Biosynthesis of Polyhydroxyalkanoate Terpolymer from Methanol via the Reverse β-Oxidation Pathway in the Presence of Lanthanide

Methylorubrum extorquens AM1 is the attractive platform for the production of value-added products from methanol. We previously demonstrated that M. extorquens equipped with PHA synthase with broad substrate specificity synthesized polyhydroxyalkanoates (PHAs) composed of (R)-3-hydroxybutyrate and small fraction of (R)-3-hydroxyvalerate (3HV) and (R)-3-hydroxyhexanoate (3HHx) units on methanol. This study further engineered M. extorquens for biosynthesis of PHAs with higher 3HV and 3HHx composition focusing on the EMC pathway involved in C1 assimilation. The introduction of ethylmalonyl-CoA decarboxylase, catalyzing a backward reaction in the EMC pathway, aiming to increase intracellular propionyl/butyryl-CoA precursors did not affect PHA composition. Reverse b-oxidation pathway and subsequent (R)-specific hydration of 2-enoyl-CoA were then enhanced by heterologous expression of four genes derived from Ralstonia eutropha for the conversion of propionyl/butyryl-CoAs to the corresponding (R)-3-hydroxyacyl-CoA monomers. The resulting strains produced PHAs with higher 3HV and 3HHx compositions, while the methylotrophic growth was severely impaired. This growth impairment was interestingly restored by the addition of La3+ without a negative impact on PHA biosynthesis, suggesting the activation of the EMC pathway by La3+. The engineered M. extorquens synthesized PHA terpolymer composed of 5.4 mol% 3HV and 0.9% of 3HHx with 41% content from methanol as a sole carbon source in the presence of La3+.

Staphylococcus aureus does not synthesize arginine from proline under physiological conditions

The Gram-positive pathogen Staphylococcus aureus is the only bacterium known to synthesize arginine from proline via the arginine-proline interconversion pathway, despite having genes for the well-conserved glutamate pathway. Since the proline-arginine interconversion pathway is repressed by CcpA-mediated carbon catabolite repression (CCR), CCR has been attributed to the arginine auxotrophy of S. aureus. Using ribose as a secondary carbon source, here, we demonstrate that S. aureus arginine auxotrophy is not due to CCR but due to the inadequate concentration of proline degradation product. Proline is degraded by proline dehydrogenase (PutA) into pyrroline-5-carboxylate (P5C). Although the PutA expression was fully induced by ribose, the P5C concentration remained insufficient to support arginine synthesis because P5C was constantly consumed by the P5C reductase ProC. When the P5C concentration was artificially increased by either PutA overexpression or proC-deletion, S. aureus could synthesize arginine from proline regardless of carbon source. In contrast, when the P5C concentration was reduced by overexpression of proC, it inhibited the growth of the ccpA-deletion mutant without arginine. Intriguingly, the ectopic expression of the glutamate pathway enzymes converted S. aureus into arginine prototroph. In an animal experiment, the arginine-proline interconversion pathway was not required for the survival of S. aureus. Based on these results, we concluded that S. aureus does not synthesize arginine from proline under physiological conditions. We also propose that arginine auxotrophy of S. aureus is not due to the CcpA-mediated CCR but due to the inactivity of the conserved glutamate pathway.

Strategies Shaping the Transcription of Carbohydrate-Active Enzyme Genes in Aspergillus nidulans

Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose, or arabinogalactan, as well as under carbon-starved conditions. We determined both carbon-stress-specific changes (weak or no carbon source vs. glucose) and carbon-source-specific changes (one type of culture vs. all other cultures). Many CAZyme genes showed carbon-stress-specific and/or carbon-source-specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan-degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan, and xylan-degrading enzyme genes was observed. Fewer upregulated genes, 81 and 107 carbon stress specific, and 6 and 16 carbon source specific, were found on lactose and in carbon-starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed carbon-source-specific upregulation on glucose, and they were enriched in β-1,4-glucanase genes. The behavioral ecological background of these characteristics was evaluated to comprehensively organize our knowledge on CAZyme production, which can lead to developing new strategies to produce enzymes for plant cell wall saccharification.

A review of exotic earthworm observations in the Canadian boreal forest and taiga zones

In the last decades, concerns have emerged that boreal forests could convert from a carbon sink to a carbon source, thus accentuating climate change. Although forest fire is generally mentioned as the main factor that could cause the boreal forest to transition to a carbon source, other factors, such as exotic earthworm activity, could also play an important role. Invasive exotic earthworms can also affect nutrient cycling, biodiversity and forest dynamics. In this context, a better knowledge of the distribution of exotic earthworms can help understand the likely changes in the ecosystems that they have colonized. Here we report the results of an exhaustive literature review of the presence of exotic earthworms in the Canadian boreal forest and taiga zones. We identified 230 sectors containing 14 earthworm species (11 exotic, 2 native and 1 putative native) in 6 provinces and 3 territories across Canada’s boreal forest and taiga zone. We also report 23 as-yet unpublished observations from the province of Quebec. We note the presence of earthworms in environments (acid soils, harsh climate) that were historically considered inadequate for their survival. This suggests that the portion of Canada’s boreal forests suitable for their presence or colonization is larger than what was previously believed. This study represents the first compilation of exotic earthworm presence in this large northern area. Factors that could affect their distribution and potential effects on boreal ecosystems are also discussed. Globally, several earthworm species seem to be overcoming the previously assumed limitation by temperature and pH.

Volatile Organic Compound Composition and Glandular Trichome Characteristics of In Vitro Propagated Clinopodium pulegium (Rochel) Bräuchler: Effect of Carbon Source

Clinopodium pulegium (Rochel) Bräuchler (Lamiaceae) is an endangered species endemic to the Southern Carpathians. It is characterized by the production of high amounts of essential oils, which emit volatile organic compounds (VOCs) that have an essential role in biotic and abiotic stress responses and in plant–plant and plant–insect interactions. The present study was initiated to phytochemically examine the influence of different carbon sources in the nutrition medium on VOC emissions of micropropagated C. pulegium plants, using gas chromatography–mass spectrometry analysis of headspace VOCs. The volatile profiles were subjected to multivariate analysis with respect to the presence, concentration and type of carbon source in the nutrient medium. In addition, the effect of different carbohydrates on the density and size of the leaf glandular trichomes, the main structures involved in the emission of VOCs, was determined. A total of 19 VOCs, primarily belonging to mono- and sesquiterpenes previously described in plants, were tentatively identified. Six VOCs were produced at levels higher than 2% of the total VOC emission, dominated by pulegone, ß-pinene and menthone. Inclusion of the carbohydrates in the culture media affected the production of the main leaf trichome-associated volatile allelochemicals although the qualitative composition of the volatiles changed only slightly. Multivariate analysis showed that the concentration, rather than the carbohydrate type, influenced the VOC profile.

Crypthecodinium cohnii Growth and Omega Fatty Acid Production in Mediums Supplemented with Extract from Recycled Biomass

Crypthecodinium cohnii is a marine heterotrophic dinoflagellate that can accumulate high amounts of omega-3 polyunsaturated fatty acids (PUFAs), and thus has the potential to replace conventional PUFAs production with eco-friendlier technology. So far, C. cohnii cultivation has been mainly carried out with the use of yeast extract (YE) as a nitrogen source. In the present study, alternative carbon and nitrogen sources were studied: the extraction ethanol (EE), remaining after lipid extraction, as a carbon source, and dinoflagellate extract (DE) from recycled algae biomass C. cohnii as a source of carbon, nitrogen, and vitamins. In mediums with glucose and DE, the highest specific biomass growth rate reached a maximum of 1.012 h−1, while the biomass yield from substrate reached 0.601 g·g−1. EE as the carbon source, in comparison to pure ethanol, showed good results in terms of stimulating the biomass growth rate (an 18.5% increase in specific biomass growth rate was observed). DE supplement to the EE-based mediums promoted both the biomass growth (the specific growth rate reached 0.701 h−1) and yield from the substrate (0.234 g·g−1). The FTIR spectroscopy data showed that mediums supplemented with EE or DE promoted the accumulation of PUFAs/docosahexaenoic acid (DHA), when compared to mediums containing glucose and commercial YE.

Isolation and Characterization of a Biosurfactant Producing Strain Planococcus sp. XW-1 from the Cold Marine Environment

One cold-adapted strain, named Planococcus sp. XW-1, was isolated from the Yellow Sea. The strain can produce biosurfactant with petroleum as sole source of carbon at low temperature (4 °C). The biosurfactant was identified as glycolipid-type biosurfactant species by thin-layer chromatography (TLC) and Fourier transform infrared spectroscopy (FTIR). It reduced the surface tension of water to 26.8 mN/m with a critical micelle concentration measurement of 60 mg/L. The produced biosurfactant possesses high surface activity at wide ranges of temperature (−18–105 °C), pH values (2–12), and salt concentrations (1–18%). The biosurfactant exhibited higher surface activity and higher growth rate of cells with hexadecane and diesel as carbon source. The strain Planococcus sp. XW-1 was also effective in degrading crude oil, after 21 days of growth at 4 °C in medium with 1% crude oil and 1% (v/v) bacteria broth, 54% of crude oil was degraded. The results suggest that Planococcus sp. XW-1 is a promising candidate for use in the bioremediation of petroleum-contaminated seawater in the Yellow Sea during winter. This study reported for the first time that Planococcus isolated from the Yellow Sea can produce biosurfactant using petroleum as the sole carbon source at low temperature (4 °C), showing its ecological role in the remediation of marine petroleum pollution.