College of Engineering
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The College of Engineering at Montana State University will serve the State of Montana and the nation by fostering lifelong learning, integrating learning and discovery, developing and sharing technical expertise, and empowering students to be tomorrow's leaders.
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Item Community-led, integrated, reproducible multi-omics with anvi’o(Springer Science and Business Media LLC, 2020-12) Eren, A. Murat; Kiefl, Evan; Shaiber, Alon; Veseli, Iva; Miller, Samuel E.; Schechter, Matthew S.; Fink, Isaac; Pan, Jessica N.; Yousef, Mahmoud; Fogarty, Emily C.; Trigodet, Florian; Watson, Andrea R.; Esen, Ozcan C.; Moore, Ryan M.; Clayssen, Quentin; Lee, Michael D.; Kivenson, Veronika; Graham, Elaina D.; Merrill, Bryan D.; Karkman, Antti; Blankenberg, Daniel; Eppley, John M.; Sjodin, Andreas; Scott, Jarrod J.; Vazquez-Campos, Xabier; McKay, Luke J.; McDaniel, Elizabeth A.; Stevens, Sarah L.R.; Anderson, Rika E.; Fuessel, Jessika; Fernandez-Guerra, Antonio; Maignien, Lois; Delmont, Tom O.; Willis, Amy D.Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.Item Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics(Springer Science and Business Media LLC, 2022-02) Schweitzer, Hannah D.; Smith, Heidi J.; Barnhart, Elliott P.; McKay, Luke J.; Gerlach, Robin; Cunningham, Alfred B.; Malmstrom, Rex R.; Goudeau, Danielle; Fields, Matthew W.Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.Item The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases(American Association for the Advancement of Science, 2021-10) Altae-Tran, Han; Kannan, Soumya; Demircioglu, F. Esra; Oshiro, Rachel; Nety, Suchita P.; McKay, Luke J.; Dlakić, Mensur; Inskeep, William P.; Makarova, Kira S.; Macrae, Rhiannon K.; Koonin, Eugene V.; Zhang, FengIscB proteins are putative nucleases encoded in a distinct family of IS200/IS605 transposons and are likely ancestors of the RNA-guided endonuclease Cas9, but the functions of IscB and its interactions with any RNA remain uncharacterized. Using evolutionary analysis, RNA sequencing, and biochemical experiments, we reconstructed the evolution of CRISPR-Cas9 systems from IS200/IS605 transposons. We found that IscB uses a single noncoding RNA for RNA-guided cleavage of double-stranded DNA and can be harnessed for genome editing in human cells. We also demonstrate the RNA-guided nuclease activity of TnpB, another IS200/IS605 transposon-encoded protein and the likely ancestor of Cas12 endonucleases. This work reveals a widespread class of transposon-encoded RNA-guided nucleases, which we name OMEGA (obligate mobile element–guided activity), with strong potential for developing as biotechnologies.Item Draft Genome Sequence of Methanothermobacter thermautotrophicus WHS, a Thermophilic Hydrogenotrophic Methanogen from Washburn Hot Springs in Yellowstone National Park, USA(American Society for Microbiology, 2021-02) McKay, Luke K.; Klingelsmith, Korinne B.; Deutschbauer, Adam M.; Inskeep, William P.; Fields, Matthew W.A thermophilic methanogen was enriched in coculture from Washburn Hot Springs (Yellowstone National Park, USA), grown on carbon dioxide and hydrogen, and subsequently sequenced. The reconstructed 1.65-Mb genome sequence for Methanothermobacter thermautotrophicus WHS contributes to our understanding of hydrogenotrophic, CO2-reducing methanogenesis in geothermal ecosystems.Item Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane(Springer Science and Business Media LLC, 2021-10) McKay, Luke J.; Smith, Heidi J.; Barnhart, Elliott P.; Schweitzer, Hannah D.; Malmstrom, Rex R.; Goudeau, Danielle; Fields, Matthew W.Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.Item Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community(2018-09) Hunt, Kristopher A.; Jennings, Ryan deM.; Inskeep, William P.; Carlson, Ross P.Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2–4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.Item DOM composition alters ecosystem function during microbial processing of isolated sources(2019-01) D'Andrilli, Juliana; Junker, James R.; Smith, Heidi J.; Scholl, Eric A.; Foreman, Christine M.Dynamics of dissolved organic matter (DOM) in ecosystems are controlled by a suite of interacting physical, chemical, and biological factors. Growing recognition of the associations between microbial communities and metabolism and intrinsic DOM characteristics, highlight the potential importance of microbe-DOM relationships to modulate the role and fate of DOM, yet these relationships are difficult to isolate because they often operate across confounding environmental gradients. In a controlled laboratory incubation (44 days), we integrated DOM bulk and molecular characterization, bacterial abundances, microbial assemblage composition, nutrient concentrations, and cellular respiration to discern the structural dynamics of biological processing among DOM sources from different allochthonous litters (grass, deciduous leaves, and evergreen needles). We identified two periods, consistent among DOM sources, where processing dynamics differed. Further, bulk fluorescent analyses showed shifts from low to high excitation and emission wavelengths, indicating the biological production of more complex/degraded materials over time. Molecular level analyses revealed similar temporal patterns among DOM sources in the production and consumption of individual chemical components varying in reactivity and heteroatomic content. Despite these similarities, total carbon (C) removed and carbon dioxide (CO2) accumulation differed by ~ 20% and 25% among DOM sources. This range in C processing was apparently tied to key chemical properties of the DOM (e.g., initial DOM composition, N content, and labile nature) as well as differential reorganization of the microbial populations that decomposed the DOM. We conclude that the production, transformation, and consumption of C in aquatic ecosystems is strongly dependent on the source and character of DOM as well as the structure of the microbial communities present, both of which change as DOM is processed over time. It is crucial that stream C processing models represent this complexity accurately.Item Phosphate starvation response controls genes required to synthesize the phosphate analog arsenate(2018-05) Wang, Qian; Kang, Yoon-Suk; Alowaifeer, Abdullah; Shi, Kaixiang; Fan, Xia; Wang, Lu; Jetter, Jonathan; Bothner, Brian; Wang, Gejiao; McDermott, Timothy R.Environmental arsenic poisoning affects roughly 200 million people worldwide. The toxicity and mobility of arsenic in the environment is significantly influenced by microbial redox reactions, with arsenite (AsIII ) being more toxic than arsenate (AsV ). Microbial oxidation of AsIII to AsV is known to be regulated by the AioXSR signal transduction system and viewed to function for detoxification or energy generation. Here, we show that AsIII oxidation is ultimately regulated by the phosphate starvation response (PSR), requiring the sensor kinase PhoR for expression of the AsIII oxidase structural genes aioBA. The PhoRB and AioSR signal transduction systems are capable of transphosphorylation cross-talk, closely integrating AsIII oxidation with the PSR. Further, under PSR conditions, AsV significantly extends bacterial growth and accumulates in the lipid fraction to the apparent exclusion of phosphorus. This could spare phosphorus for nucleic acid synthesis or triphosphate metabolism wherein unstable arsenic esters are not tolerated, thereby enhancing cell survival potential. We conclude that AsIII oxidation is logically part of the bacterial PSR, enabling the synthesis of the phosphate analog AsV to replace phosphorus in specific biomolecules or to synthesize other molecules capable of a similar function, although not for total replacement of cellular phosphate.Item A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice(2018-02) Biyiklioglu, Sezgi; Alptekin, Burcu; Akpinar, B. Ani; Varella, Andrea C.; Hofland, Megan L.; Weaver, David K.; Bothner, Brian; Budak, HikmetThe wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae), is an important pest of wheat and other cereals, threatening the quality and quantity of grain production. WSS larvae feed and develop inside the stem where they are protected from the external environment; therefore, pest management strategies primarily rely on host plant resistance. A major locus on the long arm of wheat chromosome 3B underlies most of the variation in stem solidness; however, the impact of stem solidness on WSS feeding has not been completely characterized. Here, we used a multiomics approach to examine the response to WSS in both solid- and semi-solid-stemmed wheat varieties. The combined transcriptomic, proteomic, and metabolomic data revealed that two important molecular pathways, phenylpropanoid and phosphate pentose, are involved in plant defense against WSS. We also detected a general downregulation of several key defense transcripts, including those encoding secondary metabolites such as DIMBOA, tricetin, and lignin, which suggested that the WSS larva might interfere with plant defense. We comparatively analyzed the stem solidness genomic region known to be associated with WSS tolerance in wild emmer, durum, and bread wheats, and described syntenic regions in the close relatives barley, Brachypodium, and rice. Additionally, microRNAs identified from the same genomic region revealed potential regulatory pathways associated with the WSS response. We propose a model outlining the molecular responses of the WSS-wheat interactions. These findings provide insight into the link between stem solidness and WSS feeding at the molecular level.Item Opportunities and Trade-offs among BECCS and the Food, Water, Energy, Biodiversity, and Social Systems Nexus at Regional Scales(2018-01) Stoy, Paul C.; Ahmed, Selena; Jarchow, Meghann; Rashford, Benjamin; Swanson, David; Albeke, Shannon; Bromley, Gabriel T.; Brookshire, E. N. Jack; Dixon, Mark D.; Haggerty, Julia Hobson; Miller, Perry R.; Peyton, Brent M.; Royem, Alisa; Spangler, Lee H.; Straub, Crista; Poulter, BenjaminCarbon dioxide must be removed from the atmosphere to limit climate change to 2°C or less. The integrated assessment models used to develop climate policy acknowledge the need to implement net negative carbon emission strategies, including bioenergy with carbon capture and storage (BECCS), to meet global climate imperatives. The implications of BECCS for the food, water, energy, biodiversity, and social systems (FWEBS) nexus at regional scales, however, remain unclear. Here, we present an interdisciplinary research framework to examine the trade-offs as well as the opportunities among BECCS scenarios and FWEBS on regional scales using the Upper Missouri River Basin (UMRB) as a case study. We describe the physical, biological, and social attributes of the UMRB, and we use grassland bird populations as an example of how biodiversity is influenced by energy transitions, including BECCS. We then outline a "conservation" BECCS strategy that incorporates societal values and emphasizes biodiversity conservation.