The regulation of respiration rate in growing bacteria

Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria

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.

Microoxic-Anoxic Niche of Beggiatoa spp.: Microelectrode Survey of Marine and Freshwater Strains

Beggiatoa spp. grow optimally in media containing opposed gradients of oxygen and soluble sulfide, although some strains also require an organic substrate. By using microelectrodes, we characterized oxygen and sulfide gradients during their initial development in uninoculated media and in cultures of marine and freshwater strains. In gradient media, Beggiatoa strains always grew some distance below the air/agar interface as a dense "plate" of constantly gliding filaments with sharply demarcated upper and lower boundaries. Within established plates, the maximum oxygen partial pressure was 0.6 to 6.0% of air saturation and not significantly lower if filaments were fixing nitrogen. Oxygen penetrated only 100 to 300 mum into the plate, and the anoxic fraction increased from less than 10% to approximately 90% during later stages of growth. For lithoautotrophically grown marine strains, the linearity of the oxygen profile above the plate plus its drop to zero therein indicated that oxygen uptake for the entire tube occurred only within the Beggiatoa plate. Consequently, oxygen consumption could be predicted solely from the distance between the air/agar interface and the top of a plate, given the diffusion coefficient for oxygen. By contrast, for freshwater strains grown heterotrophically (with sulfide also in the medium), oxygen profiles were frequently nonlinear because of nonbiological reaction with sulfide which had diffused past the aggregated filaments. For all strains tested, microoxic aggregation also occurred in the absence of sulfide, apparently reflecting a step-up phobic response to oxygen.

Regulation of Dissimilatory Fe(III) Reduction Activity in Shewanella putrefaciens

Under anaerobic conditions, Shewanella putrefaciens is capable of respiratory-chain-linked, high-rate dissimilatory iron reduction via both a constitutive and inducible Fe(III)-reducing system. In the presence of low levels of dissolved oxygen, however, iron reduction by this microorganism is extremely slow. Fe(II)-trapping experiments in which Fe(III) and O(2) were presented simultaneously to batch cultures of S. putrefaciens indicated that autoxidation of Fe(II) was not responsible for the absence of Fe(III) reduction. Inhibition of cytochrome oxidase with CN resulted in a high rate of Fe(III) reduction in the presence of dissolved O(2), which suggested that respiratory control mechanisms did not involve inhibition of Fe(III) reductase activities or Fe(III) transport by molecular oxygen. Decreasing the intracellular ATP concentrations by using an uncoupler, 2,4-dinitrophenol, did not increase Fe(III) reduction, indicating that the reduction rate was not controlled by the energy status of the cell. Control of electron transport at branch points could account for the observed pattern of respiration in the presence of the competing electron acceptors Fe(III) and O(2).

Effect of total and partial pressure (oxygen and carbon dioxide) on aerobic microbial processes

In industrial bioreactors, levels and gradients of total and partial pressures are considerably higher than on the laboratory scale. In the relevant range (in general up to 2 or 3 bar, maximum approx. 10 bar), effects of total pressure on aerobic cultures are negligibly small. CO2 partial pressures of more than approx. 100 mbar may have inhibitory effects on aerobic cultures. Growth of aerobic cultures can be enhanced by O2 partial pressures higher than 210 mbar (corresponding to air at 1 bar), if oxygen transfer is limited. In many cases, however, increased O2 partial pressure (higher than approx. 1 bar) is toxic to aerobic cultures and inhibits microbial growth and product formation. Stepwise and cyclic variations of O2 partial pressure may have positive or negative effects, depending on strain of microorganism, culturing conditions, and range of dissolved oxygen concentration. Knowledge of these effects is required in process development and bioreactor scale-up.

Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldehyde detoxification

Formaldehyde is a highly toxic chemical common in industrial effluents, and it is also an intermediate in bacterial metabolism of one-carbon growth substrates, although its role as a bacterial growth substrate per se has not been extensively reported. This study investigated two highly formaldehyde-resistant formaldehyde utilizers, strains BIP and ROS1; the former strain has been used for industrial remediation of formaldehyde-containing effluents. The two strains were shown by means of 16S rRNA characterization to be closely related members of the genus Methylobacterium. Both strains were able to use formaldehyde, methanol and a range of multicarbon compounds as their principal growth substrate. Growth on formaldehyde was possible up to a concentration of at least 58 mM, and survival at up to 100 mM was possible after stepwise acclimatization by growth at increasing concentrations of formaldehyde. At such high concentrations of formaldehyde, the cultures underwent a period of formaldehyde removal without growth before the formaldehyde concentration fell below 60 mM, and growth could resume. Two-dimensional electrophoresis and MS characterization of formaldehyde-induced proteins in strain BIP revealed that the pathways of formaldehyde metabolism, and adaptations to methylotrophic growth, were very similar to those seen in the well-characterized methanol-utilizing methylotroph Methylobacterium extorquens AM1. Thus, it appears that many of the changes in protein expression that allow strain BIP to grow using high formaldehyde concentrations are associated with expression of the same enzymes used by M. extorquens AM1 to process formaldehyde as a metabolic intermediate during growth on methanol.

Alternative Function of the Electron Transport System in Azotobacter vinelandii: Removal of Excess Reductant by the Cytochrome d Pathway

The N(inf2)-fixing bacterium Azotobacter vinelandii was grown in an O(inf2)-regulated chemostat with glucose or galactose as substrate. Increasing the O(inf2) partial pressure resulted in identical synthesis of the noncoupled cytochrome d terminal oxidase, which is consistent with the hypothesis that A. vinelandii uses high rates of respiration to protect the nitrogenase from oxygen. However, cell growth on glucose showed a lower yield of biomass, higher glycolytic rate, higher respiratory rate, and lower cytochrome o content than cell growth on galactose. Elemental analysis indicated no appreciable change in the C-to-N ratio of cell cultures, suggesting that the major composition of the cell was not influenced by the carbon source. A poor coordination of glucose and nitrogen metabolisms in A. vinelandii was suggested. The rapid hydrolysis of glucose resulted in carbonaceous accumulation in cells. Thus, Azotobacter species must induce a futile electron transport to protect cells from the high rates of glucose uptake and glycolysis.

Control of respiration rate in non-growing cells of Paracoccus denitrificans

By means of fluorimetric measurement and by direct determination of intracellular NAD+ and NADH contents, it was proved that the respiration rate of Paracoccus denitrificans cells utilizing glucose is limited by processes preceding NADH oxidation in the respiratory chain, so that the membrane NADH dehydrogenase is not saturated by its substrate. In the separated membrane fraction on saturation with exogenous NADH the main limiting factor is represented by NADH: ubiquinone oxidoreductase.

On the absence of correlation between cyanide-resistant respiration and cytochrome d content in bacteria

The regularity of appearance of cyanide-resistant respiration and cytochrome d in various bacteria as well as the relationship between the degree of resistance of respiration to cyanide and cytochrome d content was studied. Bacteria able to synthesize cyanide-resistant respiration were shown to appear during transition of culture to the stationary phase of growth caused by the exhaustion of carbon source. No regulatory of appearance of cytochrome d was observed. There is no correlation between the degree of resistance to cyanide and cytochrome d content. It was concluded that the cyanide-resistant respiration of bacteria and eukaryotic microorganisms may be associated with the functioning of a non-cytochrome nature oxidase.

L-serine degradation in Escherichia coli K-12: a combination of L-serine, glycine, and leucine used as a source of carbon

Escherichia coli K-12 strain CU1008 cannot use L-serine as the sole carbon source, but it could use L-serine as an auxiliary carbon source with glucose, L-alanine, or pyruvate and could derive energy from L-serine to support oxygen uptake. CU1008 grew with L-serine if it was also provided with glycine and leucine. These may act by increasing the available activity of L-serine deaminase; other explanations are also explored.

[Cytochrome pattern of methylotropic acetic acid bacterium MB 58 as dependent on growth conditions]

In contrast to methylotrophic bacteria investigated up to now the facultative methylotrophic Bacterium MB 58 (Acetobactersp. MB 58) does not possess a cytochrome aa3-complex, but we could find out cytochrome, cytochrome cco, cytochrome a1, and moreover cytochrome d in dependence on the growth conditions. Cytochrome d was found only in stationary phase of heterotrophic growth. Under methylotrophic growth conditions cytochrome d could be demonstrated only by lowering of the aeration rate during the fermentation, by variation the pH-value of the growth medium from 4.0 to 6.5 and with low growth rates (low dilution rates) during continuous fermentation. The addition of cyanide to the oxidized suspension of bacteria during the registration of the cytochrome-redox-difference spectrum allowed the selective representation of cytochrome d under all conditions even if no identification was possible in the spectrum normally. The oxidation of cytochrome d of Acetobacter sp. MB 58 in the presence of cyanide is an indication of its cyanide insensitivity. The low level of b-type cytochromes could be represented by a special technique for registration of spectra. In this connection a unknown absorption peak at 570 nm was registered. The cyanide insensitivity of cytochrome d from Acetobacter sp. MB 58 and the occurrence of several terminal oxidases is appreciated as a hint for a branched respiratory chain.

Regulation of exoprotease production by temperature and oxygen in Vibrio alginolyticus

The production of an extracellular collagenase and alkaline protease by Vibrio alginolyticus during stationary phase was inhibited by a temperature shift from 30 to 37 degrees C and by a lack of oxygen. The stability of the exoproteases was unaffected by incubation at 37 degrees C and aeration. The optimum growth temperature for the V. alginolyticus strain was 33.5 degrees C and there was no difference in the growth rate at 30 and 37 degrees C. Aeration enhanced the rate of growth of exponential phase cells. Temperature and oxygen did not affect the growth of stationary phase cells when the exoproteases were being produced. Macromolecular synthesis in stationary phase cells was not affected by temperature. There was no rapid release of the exoproteases after temperature shift down and chloramphenicol inhibited the production of the enzymes when added at time of temperature shift down from 37 to 30 degrees C. The regulation of exoprotease production by temperature and oxygen was specific and has implications regarding the ecology of V. alginolyticus. Cerulenin, quinacrine and O-phenanthroline inhibited the production of the exoproteases.

Nitrogen fixation gene (nifL) involved in oxygen regulation of nitrogenase synthesis in K. pneumoniae

The enzyme complex nitrogenase, which reduces N2 to NH+4, involves two redox proteins, both irreversibly damaged by O2 (ref. 1). Enzyme activity therefore requires anaerobic conditions, a source of reductant and a large amount of ATP (approximately 16 ATPs per N2). In both aerobic and facultative anaerobic N2-fixing bacteria, nitrogenase synthesis is regulated by O2 and NH+4, but in the aerobes there are also processes to protect the enzyme from O2 damage. The mechanisms of repression by O2 and NH+4 seem to be independent in the organisms so far examined. In the facultative anaerobe, Klebsiella pneumoniae, O2 was shown to repress nitrogenase synthesis in an NH+4-constitutive strain. The fusion of the Escherichia coli lacZ gene into each transcriptional unit of the nitrogen fixation (nif) gene cluster in K. pneumoniae has facilitated studies with O2, because expression from the various nif promoters results in an O2-stable product (beta-galactosidase). Notably, the nifHDK operon (the nitrogenase structural genes) was more sensitive to O2 repression than the nifLA operon (regulatory genes). The characterization of mutants, reported here, indicates the involvement of a nif-regulatory gene product in the mechanism of O2 control of nitrogenase synthesis.

Are growth rates of Escherichia coli in batch cultures limited by respiration?

Batch cultures of Escherichia coli were grown in minimal media supplemented with various carbon sources which supported growth at specific growth rates from 0.2 to 1.3/h. The respiration rates of the cultures were measured continuously. With few exceptions, the specific rate of oxygen consumption was about 20 mmol of O2/h per g (dry weight), suggesting that the respiratory capacity was limited at this value. The adenosine triphosphate (ATP) required for the production of cell material from the different carbon sources was calculated on the basis of known ATP requirements in the biochemical pathways and routes of macromolecular synthesis. The calculated ATP requirements, together with the measured growth rates and growth yields on the different carbon sources, were used to calculate the rate of ATP synthesis by oxidative phosphorylation. This rate was closely related to the respiration rate. We suggest that aerobic growth of E. coli in batch cultures is limited by the rate of respiration and the concomitant rate of ATP generation through oxidative phosphorylation.

Regulative influence of o-aminobenzoic acid on the biosynthesis of nourseothricin in cultures of Streptomyces noursei JA 3890b. IV. Bistability of metabolism and the mechanism of action of aminobenzoic acids

Using the semi-continuous cultivation technique we could establish that specifically in Streptomyces noursei JA 3890b during growth on a medium supplied with D,L-alanine, NH4+, and maize starch there are two different phenotypes of the organism and stationary states of metabolism, respectively. The expression of either the metabolic state I with an enhanced capacity to oxidative deamination of alanine via the NAD+-dependent alanaine dehydrogenase or the metabolic state 2 which may be characterized by the preferred use of ammonium ions via the NADP+-dependent glutamate dehydrogenase was shown to depend strongly on the conditions of inoculum cultivation. When the amino acid permeases were derepressed by cultivating the inoculum cells on amino acid media, probably due to the defective mechanism of negative feedback control of amino acid influx in this strain an abnormously high uptake of alanine was observed that, consequently, was correlated to the enhanced oxidation of this amino acid as well as to the intensive production of ammonia within the cell. This overproduction of cellular NH4+ seems to bring about the subsequent repression of biosynthetic glutamate dehydrogenase and so on the accumulation of ammonia autocatalytically may rise up (metabolic state I). On the other hand, if the influx of alanine was kept low and the NADH oxidation was less efficient, respectively, or when there was high cellular activity of glutamate dehydrogenase the level of ammonia never did exceed the respressory limit and, accordingly, the expression of the metabolic state 2 was observed. Switching-over of metabolic flux from the state 2 towards the state 1 can be brought about either by increasing the level of nitrogen sources in the medium or by adding buffers pH greater than 7.5. In contrast, decrease of cellular level of NH4+ was shown to induce the transition of metabolic state 1 into the state 2. This can be achieved not only by limitation of nitrogen source but also by adding different aminobenzoic acids and, alternatively, effectors of membrane function (short-chain alcohols), inhibitors of cytochrome oxidases (sodium azide, potassium cyanide), heavy metal (Fe++)-chelating agents (catechol, 2,5'-dipyridyl, o-phenanthroline), beta-alanine, and buffers pH less than 7. This suggests that these effectors are capable of preventing the abnormously high influx of amino acids as well as its wasteful catabolism within the cell of S. noursei JA 3890b. Therefore, it seems likely that by this way the aminobenzoic acids and similar effectors can diminish the catabolite repression or inhibition of secondary metabolism by cellular excess of some nitrogen compounds in good agreement with its well-known stimulatory action on the biosynthesis of the antibiotic nourseothricin in this strain.