Stability and performance of Xanthobacter autotrophicus GJ10 during 1,2-dichloroethane biodegradation

A nucleic acid-based approach was used to investigate the dynamics of a microbial community dominated by Xanthobacter autotrophicus GJ10 in the degradation of synthetic wastewater containing 1,2-dichloroethane (DCE). This study was performed over a 140-day period in a nonsterile continuous stirred-tank bioreactor (CSTB) subjected to different operational regimens: nutrient-limiting conditions, baseline operation, and the introduction of glucose as a cosubstrate. The microbial community was analyzed by a combination of fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Under nutrient-limiting conditions, DCE degradation was restricted, but this did not affect the dominance of strain GJ10, determined by FISH to comprise 85% of the active population. During baseline operation, DCE degradation improved significantly to over 99.5% and then remained constant throughout the subsequent experimental period. DGGE profiles revealed a stable, complex community, while FISH indicated that strain GJ10 remained the dominant species. During the addition of glucose as a cosubstrate, DGGE profiles showed a proliferation of other species in the CSTB. The percentage of strain GJ10 dropped to 8% of the active population in just 5 days, although this did not affect the DCE biodegradation performance. The return to baseline conditions was accompanied by the reestablishment of strain GJ10 as the dominant species, suggesting that this system responds robustly to external perturbations, both at the functional biodegradation level and at the individual strain level.     

Evidence of Substantial Carbon Isotope Fractionation among Substrate, Inorganic Carbon, and Biomass during Aerobic Mineralization of 1,2-Dichloroethane by Xanthobacter autotrophicus

Carbon isotope fractionation during aerobic mineralization of 1,2-dichloroethane (1,2-DCA) by Xanthobacter autotrophicus GJ10 was investigated. A strong enrichment of ¹³C in residual 1,2-DCA was observed, with a mean fractionation factor α ± standard deviation of 0.968 ± 0.0013 to 0.973 ± 0.0015. In addition, a large carbon isotope fractionation between biomass and inorganic carbon occurred. A mechanistic model that links the fractionation factor α to the rate constants of the first catabolic enzyme was developed. Based on the model, it was concluded that the strong enrichment of ¹³C in 1,2-DCA arises because the first irreversible step of the initial enzymatic transformation of 1,2-DCA consists of an S_N2 nucleophilic substitution. S_N2 reactions are accompanied by a large kinetic isotope effect. The substantial carbon isotope fractionation between biomass and inorganic carbon could be explained by the kinetic isotope effect associated with the initial 1,2-DCA transformation and by the metabolic pathway of 1,2-DCA degradation. Carbon isotope fractionation during 1,2-DCA mineralization leads to 1,2-DCA, inorganic carbon, and biomass with characteristic carbon isotope compositions, which may be used to trace the process in contaminated environments.     

Stable carbon isotope fractionation during degradation of dichloromethane by methylotrophic bacteria

Stable carbon isotope fractionation during dichloromethane (DCM) degradation by methylotrophic bacteria was investigated under aerobic and nitrate-reducing conditions. The strains studied comprise several Hyphomicrobium strains, Methylobacterium, Methylopila, Methylophilus and Methylorhabdus spp. that are considered to degrade DCM by a glutathione (GSH)-dependent dehalogenase enzyme system in the initial step. The stable carbon isotope fractionation factors (alphaC) of the strains varied under aerobic conditions between 1.043 and 1.071 and under nitrate-reducing conditions between 1.048 and 1.065. Comparison of isotope fractionation under aerobic and nitrate-reducing conditions by individual strains revealed only minor to no differences. The variability in isotope fractionation among strains was found to be related to the polymorphism of the functional genes encoding the DCM dehalogenase.     

Carbon and hydrogen stable isotope fractionation during aerobic bacterial degradation of aromatic hydrocarbons

13C/(12)C and D/H stable isotope fractionation during aerobic degradation was determined for Pseudomonas putida strain mt-2, Pseudomonas putida strain F1, Ralstonia pickettii strain PKO1, and Pseudomonas putida strain NCIB 9816 grown with toluene, xylenes, and naphthalene. Different types of initial reactions used by the respective bacterial strains could be linked with certain extents of stable isotope fractionation during substrate degradation.     

Sources of organic and inorganic carbon in a headwater stream: Evidence from carbon isotope studies

A combination of stable isotope studies and ¹⁴Cdating were used to identify the main sources andprocesses controlling streamwater DOC and TIC in atemperate non-forested watershed. ¹³Cvalues for terrestrial (–24.9 to –29.1) and aquatic(–30.5 to –33.5) plants were similar to valuesreported in the literature for similar ecosystems.¹³C values for DOC in soil solution andstreamwater were consistent with soil and terrestrialvegetation, indicating that the terrestrial ecosystemis the dominant source of aquatic DOC in thiswatershed. ¹³C values of soil atmosphereCO₂ (–17.2 to –25.2) were slightly lessnegative than would be expected for production viaaerobic soil microbial decomposition and rootrespiration. There was a close correspondence between¹³C values (–15.5 to –21.5) forstreamwater TIC and soil atmospheric CO₂ in thecentral part of the catchment where the stream drainsCO₂-rich peats. ¹⁴C dating showed thatalthough peat has been accumulating in the watershedfor at least 2700 years, DOC in soil pore water andstreamwater contains carbon of predominantly recentorigin (post-AD 1955).     

Mechanisms of CO2 fixation in bacterial photosynthesis studied by the carbon isotope fractionation technique

1. The carbon isotope discrimination properties of a representative of each of the three types of photosynthetic bacteria Chlorobium thiosulfatophilum, Rhodospirillum rubrum and Chromatium and of the C₃-alga Chlamydomonas reinhardii were determined by measuring the ratio of ¹³CO₂ to ¹²CO₂ incorporated during photoautotrophic growth. 2. Chromatium and R. rubrum had isotope selection properties similar to those of C₃-plants, whereas Chlorobium was significantly different. 3. The results suggest that Chromatium and R. rubrum assimilate CO₂ mainly via ribulose 1,5-diphosphate carboxylase and the associated reactions of the reductive pentose phosphate cycle, whereas Chlorobium utilizes other mechanisms. Such mechanisms would include the ferredoxin-linked carboxylation enzymes and associated reactions of the reductive carboxylic acid cycle.Abbreviations RuDP ribulose 1,5-disphosphate - PEP phosphoenolpyruvate     

Carbon isotope fractionation during aerobic biodegradation of trichloroethene by Burkholderia cepacia G4: a tool to map degradation mechanisms

The strain Burkholderia cepacia G4 aerobically mineralized trichloroethene (TCE) to CO(2) over a time period of approximately 20 h. Three biodegradation experiments were conducted with different bacterial optical densities at 540 nm (OD(540)s) in order to test whether isotope fractionation was consistent. The resulting TCE degradation was 93, 83.8, and 57.2% (i.e., 7.0, 16.2, and 42.8% TCE remaining) at OD(540)s of 2.0, 1.1, and 0.6, respectively. ODs also correlated linearly with zero-order degradation rates (1.99, 1.11, and 0.64 micromol h(-1)). While initial nonequilibrium mass losses of TCE produced only minor carbon isotope shifts (expressed in per mille delta(13)C(VPDB)), they were 57.2, 39.6, and 17.0 per thousand between the initial and final TCE levels for the three experiments, in decreasing order of their OD(540)s. Despite these strong isotope shifts, we found a largely uniform isotope fractionation. The latter is expressed with a Rayleigh enrichment factor, epsilon, and was -18.2 when all experiments were grouped to a common point of 42.8% TCE remaining. Although, decreases of epsilon to -20.7 were observed near complete degradation, our enrichment factors were significantly more negative than those reported for anaerobic dehalogenation of TCE. This indicates typical isotope fractionation for specific enzymatic mechanisms that can help to differentiate between degradation pathways.     

Determination of isotope fractionation factors and quantification of carbon flow by stable carbon isotope signatures in a methanogenic rice root model system

Methanogenic processes can be quantified by stable carbon isotopes, if necessary modeling parameters, especially fractionation factors, are known. Anoxically incubated rice roots are a model system with a dynamic microbial community and thus suitable to investigate principal geochemical processes in anoxic natural systems. Here we applied an inhibitor of acetoclastic methanogenesis (methyl fluoride), calculated the thermodynamics of the involved processes, and analyzed the carbon stable isotope signatures of CO₂, CH₄, propionate, acetate and the methyl carbon of acetate to characterize the carbon flow during anaerobic degradation of rice roots to the final products CO₂ and CH₄. Methyl fluoride inhibited acetoclastic methanogenesis and thus allowed to quantify the fractionation factor of CH₄ production from H₂/CO₂. Since our model system was not affected by H₂ gradients, the fractionation factor could alternatively be determined from the Gibbs free energies of hydrogenotrophic methanogenesis. The fractionation factor of acetoclastic methanogenesis was also experimentally determined. The data were used for successfully modeling the carbon flow. The model results were in agreement with the measured process data, but were sensitive to even small changes in the fractionation factor of hydrogenotrophic methanogenesis. Our study demonstrates that stable carbon isotope signatures are a proper tool to quantify carbon flow, if fractionation factors are determined precisely.     

Minor stable carbon isotope fractionation between respired carbon dioxide and bulk soil organic matter during laboratory incubation of topsoil

A common assumption in paleoenvironmental reconstructions using soils is that the carbon isotope composition of soil-respired CO₂ is equivalent to the carbon isotope composition of bulk soil organic matter (SOM). However, the occurrence of a non-zero per mil carbon isotope enrichment factor between CO₂ and SOM (\(\varepsilon_{{{\text{CO}}_{ 2} - {\text{SOM}}}}\)) during soil respiration is the most widely accepted explanation for the down-profile increase in SOM δ¹³C values commonly observed in well-drained soils. In order to shed light on this apparent discrepancy, we incubated soil samples collected from the top 2 cm of soils with pure C₃ vegetation and compared the δ¹³C values of soil-respired CO₂ to the δ¹³C values of bulk SOM. Our results show near-zero \(\varepsilon_{{{\text{CO}}_{ 2} - {\text{SOM}}}}\) values (?0.3 to 0.4 ‰), supporting the use of paleosol organic matter as a proxy for paleo soil-respired CO₂. Significantly more negative \(\varepsilon_{{{\text{CO}}_{ 2} - {\text{SOM}}}}\) values are required to explain the typical δ¹³C profiles of SOM in well-drained soils. Therefore our results also suggest that typical SOM δ¹³C profiles result from either (1) a process other than carbon isotope fractionation between CO₂ and SOM during soil respiration or (2) \(\varepsilon_{{{\text{CO}}_{ 2} - {\text{SOM}}}}\) values that become increasingly negative as SOM matures.     

Use of glucose and carbon isotope fractionation by microbial cells immobilized on solid-phase surface

By the example of glucose uptake by the soil bacteria Pseudomonas aureofaciens BS1393(pBS216) and Rhodococcus sp. 3–30 immobilized on a solid-phase surface (quartz sand), their growth parameters were determined: growth rate (doubling time), total CO₂ production, CO₂ production per cell, lag period with respect to substrate uptake, respiratory quotient. The growth of P. aureofaciens and Rhodococcus sp. on glucose revealed (1) differences of the lag period with respect to substrate (lag time of ～4 h for P. aureofaciens and ～26 h for Rhodococcus sp.); (2) differences between the maximal rates of CO₂ production (～50 μg C-CO₂ g^?1 sand h^?1 for P. aureofaciens and ～8.5 μg C-CO₂ g^?1 sand h^?1 for Rhodococcus sp.); (3) differences in CO₂ production per cell (～1.94 × 10^?9 μM CO₂/CFU for P. aureofaciens and more than ～3.4 × 10^?9 μM CO₂/CFU for Rhodococcus sp.). The kinetics of the metabolic CO₂ isotopic composition was shown to be determined by the difference in the carbon isotopic characteristics of products in the cell. Upon introduction of glucose into the medium (the preparatory stage of the metabolism), the uptake of intracellular ¹³C-depleted products (lipids) is noted; at the stage of the maximal cell growth rate, introduced glucose is mainly metabolized; and at the final stage, upon exhaustion of substrate, the “stored” products—the lipid fraction—get involved in the metabolism. At the maximal rate of glucose uptake, the CO₂ carbon isotopic fractionation coefficient relative to organic products of microbial biosynthesis was determined to be α = 1.009 ± 0.002.     

Sulfur isotope fractionation by Salmonella heidelberg: inverse isotope effects during growth on high concentrations of Na2SO3

During growth on minimal salts - glucose media supplemented with high concentrations of Na2SO3 (10-3 and 10-2 M), Salmonella heidelberg exhibited cytological and growth responses which indicated increased cellular toxicity with increasing sulfite concentrations. The large quantities of sulfide evolved during growth at both SO32- concentrations were accompanied by large normal and inverse isotope effects. Consistent with earlier findings, this organism was found capable of rapidly metabolizing both the sulfane and sulfonate sulfur of thiosulfate. Therefore, the isotope effects do not appear to be caused by extracellular chemical thiosulfate formation.     

Stable isotope fractionation by Clostridium pasteurianum. 2. Regulation of sulfite reductases by sulfur amino acids and their influence on sulfur isotope fractionation during SO32- and SO42- reduction

In addition to an assimilatory sulfite reductase, studies of cultures of Clostridium pasteurianum supplemented with methionine, cysteine, and 35SO42- provides evidence for another reductase which is induced by SO32-. This inducible reductase appears to be dissimaltory because of the copious sulfide production arising when the cells are grown on SO32-. Cysteine can repress the assimilatory sulfite reductase but does not affect the inducible reductase. During late logarithmic growth on 1 mM SO42- + 10mM cysteine, depression of the inducible reductase occurred along with increased sulfide production. The presence of 1 mM cysteine and (or) 1 mM cysteine and (or) 1 mM methionine does not affect the inverse sulfur isotope effect for evolved H2S. However, 5 and 10 mM cysteine reduce the maximum delta34S value for released H2S from +40 to 10%. A small conversion of cysteine to H2S by C. pasteurianum occurs, but only in the stationary phase.     

Factors controlling the carbon isotope fractionation of tetra- and trichloroethene during reductive dechlorination by Sulfurospirillum ssp. and Desulfitobacterium sp. strain PCE-S

Carbon stable isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE) was investigated during reductive dechlorination. Growing cells of Sulfurospirillum multivorans, Sulfurospirillum halorespirans, or Desulfitobacterium sp. strain PCE-S, the respective crude extracts and the abiotic reaction with cyanocobalamin (vitamin B(12)) were used. Fractionation of TCE (alphaC=1.0132-1.0187) by S. multivorans was more than one order of magnitude higher than values previously observed for tetrachloroethene (PCE) (alphaC=1.00042-1.0017). Similar differences in fractionation were observed during reductive dehalogenation by the close relative S. halorespirans with alphaC=1.0046-1.032 and alphaC=1.0187-1.0229 for PCE and TCE respectively. TCE carbon isotope fractionation (alphaC=1.0150) by the purified PCE-reductive dehalogenase from S. multivorans was more than one order of magnitude higher than fractionation of PCE (alphaC=1.0017). Carbon isotope fractionation of TCE by Desulfitobacterium sp. strain PCE-S (alphaC=1.0109-1.0122) as well as during the abiotic reaction with cyanocobalamin (alphaC=1.0154) was in a similar range to previously reported values for fractionation by mixed microbial cultures. In contrast with previous results with PCE, no effects due to rate limitations, uptake or transport of the substrate to the reactive site could be observed during TCE dechlorination. Our results show that prior to a mechanistic interpretation of stable isotope fractionation factors it has to be carefully verified how other factors such as uptake or transport affect the isotope fractionation during degradation experiments with microbial cultures.     

Stable isotope fractionation by Clostridium pasteurianum. 1. 34S/32S: inverse isotope effects during SO4-2- and SO3-2- reduction.

During growth on minimal salts--sucrose media supplemented with various concentrations (10-4-10-2 M) of sodium sulfate, Clostridium pasteurianum grew at a normal rate and only evolved sulfide in late stages of growth on 10-2 M SO4-2-. The evolved sulfide was slightly enriched in 34S as compared to the medium sulfur. On the other hand, sulfide was evolved during growth on all concentrations of sulfite tested. Large normal and inverse isotopic effects were observed in the evolved sulfide during SO3-2- reductions. In contrast, the intracellular sulfur showed much smaller fractionations. The complexity of the isotopic patterns suggests that a dissimilatory sulfite reductase system may be induced by high concentrations of sulfite.     

Metabolism of mono- and dihalogenated C1 and C2 compounds by <Emphasis Type="Italic">Xanthobacter autotrophicus</Emphasis> growing on 1,2-dichloroethane

The conversion of and toxic effects exerted by several mono- and dihalogenated C1 and C2 compounds on cultures of Xanthobacter autotrophicus GJ10 growing on 1,2-dichloroethane were investigated. Bromochloromethane, dibromomethane and 1-bromo-2-chloroethane were utilized by strain GJ10 in batch culture as a cosubstrate and sole carbon source. The rate of degradation of dihalomethanes by whole cells was lower than that of 1,2-dichloroethane, but a significant increase of the rate of dihalomethane biodegradation was observed when methanol or ethanol were added as a cosubstrate. Products of the degradation of several tested compounds by haloalkane dehalogenase were analyzed and a new metabolic pathway based on hydrolytic conversion to formaldehyde was proposed for the dihalomethanes. Strain GJ10 growing on 1,2-dichloroethane converted 2-fluoroethanol and 1-chloro-2-fluoroethane to 2-fluoroacetate, which was tolerated up to a concentration of 2.5 mM. On the basis of the results from batch cultures an inert (dichloromethane), a growth-supporting (dibromomethane) and a toxic (1,2-dibromoethane) compound were selected for testing their effects on a continuous culture of strain GJ10 growing on 1,2-dichloroethane. The compounds were added as pulses to a steady-state chemostat and the response of the culture was followed. The effects varied from a temporary decrease in cell density for dibromomethane to severe toxicity and culture washout with 1,2-dibromoethane. Our results extend the spectrum of halogenated C1 and C2 compounds that are known to be degraded by strain GJ10 and provide information on toxic effects and transformation of compounds not serving as a carbon source for this bacterium.     

Evidence for recycling of inorganic phosphate by wheat chloroplasts during photosynthesis at air levels of CO2 and O2

Phosphate recycling under photorespiratory conditions was investigated using intact wheat chloroplasts from Triticum aestivum (cv. Maris dove). A decline in the optimal Pi level needed to support steady-state photosynthesis was observed (a) as the bicarbonate supply became limiting, or (b) as oxygen concentrations were increased. Further, at subsaturating CO2 and elevated O2 (52%), photosynthetic induction periods were shortest in the absence of exogenous Pi, and severely extended by its addition. Thus, photosynthesis under low CO2 levels which favor ribulose 1,5 bisphosphate (RuBP) oxygenase activity and glycolate synthesis by chloroplasts decreases their dependency on exogenous Pi from the initial illumination of chloroplasts through to the attainment of steady state rates of O2 evolution. Uptake of phosphate (Pi) was directly measured at ambient O2 concentrations and showed the stoichiometry of O2 evolved to Pi consumed at 10 mmol/L bicarbonate (saturating) had a mean value of 3.0, and was increased to 5.4 at 2.5 mmol/L bicarbonate and to > 8.0 at 1.0 mmol/L bicarbonate. The observation is consistent with enhanced stromal recycling of Pi released during hydrolysis of phosphoglycolate produced in greater quantities as the ratio of RuBP carboxylase relative to oxygenase activities (vc/vo) declines. The theoretical relationship between vc/vo and O2/Pi stoichiometries was derived and compared favorably to experimental data obtained.     

Genotypic variations in carbon isotope discrimination, transpiration efficiency, and biomass production in rice as affected by soil water conditions and N

Genotypic and environmental (soil water regime and N level) variation in carbon isotope discrimination (CID) in relation to the gas exchange, transpiration efficiency (A/T), and biomass production were investigated in field experiments using eleven rice (Oryza sativa L.) genotypes. The results showed that genotype was more dominant for variation in CID than in total biomass. Genotypic ranking in CID was consistent across environments because of small genotype × environment interactions. Japonica genotypes tended to have lower CID than indica genotypes. Higher soil water and lower N rate significantly increased CID. Variation in CID was slightly smaller for water regime than for genotype. There was a negative correlation between CID andA/T among genotypes within water regimes. Genotypic variation in CID was associated mainly with variation in stomatal conductance under all soil water regimes and with photosynthetic capacity in late growth stages under aerobic soil conditions. The decrease in CID at higher N was probably due to lower stomatal conductance under aerobic soil conditions and to higher photosynthetic rates under submerged soil conditions. The correlation between biomass and CID was not clear in aerobic soil, whereas it was positive in submerged soil, which indicated that the significance of lower or higher CID for improving biomass productivity may differ under different soil water regimes. Overall, the results implied a possible use of CID as a selection criterion for genotypic improvement inA/T and productivity in rice.