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1. Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soil Pseudomonas species

   https://doi.org/10.1073/pnas.2016380117  

   Mendonca, Caroll M.; Yoshitake, Sho; Wei, Hua; Werner, Anne; Sasnow, Samantha S.; Thannhauser, Theodore W.; Aristilde, Ludmilla (December 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   High-affinity iron (Fe) scavenging compounds, or siderophores, are widely employed by soil bacteria to survive scarcity in bioavailable Fe. Siderophore biosynthesis relies on cellular carbon metabolism, despite reported decrease in both carbon uptake and Fe-containing metabolic proteins in Fe-deficient cells. Given this paradox, the metabolic network required to sustain the Fe-scavenging strategy is poorly understood. Here, through multiple 13 C-metabolomics experiments with Fe-replete and Fe-limited cells, we uncover how soil Pseudomonas species reprogram their metabolic pathways to prioritize siderophore biosynthesis. Across the three species investigated ( Pseudomonas putida KT2440, Pseudomonas protegens Pf-5, and Pseudomonas putida S12), siderophore secretion is higher during growth on gluconeogenic substrates than during growth on glycolytic substrates. In response to Fe limitation, we capture decreased flux toward the tricarboxylic acid (TCA) cycle during the metabolism of glycolytic substrates but, due to carbon recycling to the TCA cycle via enhanced anaplerosis, the metabolism of gluconeogenic substrates results in an increase in both siderophore secretion (up to threefold) and Fe extraction (up to sixfold) from soil minerals. During simultaneous feeding on the different substrate types, Fe deficiency triggers a hierarchy in substrate utilization, which is facilitated by changes in protein abundances for substrate uptake and initial catabolism. Rerouted metabolism further promotes favorable fluxes in the TCA cycle and the gluconeogenesis–anaplerosis nodes, despite decrease in several proteins in these pathways, to meet carbon and energy demands for siderophore precursors in accordance with increased proteins for siderophore biosynthesis. Hierarchical carbon metabolism thus serves as a critical survival strategy during the metal nutrient deficiency. 

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2. Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron

   https://doi.org/10.1128/mSystems.00252-20  

   Catlett, Jennie L.; Catazaro, Jonathan; Cashman, Mikaela; Carr, Sean; Powers, Robert; Cohen, Myra B.; Buan, Nicole R. (October 2020, mSystems)

   Lal, Rup (Ed.)

   ABSTRACT Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron ( B. theta ) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic bioenergetics but instead redirects carbon and energy to CO 2 and H 2 . Flux balance analysis modeling showed increased flux through CO 2 -producing reactions under glucose-limiting growth conditions. The metabolic dynamics observed for B. theta , a keystone symbiont organism, underscores the need for metabolic modeling to complement genomic predictions of microbial metabolism to infer mechanisms of microbe-microbe and microbe-host interactions. IMPORTANCE Bacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron ( B. theta ) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s) and metabolic interactions under changing nutrient conditions such as those that occur in complex gut communities. Our study shows B. theta prioritizes energy conservation and suppresses secretion of “overflow metabolites” such as organic acids and amino acids when concentrations of acetate are high. Secreted metabolites, especially amino acids, can be a source of nutrients or signals for the host or other microbes in the community. Our study suggests that when metabolically stressed by acetate, B. theta stops sharing with its ecological partners. 

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3. Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β‐glucosidase function in Cellvibrio japonicus

   https://doi.org/10.1002/bit.27544  

   Hwang, Jeanice; Hari, Archana; Cheng, Raymond; Gardner, Jeffrey_G; Lobo, Daniel (September 2020, Biotechnology and Bioengineering)

   Abstract Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene‐deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacteriumCellvibrio japonicusgrown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics ofC. japonicususing either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild‐type strain as well as in β‐glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non‐diauxic growth and metabolite consumptions of the wild‐type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially‐useful strains. Importantly, the model is able to explain the role of the different β‐glucosidases and their behavior under genetic perturbations. This integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates. 

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4. Long‐term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest

   https://doi.org/10.1111/gcb.16718  

   Wang, Xiaohong; Li, Shiyining; Zhu, Biao; Homyak, Peter M.; Chen, Guangshui; Yao, Xiaodong; Wu, Dongmei; Yang, Zhijie; Lyu, Maokui; Yang, Yusheng (April 2023, Global Change Biology)

   Abstract It is widely accepted that phosphorus (P) limits microbial metabolic processes and thus soil organic carbon (SOC) decomposition in tropical forests. Global change factors like elevated atmospheric nitrogen (N) deposition can enhance P limitation, raising concerns about the fate of SOC. However, how elevated N deposition affects the soil priming effect (PE) (i.e., fresh C inputs induced changes in SOC decomposition) in tropical forests remains unclear. We incubated soils exposed to 9 years of experimental N deposition in a subtropical evergreen broadleaved forest with two types of¹³C‐labeled substrates of contrasting bioavailability (glucose and cellulose) with and without P amendments. We found that N deposition decreased soil total P and microbial biomass P, suggesting enhanced P limitation. In P unamended soils, N deposition significantly inhibited the PE. In contrast, adding P significantly increased the PE under N deposition and by a larger extent for the PE of cellulose (PE_cellu) than the PE of glucose (PE_glu). Relative to adding glucose or cellulose solely, adding P with glucose alleviated the suppression of soil microbial biomass and C‐acquiring enzymes induced by N deposition, whereas adding P with cellulose attenuated the stimulation of acid phosphatase (AP) induced by N deposition. Across treatments, the PE_gluincreased as C‐acquiring enzyme activity increased, whereas the PE_celluincreased as AP activity decreased. This suggests that P limitation, enhanced by N deposition, inhibits the soil PE through varying mechanisms depending on substrate bioavailability; that is, P limitation regulates the PE_gluby affecting soil microbial growth and investment in C acquisition, whereas regulates the PE_celluby affecting microbial investment in P acquisition. These findings provide new insights for tropical forests impacted by N loading, suggesting that expected changes in C quality and P limitation can affect the long‐term regulation of the soil PE. 

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5. Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria

   https://doi.org/10.1128/mBio.02293-19  

   Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.; Frey, Serita D.; Sistla, Seeta A.; DeAngelis, Kristen M. (February 2020, mBio)

   Giovannoni, Stephen J. (Ed.)

   ABSTRACT The strategy that microbial decomposers take with respect to using substrate for growth versus maintenance is one essential biological determinant of the propensity of carbon to remain in soil. To quantify the environmental sensitivity of this key physiological trade-off, we characterized the carbon use efficiency (CUE) of 23 soil bacterial isolates across seven phyla at three temperatures and with up to four substrates. Temperature altered CUE in both an isolate-specific manner and a substrate-specific manner. We searched for genes correlated with the temperature sensitivity of CUE on glucose and deemed those functional genes which were similarly correlated with CUE on other substrates to be validated as markers of CUE. Ultimately, we did not identify any such robust functional gene markers of CUE or its temperature sensitivity. However, we found a positive correlation between rRNA operon copy number and CUE, opposite what was expected. We also found that inefficient taxa increased their CUE with temperature, while those with high CUE showed a decrease in CUE with temperature. Together, our results indicate that CUE is a flexible parameter within bacterial taxa and that the temperature sensitivity of CUE is better explained by observed physiology than by genomic composition across diverse taxa. We conclude that the bacterial CUE response to temperature and substrate is more variable than previously thought. IMPORTANCE Soil microbes respond to environmental change by altering how they allocate carbon to growth versus respiration—or carbon use efficiency (CUE). Ecosystem and Earth System models, used to project how global soil C stocks will continue to respond to the climate crisis, often assume that microbes respond homogeneously to changes in the environment. In this study, we quantified how CUE varies with changes in temperature and substrate quality in soil bacteria and evaluated why CUE characteristics may differ between bacterial isolates and in response to altered growth conditions. We found that bacterial taxa capable of rapid growth were more efficient than those limited to slow growth and that taxa with high CUE were more likely to become less efficient at higher temperatures than those that were less efficient to begin with. Together, our results support the idea that the CUE temperature response is constrained by both growth rate and CUE and that this partly explains how bacteria acclimate to a warming world. 

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