Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13 C-fingerprinting, 13C metabolic flux analysis ( 13 C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO 2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO 2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13 C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.

BackgroundEngineering strategies to create promoters that are both higher strength and tunable in the presence of inexpensive compounds are of high importance to develop metabolic engineering technologies that can be commercialized. Lignocellulosic biomass stands out as the most abundant renewable feedstock for the production of biofuels and chemicals. However, lignin a major polymeric component of the biomass is made up of aromatic units and remains as an untapped resource. Novel synthetic biology tools for the expression of heterologous proteins are critical for the effective engineering of a microbe to valorize lignin. This study demonstrates the first successful attempt in the creation of engineered promoters that can be induced by aromatics present in lignocellulosic hydrolysates to increase heterologous protein production.ResultsA hybrid promoter engineering approach was utilized for the construction of phenolic-inducible promoters of higher strength. The hybrid promoters were constructed by replacing the spacer region of an endogenous promoter, PemrR present in E. coli that was naturally inducible by phenolics. In the presence of vanillin, the engineered promoters Pvtac, Pvtrc, and Pvtic increased protein expression by 4.6-, 3.0-, and 1.5-fold, respectively, in comparison with a native promoter, PemrR. In the presence of vanillic acid, Pvtac, Pvtrc, and Pvtic improved protein expression by 9.5-, 6.8-, and 2.1-fold, respectively, in comparison with PemrR. Among the cells induced with vanillin, the emergence of a sub-population constituting the healthy and dividing cells using flow cytometry was observed. The analysis also revealed this smaller sub-population to be the primary contributor for the increased expression that was observed with the engineered promoters.ConclusionsThis study demonstrates the first successful attempt in the creation of engineered promoters that can be induced by aromatics to increase heterologous protein production. Employing promoters inducible by phenolics will provide the following advantages: (1) develop substrate inducible systems; (2) lower operating costs by replacing expensive IPTG currently used for induction; (3) develop dynamic regulatory systems; and (4) provide flexibility in operating conditions. The flow cytometry findings strongly suggest the need for novel approaches to maintain a healthy cell population in the presence of phenolics to achieve increased heterologous protein expression and, thereby, valorize lignin efficiently.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1179-8) contains supplementary material, which is available to authorized users.

Predation is a common cause of early life stage mortality in fishes, with reduced risk as individuals grow and become too large to be consumed by gape-limited predatory fishes. Large-bodied species, such as sturgeon, may reach this size-refuge within the first year. However, there is limited understanding of what this size threshold is despite the value of this information for conservation management. We conducted laboratory-based predation experiments on juvenile green sturgeon, Acipenser medirostris, to estimate vulnerability to predation during outmigration from their natal reaches in California to the Pacific Ocean. Two highly abundant and non-native predatory fish species (largemouth bass, Micropterus salmoides, and striped bass, Morone saxatilis) were captured in the wild to be tested with developing juvenile green sturgeon from the UC Davis Green Sturgeon Broodstock Program. Experimental tanks, each containing five predators, received thirty prey for 24-hr exposures. Between sturgeon prey trials, predators were exposed to alternative prey species to confirm predators were exhibiting normal feeding behaviors. In addition to green sturgeon mortality data, trials were video recorded and predatory behaviors were quantified.Overall, these predator species displayed much lower rates of predation on juvenile green sturgeon than alternate prey. Predation decreased with green sturgeon size, and predation risk diminished to zero once sturgeon reached a length threshold of roughly 20-22 cm total length, or between 38% and 58% of predator total length. Behavioral analyses showed low motivation to feed on green sturgeon, with both predators attempting predation less frequently as sturgeon grew. Results of this study imply that optimizing growth rates for larval and juvenile sturgeon would shorten the time in which they are vulnerable to predation. Future experiments should assess predation risk of juvenile green sturgeon by additional predator species common to the Sacramento-San Joaquin watershed. K E Y W O R D S green sturgeon, largemouth bass, predation, striped bass 1 | INTRODUC TI ON Sturgeon populations across the globe have been experiencing drastic population declines. Consequently, sturgeon are the most threatened group of animals on the IUCN Red List of Threatened Species, with 63% of the species listed as Critically Endangered and 85% at risk of extinction (IUCN 2019). Sturgeon are large-bodied and long-lived, with unique reproductive strategies such as late maturation and infrequent | 15 BAIRD et Al. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Baird SE, Steel AE, Cocherell DE, Poletto JB, Follenfant R, Fangue NA. Experimental assessment of predation risk for juvenile green sturgeon, Acipenser medirostris, by two predatory fishes. J Appl Ichthyol.