Browsing by Author "Schwarz, Cory"

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    Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress
    (Springer Nature, 2021) Huang, Dan; Yu, Pingfeng; Ye, Mao; Schwarz, Cory; Jiang, Xin; Alvarez, Pedro J.J.
    Background: Microbe–virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify the ecological function of viral communities and understand microbiome environmental adaptation. Heavy metal-contaminated soils represent a relevant ecosystem to study the interplay between microbes, viruses, and environmental stressors. Results: Metagenomic analysis revealed that Cr pollution adversely altered the abundance, diversity, and composition of viral and bacterial communities. Host–phage linkage based on CRISPR indicated that, in soils with high Cr contamination, the abundance of phages associated with heavy metal-tolerant hosts increased, as did the relative abundance of phages with broad host ranges (identified as host–phage linkages across genera), which would facilitate transfection and broader distribution of heavy metal resistance genes in the bacterial community. Examining variations along the pollutant gradient, enhanced mutualistic phage–bacterium interactions were observed in the face of greater environmental stresses. Specifically, the fractions of lysogens in bacterial communities (identified by integrase genes within bacterial genomes and prophage induction assay by mitomycin-C) were positively correlated with Cr contamination levels. Furthermore, viral genomic analysis demonstrated that lysogenic phages under higher Cr-induced stresses carried more auxiliary metabolic genes regulating microbial heavy metal detoxification. Conclusion: With the intensification of Cr-induced environmental stresses, the composition, replication strategy, and ecological function of the phage community all evolve alongside the bacterial community to adapt to extreme habitats. These result in a transformation of the phage–bacterium interaction from parasitism to mutualism in extreme environments and underscore the influential role of phages in bacterial adaptation to pollution-related stress and in related biogeochemical processes.
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    Rapid Metabolism of 1,4-Dioxane to below Health Advisory Levels by Thiamine-Amended Rhodococcus ruber Strain 219
    (American Chemical Society, 2021) Simmer, Reid A.; Richards, Patrick M.; Ewald, Jessica M.; Schwarz, Cory; da Silva, Marcio L.B.; Mathieu, Jacques; Alvarez, Pedro J.J.; Schnoor, Jerald L.
    Bioremediation is a promising treatment technology for 1,4-dioxane-contaminated groundwater. However, metabolic dioxane-degrading bacteria identified to date are limited by their slow kinetics and inability to sustain growth at low dioxane concentrations (<100 μg/L). Furthermore, strains may underperform because of missing growth factors, such as amino acids or vitamins. In this work, we reevaluate Rhodococcus ruber strain 219 as a dioxane-degrading strain with bioaugmentation potential. We report rapid growth and metabolic dioxane degradation by R. ruber 219 when supplemented with thiamine (vitamin B1). We also discern that the strain lacks a complete de novo thiamine synthesis pathway, indicating that R. ruber 219 is a probable thiamine auxotroph. However, when supplemented with thiamine, the strain’s Monod kinetics (Ks = 0.015 ± 0.03 μg/L) and exceedingly low Smin (0.49 ± 1.16 μg/L) suggest this strain can maintain growth at very low dioxane concentrations (<100 μg/L). Accordingly, we demonstrate that thiamine-grown R. ruber 219 sustains degradation of dilute dioxane (<100 μg/L) to below health advisory levels. This is the first study to report sustained metabolic dioxane biodegradation to below health advisory levels of 0.35 μg/L. Overall, our findings solidify R. ruber 219 as a promising candidate for bioremediation of dioxane-contaminated groundwater.