Detection of luciferase gene sequences in nonluminescent bacteria from the Chesapeake Bay

Washed excised roots of rice (Oryza sativa) produced H(2), CH(4) and fatty acids (millimolar concentrations of acetate, propionate, butyrate; micromolar concentrations of isovalerate, valerate) when incubated under anoxic conditions. Surface sterilization of the root material resulted in the inactivation of the production of CH(4), a strong reduction of the production of fatty acids and a transient (75 h) but complete inhibition of the production of H(2). Radioactive bicarbonate was incorporated into CH(4), acetate, propionate and butyrate. About 20-40% of the fatty acid carbon originated from CO(2) reduction. In the presence of phosphate, CH(4) was exclusively produced from H(2)/CO(2), since phosphate selectively inhibited acetoclastic methanogenesis. Acetoclastic methanogenesis was also selectively inhibited by methyl fluoride, while chloroform or 2-bromoethane sulfonate inhibited CH(4) production completely. Production of CH(4), acetate, propionate and butyrate from H(2)/CO(2) was always exergonic with Gibbs free energies <-20 kJ mol(-1) product. Chloroform inhibited the production of acetate and the incorporation of radioactive CO(2) into acetate. Simultaneously, H(2) was no longer consumed and accumulated, indicating that acetate was produced from H(2)/CO(2). Chloroform also resulted in increased production of propionate and butyrate whose formation from CO(2) became more exergonic upon addition of chloroform. Nevertheless, the incorporation of radioactive CO(2) into propionate and butyrate was inhibited by chloroform. The accumulation of propionate and butyrate in the presence of chloroform probably occurred by fermentation of organic matter, rather than by reduction of acetate and CO(2). [U-(14)C]Glucose was indeed converted to acetate, propionate, butyrate, CO(2) and CH(4). Radioactive acetate, CO(2) and CH(4) were also products of the degradation of [U-(14)C]cellulose and [U-(14)C]xylose. Addition of chloroform and methyl fluoride did not affect the product spectrum of [U-(14)C]glucose degradation. The application of combinations of selective inhibitors may be useful to elucidate anaerobic metabolic pathways in mixed microbial cultures and natural microbial communities.     

Effect of algal deposition on acetate and methane concentrations in the profundal sediment of a deep lake (Lake Constance)

Abstract In the profundal sediment ot Lake Constance (143 m depth) the temperature is constant at 4 °C. Despite the constant temperature, CH₄ concentrations changed with season between about 120 μM in winter and about 750 μM in summer, measured down to 30 cm depth. The acetate concentration profiles also varied between seasons. In summer, acetate concentration reached a maximum at about 100 μM in 2 or 4 cm depth. In winter, maximal concentrations of about 5 μM were observed over the entire depth. Input of organic material in late spring may be the reason for the seasonal change of both compounds. To simulate such a sedimentation event, intact sediment cores were covered with suspensions of Porphyridium aerugenium or Synechococcus sp. The addition of the phytoplankton material resulted in a drastic increase of acetate concentrations with a maximum at 2 cm depth, similar to in situ acetate concentrations measured in summer. The same applies for CH₄ for which increased concentrations were observed down to 6 cm depth. H₂ concentrations, on the other hand, showed no distinct increase. Treatment of intact sediment cores with ¹⁴C-labeled Synechococcus cells resulted in the formation of ¹⁴C-acetate, ¹⁴CH₄ and ¹⁴CO₂. Maximum concentrations of ¹⁴CH₄ were found at 4 cm depth, i.e. just above the depth to which ¹⁴C-acetate penetrated. The results show that phytoplankton blooms may cause a seasonal variation of acetate and CH₄ in profundal sediments of deep lakes despite the constant low temperature. They also indicate that acetate is the dominant substrate for methanogenic bacteria in the profundal sediments of Lake Constance.     

Influence of uncertainties in pH,pMg, activity coefficients,metabolite concentrations,and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

Thermodynamic feasibility analysis (TFA) has been used as a tool capable of providing additional constraints to the mass balance‐based methods of analysis of metabolic networks (e.g., flux balance analysis). Several publications have recently appeared in which TFA of different metabolic pathways from relatively simple to the genome‐scale networks was described as a means of detecting the possible metabolic control steps. However, in order to perform TFA, many simplifying assumptions were necessary. On the other hand, it has been shown by applying TFA to the well‐known pathway of glycolysis that erroneous simplifying assumptions may seriously bias the results of the analysis. A quantitative analysis of the influence of non‐ideality of the biochemical system, pH, temperature, and complexation of the metabolites with Mg²⁺ ions as well as a number of other factors on the TFA is reported. It is shown that the feasibility of glycolysis is very seriously limited by the reaction of oxidative phosphorylation of glyceraldehyde phosphate, and that the intracellular concentration of the main product of this reaction, biphosphoglycerate, must be anywhere from 10 to 100 times lower than published values. In addition, the driving force for this reaction, and consequently the feasibility of the entire pathway depend strongly on the intracellular pH and ionic strength and to a lesser extent on pMg and temperature. The analysis may also be influenced by uncertainties of the dissociation and magnesium complexation constants of glyceraldehyde phosphate. The analysis demonstrates the crucial importance of taking such factors into account when performing TFA. It also suggests an urgent need for experimental determinations of such factors as a prerequisite for sensible thermodynamic analysis of metabolism on a genome‐wide scale. Biotechnol. Bioeng. 2009;103: 780–795. © 2009 Wiley Periodicals, Inc.     

Influence of temperature, salinity and nutrient limitation on yessotoxin production and release by the dinoflagellate Protoceratium reticulatum in batch-cultures

The toxic dinoflagellate Protoceratium reticulatum (Claparède & Lachmann) Buetschli is recurrently present in the Adriatic sea. It is the producing organism of yessotoxin (YTX) and some of its analogues and thus its presence in seawater often results in shellfish farm closure for long periods. However, molluscs become highly toxic also at the presence of low cell concentrations, due to the high YTX content present in most algal strains. As no data were available on the environmental conditions favouring growth and YTX production by Adriatic P. reticulatum strains, in the present work, we investigated the effect of nutrient limitation, salinity and temperature on growth and YTX content in P. reticulatum cultures. Liquid chromatography–mass spectrometry (LC–MS) analyses were carried out to determine YTX production as well as the difference between the YTX amount retained in cells and that released in growth medium, in order to relate cell content to excretion mechanisms. The toxin content was determined in cells collected at the stationary phase, since both toxin production and release were found to be higher in this growth stage than in the exponential phase. As for nutrient-effect, a severe P-limitation strongly affected cell growth and favoured toxin accumulation, as consequences of both impaired cell division and lower toxin release. N-limited cultures, on the contrary, had a toxin content similar to controls and the highest percentage of release. P. reticulatum was confirmed to be tolerant towards salinity changes as it could grow at salinity values in the range of 22–42. The highest YTX production was observed at intermediate salinity values (32) whereas toxin release, expressed as percentage of the total amount produced, decreased as salinity increased. P. reticulatum growth was impaired in cultures kept at 26 °C in respect to those grown at 16 and 20 °C. YTX release decreased as temperature increased; however, cells kept at 26 °C displayed a very high YTX content. The environmental implications of these physiological behaviours highlight that farmed molluscs can become less toxic in colder waters at lower salinity values.     

The capacity of hydrogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor

The effect of different electron acceptors on substrate degradation was studied in pure and mixed cultures of various hydrogenotrophic homoacetogenic, methanogenic, sulfate-reducing, fumarate-reducing and nitrate-ammonifying bacteria. Two different species of these bacteria which during organic substrate degradation produce and consume hydrogen, were cocultured on a substrate which was utilized only by one of them. Hydrogen, which was excreted as intermediate by the first strain (and reoxidized in pure culture), could, depending on the hydrogen acceptor present, also be used by the second organism, resulting in interspecies hydrogen transfer. The efficiency of H₂ transfer was similar when methanol, lactate or fructose were used as organic substrate, although the free energy changes of fermentative H₂ formation of these substrates are considerably different. In coculture experiments nitrate or fumarate>sulfate> CO₂/CH₄>sulfur or CO₂/acetate were the preferred electron acceptors, and an increasing percentage of H₂ was transferred to that bacterium which was able to utilize the preferred electron acceptor. In pure culture the threshold values for hydrogen oxidation decreased in the same order from 1,100 ppm for homoacetogenic bacteria to about 0.03 ppm for nitrate or fumarate reducing bacteria. The determined H₂-threshold values as well as the percentage of H₂ transfer in cocultures were related to the Gibbs free energy change of the respective hydrogen oxidizing reaction.Parts of this work (grant to R C-R) was supported by the European Community (ST2A-0022)     

Influence of temperature on energetics of hydrogen metabolism in homoacetogenic,methanogenic, and other anaerobic bacteria

Hydrogen consumption by various thermophilic, mesophilic and/or psychrotrophic homoacetogens and methanogens was measured at temperatures between 4 and 80°C. Within the tolerated temperature range H₂ was consumed until a final H₂ threshold partial pressure was reached. H₂ thresholds generally decreased with temperature, parallel to the values calculated from the thermodynamics prevailing under culture conditions, i.e. the Gibbs free energy (G) of H₂ oxidation corrected for temperature by both the free-energy form of the Nernst equation and the Van't Hoff equation. The difference between the observed and the calculated H₂ partial pressures gives the minimum energy required for H₂ utilization being about-5 to-6 kJ/mol H₂ for the homoacetogenes and-9 to-12 kJ/mol H₂ for methanogens. The temperature dependence of the standard Gibbs free energy (G⁰) as described by the Van't Hoff equation apparently became the more important for thermodynamics as well as H₂ thresholds the more the temperature deviated from standard conditions (i.e. 25°C). Correction factors for calculation of temperature-corrected G _infT ^sup0 are presented for various H₂-producing and H₂-consuming reactions.     

Influence of temperature and size of females on the timing of spawning of perch,Perca fluviatilis,in Lake Geneva from 1984 to 1993

Synopsis The influence of temperature and the size of reproducing females on the timing of spawning of perch in Lake Geneva has been studied for 10 consecutive years (1984–1993) by means of artificial spawning substrates. The clutch of perch is an egg ribbon with a width proportional to the size of the reproducing female, so that the size structure distribution of the female population can be estimated from measurements of the width of the egg ribbons. The survey of egg-ribbon size revealed a succession of 3 cycles (period of increasing mean size followed by a sharp decrease) lasting 3, 3 and 4 years which were due to the occurrence of 3 strong year classes born in 1982, 1985 and 1988 respectively. This phenomenon can be explained by the effect of intraspecific predation exerted by strong year classes on the offspring of the 2 following years rather than by fluctuations in the success of reproduction in relation to climatic changes. In Lake Geneva, perch spawn in May. The water temperature exerted only a minor influence on the date of the beginning of the spawning period but had a greater effect on its intensity. A rise in temperature in May stimulated spawning while bad weather decreased spawning intensity. The larger perch had a tendency to spawn later than the small ones. The date of the mid-spawning period was well correlated with the yearly mean width of perch egg ribbons but no correlation could be detected between it and the water temperature.