Imbalance in Carbon and Nitrogen Metabolism in <i>Comamonas testosteroni</i> R2 Is Caused by Negative Feedback and Rescued by L-arginine

Abstract

The collapse of Comamonas testosteroni R2 under chemostat conditions and the aerobic growth of strain R2 under batch conditions with phenol as the sole carbon source were investigated using physiological and transcriptomic techniques. Phenol-/catechol-degrading activities under chemostat conditions gradually decreased, suggesting that metabolites produced from strain R2 accumulated in the culture, which caused negative feedback. The competitive inhibition of phenol hydroxylase and catechol dioxygenase was observed in a crude extract of the supernatant collected from the collapsed culture. Transcriptomic analyses showed that genes related to nitrogen transport were up-regulated; the ammonium transporter amtB was up-regulated approximately 190-fold in the collapsed status, suggesting an increase in the concentration of ammonium in cells. The transcriptional levels of most of the genes related to gluconeogenesis, glycolysis, the pentose phosphate pathway, and the TCA and urea cycles decreased by ~0.7-fold in the stable status, whereas the activities of glutamate synthase and glutamine synthetase increased by ~2-fold. These results suggest that ammonium was assimilated into glutamate and glutamine via 2-oxoglutarate under the limited supply of carbon skeletons, whereas the synthesis of other amino acids and nucleotides was repressed by 0.6-fold. Furthermore, negative feedback appeared to cause an imbalance between carbon and nitrogen metabolism, resulting in collapse. The effects of amino acids on negative feedback were investigated. L-arginine allowed strain R2 to grow normally, even under growth-inhibiting conditions, suggesting that the imbalance was corrected by the stimulation of the urea cycle, resulting in the rescue of strain R2.

Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity

“…Metabolic networks play roles in the functional stability of a whole system by supporting common goods ( Morris et al , 2013 ; Niehaus et al , 2019 ; Smith and Schuster, 2019 ) and removing toxic metabolic byproducts that inhibit the growth of other bacteria ( Luli and Strohl, 1990 ; Lilja and Johnson, 2016 ; Aziz et al , 2021 ; Mohd Din et al , 2021 ). Pure and synthetic microbial cultures collapse with feedback inhibition caused by the accumulation of metabolites ( Aziz et al , 2015 ; Mohd Din et al , 2021 ), suggesting that a fixed metabolic network is incapable of maintaining a stable state, even in complex systems. Among the 13 core OTUs, the abundance of OTUs_9947, 2765, and 2727 was mostly maintained and they kept their dominant states ( Fig.…”