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

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

Observations of the very young Type Ia Supernova 2019np with early-excess emission

H. Sai et al.Early-time radiative signals from Type Ia supernovae (SNe Ia) can provide important constraints on the explosion mechanism and the progenitor system. We present observations and analysis of SN 2019np, a nearby SN Ia discovered within 1–2 days after the explosion. Follow-up observations were conducted in optical, ultraviolet, and near-infrared bands, covering the phases from ∼−16.7 d to ∼+ 367.8 d relative to its B-band peak luminosity. The photometric and spectral evolutions of SN 2019np resemble the average behaviour of normal SNe Ia. The absolute B-band peak magnitude and the post-peak decline rate are Mmax(B) = −19.52 ± 0.47 mag and Δm15(B) = 1.04 ± 0.04 mag, respectively. No Hydrogen line has been detected in the nebular-phase spectra of SN 2019np. Assuming that the 56Ni powering the light curve is centrally located, we find that the bolometric light curve of SN 2019np shows a flux excess up to 5.0 per cent in the early phase compared to the radiative diffusion model. Such an extra radiation perhaps suggests the presence of an additional energy source beyond the radioactive decay of central nickel. Comparing the observed colour evolution with that predicted by different models, such as interactions of SN ejecta with circumstellar matter (CSM)/companion star, a double-detonation explosion from a sub-Chandrasekhar mass white dwarf (WD) and surface 56Ni mixing, we propose that the nickel mixing is more favoured for SN 2019np.Financial support for this work has been provided by the National Science Foundation of China (NSFC grants 12033003 and 11633002), the Scholar Program of Beijing Academy of Science and Technology (DZ:BS202002), and the Tencent XPLORER Prize. This work was partially supported by the Open Project Program of the Key Laboratory of Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences. J.Z. is supported by the National Natural Science Foundation of China (NSFC, grants 11773067, 12173082, 11403096), by the Youth Innovation Promotion Association, CAS (grant 2018081), and by the Ten Thousand Talents Program of Yunnan for Top-notch Young Talents. A.R. acknowledges support from ANID BECAS/DOCTORADO NACIONAL 21202412. SY acknowledge support from the G.R.E.A.T research environment, funded by Vetenskapsrådet, the Swedish Research Council, project number 2016-06012. Y.-Z. Cai is funded by China Postdoctoral Science Foundation (grant no. 2021M691821). This work has been supported by MINECO grant ESP2017-82674-R, by EU FEDER funds and by grants 2014SGR1458 and CERCA Programe of the Generalitat de Catalunya (JI). The research of Y.Y. is supported through the Bengier-Winslow-Robertson Fellowship. M. Stritzinger is supported by grants from the Villum Fonden (grant number 28021) and the Independent Research Fund Denmark (IRFD; 8021-00170B). Lingzhi Wang is sponsored (in part) by the Chinese Academy of Sciences (CAS), through a grant to the CAS South America Center for Astronomy (CASSACA) in Santiago, Chile. CYW is supported by the National Natural Science Foundation of China (NSFC grants 12003013). BW is supported by the National Key R&D Program of China (No. 2021YFA1600404), the Western Light Project of CAS (No. XBZG-ZDSYS-202117), the science research grants from the China Manned Space Project (No CMS-CSST-2021-A13).Peer reviewe

Thyroid hormone reverses aging-induced myocardial fatty acid oxidation defects and improves the response to acutely increased afterload.

Subclinical hypothyroidism occurs during aging in humans and mice and may contribute to the development of heart failure. Aging also impairs myocardial fatty acid oxidation, causing increased reliance on flux through pyruvate dehydrogenase (PDH) to maintain function. We hypothesize that the metabolic changes in aged hearts make them less tolerant to acutely increased work and that thyroid hormone supplementation reverses these defects.Studies were performed on young (Young, 4-6 months) and aged (Old, 22-24 months) C57/BL6 mice at standard (50 mmHg) and high afterload (80 mmHg). Another aged group received thyroid hormone for 3 weeks (Old-TH, high afterload only). Function was measured in isolated working hearts along with substrate fractional contributions (Fc) to the citric acid cycle (CAC) using perfusate with (13)C labeled lactate, pyruvate, glucose and unlabeled palmitate and insulin.Old mice maintained cardiac function under standard workload conditions, despite a marked decrease in unlabeled (presumably palmitate) Fc and relatively similar individual carbohydrate contributions. However, old mice exhibited reduced palmitate oxidation with diastolic dysfunction exemplified by lower -dP/dT. Thyroid hormone abrogated the functional and substrate flux abnormalities in aged mice.The aged heart shows diminished ability to increase cardiac work due to substrate limitations, primarily impaired fatty acid oxidation. The heart accommodates slightly by increasing efficiency through oxidation of carbohydrate substrates. Thyroid hormone supplementation in aged mice significantly improves cardiac function potentially through restoration of fatty acid oxidation

Structural Insights into the Interaction Between a Potent Anti-Inflammatory Protein, Viral CC Chemokine Inhibitor (vCCI), and the Human CC Chemokine, Eotaxin-1

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N terminus, 20s region and 40s loop. However, the interactions between vCCI and other CC chemokines have not yet been fully explored. Here, we used NMR and fluorescence anisotropy to study the interaction between vCCI and eotaxin-1 (CCL11), a CC chemokine that is an important factor in the asthma response. NMR results reveal that the binding pattern is very similar to the vCCI·MIP-1β complex and suggest that electrostatic interactions provide a major contribution to binding. Fluorescence anisotropy results on variants of eotaxin-1 further confirm the critical roles of the charged residues in eotaxin-1. In addition, the binding affinity between vCCI and other wild type CC chemokines, MCP-1 (monocyte chemoattractant protein-1), MIP-1β, and RANTES (regulated on activation normal T cell expressed and secreted), were determined as 1.1, 1.2, and 0.22 nM, respectively. To our knowledge, this is the first work quantitatively measuring the binding affinity between vCCI and multiple CC chemokines