The pathway of carbon dioxide assimilation in rhodospirillum rubrum grown in turbidostat continuous-flow culture

Summary A comparison of light and dark short-term incorporation of [¹⁴C]-carbon dioxide by Rhodospirillum rubrum grown in turbidostat continuous-flow culture at two different steady states on medium containing malate has shown that the labelling of phosphate esters was the main light-dependent process. Thus, the reductive pentose phosphate cycle appears to be the major pathway of carbon dioxide assimilation in the light under these growth conditions.The labelling of glutamate was also light-dependent and was most marked in the most rapidly growing steady state culture.The assimilated [¹⁴C]carbon was transferred to metabolites of the tricarboxylic acid cycle, particularly C₄-dicarboxylic acids, and the transfer involved additional carboxylations which were not light-dependent. The activity of these reactions accounted for initial high rates of carbon dioxide assimilation in the dark.In the dark assimilated [¹⁴C]carbon accumulated in succinate.     

Microcalorimetry of microorganism metabolism of monosaccharides and simple aromatic compounds

Heat conduction solution enable rapid determination of the heats of aerobic and anaerobic metabolism of substrate by microorganisms. Aliquots of 1.0 ml cell suspension, 5 × 10⁹ cell/ml, were mixed with a few dozen nmol substrate contained in 0.5 ml, under a controlled atmosphere of air, O₂, or N₂. At these substrate concentration, with adapted microorganisms, metabolism and its heat generation are usually complete within 300 to 600 sec. The raw data yield ΔH_app values. The ΔH_app were determined in the range 0.001 to 0.010% substrate, and extrapolated (limit substrate concentration →0), to yield Δ⁰H?, the limiting differential molar heat of metabolism. The Δ⁰H? values express the heat generated when there is rapid metabolism but little new growth, minimal contribution by H⁺ transfer from metabolites, and maintenance of aerobicity or anaerobicity as specified. Escherichiacoli B/5 was used for aerobic and anaerobic combustion of eight sugars. Pseudomonas multivorans, and an Acinetobacter, strain B-1, were used for aerobic metabolism of benzene, toluene, naphthalene, and a methylnaphthalene. The larger heats of combustion of the hydrocarbons enable the use of aqueous solutions of hydrocarbons well below their solubility limits. The quotient Δ⁰H?/n (n = atoms carbon/molecule substrate) varies from (-)36 to (-)67 kcal/mol carbon for the sugars. The most reduced sugar yields the largest exothermic heats. The quotient varies from (-)27 to (-)81 kcal/mol carbon for the aromatic hydrocarbons. Comparison of the calorimetric heats of metabolism of those from total aerobic combustion in aquo (where available) give measure of the efficiencies with which the heat contents of the aqueous substrate are used by the bacteria.     

Sulfonate-sulfur can be assimilated for fermentative growth

Abstract Bacterial assimilation of sulfonate-sulfur under anaerobic conditions has been demonstrated. Two different bacteria able to grow fermentatively using sulfonate-sulfur as sole sulfur source were isolated by enrichment culture; neither were able to utilize sulfonates as sole source of carbon and energy for growth. The isolate of Clostridium pasteurianum assimilated the sulfur of isethionate (2-hydroxyethanesulfonate), taurine (2-aminoethanesulfonate), or p -toluenesulfonate. A facultatively fermentative Klebsiella strain did not utilize the sulfur of any of these sulfonates, but assimilated cysteate-sulfur; in contrast, when growing by aerobic respiration, the range of sulfonates able to serve as sulfur source was greater. Both bacteria displayed a preferential utilization of sulfate-sulfur to that of the sulfonates tested. Thus, bacterial assimilation of sulfonate-sulfur during anaerobic growth has direct parallels with features until now recognized only for aerobic assimilatory processes.     

The feeding biology of Hydrobia ventrosa (Montagu). II. Allocation of the components of the carbon-budget and the significance of the secretion of dissolved organic material

The deposit-feeding prosobranch Hydrobia ventrosa (Montagu) was fed ¹⁴C-labelled food for a short period. As food, sterile detritus (homogenously ¹⁴C-labelled, dried barley hay), detritus with attached bacteria, and pure bacteria were used. The distribution of the ingested ¹⁴C was followed for a 24-h period. It was found that the assimilation efficiencies of sterile hay, hay with bacteria, and pure bacteria were 34, 56, and 70 %, respectively. This indicates a significance of bacteria for deposit-feeders. There is a considerable loss of dissolved organic material, in part due to leakage from faecal pellets (13 % of the ingested C in the case of a pure bacterial meal and 7 % of the ingested C in the case of sterile hay). The animals also excrete about 30 % of the assimilated carbon. Excretion of mucus constitutes about 9 % of the assimilated carbon. The fraction of assimilated carbon respired depends on the nature of the food. For sterile hay, hay with bacteria, and pure bacteria the percentage respired was 53, 30, and 38 %, respectively. Growth efficiency is, therefore, higher when protein-rich bacteria are included in the diet.     

Regulation of autotrophic and heterotrophic metabolism in Pseudomonas oxalaticus OX1: Growth on mixtures of acetate and formate in continuous culture

Growth of Pseudomonas oxalaticus in carbon- and energy-limited continuous cultures with mixtures of acetate and formate resulted in the simultaneous utilization of both substrates at all dilution rates tested. During growth on these mixtures, acetate repressed the synthesis of ribulosebisphosphate carboxylase. The degree of this repression was dependent on the dilution rate and on the ratio of acetate and formate in the medium reservoir. At fixed acetate and formate concentrations in the inflowing medium of 30 and 100 mM, respectively, and dilution rates above 0.10h^-1, the severe repression of autotrophic enzymes resulted in a marked increase in bacterial dry weight compared to the growth yield of the organisms on the two substrates separately. Also, at these dilution rates a significant increase in isocitrate lyase activity was observed in the cells as compared to growth on acetate alone. This indicated that under these conditions more acetate was assimilated and less dissimilated since acetate was partly replaced by formate as the energy source. When formate was added to the reservoir of an acetate-limited culture (S_R=30 mM), derepression of RuBPCase synthesis was observed at formate concentrations of 50 mM and above. Below this concentration formate only served as an energy source for acetate assimilation; when its concentration was increased above 50 mM a progressively increasing contribution of carbon dioxide fixation to the total carbon assimilation was observed as the activity of RuBPCase in the cells increased. It is concluded that in Pseudomonas oxalaticus the synthesis of enzymes involved in autotrophic carbon dioxide fixation via the Calvin cycle is regulated by a repression/derepression mechanism.Abbreviations RuBPCase ribulosebisphosphate carboxylase - PMS phenazine methosulphate - DCPIP 2,6-dichlorophenol-indophenol - FDH formate dehydrogenase - S_R concentration of growth-limiting substrate in reservoir     

Mixotrophic growth of Thiobacillus A2 on acetate and thiosulfate as growth limiting substrates in the chemostat

During heterotrophic growth on acetate, in batch culture, the autotrophic growth potential of Thiobacillus A2, i.e. the capacity to oxidize thiosulfate and to fix carbon dioxide via the Calvin cycle, was completely repressed. The presence of thiosulfate in a batch culture with acetate as the organic substrate partly released the repression of the thiosulfate oxidizing system. Cultivation of the organism in continuous culture at a dilution rate of 0.05 h^-1 with different concentration ratios of thiosulfate and acetate in the reservoir medium led to mixotrophic growth under dual substrate limitation. Growth on the different mixtures of acetate and thiosulfate yielded upto 30% more cell dry weight than predicted from the growth yields on comparable amounts of these substrates separately. The extent to which the carbon dioxide fixation capacity and the maximum thiosulfate and acetate oxidation capacity are repressed appeared to be a function of the thiosulfate to acetate concentration ratio in the reservoir medium. The results of ¹⁴C-acetate assimilation experiments and of gas-analysis demonstrated that the extent to which acetate was assimilated depended also on the substrate ratio in the inflowing medium. Under the different growth conditions surprisingly little variation was found in some tri-carboxylic acid cycle enzyme activities. Cultivation of T. A2 at different growth rates with a fixed mixture of thiosulfate (18 mM) and acetate (11 mM) in the medium, showed that dual substrate limitation occured at dilution rates ranging from 0.03–0.20 h^-1.Abbreviations PPO 2,5-diphenoloxazol - RubPCase Ribulose-1,5-bisphophate carboxylase - Tris tris (hydroxymethyl) aminomethane - EDTA ethylenediaminetetra-acetic acid     

Biochemical limits to microbial growth yields: An analysis of mixed substrate utilization

A theoretical analysis has been made of carbon conversion efficiency during heterotrophic microbial growth. The expectation was that the maximal growth yield occurs when all the substrate is assimilated and the net flow of carbon through dissimilation is zero. This, however, is not identical to a 100% carbon conversion, since assimilatory pathways lead to a net production of CO(2). It can be shown that the amount of CO(2) produced by way of assimilatory processes is dependent upon the nature of the carbon source, but independent of its degree of reduction and varies between 12 and 29% of the substrate carbon. An analysis of published yield data reveals that nearly complete assimilation can occur during growth on substrates with a high energy content. This holds for substrates with a heat of combustion of ca. 550 kJ/mol C, or a degree of reduction higher than 5 (e.g. ethane, ethanol, and methanol). Complete assimilation can also be achieved on substrates with a lower energy content, provided that an auxiliary energy source is present that cannot be used as a carbon source. This is evident from the cell yields reported for Candida utilis grown on glucose plus formate and for Thiobacillus versutus grown on acetate plus thiosulfate. This evaluation of the carbon conversion efficiency during assimilation also made it possible to compare the energy content of the auxiliary energy substrate added with the quantity of the carbon source it had replaced. It will be shown that utilization of the auxiliary energy source may lead to extreme changes in the efficiency of dissimilatory processes.     

PRODUCTS OF THE OXIDATION OF THIOSULFATE BY BACTERIA IN MINERAL MEDIA

Various cultures (previously described), which oxidize thiosulfate in mineral media have been studied in an attempt to determine the products of oxidation. The transformation of sodium thiosulfate by Cultures B, T, and K yields sodium tetrathionate and sodium hydroxide; secondary chemical reactions result in the accumulation of some tri- and pentathionates, sulfate, and elemental sulfur. As a result of the initial reaction, the pH increases; the secondary reactions cause a drop in pH after this initial rise. The primary reaction yields much less energy than the reactions effected by autotrophic bacteria. No significant amounts of assimilated organic carbon were detected in media supporting representatives of these cultures. It is concluded that they are heterotrophic bacteria. Th. novellus oxidizes sodium thiosulfate to sodium sulfate and sulfuric acid; the pH drops progressively with growth and oxidation. Carbon assimilation typical of autotrophic bacteria was detected; the ratio of sulfate-sulfur formed to carbon assimilated was 56:1. It is calculated that 5.1 per cent of the energy yielded by the oxidation of thiosulfate is accounted for in the organic cell substance synthesized from inorganic materials. This organism is a facultative autotroph. The products of oxidation of sodium thiosulfate by Th. thioparus are sodium sulfate, sulfuric acid, and elemental sulfur; the ratio of sulfate sulfur to elemental sulfur is 3 to 2. The pH decreases during growth and oxidation. The elemental sulfur is produced by the primary reaction and is not a product of secondary chemical changes. The bacterium synthesizes organic compounds from mineral substances during growth. The ratio of thiosulfate-sulfur oxidized to carbon assimilated was 125:1, with 4.7 per cent of the energy of oxidation recovered as organic cell substance. This bacterium is a strict autotroph.     

Assimilation of Polysaccharides and Glucose by Major Bacterial Groups in the Delaware Estuary

The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively. Actinobacteria contributed 70% to glucose assimilation in freshwater, while Alphaproteobacteria assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS. Actinobacteria and Betaproteobacteria contributed the most in the freshwater section, whereas Cytophaga-like bacteria and Alpha- and Gammaproteobacteria participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by “bottom-up” factors such as dissolved organic matter.     

Commensalism during submerged mixed culture of Geotrichum candidum and Penicillium camembertii on glutamate and lactate

Geotrichum candidum and Penicillium camembertii were cultivated in pure and mixed cultures on glutamate- and lactate-based medium. In pure culture, P. camembertii assimilated simultaneously glutamate, as a nitrogen and carbon source for biosynthesis, and lactate as an energy source. On the contrary, G. candidum grew on glutamate alone. The mixed culture led to higher growth rates and then higher rates of substrate consumption and metabolite production than each pure culture; however, the behaviour recorded was similar to that observed during G. candidum pure culture, in particular the absence of lactate assimilation during growth, illustrating a commensalism between both species. The presence of G. candidum induced a form of “competition” and then a better assimilation by P. camembertii of the sole nitrogen source, glutamate, which was therefore used as an energy source in addition to be a carbon (and nitrogen) source. Lactate was only used for energy supply during stationary state, as also recorded during G. candidum pure culture.     

Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary

The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively. Actinobacteria contributed 70% to glucose assimilation in freshwater, while Alphaproteobacteria assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS. Actinobacteria and Betaproteobacteria contributed the most in the freshwater section, whereas Cytophaga-like bacteria and Alpha- and Gammaproteobacteria participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by "bottom-up" factors such as dissolved organic matter.     

Dynamics of production of extracellular polysaccharides by nodule bacteria

The dynamics of the accumulation of the extracellular polysaccharides synthesized by nodule bacteria and the possibility of their assimilation by these bacteria as a source of carbon was studied. When nodule bacteria were cultured for 20 days in a medium containing glucose, an increase in the titer of the bacteria and the accumulation of extracellular polysaccharides was observed in the first three days. After this the titer of the nodule bacteria decreased with a decrease in the glucose in the medium, but the amount of extracellular polysaccharide synthesized did not increase. These data suggest that extracellular polysaccharides are not assimilated by nodule bacteria as a source of carbon and evidently are protective substances for the cells.     

Uptake of glycollate by Skeletonema costatum (Grev.) Cleve in bacterized culture

Glycollic acid, supplied at a concentration of 1 mg l^?1, increased the relative growth rate of Skeletonema costatum (Grev.) Cleve growing in bacterized culture at limiting light intensities. There was little or no such effect at intensities approaching saturation. The presence in the medium of alumina, an adsorbent for glycollate, prolonged the lag phase, the cells remaining viable for up to 5 days. Uptake of glycollate was not appreciably affected by the bicarbonate concentration of the medium. After 3 h, 80–92% of the glycollate carbon assimilated was found in the alcohol and benzene insoluble fraction of the cells. This is in agreement with the supposition that glycollate carbon is as-similated directly by the diatom rather than after degradation by bacteria to carbon dioxide.     

Increased Light Availability Reduces the Importance of Bacterial Carbon in Headwater Stream Food Webs

Many ecosystems rely on subsidies of carbon and nutrients from surrounding environments. In headwater streams that are heavily shaded by riparian forests, allochthonous inputs from terrestrial systems often comprise a major part of the organic matter budget. Bacteria play a key role in organic matter cycling in streams, but there is limited evidence about how much bacterial carbon is actually assimilated by invertebrate and fish consumers, and how bacterial carbon assimilation varies among streams. We conducted stable isotope tracer additions of ¹³C-acetate, that is assimilated only by bacteria, and ¹⁵N-ammonium, that is assimilated by both bacteria and algae, in two small, shaded streams in the Adirondack region of New York State, USA. Our goal was to determine whether there is an important trophic link between bacteria and macroconsumers, and whether the link changes when the light environment is experimentally altered. In 2009, we evaluated bacterial carbon use in both streams with natural canopy cover using 10-day dual-isotope tracer releases. The canopy was then thinned in one stream to increase light availability and primary production and tracer experiments were repeated in 2010. As part of the tracer experiments, we developed a respiration assay to measure the δ ¹³C content of live bacteria, which provided critical information for determining how much of the carbon assimilated by invertebrate consumers is from bacterial sources. Some invertebrate taxa, including scraper mayflies (Heptagenia spp.) that feed largely on biofilms assimilated over 70% of their carbon from bacterial sources, whereas shredder caddisflies (Pycnopsyche spp.) that feed on decomposing leaves assimilated less than 1% of their carbon from bacteria. Increased light availability led to strong declines in the magnitude of bacterial carbon fluxes to different consumers (varying from ?17 to ?91% decrease across invertebrate taxa), suggesting that bacterial energy assimilation differs not only among consumer taxa but also within the same consumer taxa in streams with different ecological contexts. Our results demonstrate that fluxes of bacterial carbon to higher trophic levels in streams can be substantial, that is over 70% for some taxa, but that invertebrate taxa vary considerably in their reliance on bacterial carbon, and that local variation in carbon sources controls how much bacterial carbon invertebrates use.     

Extracellular dissolved organic carbon released from phytoplankton as a source of carbon for heterotrophic bacteria in lakes of different humic content

The quantitative importance of photosynthetically produced dissolved organic carbon (PDOC) released from phytoplankton as a source of carbon for pelagic, heterotrophic bacteria was investigated in four temperate Swedish lakes, of which two had low (≈20 mg Pt 1⁻¹), and two moderately high (60–80 mg Pt 1⁻¹) humic content. The bacterial assimilation of PDOC was estimated with the ¹⁴C method, and the total production of the heterotrophic bacteria was estimated with the [3H]thymidine incorporation method. The release of PDOC from natural communities of phytoplankton was not restricted to periods of photosynthesis, but often continued during periods of darkness. Heterotrophic bacteria often assimilated the labile components of the PDOC at high rates (up to 73% of the released PDOC was assimilated during the incubation in our experiments). The contribution of PDOC to bacterial production exhibited large within-lake seasonal variations, but PDOC was at certain times, both in humic and non-humic lakes, a quantitatively very important carbon source for the heterotrophic bacteria. Under periods of comparatively low primary production, heterotrophic bacteria in humic lakes appear to utilize allochthonous, humic substances as a substrate.     

Extracellular release in Chlorella vulgaris culture and the role of bacteria accompanying - algae in this process.

The effect of different concentrations of nitrogen and phosphorus on extracellular release was investigated. Phosphorus induced the enhanced extracellular release of metabolites by Chlorella vulgaris. No influence of nitrogen on extracellular release was observed. In the initial stages of C. vulgaris culture the algae release was observed. In the initial stages of C. vulgaris culture the algae release compounds readily assimilated by the accompanying bacteria, hence the observed drop of percentage of extracellular release (PER) in culture medium caused by the bacteria. Both, the glycolic acid and the products of photoassimilation released to the environment in the first stages of cultivation were assimilated by the bacteria accompanying-algae at a similar rate. The ageing of C. vulgaris culture resulted in the accumulation of extracellularly released metabolites and increase of PER. These products were not assimilated by the bacteria present in the algal culture.     

A calorimetrically based method to convert toxic compounds into poly-3-hydroxybutyrate and to determine the efficiency and velocity of conversion

A fed-batch method for converting toxic substrates into poly-3-hydroxybutyrate is presented. The method involves a series of batch-growth processes, regulated by adding small amounts of carbon substrate, during the course of which the concentration of the nitrogen source decreases and controls the distribution of the substrate-carbon assimilated. The addition of carbon substrate is controlled, and the small changes that occur in the growth pattern are interpreted using high-resolution reaction calorimetry. The method was tested with Ralstonia eutropha DSM 4058 growing on phenol, and Variovorax paradoxus DSM 4065 growing on sodium benzoate. The maximum carbon conversion efficiencies (CCEs) obtained, 23% and 27% respectively, were compared with the theoretically possible values.     

Carbon Use Efficiency and Cell Expansion of NaCl-Adapted Tobacco Cells

Carbon use efficiencies (gram cell organic dry weight accumulated per gram sugar assimilated from the medium) of unadapted and NaCl-adapted (428 millimolar) cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) were determined to evaluate metabolic costs associated with growth and survival in a saline environment. No net increase in carbon costs was associated with salt adaptation. At low substrate levels, carbon use efficiencies of unadapted and NaCl-adapted cells were not appreciably different (0.495 and 0.422, respectively) and at higher substrate levels carbon use efficiency of NaCl-adapted cells was clearly higher than that of unadapted cells. These results indicate that a homeostasis of metabolic efficiency is established after cells have adapted to NaCl. Altered carbon availability does not cause the reduced cell volume that results from adaptation to NaCl. This does not preclude, however, the possibility that altered intracellular partitioning of carbon affects cell expansion.     

Contribution of SAR11 Bacteria to Dissolved Dimethylsulfoniopropionate and Amino Acid Uptake in the North Atlantic Ocean

SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of ³H-amino acids and [³⁵S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.     

Autotrophic assimilation of CO2 and C1-compounds by pathogenic bacteria

We demonstrate for the first time that the pathogenic bacteria Yersinia pseudotuberculosis and Listeria monocytogenes (pathogens of saprozoonoses) are capable of chemolithoautotrophic assimilation of CO2. Low temperature is favorable for better absorption of CO2 by these bacteria; this is supported by increased enzymatic activity of carbonic anhydrase acting as the supplier of the substrate to the site of carboxylation. Data of radioisotopic methods indicate that assimilated labeled carbon of CO2 is incorporated into all major cell biopolymers. The bacteria can utilize not only CO2, but also other C1-compounds for biosynthesis.