Publications by Colleges and Departments (MSU - Bozeman)
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Item Functional traits underlie specialist-generalist strategies in whitebark pine and limber pine(Elsevier BV, 2023-08) Ulrich, Danielle E. M.; Wasteneys, Chloe; Hoy-Skubik, Sean; Alongi, FranklinPlant species life history strategies are described by functional variation spanning an acquisitive and conservative resource use continuum. Specialist species can exhibit traits promoting one end of the continuum, while generalist species can display traits promoting both acquisitive and conservative resource use. Whitebark pine (Pinus albicaulis, PIAL) and limber pine (Pinus flexilis, PIFL) are two high-elevation pines that have similar growth and morphology, yet contrasting elevational distributions with PIAL viewed as a specialist inhabiting a narrower elevation range, and PIFL as a generalist inhabiting a broader elevation range. We compared the physiological and morphological traits of greenhouse-grown 5-year-old PIAL and PIFL. Our results suggest that PIFL’s acquisitive and conservative resource use traits contribute to its generalist strategy and ability to inhabit a greater range of elevations than PIAL. PIFL had greater acquisitive resource use traits including: high-light tolerance (greater Qsat, greater fascicle density), increased biomass allocation to photosynthetic tissue (higher needle biomass, aboveground:belowground biomass, needle:branch + stem biomass), and higher C and water uptake (greater stomatal density and size, higher C assimilation rate), as well as greater conservative resource use traits including: greater physical stress resistance (shorter height, higher stem and branch diameters, greater branch and stem diameter:length), drought tolerance (higher SWC, leaf starch proportion), and drought avoidance (earlier budburst phenology, smaller hydroscape area) than PIAL. Our results suggest that PIFL may make more efficient use of high-light loads and maximize C and water uptake when moisture is abundant during spring snowmelt before the onset of dry summer conditions. Other conservative resource use traits describing cold tolerance, heat tolerance, and drought tolerance did not differ between species, suggesting that both species exhibit traits that promote similar conservative resource use enabling their overlapping persistence at higher elevations. Comparing the physiology of PIAL and PIFL within the same environment enables us to identify physiological mechanisms that underlie species establishment and survival, and how juvenile physiology contributes to their contrasting distributions and their generalist-specialist strategies.Item Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in Bacteria(2013-12) Rodionova, I. A.; Li, X.; Thiel, Vera; Stolyar, S.; Stanton, K.; Frederickson, J. K.; Bryant, Donald A.; Osterman, A. L.; Best, A. A.; Rodionov, D. A.L-rhamnose (L-Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L-Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and L-Rha-containing polymers. Large-scale regulon inference using bioinformatics revealed remarkable variations in transcriptional regulators for L-Rha utilization genes among bacteria. A novel bifunctional enzyme, L-rhamnulose-phosphate aldolase (RhaE) fused to L-lactaldehyde dehydrogenase (RhaW), which is not homologous to previously characterized L-Rha catabolic enzymes, was identified in diverse bacteria including Chloroflexi, Bacilli, and Alphaproteobacteria. By using in vitro biochemical assays we validated both enzymatic activities of the purified recombinant RhaEW proteins from Chloroflexus aurantiacus and Bacillus subtilis. Another novel enzyme of the L-Rha catabolism, L-lactaldehyde reductase (RhaZ), was identified in Gammaproteobacteria and experimentally validated by in vitro enzymatic assays using the recombinant protein from Salmonella typhimurium. C. aurantiacus induced transcription of the predicted L-Rha utilization genes when L-Rha was present in the growth medium and consumed L-Rha from the medium. This study provided comprehensive insights to L-Rha catabolism and its regulation in diverse Bacteria.Item An endophytic Nodulisporium sp. producing volatile organic compounds having bioactivity and fuel potential(2012) Mends, Morgan Tess; Yu, Eizadora; Strobel, Gary A.; Hassan, S. R. U.; Booth, Eric; Geary, Brad; Sears, Joe; Taatjes, C. A.; Hadi, M.Nodulisporium sp. has been isolated as an endophyte of Myroxylon balsamum found in the upper Napo region of the Ecuadorian Amazon. This organism produces volatile organic compounds (VOCs) that have both fuel and biological potential.Under microaerophilic growth environments, the organism produces 1, 4-cyclohexadiene, 1 methyl-,1-4 pentadiene and cyclohexene, 1-methyl-4-(1-methylethenyl)- along with some alcohols and terpenoids of interest as potential fuels. The fungus was scaled up in an aerated large fermentation flask, and the VOCs trapped by Carbotrap technology and analyzed by headspace solid –phase microextraction (SPME) fiber-GC/MS. Under these conditions, Nodulisporium sp. produces a series of alkyl alcohols starting with 1-butanol-3-methyl, 1- propanol-2-methyl, 1- pentanol, 1-hexanol, 1-heptanol, 1- octanol, 1-nonanol along with phenylethyl alcohol.The organism also produces secondary alkyl alcohols, esters, ketones, benzene derivatives, a few terpenoids, and some hydrocarbons. It appears that many of the products have fuel potential. Furthermore, the VOCs of Nodulisporium sp. were active against a number of pathogens causing death to both Aspergillus fumigatus and Rhizoctonia solani and severe growth inhibition produced in Phytophthora cinnamomi and Sclerotinia sclerotiorum within 48 hr of exposure. The Carbotrapped materials somewhat mimicked the bioactivities of the culture itself when certain test organisms were exposed to these VOCs. A brief discussion on the relationship of these fungal VOCs to those compounds found in transportation fuels is presented.Item The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem.(2013-05) Inskeep, William P.; Jay, Zackary J.; Tringe, Susannah G.; Herrgard, M.; Rusch, Douglas B.; YNP Metagenome Project Steering Committee and Working Group MembersThe Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential, and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1) phototrophic mats, (2) “filamentous streamer” communities, and (3) archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments.Item Components and evolution of oxidative sulfur metabolism in green sulfur bacteria(2011-05) Gregersen, L. H.; Bryant, Donald A.; Frigaard, N. U.Green sulfur bacteria (GSB) constitute a closely related group of photoautotrophic and thiotrophic bacteria with limited phenotypic variation. They typically oxidize sulfide and thiosulfate to sulfate with sulfur globules as an intermediate. Based on genome sequence information from 15 strains, the distribution and phylogeny of enzymes involved in their oxidative sulfur metabolism was investigated. At least one homolog of sulfide:quinone oxidoreductase (SQR) is present in all strains. In all sulfur-oxidizing GSB strains except the earliest diverging Chloroherpeton thalassium, the sulfide oxidation product is further oxidized to sulfite by the dissimilatory sulfite reductase (DSR) system. This system consists of components horizontally acquired partly from sulfide-oxidizing and partly from sulfate-reducing bacteria. Depending on the strain, the sulfite is probably oxidized to sulfate by one of two different mechanisms that have different evolutionary origins: adenosine-5′-phosphosulfate reductase or polysulfide reductase-like complex 3. Thiosulfate utilization by the SOX system in GSB has apparently been acquired horizontally from Proteobacteria. SoxCD does not occur in GSB, and its function in sulfate formation in other bacteria has been replaced by the DSR system in GSB. Sequence analyses suggested that the conserved soxJXYZAKBW gene cluster was horizontally acquired by Chlorobium phaeovibrioides DSM 265 from the Chlorobaculum lineage and that this acquisition was mediated by a mobile genetic element. Thus, the last common ancestor of currently known GSB was probably photoautotrophic, hydrogenotrophic, and contained SQR but not DSR or SOX. In addition, the predominance of the Chlorobium–Chlorobaculum–Prosthecochloris lineage among cultured GSB could be due to the horizontally acquired DSR and SOX systems. Finally, based upon structural, biochemical, and phylogenetic analyses, a uniform nomenclature is suggested for sqr genes in prokaryotes.