The methanogenic fermentation of aromatic substrates

The role of terrestrially derived organic carbon in the coastal ocean: a changing paradigm and the priming effect

One of the major conundrums in oceanography for the past 20 y has been that, although the total flux of dissolved organic carbon (OC; DOC) discharged annually to the global ocean can account for the turnover time of all oceanic DOC (ca. 4,000-6,000 y), chemical biomarker and stable isotopic data indicate that there is very little terrestrially derived OC (TerrOC) in the global ocean. Similarly, it has been estimated that only 30% of the TerrOC buried in marine sediments is of terrestrial origin in muddy deltaic regions with high sedimentation rates. If vascular plant material--assumed to be highly resistant to decay--makes up much of the DOC and particulate OC of riverine OC (along with soil OC), why do we not see more TerrOC in coastal and oceanic waters and sediments? An explanation for this "missing" TerrOC in the ocean is critical in our understanding of the global carbon cycle. Here, I consider the origin of vascular plants, the major component of TerrOC, and how their appearance affected the overall cycling of OC on land. I also examine the role vascular plant material plays in soil OC, inland aquatic ecosystems, and the ocean, and how our understanding of TerrOC and "priming" processes in these natural systems has gained considerable interests in the terrestrial literature, but has largely been ignored in the aquatic sciences. Finally, I close by postulating that priming is in fact an important process that needs to be incorporated into global carbon models in the context of climate change.

Catabolism of phloroglucinol by the rumen anaerobe coprococcus

A rumen isolate, Coprococcus, sp. Pe(1)5, was found to carry phloroglucinol reductase, which catalyzed the initial step in the breakdown of phloroglucinol. The organism uses phloroglucinol as the sole source of carbon and energy when grown in the absence of oxygen. Induced levels of enzyme were detected in cells grown either on phloroglucinol or on other carbon sources in the presence of limiting quantities of phloroglucinol. Although the organism is a strict anaerobe, the enzyme from anaerobically grown cells was insensitive to air. The partially purified enzyme required reduced nicotinamide adenine dinucleotide phosphate as an electron donor and was specific for phloroglucinol. However, partial enzyme activity (14 to 17%) was also detected in the presence of 2-methyl-1,4-naphthoquinone but not in the presence of several other phenolic compounds. The enzyme exhibited a higher affinity for phloroglucinol than for reduced nicotinamide adenine dinucleotide phosphate, with K(m) values of 3.0 x 10 M and 29.0 x 10 M, respectively. The optimum pH for maximal enzyme activity was 7.4, and the molecular weight of the native protein was about 130,000, as determined by the Sephadex gel filtration technique.

Effect of oxidized leachate on degradation of lignin by sulfate-reducing bacteria

Municipal solid waste materials (MSWs) in landfills need a long period of stabilization because lignin compounds in MSWs and leachate are not readily biodegraded, but inhibit methanogenic metabolism. Recirculation of leachate into the landfill offers the potential advantage of increasing the rate of decomposition of organic matter. However, the degradation of lignin by leachate recirculation alone is quite difficult. Several recent studies have demonstrated that sulfate-reducing bacteria (SRB) were able to degrade lignin compounds. In this study, batch tests were conducted to investigate the impacts of SRB enrichment on lignin decomposition rates as well as the decomposition of other biodegradable organics. Further, the effects of nitrite and nitrate on lignin degradation rates were also studied. A 16S rRNA assay showed that the SRB used herein, which were obtained by enriching solid waste collected from a closed MSW landfill, were Thaurea sp. and Desulfovibrio sp. Lignin was found to be biodegraded by the SRB and the rate of lignin removal per unit of waste volatile suspended solid was 2.9 mg lignin g—1 VSS day— 1. It was found that the initial degradation rate increased under higher initial lignin concentrations. However, the degradation rate during days 6—19 became slower than that during the initial 9 days because lignin consisted of complexly bonded aromatic compounds that were not readily biodegradable. Adding other organics such as lactate seemed to improve the rate and amount of lignin degradation, probably due to the increase in SRB associated with consumption of the additional organics. The lignin removal percentage decreased with increases in oxidized nitrogen (nitrite or nitrate) concentrations, indicating that oxidized nitrogen could inhibit SRB activity. Conclusively, the study verified the existence of SRB in the landfill and showed that the SRB could be activated for the degradation of lignin by the recirculation of the leachate, which is consistent with other studies showing that leachate recirculation could shorten the stabilization period of the landfill.

Degradation of 3-chlorobenzoate under low-oxygen conditions in pure and mixed cultures of the anoxygenic photoheterotroph Rhodopseudomonas palustris DCP3 and an aerobic Alcaligenes species

The presence or absence of molecular oxygen has been shown to play a crucial role in the degradability of haloaromatic compounds. In the present study, it was shown that anaerobic phototrophic 3-chlorobenzoate (3CBA) metabolism by Rhodopseudomonas palustris DCP3 is oxygen tolerant up to a concentration of 3 microM O2. Simultaneous oxidation of an additional carbon source permitted light-dependent anaerobic 3CBA degradation at oxygen input levels which, in the absence of such an additional compound, would result in inhibition of light-dependent dehalogenation. Experiments under the same experimental conditions with strain DCP3 in coculture with an aerobic 3CBA-utilizing heterotroph, Alcaligenes sp. strain L6, revealed that light-dependent dehalogenation of 3CBA did not occur. Under both oxygen limitation (O2 < 0.1 microM) and low oxygen concentrations (3 microM O2), all the 3CBA was metabolized by the aerobic heterotroph. These data suggest that biodegradation of (halo)aromatics by photoheterotrophic bacteria such as R. palustris DCP3 may be restricted to anoxic photic environments.

The bacterial degradation of benzoic acid and benzenoid compounds under anaerobic conditions: unifying trends and new perspectives

Simple homocyclic aromatic compounds are extremely abundant in the environment and are derived largely from lignin. Such compounds may enter anaerobic environments and several groups of bacteria, exhibiting diverse energy-yielding mechanisms, have evolved the capacity to overcome the thermodynamic stability of the benzene nucleus and degrade aromatic compounds under these conditions. Over the last few years considerable advances have been made in our understanding of the biochemical strategies underlying the bacterial degradation of aromatic compounds in anoxic environments. The study of the biochemistry, and more recently the molecular genetics of the photosynthetic bacterium Rhodopseudomonas palustris and several strains of denitrifying pseudomonads, has provided the greatest insight into the mechanism and regulation of aromatic degradation under anaerobic conditions. Research has centred around the anaerobic degradation of benzoic acid. This involves the initial activation to form benzoyl-Coenzyme A, reduction of the aromatic nucleus--a reaction that has only recently been demonstrated in vitro--and the subsequent degradation of the alicyclic intermediates. Recently, much information regarding the exact nature of these intermediates has been obtained. Also through recent studies, it has become increasingly clear that benzoyl-CoA is a central metabolic intermediate during the anaerobic degradation of structurally diverse aromatic compounds. The initial metabolism of these compounds involves the formation of a carboxyl group on the aromatic nucleus (if necessary) and the synthesis of the respective Coenzyme A thioester; this results in the direct formation of benzoyl-Coenzyme A rather than benzoate. In many cases of anaerobic aromatic degradation studied in batch culture, aromatic intermediates are transiently excreted into the medium. It is argued that the study of this phenomenon may facilitate the understanding of the regulation and kinetics of the aromatic degradative pathways.

Anaerobic degradation of trans-cinnamate and omega-phenylalkane carboxylic acids by the photosynthetic bacterium Rhodopseudomonas palustris: evidence for a beta-oxidation mechanism

The mechanism responsible for the initial steps in the anaerobic degradation of trans-cinnamate and omega-phenylalkane carboxylates by the purple non-sulphur photosynthetic bacterium Rhodopseudomonas palustris was investigated. Phenylacetate did not support growth and there was a marked CO2 dependence for growth on acids with greater side-chain lengths. Here, CO2 was presumably acting as a redox sink for the disposal of excess reducing equivalents. Growth on benzoate did not require the addition of exogenous CO2. Aromatic acids with an odd number of side-chain carbon atoms (3-phenylpropionate, 5-phenylvalerate, 7-phenylheptanoate) gave greater apparent molar growth yields than those with an even number of side-chain carbon atoms (4-phenylbutyrate, 6-phenylhexanoate, 8-phenyloctanoate). HPLC analysis revealed that phenylacetate accumulated and persisted in the culture medium during growth on these latter compounds. Cinnamate and benzoate transiently accumulated in the culture medium during growth on 3-phenylpropionate, and benzoate alone accumulated transiently during the course of trans-cinnamate degradation. The transient accumulation of 4-phenyl-2-butenoic acid occurred during growth on 4-phenylbutyrate, and phenylacetate accumulated to a 1:1 molar stoichiometry with the initial 4-phenylbutyrate concentration. It is proposed that the initial steps in the anaerobic degradation of trans-cinnamate and the group of acids from 3-phenylpropionate to 8-phenyloctanoate involves beta-oxidation of the side-chain.

Anaerobic phototrophic metabolism of 3-chlorobenzoate by Rhodopseudomonas palustris WS17

A mixed phototrophic culture was found to reductively metabolize 3-chlorobenzoate in the presence of benzoate following adaptation for a period of 7 weeks. The dominant bacterial isolate from this mixed culture, identified as Rhodopseudomonas palustris WS17, metabolized 3-chlorobenzoate completely in the presence of benzoate and light and in the absence of oxygen. [14C]3-chlorobenzoate was converted to 14CO2 and cell 3-chlorobenzoate metabolism is a common phenomenon in this species.

Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris

The purple nonsulfur photosynthetic bacterium Rhodopseudomonas palustris used diverse aromatic compounds for growth under anaerobic and aerobic conditions. Many phenolic, dihydroxylated, and methoxylated aromatic acids, as well as aromatic aldehydes and hydroaromatic acids, supported growth of strain CGA001 in both the presence and absence of oxygen. Some compounds were metabolized under only aerobic or under only anaerobic conditions. Two other strains, CGC023 and CGD052, had similar anaerobic substrate utilization patterns, but CGD052 was able to use a slightly larger number of compounds for growth. These results show that R. palustris is far more versatile in terms of aromatic degradation than had been previously demonstrated. A mutant (CGA033) blocked in aerobic aromatic metabolism remained wild type with respect to anaerobic degradative abilities, indicating that separate metabolic pathways mediate aerobic and anaerobic breakdown of diverse aromatics. Another mutant (CGA047) was unable to grow anaerobically on either benzoate or 4-hydroxybenzoate, and these compounds accumulated in growth media when cells were grown on more complex aromatic compounds. This indicates that R. palustris has two major anaerobic routes for aromatic ring fission, one that passes through benzoate and one that passes through 4-hydroxybenzoate.

Methane Fermentation of Ferulate and Benzoate: Anaerobic Degradation Pathways

The anaerobic biodegradation of ferulate and benzoate in stabilized methanogenic consortia was examined in detail. Up to 99% of the ferulate and 98% of the benzoate were converted to carbon dioxide and methane. Methanogenesis was inhibited with 2-bromoethanesulfonic acid, which reduced the gas production and enhanced the buildup of intermediates. Use of high-performance liquid chromatography and two gas chromatographic procedures yielded identification of the following compounds: caffeate, p -hydroxycinnamate, cinnamate, phenylpropionate, phenylacetate, benzoate, and toluene during ferulate degradation; and benzene, cyclohexane, methylcyclohexane, cyclohexanecarboxylate, cyclohexanone, 1-methylcyclohexanone, pimelate, adipate, succinate, lactate, heptanoate, caproate, isocaproate, valerate, butyrate, isobutyrate, propionate, and acetate during the degradation of either benzoate or ferulate. Based on the identification of the above compounds, more complete reductive pathways for ferulate and benzoate are proposed.

Absence of microbial mineralization of lignin in anaerobic enrichment cultures

The existence of anaerobic biodegradation of lignin was examined in mixed microflora. Egyptian soil samples, in which rapid mineralization of organic matter takes place in the presence of an important anaerobic microflora, were used to obtain the anaerobic enrichment cultures for this study. Specifically, 14CO2 or [14C]lignin wood was used to investigate the release of labeled gaseous or soluble degradation products of lignin in microbial cultures. No conversion of 14C-labeled lignin to 14CO2 or 14CH4 was observed after 6 months of incubation at 30 degrees C in anaerobic conditions with or without NO3-. A small increase in soluble radioactivity was observed in certain cultures, but it could not be related to the release of catabolic products during the anaerobic biodegradation of lignin.

The origin of urinary aromatic compounds excreted by ruminants. 3. The metabolism of phenolic compounds to simple phenols

Dietary phenolic cinnamic acids are hydrogenated in the side-chain, demethylated and dehydroxylated in the rumen and are responsible for the large urinary output of benzoic acid by ruminants. 2. Decarboxylation of phenolic acids to simple phenols is another reaction of the intestinal microflora and experiments were made to determine the extent of this reaction in the rumen of sheep. 3. In five experiments phenolic compounds, quinic acid or casein were infused into the rumen or abomasum of sheep and increments in urinary outputs of phenolic acids and phenols determined by thin-layer and gas-liquid chromatography. 4. Production of phenols was almost exclusively confined to reactions in the rumen. 5. Rumen administration of phenolic benzoic or phenylacetic acids which contained a 4-hydroxy substituent yielded large increments in urinary phenol outputs. Other phenolic benzoic and phenylacetic acids were not decarboxylated. Rumen decarboxylation of 4-hydroxy-3-phenylpropionic acid did not occur and decarboxylation of 4-hydroxycinnamic acids was slight. 6. Nearly half the tyrosine content of rumen-administered casein was excreted as p-cresol, a decarboxylation product of 4-hydroxyphenylacetic acid, p-Cresol was the principal phenol found in sheep urine. 7. Catechol and phenol were consistently found in sheep urine samples and p-ethylphenol, resorcinol, quinol, 4-methylcatechol, orcinol and pyrogallol were also found when suitable precursors were infused to the rumen. 8. It is concluded that p-cresol is a rumen metabolite of tyrosine. The other phenols found are microbial metabolites of phenolic precursors which are either widely distributed in plants such as 4-hydroxybenzoic, protocatechuic and vanillic acids or of more limited distribution such as the orcinol glycosides of some Ericaceous plants.

The origin of urinary aromatic compounds excreted by ruminants. 1. The metabolism of quinic, cyclohexanecarboxylic and non-phenolic aromatic acids to benzoic acid

1. The contribution of dietary constituents to the large urinary output of benzoic acid characteristic of ruminants and some herbivores is not well understood. 2. Methods for the analysis of quinic, cyclohexanecarboxylic, benzoic, phenylacetic, 3-phenylpropionic and cinnamic acids in urine and in rumen fluids were developed. 3. The urinary output of aromatic acids by sheep given seven-rations was determined: benzoic acid output varied between 2.8 and 7.8 g/d; phenylacetic acid output between 0.16 and 1.3 g/d; cinnamic acid between 0.08 and 0.25 g/d and small amounts of 3-phenylpropionic acid were found in some samples. 4. Increments in urinary aromatic acid excretion were determined when the acids listed in paragraph 2 were infused via rumen or abomasal cannulas. 5. When cyclohexanecarboxylic acid was infused 40% of the dose was excreted as urinary benzoic acid after either route of infusion. Quinic acid was completely metabolized in the rumen; following rumen infusion between 16 and 53% of the infused acid was recovered as urinary benzoic acid; none was so recovered after abomasal infusion. 6. Urinary recoveries of rumen- and abomasally-infused aromatic acids were: benzoic acid 90 and 88% respectively as benzoic acid, phenylacetic acid 78 and 83% respectively as phenylacetic acid, 3-phenylpropionic acid 96 and 105% respectively as benzoic acid and cinnamic acid, 70 and 70% respectively as benzoic acid. 7. The concentration of aromatic acids in rumen fluid varied with time after feeding: cyclohexanecarboxylic acid was maximal (7 mg/l) 1 h after feeding, benzoic acid was always a minor component (0.5 +/- 0.5 mg/l), phenylacetic acid varied between 0 and 35 mg/l and 3-phenylpropionic acid between 25 and 47 mg/l. Cinnamic acid was not found in rumen fluid but on rumen infusion of this acid the concentration of 3-phenylpropionic acid in rumen fluid increased by 10 mg/l rumen fluid per g infused per d. 8. The incomplete metabolism of quinic and cyclohexanecarboxylic acids to urinary benzoic acid is discussed. It is concluded that the principal dietary precursors of urinary benzoic acid in ruminants are compounds yielding 3-phenylpropionic acid on microbial fermentation in the rumen. The small amount of cinnamic acid characteristic of ruminant urine arises as an intermediate in the beta-oxidation of 3-phenylpropionic acid in the body tissues.

Methanogenic Decomposition of Ferulic Acid, a Model Lignin Derivative

Ferulic acid, a model lignin derivative, was observed to be biodegradable to methane and carbon dioxide under strict anaerobic conditions. This conversion appears to be carried out by a consortium of bacteria similar to that previously described for the methanogenic degradation of benzoic acid. A temporary buildup of acetate in these cultures indicates that it is a likely intermediate and precursor for methane formation. An analog of coenzyme M, 2-bromoethanesulfonic acid (BESA), inhibited gas production and enhanced the buildup of propionate, butyrate, isobutyrate, and isovalerate. Phenylacetate, cinnamate, 3-phenylpropionate, benzoate, cyclohexane carboxylate, adipate, and pimelate were also detected in BESA-inhibited cultures. A pathway is proposed which includes these various acids as possible intermediates in the methanogenic degradation of ferulic acid. This model overlaps previously described benzoic acid degradation pathways, suggesting that this type of anaerobic degradation may be common for aromatic compounds.

Biochemistry of the bacterial catabolism of aromatic compounds in anaerobic environments

Methods of aerobic degradation of aromatic compounds in the biosphere are well understood, but it is only relatively recently that it has been shown how some bacteria can also degrade these substrates in the absence of molecular oxygen. This occurs by photometabolism (Athiorhodaceae), nitrate respiration (Pseudomonas and Moraxella sp.) and methanogenic fermentation (a consortium) in which the benzene nucleus is first reduced and then cleaved by hydrolysis to yield aliphatic acids for cell growth. These methods may be used by microbial communities to catabolise man-made pollutants.

Methanogenic fermentation of benzoate in an enrichment culture

Enrichment cultures inoculated with black mud fermented benzoate according to the stoichiometric equation: 4 C6H5CO2H+18 H2O → 15 CH4+13 CO2.Trans-2-hydroxycyclohexanecarboxylate, 2-oxo-cyclohexanecarboxylate, pimelate, caproate, butyrate, acetate, and molecular hydrogen were shown to be regular components of the culture fluid occurring in low concentrations. Inhibition of methanogenesis by chloroform, 4-chlorobutyrate, or 2-bromooctanoate resulted in a cessation of the benzoate breakdown after all intermediates had accumulated. It is proposed that benzoate is fermented via a direct reductive pathway to butyrate, acetate, H2, and CO2, whereafter butyrate is converted to acetate and H2, and the latter substrates are fermented to CH4 and CO2 by methane producers.