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1. The Role of Biochar in Regulating the Carbon, Phosphorus, and Nitrogen Cycles Exemplified by Soil Systems

   https://doi.org/10.3390/su13105612  

   Pan, Shu-Yuan; Dong, Cheng-Di; Su, Jenn-Fang; Wang, Po-Yen; Chen, Chiu-Wen; Chang, Jo-Shu; Kim, Hyunook; Huang, Chin-Pao; Hung, Chang-Mao (May 2021, Sustainability)

   null (Ed.)

   Biochar is a carbon-rich material prepared from the pyrolysis of biomass under various conditions. Recently, biochar drew great attention due to its promising potential in climate change mitigation, soil amendment, and environmental control. Obviously, biochar can be a beneficial soil amendment in several ways including preventing nutrients loss due to leaching, increasing N and P mineralization, and enabling the microbial mediation of N2O and CO2 emissions. However, there are also conflicting reports on biochar effects, such as water logging and weathering induced change of surface properties that ultimately affects microbial growth and soil fertility. Despite the voluminous reports on soil and biochar properties, few studies have systematically addressed the effects of biochar on the sequestration of carbon, nitrogen, and phosphorus in soils. Information on microbially-mediated transformation of carbon (C), nitrogen (N), and phosphorus (P) species in the soil environment remains relatively uncertain. A systematic documentation of how biochar influences the fate and transport of carbon, phosphorus, and nitrogen in soil is crucial to promoting biochar applications toward environmental sustainability. This report first provides an overview on the adsorption of carbon, phosphorus, and nitrogen species on biochar, particularly in soil systems. Then, the biochar-mediated transformation of organic species, and the transport of carbon, nitrogen, and phosphorus in soil systems are discussed. This review also reports on the weathering process of biochar and implications in the soil environment. Lastly, the current knowledge gaps and priority research directions for the biochar-amended systems in the future are assessed. This review focuses on literatures published in the past decade (2009–2021) on the adsorption, degradation, transport, weathering, and transformation of C, N, and P species in soil systems with respect to biochar applications. 

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2. Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants

   https://doi.org/10.1128/AEM.00487-21  

   Moxley, W. Chris; Eiteman, Mark A. (June 2021, Applied and Environmental Microbiology)

   Atomi, Haruyuki (Ed.)

   ABSTRACT Altering metabolic flux at a key branch point in metabolism has commonly been accomplished through gene knockouts or by modulating gene expression. An alternative approach to direct metabolic flux preferentially toward a product is decreasing the activity of a key enzyme through protein engineering. In Escherichia coli , pyruvate can accumulate from glucose when carbon flux through the pyruvate dehydrogenase complex is suppressed. Based on this principle, 16 chromosomally expressed AceE variants were constructed in E. coli C and compared for growth rate and pyruvate accumulation using glucose as the sole carbon source. To prevent conversion of pyruvate to other products, the strains also contained deletions in two nonessential pathways: lactate dehydrogenase ( ldhA ) and pyruvate oxidase ( poxB ). The effect of deleting phosphoenolpyruvate synthase ( ppsA ) on pyruvate assimilation was also examined. The best pyruvate-accumulating strains were examined in controlled batch and continuous processes. In a nitrogen-limited chemostat process at steady-state growth rates of 0.15 to 0.28 h −1 , an engineered strain expressing the AceE[H106V] variant accumulated pyruvate at a yield of 0.59 to 0.66 g pyruvate/g glucose with a specific productivity of 0.78 to 0.92 g pyruvate/g cells·h. These results provide proof of concept that pyruvate dehydrogenase complex variants can effectively shift carbon flux away from central carbon metabolism to allow pyruvate accumulation. This approach can potentially be applied to other key enzymes in metabolism to direct carbon toward a biochemical product. IMPORTANCE Microbial production of biochemicals from renewable resources has become an efficient and cost-effective alternative to traditional chemical synthesis methods. Metabolic engineering tools are important for optimizing a process to perform at an economically feasible level. This study describes an additional tool to modify central metabolism and direct metabolic flux to a product. We have shown that variants of the pyruvate dehydrogenase complex can direct metabolic flux away from cell growth to increase pyruvate production in Escherichia coli . This approach could be paired with existing strategies to optimize metabolism and create industrially relevant and economically feasible processes. 

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3. Treatment of Dairy Farm Runoff in Vegetated Bioretention Systems Amended with Biochar

   https://doi.org/10.3390/w16101347  

   Rahman, Md_Yeasir A; Richardson, Nicholas; Nachabe, Mahmood H; Ergas, Sarina J (May 2024, Water)

   Nitrogen and fecal indicator bacteria (FIB) in runoff from concentrated animal feeding operations (CAFOs) can impair surface and groundwater quality. Bioretention systems are low impact nature-based technologies that can effectively treat CAFO runoff if modified with an internal water storage zone (IWSZ) or amended with biochar. In this study, the performances of four pilot-scale modified bioretention systems were compared to assess the impacts of (1) amending bioretention media with biochar and (2) planting the systems with Muhlenbergia. The system with both plants and biochar amendment had the best performance, with an average of 5.58 log reduction in E. coli and 98% removal of total nitrogen (TN). All systems treated the first pore volume well as new runoff flushed the treated water from the IWSZ. Biochar improved TN and FIB removal due to its high capacity to adsorb or retain ammonium (NH4+), dissolved organic nitrogen, dissolved organic carbon, and E. coli. Planting improved performance, possibly by increasing rhizosphere microbial activity. 

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4. Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth

   https://doi.org/10.1128/mbio.03259-21  

   Wilkes, Rebecca A.; Waldbauer, Jacob; Aristilde, Ludmilla (December 2021, mBio)

   Dunn, Anne K.; Ruby, Edward G. (Ed.)

   ABSTRACT Gluconeogenic carbon metabolism is not well understood, especially within the context of flux partitioning between energy generation and biomass production, despite the importance of gluconeogenic carbon substrates in natural and engineered carbon processing. Here, using multiple omics approaches, we elucidate the metabolic mechanisms that facilitate gluconeogenic fast-growth phenotypes in Pseudomonas putida and Comamonas testosteroni , two Proteobacteria species with distinct metabolic networks. In contrast to the genetic constraint of C. testosteroni , which lacks the enzymes required for both sugar uptake and a complete oxidative pentose phosphate (PP) pathway, sugar metabolism in P. putida is known to generate surplus NADPH by relying on the oxidative PP pathway within its characteristic cyclic connection between the Entner-Doudoroff (ED) and Embden-Meyerhoff-Parnas (EMP) pathways. Remarkably, similar to the genome-based metabolic decoupling in C. testosteroni , our 13 C-fluxomics reveals an inactive oxidative PP pathway and disconnected EMP and ED pathways in P. putida during gluconeogenic feeding, thus requiring transhydrogenase reactions to supply NADPH for anabolism in both species by leveraging the high tricarboxylic acid cycle flux during gluconeogenic growth. Furthermore, metabolomics and proteomics analyses of both species during gluconeogenic feeding, relative to glycolytic feeding, demonstrate a 5-fold depletion in phosphorylated metabolites and the absence of or up to a 17-fold decrease in proteins of the PP and ED pathways. Such metabolic remodeling, which is reportedly lacking in Escherichia coli exhibiting a gluconeogenic slow-growth phenotype, may serve to minimize futile carbon cycling while favoring the gluconeogenic metabolic regime in relevant proteobacterial species. IMPORTANCE Glycolytic metabolism of sugars is extensively studied in the Proteobacteria , but gluconeogenic carbon sources (e.g., organic acids, amino acids, aromatics) that feed into the tricarboxylic acid (TCA) cycle are widely reported to produce a fast-growth phenotype, particularly in species with biotechnological relevance. Much remains unknown about the importance of glycolysis-associated pathways in the metabolism of gluconeogenic carbon substrates. Here, we demonstrate that two distinct proteobacterial species, through genetic constraints or metabolic regulation at specific metabolic nodes, bypass the oxidative PP pathway during gluconeogenic growth and avoid unnecessary carbon fluxes by depleting protein investment into connected glycolysis pathways. Both species can leverage instead the high TCA cycle flux during gluconeogenic feeding to meet NADPH demand. Importantly, lack of a complete oxidative pentose phosphate pathway is a widespread metabolic trait in Proteobacteria with a gluconeogenic carbon preference, thus highlighting the important relevance of our findings toward elucidating the metabolic architecture in these bacteria. 

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5. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions

   https://doi.org/10.1093/jxb/erab435  

   Chowdhury, Niaz Bahar; Schroeder, Wheaton L; Sarkar, Debolina; Amiour, Nardjis; Quilleré, Isabelle; Hirel, Bertrand; Maranas, Costas D; Saha, Rajib (September 2021, Journal of Experimental Botany)

   Gibon, Yves (Ed.)

   Abstract The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N−) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes. 

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