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1. Metabolomic Responses of Green Alga Chlamydomonas reinhardtii Exposed to Sublethal Concentrations of Inorganic and Methylmercury.

   https://doi.org/10.1021/ acs.est.0c08416  

   Slaveykova, Vera I. ; Majumdar, Sanghamitra ; Regier, Nicole ; Li, Weiwei ; Keller, Arturo A. ( February 2021 , Environmental science and technology)

   Metabolomics characterizes low-molecular-weight molecules involved in different biochemical reactions and provides an integrated assessment of the physiological state of an organism. By using liquid chromatography–mass spectrometry targeted metabolomics, we examined the response of green alga Chlamydomonas reinhardtii to sublethal concentrations of inorganic mercury (IHg) and monomethylmercury (MeHg). We quantified the changes in the levels of 93 metabolites preselected based on the disturbed metabolic pathways obtained in a previous transcriptomics study. Metabolites are downstream products of the gene transcription; hence, metabolite quantification provided information about the biochemical status of the algal cells exposed to Hg compounds. The results showed that the alga adjusts its metabolism during 2 h exposure to 5 × 10–9 and 5 × 10–8 mol L–1 IHg and MeHg by increasing the level of various metabolites involved in amino acid and nucleotide metabolism, photorespiration, and tricarboxylic acid (TCA) cycle, as well as the metabolism of fatty acids, carbohydrates, and antioxidants. Most of the metabolic perturbations in the alga were common for IHg and MeHg treatments. However, the exposure to IHg resulted in more pronounced perturbations in the fatty acid and TCA metabolism as compared with the exposure to MeHg. The observed metabolic perturbations were generally consistent with ourmore »previously published transcriptomics results for C. reinhardtii exposed to the comparable level of IHg and MeHg. The results highlight the potential of metabolomics for toxicity evaluation, especially to detect effects at an early stage of exposure prior to their physiological appearance.« less
2. Metabolite shift in Medicago truncatula occurs in phosphorus deprivation

   https://doi.org/10.1093/jxb/erab559  

   Dokwal, Dhiraj ; Cocuron, Jean-Christophe ; Alonso, Ana Paula ; Dickstein, Rebecca ; Nakamura, ed., Yuki ( December 2021 , Journal of Experimental Botany)

   Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in –P leaves, with a moderate reduction in –P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.
3. 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 itsmore »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.« less
4. Emerging investigator series: linking chemical transformations of silver and silver nanoparticles in the extracellular and intracellular environments to their bio-reactivity

   https://doi.org/10.1039/c9en00710e  

   Minghetti, Matteo ; Dudefoi, William ; Ma, Qing ; Catalano, Jeffrey G. ( October 2019 , Environmental Science: Nano)

   The fish intestine is an important barrier for environmental toxicants, including metals and metal nanoparticles. Tracking chemical transformation at the interface between the intestinal epithelium and the intestinal lumen can inform us about chemicals' bio-reactivity and toxicity but is challenging due to the lack of appropriate models. To allow for such investigations, a model of the fish intestine derived from rainbow trout ( Oncorhynchus mykiss ), the RTgutGC cell line, was used. Cells were exposed to silver nitrate (AgNO 3 ) or citrate coated silver nanoparticles (cit-AgNPs) in Leibovitz's L-15 medium without amino acids and vitamins (L-15/ex), which allowed the determination of the extracellular silver species using a chemical equilibrium model. X-ray absorption spectroscopy (XAS) was used to track intracellular silver speciation. Cellular toxicity, silver accumulation, and metallothionein (MT) mRNA levels were also measured. Cells accumulated the same concentrations of silver when exposed to equimolar amounts ( i.e. 1, 5 and 10 μM) of AgNO 3 or cit-AgNPs. However, AgNO 3 was shown to be more toxic than cit-AgNPs. Intracellular silver speciation changed over time in both exposure series. After 1 hour, intracellular silver speciation was dominated by chloride complexation in both exposures. After 24 and 72 hours of exposuremore »to cit-AgNPs, ∼7% of silver was complexed to cysteine, whereas the remaining silver was AgNPs. In cells exposed to AgNO 3 for 72 hours, 97% of Ag was complexed to cysteine. A significant increase, compared to controls, in metallothionein mRNA levels at 24 and 72 hours of exposure to AgNO 3 and cit-AgNPs can explain the formation of Ag–cysteine complexes. In summary, these data show that silver chloride species are bioavailable and that complexation to cysteine scavenges intracellular dissolved silver ions, thus preventing toxicity. Silver nanoparticles present a similar but attenuated toxic response to AgNO 3 . Thus, at least in acute exposures, existing risk assessment for dissolved silver species could be protective for nanosilver.« less
5. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

   https://doi.org/10.1038/s41396-020-00828-3  

   Bayer, Barbara ; Saito, Mak A. ; McIlvin, Matthew R. ; Lücker, Sebastian ; Moran, Dawn M. ; Lankiewicz, Thomas S. ; Dupont, Christopher L. ; Santoro, Alyson E. ( November 2020 , The ISME Journal)

   The genusNitrospirais the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marinaNb-295^Twas isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential ofN. marinabased on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm thatN. marinabenefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolvedpCO₂, and requires exogenous vitamin B₁₂. In addition,N. marinais able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response ofN. marinato low (∼5.6 µM) O₂concentrations. The abundance of a potentially more efficient CO₂-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinitycbb₃-type terminal oxidase increased under O₂limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O₂-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O₂conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, themore »genome and proteome of the first marineNitrospiraisolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.

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