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Creators/Authors contains: "Alfred, M."

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  1. Abstract

    Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.

     
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  2. Abstract An electrodynamic levitation thermal-gradient diffusion chamber was used to grow 268 individual, small ice particles (initial radii of 8–26 μ m) from the vapor, at temperatures ranging from −65° to −40°C, and supersaturations up to liquid saturation. Growth limited by attachment kinetics was frequently measured at low supersaturation, as shown in prior work. At high supersaturation, enhanced growth was measured, likely due to the development of branches and hollowed facets. The effects of branching and hollowing on particle growth are often treated with an effective density ρ eff . We fit the measured time series with two different models to estimate size-dependent ρ eff values: the first model decreases ρ eff to an asymptotic deposition density ρ dep , and the second models ρ eff by a power law with exponent P . Both methods produce similar results, though the fits with ρ dep typically have lower relative errors. The fit results do not correspond well with models of isometric or planar single-crystalline growth. While single-crystalline columnar crystals correspond to some of the highest growth rates, a newly constructed geometric model of budding rosette crystals produces the best match with the growth data. The relative frequency of occurrence of ρ dep and P values show a clear dependence on ice supersaturation normalized to liquid saturation. We use these relative frequencies of ρ dep and P to derive two supersaturation-dependent mass–size relationships suitable for cloud modeling applications. 
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  3. There are few measurements of the vapor growth of small ice crystals at temperatures below -30°C. Presented here are mass-growth measurements of heterogeneously and homogeneously frozen ice particles grown within an electrodynamic levitation diffusion chamber at temperatures between -44 and -30°C and supersaturations ( s i ) between 3 and 29%. These growth data are analyzed with two methods devised to estimate the deposition coefficient ( α) without the direct use of s i . Measurements of s i are typically uncertain, which has called past estimates of α into question. We find that the deposition coefficient ranges from 0.002 to unity and is scattered with temperature, as shown in prior measurements. The data collectively also show a relationship between α and s i , with α rising (falling) with increasing s i for homogeneously (heterogeneously) frozen ice. Analysis of the normalized mass growth rates reveals that heterogeneously-frozen crystals grow near the maximum rate at low s i , but show increasingly inhibited (low α) growth at high s i . Additionally, 7 of the 17 homogeneously frozen crystals cannot be modeled with faceted growth theory or constant α. These cases require the growth mode to transition from efficient to inefficient in time, leading to a large decline in α. Such transitions may be, in part, responsible for the inconsistency in prior measurements of α. 
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  5. Summary

    Direct electron uptake is emerging as a key process for electron transfer in anaerobic microbial communities, both between species and from extracellular sources, such as zero‐valent iron (Fe0) or cathodic surfaces. In this study, we investigated cathodic electron uptake by Fe0‐corrodingDesulfovibrio ferrophilusIS5 and showed that electron uptake is dependent on direct cell contact via a biofilm on the cathode surface rather than through secreted intermediates. Induction of cathodic electron uptake by lactate‐starvedD. ferrophilusIS5 cells resulted in the expression of all components necessary for electron uptake; however, protein synthesis was required for full biofilm formation. Notably, proteinase K treatment uncoupled electron uptake from biofilm formation, likely through proteolytic degradation of proteinaceous components of the electron uptake machinery. We also showed that cathodic electron uptake is dependent on SO42−reduction. The insensitivity of Fe0corrosion to proteinase K treatment suggests that electron uptake from a cathode might involve different mechanism(s) than those involved in Fe0corrosion.

     
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  6. Free, publicly-accessible full text available March 1, 2024