Bioenergetic Conditions of Butyrate Metabolism by a Syntrophic, Anaerobic Bacterium in Coculture with Hydrogen-Oxidizing Methanogenic and Sulfidogenic Bacteria

The butyrate-oxidizing, proton-reducing, obligately anaerobic bacterium NSF-2 was grown in batch cocultures with either the hydrogen-oxidizing bacterium Methanospirillum hungatei PM-1 or Desulfovibrio sp. strain PS-1. Metabolism of butyrate occurred in two phases. The first phase exhibited exponential growth kinetics (phase a) and had a doubling time of 10 h. This value was independent of whether NSF-2 was cultured with a methanogen or a sulfate reducer and likely represents the maximum specific growth rate of NSF-2. This exponential growth phase was followed by a second phase with a nearly constant rate of degradation (phase b) which dominated the time course of butyrate degradation. The specific activity of H₂ uptake by the hydrogen-oxidizing bacterium controlled the bioenergetic conditions of metabolism in phase b. During this phase both the Gibbs free energy (ΔG′) and the butyrate degradation rate (v) were greater for NSF-2-Desulfovibrio sp. strain PS-1 (ΔG′ = −17.0 kJ/mol; v = 0.20 mM/h) than for NSF-2-M. hungatei PM-1 (ΔG′ = −3.8 kJ/mol, v = 0.12 mM/h). The ΔG′ value remained stable and characteristic of the two hydrogen oxidizers during phase b. The stable ΔG′ resulted from the close coupling of the rates of butyrate and H₂ oxidation. The addition of 2-bromoethanesulfonate to a NSF-2-methanogen coculture resulted in the total inhibition of butyrate degradation; the inhibition was relieved when Desulfovibrio sp. strain PS-1 was added as a new H₂ sink. When the specific activity of H₂ consumption was increased by adding higher densities of the Desulfovibrio sp. to 2-bromoethanesulfonate-inhibited NSF-2-methanogen cocultures, lower H₂ pool sizes and higher rates of butyrate degradation resulted. Thus, it is the kinetic parameters of H₂ consumption, not the type of H₂ consumer per se, that establishes the thermodynamic conditions which in turn control the rate of fatty acid degradation. The bioenergetic homeostasis we observed in phase b was a result of the kinetics of the coculture members and the feedback inhibition by hydrogen which prevents butyrate degradation rates from reaching their theoretical V_max.     

Anaerobic bacteria that dechlorinate perchloroethene.

In this study, we identified specific cultures of anaerobic bacteria that dechlorinate perchlorethene (PCE). The bacteria that significantly dechlorinated PCE were strain DCB-1, an obligate anaerobe previously shown to dechlorinate chlorobenzoate, and two strains of Methanosarcina. The rate of PCE dechlorination by DCB-1 compared favorably with reported rates of trichloroethene bio-oxidation by methanotrophs. Even higher PCE dechlorination rates were achieved when DCB-1 was grown in a methanogenic consortium.     

Clostridium quercicolum sp.n., isolated from discolored tissues in living oak trees

Characteristics of an obligate anaerobe isolated from discolored tissues in living oaks were determined. The bacterium was found to be a motile, sporeforming, gram-negative rod which was catalase- and oxidase-negative. The isolate was weakly fermentative and non-proteolytic. Differences in biochemical activities and DNA base composition between the tree isolate and those of recognized species of Clostridia were considered significant enough to propose the new species,Clostridium quercicolum.     

Kinetics of two complementary hydrogen sink reactions in a defined 3-chlorobenzoate degrading methanogenic co-culture

Abstract The interrelationships between an obligate hydrogen-producing and two different hydrogen-scavenging populations grown as synthrophic members of a 3-chlorobenzoate degrading methanogenic consortium were studied. The hydrogen producer was a benzoate degrader (strain BZ-2), and the hydrogen consumers were a 3-chlorobenzoate dechlorinating bacterium ( Desulfomonile tiedjei ) and a hydrogenotropic methanogen ( Methanospirillum strain PM-1). When a mixture of 3-chlorobenzoate plus benzoate was added to this consortium, the rate of benzoate degradation was 50% higher, at slightly lower H₂ concentrations, than when benzoate alone was added. The enhanced benzoate degradation rate was apparantly triggered by the lower H₂ concentration, as the rate of benzoate degradation was shown to be a function of the H₂ concentration. By offering a hydrogen sink, in addition to methanogenesis, the dechlorinating hydrogen-scavenging population stimulated the rate of benzoate degradation. The lowering of the H₂ concentration was very small, which was in agreement with the observation that the rate of methanogenesis was hardly affected by this lower hydrogen concentration. Thus there was no significant competition for H₂ between the two hydrogen-scavenging populations in the consortium, as they practically complemented each other's hydrogen-scavenging potential at in situ hydrogen concentrations during the degradation of 3-chlorobenzoate. The H₂ concentrations at which hydrogen driven methanogenesis by Methanospirillum occurred in the consortium were well below the threshold concentration extrapolated for this methanogen after growth at high H₂ concentrations.     

Anaerobic bacteria that dechlorinate perchloroethene

In this study, we identified specific cultures of anaerobic bacteria that dechlorinate perchlorethene (PCE). The bacteria that significantly dechlorinated PCE were strain DCB-1, an obligate anaerobe previously shown to dechlorinate chlorobenzoate, and two strains of Methanosarcina. The rate of PCE dechlorination by DCB-1 compared favorably with reported rates of trichloroethene bio-oxidation by methanotrophs. Even higher PCE dechlorination rates were achieved when DCB-1 was grown in a methanogenic consortium.     

Hydrogen cycling in a three-tiered food web growing on the methanogenic conversion of 3-chlorobenzoate

Abstract A defined 3-chlorobenzoate-degrading methanogenic consortium was constructed by recombining key organisms isolated from a 3-chlorobenzoate-degrading methanogenic sludge enrichment. The organisms comprise a three-tiered food chain which includes: (1) reductive dechlorination of 3-chlorobenzoate; (2) oxidation of benzoate to acetate, H₂ and CO₂; (3) removal of H₂ plus CO₂ by conversion into methane. The defined consortium, consisting of a dechlorinating organism (DCB-1), a benzoate degrader (BZ-1) and a lithotrophic methanogen ( Methanospirillum strain PM-1) grew well in a basal salts medium supplemented with 3-chlorobenzoate (3.2 mM) as the sole energy source. The chlorine released from the aromatic ringe was recovered in stoichiometric amounts as the chloride ion. The reducing power required for reductive dechlorination was obtained from the hydrogen produced in the acetogenic oxidation of benzoate. One-third of the benzoate-derived hydrogen was recycled via the reductive dechlorination of 3-chlorobenzoate, indicating that the consortium operated as a food web rather than a food chain.     

Assignment of Clostridium bryantii to Syntrophospora bryantii gen. nov., comb. nov. on the basis of a 16S rRNA sequence analysis of its crotonate-grown pure culture.

The Clostridium bryantii-Methanospirillum hungatei syntrophic coculture, grown on caproate, was adapted to grow on crotonate. Then, C. bryantii was isolated in pure culture from crotonate bottle plates. A 16S rRNA sequence analysis of the pure subculture revealed that, as a member of the gram-positive phylum, it was not closely related to any of the Clostridium species with which it was compared or to any of the other clusters in the gram-positive phylum with which it was compared. However, it was closely related to another syntrophic fatty acid-degrading bacterium, Syntrophomonas wolfei. On the basis of its phylogeny, physiology, and cell wall ultrastructure, we propose assignment of C. bryantii to Syntrophospora bryantii gen. nov., nov. comb.     

Acetate Inhibition of Methanogenic, Syntrophic Benzoate Degradation

Acetate inhibited benzoate degradation by a syntrophic coculture of an anaerobic benzoate degrader (strain BZ-2) and Methanospirillum strain PM-1; the apparent K_i for acetate was approximately 40 mM. The addition of acetate resulted in a decrease in the hydrogen concentration in the coculture, indicating that phenomena related to interspecies hydrogen transfer affected this value and that the effect of acetate on the benzoate-degrading partner was probably greater than the apparent K_i for the coculture suggests.     

Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs

The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture sufficiently supplied with H(2) plus CO(2) and in a coculture with an acetate-oxidizing hydrogen-producing bacterium, Thermacetogenium phaeum strain PB, in which hydrogen partial pressure was constantly kept very low (20 to 80 Pa). Northern blot analysis indicated that only the mcr gene, which encodes methyl coenzyme M reductase I (MRI), catalyzing the final step of methanogenesis, was expressed in the coculture, whereas mcr and mrt, which encodes methyl coenzyme M reductase II (MRII), the isofunctional enzyme of MRI, were expressed at the early to late stage of growth in the pure culture. In contrast to these two genes, two isofunctional genes (mtd and mth) for N(5),N(10)-methylene-tetrahydromethanopterin dehydrogenase, which catalyzes the fourth step of methanogenesis, and two hydrogenase genes (frh and mvh) were expressed both in a pure culture and in a coculture at the early and late stages of growth. The same expression pattern was observed for Methanothermobacter thermoautotrophicus strain DeltaH cocultured with a thermophilic butyrate-oxidizing syntroph, Syntrophothermus lipocalidus strain TGB-C1. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole proteins of M. thermoautotrophicus strain TM obtained from a pure culture and a coculture with the acetate-oxidizing syntroph and subsequent N-terminal amino acid sequence analysis confirmed that MRI and MRII were produced in the pure culture, while only MRI was produced in the coculture. These results indicate that under syntrophic growth conditions, the methanogen preferentially utilizes MRI but not MRII. Considering that hydrogenotrophic methanogens are strictly dependent for growth on hydrogen-producing fermentative microbes in the natural environment and that the hydrogen supply occurs constantly at very low concentrations compared with the supply in pure cultures in the laboratory, the results suggest that MRI is an enzyme primarily functioning in natural methanogenic ecosystems.     

Catabolic thiosulfate disproportionation and carbon dioxide reduction in strain DCB-1, a reductively dechlorinating anaerobe.

Strain DCB-1 is a strict anaerobe capable of reductive dehalogenation. We elucidated metabolic processes in DCB-1 which may be related to dehalogenation and which further characterize the organism physiologically. Sulfoxy anions and CO2 were used by DCB-1 as catabolic electron acceptors. With suitable electron donors, sulfate and thiosulfate were reduced to sulfide. Sulfate and thiosulfate supported growth with formate or hydrogen as the electron donor and thus are probably respiratory electron acceptors. Other electron donors supporting growth with sulfate were CO, lactate, pyruvate, butyrate, and 3-methoxybenzoate. Thiosulfate also supported growth without an additional electron donor, being disproportionated to sulfide and sulfate. In the absence of other electron acceptors, CO2 reduction to acetate plus cell material was coupled to pyruvate oxidation to acetate plus CO2. Pyruvate could not be fermented without an electron acceptor. Carbon monoxide dehydrogenase activity was found in whole cells, indicating that CO2 reduction probably occurred via the acetyl coenzyme A pathway. Autotrophic growth occurred on H2 plus thiosulfate or sulfate. Diazotrophic growth occurred, and whole cells had nitrogenase activity. On the basis of these physiological characteristics, DCB-1 is a thiosulfate-disproportionating bacterium unlike those previously described.     

Isolation of a Butyrate-Utilizing Bacterium in Coculture with Methanobacterium thermoautotrophicum from a Thermophilic Digester

Sludge from a thermophilic, 55 degrees C digester produced methane without a lag period when enriched with butyrate. The sludge was found by most-probable-number enumeration to have ca. 5 x 10 butyrate-utilizing bacteria per ml. A thermophilic butyrate-utilizing bacterium was isolated in coculture with Methanobacterium thermoautotrophicum. This bacterium was a gram-negative, slightly curved rod, occurred singly, was nonmotile, and did not appear to produce spores. When this coculture was incubated with Methanospirillum hungatei at 37 degrees C, the quantity of methane produced was less than 5% of the methane produced when the coculture was incubated at 55 degrees C, the routine incubation temperature. The coculture required clarified digester fluid. The addition of yeast extract to medium containing 5% clarified digester fluid stimulated methane production when a Methanosarcina sp. was present. Hydrogen in the gas phase prevented butyrate utilization. However, when the hydrogen was removed, butyrate utilization began. Penicillin G and d-cycloserine caused the complete inhibition of butyrate utilization by the coculture. The ability of various ecosystems to convert butyrate to methane was studied. Marine sediments enriched with butyrate required a 2-week incubation period before methanogenesis began. Hypersaline sediments did not produce methane after 3 months when enriched with butyrate.     

Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.

Desulfomonile tiedjei DCB-1 is a strict anaerobe capable of reductively dechlorinating meta-chlorobenzoates. To probe the mechanism of this aryl dechlorination, we incubated cell suspensions of D. tiedjei in D2O and with 2,5-dichlorobenzoate. The deuterium was incorporated into the dechlorination product exclusively at the position of dehalogenation, as shown by gas chromatography-mass spectrometry and proton magnetic resonance analyses. These results favor a model for dechlorination that should not allow proton exchange at other positions, as would be the case if partial ring reduction occurred.     

Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.

Desulfomonile tiedjei DCB-1 is a strict anaerobe capable of reductively dechlorinating meta-chlorobenzoates. To probe the mechanism of this aryl dechlorination, we incubated cell suspensions of D. tiedjei in D2O and with 2,5-dichlorobenzoate. The deuterium was incorporated into the dechlorination product exclusively at the position of dehalogenation, as shown by gas chromatography-mass spectrometry and proton magnetic resonance analyses. These results favor a model for dechlorination that should not allow proton exchange at other positions, as would be the case if partial ring reduction occurred.     

Growth of the syntrophic anaerobic acetogen, strain PA-1, with glucose or succinate as energy source.

Strain PA-1 (S. Barik, W.J. Brulla, and M.P. Bryant, Appl. Environ. Microbiol. 50:304-310, 1985) is an anaerobic, gram-negative rod that in pure culture decarboxylates succinate to propionate and that grows syntrophically as an acetogen with the H2 utilizer Methanospirillum hungatei if glucose, pyruvate, aspartate, or fumarate is provided. In pure culture, strain PA-1 grows optimally in a medium containing 5% ruminal fluid, 0.1% yeast extract, a 4:1 N2-CO2 gas phase, and 20 mM succinate. With the PA-1 plus M. hungatei coculture, good growth was obtained with 7.5 mM glucose and tryptophan could replace the yeast extract. Strain PA-1 in pure culture grew quite well in glucose medium if the large headspace was flushed intermittently with N2. Flushing with H2 inhibited this growth.     

Growth of the syntrophic anaerobic acetogen, strain PA-1, with glucose or succinate as energy source

Strain PA-1 (S. Barik, W.J. Brulla, and M.P. Bryant, Appl. Environ. Microbiol. 50:304-310, 1985) is an anaerobic, gram-negative rod that in pure culture decarboxylates succinate to propionate and that grows syntrophically as an acetogen with the H2 utilizer Methanospirillum hungatei if glucose, pyruvate, aspartate, or fumarate is provided. In pure culture, strain PA-1 grows optimally in a medium containing 5% ruminal fluid, 0.1% yeast extract, a 4:1 N2-CO2 gas phase, and 20 mM succinate. With the PA-1 plus M. hungatei coculture, good growth was obtained with 7.5 mM glucose and tryptophan could replace the yeast extract. Strain PA-1 in pure culture grew quite well in glucose medium if the large headspace was flushed intermittently with N2. Flushing with H2 inhibited this growth.     

Reciprocal Isomerization of Butyrate and Isobutyrate by the Strictly Anaerobic Bacterium Strain WoG13 and Methanogenic Isobutyrate Degradation by a Defined Triculture

Isomerization of butyrate and isobutyrate was investigated with the recently isolated strictly anaerobic bacterium strain WoG13 which ferments glutarate to butyrate, isobutyrate, CO₂, and small amounts of acetate. Dense cell suspensions converted butyrate to isobutyrate and isobutyrate to butyrate. ¹³C-nuclear magnetic resonance experiments proved that this isomerization was accomplished by migration of the carboxyl group to the adjacent carbon atom. In cell extracts, both butyrate and isobutyrate were activated to their coenzyme A (CoA) esters by acyl-CoA:acetate CoA-transferases. The reciprocal rearrangement of butyryl-CoA and isobutyryl-CoA was catalyzed by a butyryl-CoA:isobutyryl-CoA mutase which depended strictly on the presence of coenzyme B₁₂. Isobutyrate was completely degraded via butyrate to acetate and methane by a defined triculture of strain WoG13, Syntrophomonas wolfei, and Methanospirillum hungatei.     

Involvement of a Collar Structure in Polar Growth and Cell Division of Strain DCB-1

Microscopic methods were used to investigate the unique collar structure of the gram-negative sulfate-reducing bacterium, strain DCB-1. Polar cell growth apparently occurred from the collar. When the daughter cell was approximately equal in length to the mother cell and the collar was thus centrally located, cell division occurred within the collar region. Division was by a novel mechanism which conserved the collar of the mother cell and gave rise to a new collar of the daughter cell. Cells of DCB-1 were also found to contain stacked internal membranes and glycogen bodies.     

A growth study of Coxiella burnetii Nine Mile Phase I and Phase II in fibroblasts

Coxiella burnetii, a slow-growing, gram-negative, obligate intracellular bacterium, is the causative agent of Q fever in humans. The avirulent Phase II C. burnetii Nine Mile strain can invade and establish persistent infections in a wide variety of laboratory cell lines, and is generally considered to be easier to grow in culture than the wild-type Phase I organism. Efforts to improve Phase I organism yield in the BHK-21 cell line demonstrated that high CO2 conditions and the use of Dulbecco's modified Eagle's medium (DMEM) with 4.5 g/l glucose supplementation resulted in higher organism yields. Phase II organisms grown in the same cell line and conditions showed lower growth rates. Analysis revealed that increased average numbers of C. burnetii Phase I organisms within fibroblasts was due to higher growth rates within the hosts rather than to increased uptake or to increased cell-to-cell spreading. Addition of the nucleoside cytidine to the growth medium stimulated growth of Phase II but not Phase I organisms.     

Characterization of the requirements and substrates for reductive dehalogenation by strain DCB-1

Summary An obligately anaerobic bacterium known as strain DCB-1 was grown under a variety of conditions to determine the requirements for dehalogenation as well as factors which stimulated or inhibited the process. Dechlorination was obligately anaerobic since introduction of O₂ immediately inhibited the reaction. Sulfuroxy anions, which also serve as electron acceptors for DCB-1, inhibited dechlorination but NO₃ ^– and fumarate did not. The optimum growth medium for dechlorination was 0.2% Na pyruvate and 20% rumen fluid in basal salts. Media with either pyruvate or rumen fluid alone did not support dechlorination. DCB-1 also consumed H₂ but typical substrate concentrations of H₂ (80 kPa) delayed dechlorination. Once the H₂ concentration was reduced to <20 M (2.67 kPa), dechlorination resumed. Dehalogenation by DCB-1 was restricted to the meta substituted benzoates as halogens in other positions and chloroaromatic compounds with other functional groups were not dechlorinated.