Phenotypic responses to interspecies competition and commensalism in a naturally derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL- 58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL- 48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability

Phenotypic responses to interspecies competition and commensalism in a naturally derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL- 58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL- 48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold

Observations of Type Ia Supernova 2014J for Nearly 900 Days and Constraints on Its Progenitor System

We present extensive ground-based and $Hubble~Space~Telescope$ ($HST$) photometry of the highly reddened, very nearby type Ia supernova (SN Ia) 2014J in M82, covering the phases from 9 days before to about 900 days after the $B$-band maximum. SN 2014J is similar to other normal SNe Ia near the maximum light, but it shows flux excess in the $B$ band in the early nebular phase. This excess flux emission can be due to light scattering by some structures of circumstellar materials located at a few 10$^{17}$ cm, consistent with a single degenerate progenitor system or a double degenerate progenitor system with mass outflows in the final evolution or magnetically driven winds around the binary system. At t$\sim$+300 to $\sim$+500 days past the $B$-band maximum, the light curve of SN 2014J shows a faster decline relative to the $^{56}$Ni decay. Such a feature can be attributed to the significant weakening of the emission features around [Fe III] $\lambda$4700 and [Fe II] $\lambda$5200 rather than the positron escape as previously suggested. Analysis of the $HST$ images taken at t$>$600 days confirms that the luminosity of SN 2014J maintains a flat evolution at the very late phase. Fitting the late-time pseudo-bolometric light curve with radioactive decay of $^{56}$Ni, $^{57}$Ni and $^{55}$Fe isotopes, we obtain the mass ratio $^{57}$Ni/$^{56}$Ni as $0.035 \pm 0.011$, which is consistent with the corresponding value predicted from the 2D and 3D delayed-detonation models. Combined with early-time analysis, we propose that delayed-detonation through single degenerate scenario is most likely favored for SN 2014J.Comment: 28 pages, 12 figures. Accepted for publication in Ap

FY-2007 PNNL Voluntary Protection Program (VPP) Program Evaluation

This document reports the results of the FY-2007 PNNL VPP Program Evaluation, which is a self-assessment of the operational and programmatic performance of the Laboratory related to worker safety and health. The report was compiled by a team of worker representatives and safety professionals who evaluated the Laboratory's worker safety and health programs on the basis of DOE-VPP criteria. The principle elements of DOE's VPP program are: Management Leadership, Employee Involvement, Worksite Analysis, Hazard Prevention and Control, and Safety and Health Training

Changing Safety Culture, One Step at a Time: The Value of the DOE-VPP Program at PNNL

The primary value of the Pacific Northwest National Laboratory (PNNL) Voluntary Protection Program (VPP) is the ongoing partnership between management and staff committed to change Laboratory safety culture one step at a time. VPP enables PNNL's safety and health program to transcend a top-down, by-the-book approach to safety, and it also raises grassroots safety consciousness by promoting a commitment to safety and health 24 hours a day, 7 days a week. PNNL VPP is a dynamic, evolving program that fosters innovative approaches to continuous improvement in safety and health performance at the Laboratory

Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics

NMR metabolomics, consisting of solid state high resolution magic angle spinning (HR-MAS) 1H-NMR, liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver. The melanoma group can be differentiated from its control group by PCA analysis of the estimates of absolute concentrations from liquid state 1H-NMR spectra on liver tissue extracts or by the estimates of absolute peak intensities of metabolites from 1H HR-MAS-NMR data on intact liver tissues. In particular, we found that the estimates of absolute concentrations of glutamate, creatine, fumarate and cholesterol are elevated in the melanoma group as compared to controls, while the estimates of absolute concentrations of succinate, glycine, glucose, and the family of linear lipids including long chain fatty acids, total choline and acyl glycerol are decreased. The ratio of glycerophosphocholine (GPC) to phosphocholine (PCho) is increased by about 1.5 fold in the melanoma group, while the estimate of absolute concentration of total choline is actually lower in melanoma mice. These results suggest the following picture in secondary melanoma metastasis: Linear lipid levels are decreased by beta oxidation in the melanoma group, which contributes to an increase in the synthesis of cholesterol, and also provides an energy source input for TCA cycle. These findings suggest a link between lipid oxidation, the TCA cycle and the hypoxia-inducible factors (HIF) signal pathway in tumor metastases. Thus, this study indicates that the metabolic profile derived from NMR analysis can provide a valuable bio-signature of malignancy and cell hypoxia in metastatic melanoma