Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture

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

A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3rd transferred cultures and stable states from the 5th to 10th transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.

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

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.