserving a chronological record of materials from Earth's past. Here, we investigate if OM composition surveys in ice core research can provide paleoecological information on the dynamic nature of our Earth through time. Temporal trends in OM composition from the early Holocene extending back to the Last Glacial Maximum (LGM) of the West Antarctic Ice Sheet Divide (WD) ice core were measured by fluorescence spectroscopy. Multivariate parallel factor (PARAFAC) analysis is widely used to isolate the chemical components that best describe the observed variation across three-dimensional fluorescence spectroscopy (excitation–emission matrices; EEMs) assays. Fluorescent OM markers identified by PARAFAC modeling of the EEMs from the LGM (27.0–18.0 kyr BP; before present 1950) through the last deglaciation (LD; 18.0–11.5 kyr BP), to the mid-Holocene (11.5–6.0 kyr BP) provided evidence of different types of fluorescent OM composition and origin in the WD ice core over 21.0 kyr. Low excitation–emission wavelength fluorescent PARAFAC component one (C1), associated with chemical species similar to simple lignin phenols was the greatest contributor throughout the ice core, suggesting a strong signature of terrestrial OM in all climate periods. The component two (C2) OM marker, encompassed distinct variability in the ice core describing chemical species similar to tannin- and phenylalanine-like material. Component three (C3), associated with humic-like terrestrial material further resistant to biodegradation, was only characteristic of the Holocene, suggesting that more complex organic polymers such as lignins or tannins may be an ecological marker of warmer climates. We suggest that fluorescent OM markers observed during the LGM were the result of greater continental dust loading of lignin precursor (monolignol) material in a drier climate, with lower marine influences when sea ice extent was higher and continents had more expansive tundra cover. As the climate warmed, the record of OM markers in the WD ice core changed, reflecting shifts in carbon productivity as a result of global ecosystem response..Item Microbial formation of labile organic carbon in Antarctic glacial environments(2017-04) Smith, Heidi J.; Foster, Rachel A.; McKnight, Diane M.; Lisle, John T.; Littmann, Sten; Kuypers, Marcel M. M.; Foreman, Christine M.Roughly six petagrams of organic carbon are stored within ice worldwide. This organic carbon is thought to be of old age and highly bioavailable. Along with storage of ancient and new atmospherically deposited organic carbon, microorganisms may contribute substantially to the glacial organic carbon pool. Models of glacial microbial carbon cycling vary from net respiration to net carbon fixation. Supraglacial streams have not been considered in models although they are amongst the largest ecosystems on most glaciers and are inhabited by diverse microbial communities. Here we investigate the biogeochemical sequence of organic carbon production and uptake in an Antarctic supraglacial stream in the McMurdo Dry Valleys using nanometre-scale secondary ion mass spectrometry, fluorescence spectroscopy, stable isotope analysis and incubation experiments. We find that heterotrophic production relies on highly labile organic carbon freshly derived from photosynthetic bacteria rather than legacy organic carbon. Exudates from primary production were utilized by heterotrophs within 24 h, and supported bacterial growth demands. The tight coupling of microbially released organic carbon and rapid uptake by heterotrophs suggests a dynamic local carbon cycle. Moreover, as temperatures increase there is the potential for positive feedback between glacial melt and microbial transformations of organic carbon.Item Biofilms on glacial surfaces: hotspots for biological activity(2016-06) Smith, Heidi J.; Schmit, Amber; Foster, Rachel A.; Littmann, Sten; Kuypers, Marcel M. M.; Foreman, Christine M.Glaciers are important constituents in the Earth’s hydrological and carbon cycles, with predicted warming leading to increases in glacial melt and the transport of nutrients to adjacent and downstream aquatic ecosystems. Microbial activity on glacial surfaces has been linked to the biological darkening of cryoconite particles, affecting albedo and increased melt. This phenomenon, however, has only been demonstrated for alpine glaciers and the Greenland Ice Sheet, excluding Antarctica. In this study, we show via confocal laser scanning microscopy that microbial communities on glacial surfaces in Antarctica persist in biofilms. Overall, ~35% of the cryoconite sediment surfaces were covered by biofilm. Nanoscale scale secondary ion mass spectrometry measured significant enrichment of 13C and 15N above background in both Bacteroidetes and filamentous cyanobacteria (i.e., Oscillatoria) when incubated in the presence of 13C–NaHCO3 and 15NH4. This transfer of newly synthesised organic compounds was dependent on the distance of heterotrophic Bacteroidetes from filamentous Oscillatoria. We conclude that the spatial organisation within these biofilms promotes efficient transfer and cycling of nutrients. Further, these results support the hypothesis that biofilm formation leads to the accumulation of organic matter on cryoconite minerals, which could influence the surface albedo of glaciers.Item Draft genome sequence and description of Janthinobacterium sp. strain CG3, a psychrotolerant antarctic Supraglacial stream bacterium(2013-11) Smith, Heidi J.; Akiyama, Tatsuya; Foreman, Christine M.; Franklin, Michael J.; Woyke, Tanja; Teshima, H; Davenport, K.; Daligault, H.; Erkkila, T.; Goodwin, L. A.; Gu, W.; Xu, Yan; Chain, P. S.Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight into the mechanisms necessary for bacteria to survive in UV-stressed icy environments.Item Genome sequence of Janthinobacterium sp. CG23_2, a violacein-producing isolate from an Antarctic supraglacial stream.(2016-01) Smith, Heidi J.; Foreman, Christine M.; Akiyama, Tatsuya; Franklin, Michael J.; Devitt, N. P.; Ramaraj, ThiruvaranganHere, we present the draft genome sequence for the violacein-producing Janthinobacterium sp. CG23_2 isolated from an Antarctic supraglacial stream. The genome is ~7.85 Mb, with a G+C content of 63.5%. The genome includes 7,247 candidate protein coding genes, which may provide insight into UV tolerance mechanisms.Item An ultrahigh-resolution mass spectrometry index to estimate natural organic matter lability(2015-12) D'Andrilli, Juliana; Cooper, William T.; Foreman, Christine M.; Marshall, Alan G.Rationale: Determining the chemical constituents of natural organic matter (NOM) by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICRMS) remains the ultimate measure for probing its source material, evolution, and transport; however, lability and the fate of organic matter (OM) in the environment remain controversial. FTICRMS-derived elemental compositions are presented in this study to validate a new interpretative method to determine the extent of NOM lability from various environments. Methods: FTICRMS data collected over the last decade from the same 9.4 tesla instrument using negative electrospray ionization at the National High Magnetic Field Laboratory in Tallahassee, Florida, was used to validate the application of a NOM lability index. Solid-phase extraction cartridges were used to isolate the NOM prior to FTICRMS; mass spectral peaks were calibrated internally by commonly identified NOM homologous series, and molecular formulae were determined for NOM composition and lability analysis. Results: A molecular lability boundary (MLB) was developed from the FTICRMS molecular data, visualized from van Krevelen diagrams, dividing the data into more and less labile constituents. NOM constituents above the MLB at H/C ≥1.5 correspond to more labile material, whereas NOM constituents below the MLB, H/C <1.5, exhibit less labile, more recalcitrant character. Of all marine, freshwater, and glacial environments considered for this study, glacial ecosystems were calculated to contain the most labile OM. Conclusions: The MLB extends our interpretation of FTICRMS NOM molecular data to include a metric of lability, and generally ranked the OM environments from most to least labile as glacial > marine > freshwater. Applying the MLB is useful not only for individual NOM FTICRMS studies, but also provides a lability threshold to compare and contrast molecular data with other FTICRMS instruments that survey NOM from around the world.