Cometabolic isoterpinolene formation from isolimonene by denitrifyingAlcaligenes defragrans

Anaerobic digestion of orange peel in a semi-continuous pilot plant: An environmentally sound way of citrus waste management in agro-ecosystems

The management of residues of citrus processing involves economic and environmental problems. In particular, the uncontrolled disposal of citrus processing waste near production sites can have heavy impacts on air, soil, surface water bodies and groundwater. Anaerobic digestion has been proposed as a viable alternative for citrus waste valorisation, if some problems, linked to the biochemical processes, are overcome. Although many experimental tests have studied the inhibitory effects of the high essential oil content of orange peel on biomethanisation processes, fewer experiences have been carried out in continuous or semi-continuous pilot digesters, more similar to the full-scale biogas plants, using real orange peel. This study has evaluated the methane production through anaerobic digestion of industrial orange peel using a pilot plant (84L) with semi-continuous feeding at increasing Organic Loading Rates (OLR) and essential oil (EO) supply rates (EOsr) until the complete process inhibition. Under mesophilic conditions, the highest daily specific methane yield was achieved at OLR of 1.0g_TVSL^-1 d^-1 and EOsr of 47.6mgL^-1d^-1. Partial inhibition of the anaerobic digestion was detected at OLR and EOsr of 1.98g_TVSL^-1d^-1 and 88.1mgL^-1 d^-1, respectively and the process irreversibly stopped when OLR and EOsr reached 2.5g_TVS L^-1 d^-1 and 111.2mgL^-1 d^-1, respectively. Under thermophilic conditions, the cumulative methane production (0.12Lg_TVS^-1) was about 25% of that under mesophilic conditions (0.46Lg_TVS^-1). The thermophilic digestion was completely inhibited at lower OLR (1.98g_TVSL^-1 d^-1) and EOsr (88.1mgL^-1 d^-1) compared to mesophilic conditions. This study confirmed the suitability of anaerobic digestion of orange peel for biomethane production (provided that the right management of the process is set), in view of an environmentally sound way of agricultural residues management in agro-ecosystems.

Limonene dehydrogenase hydroxylates the allylic methyl group of cyclic monoterpenes in the anaerobic terpene degradation by Castellaniella defragrans

The enzymatic functionalization of hydrocarbons is a central step in the global carbon cycle initiating the mineralization of methane, isoprenes, and monoterpenes, the most abundant biologically produced hydrocarbons. Also, terpene-modifying enzymes have found many applications in the energy-economic biotechnological production of fine chemicals. Here, we describe a limonene dehydrogenase that was purified from the facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen grown on monoterpenes under denitrifying conditions in the absence of molecular oxygen. The purified limonene:ferrocenium oxidoreductase activity hydroxylated the methyl group of limonene (1-methyl-4-(1-methylethenyl)-cyclohex-1-ene) yielding perillyl alcohol ([4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol). The enzyme had a DTT:perillyl alcohol oxidoreductase activity yielding limonene. Mass spectrometry and molecular size determinations revealed a heterodimeric enzyme comprising CtmA and CtmB. Recently, the two proteins had been identified by transposon mutagenesis and proteomics as part of the cyclic terpene metabolism (ctm) in C. defragrans and are annotated as FAD-dependent oxidoreductases of the protein domain family phytoene dehydrogenases and related proteins (COG1233). CtmAB is the first heterodimeric enzyme in this protein superfamily. Flavins in the purified CtmAB are oxidized by ferrocenium and are reduced by limonene. Heterologous expression of CtmA, CtmB, and CtmAB in Escherichia coli demonstrated that limonene dehydrogenase activity required both subunits, each carrying a flavin cofactor. Native CtmAB oxidized a wide range of monocyclic monoterpenes containing the allylic methyl group motif (1-methyl-cyclohex-1-ene). In conclusion, we have identified CtmAB as a hydroxylating limonene dehydrogenase and the first heteromer in a family of FAD-dependent dehydrogenases acting on allylic methylene or methyl CH-bonds. We suggest placing in Enzyme Nomenclature as new entry EC 1.17.99.8.

Citrus essential oils and their influence on the anaerobic digestion process: an overview

Citrus waste accounts for more than half of the whole fruit when processed for juice extraction. Among valorisation possibilities, anaerobic digestion for methane generation appears to be the most technically feasible and environmentally friendly alternative. However, citrus essential oils can inhibit this biological process. In this paper, the characteristics of citrus essential oils, as well as the mechanisms of their antimicrobial effects and potential adaptation mechanisms are reviewed. Previous studies of anaerobic digestion of citrus waste under different conditions are presented; however, some controversy exists regarding the limiting dosage of limonene for a stable process (24-192 mg of citrus essential oil per liter of digester and day). Successful strategies to avoid process inhibition by citrus essential oils are based either on recovery or removal of the limonene, by extraction or fungal pre-treatment respectively.

The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen

Background

The facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen utilizes acyclic, monocyclic and bicyclic monoterpenes as sole carbon source under oxic as well as anoxic conditions. A biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. An in-frame deletion mutant did not use myrcene, but was able to grow on monocyclic monoterpenes. The genome sequence and a comparative proteome analysis together with a random transposon mutagenesis were conducted to identify genes involved in the monocyclic monoterpene metabolism. Metabolites accumulating in cultures of transposon and in-frame deletion mutants disclosed the degradation pathway.

Results

Castellaniella defragrans 65Phen oxidizes the monocyclic monoterpene limonene at the primary methyl group forming perillyl alcohol. The genome of 3.95 Mb contained a 70 kb genome island coding for over 50 proteins involved in the monoterpene metabolism. This island showed higher homology to genes of another monoterpene-mineralizing betaproteobacterium, Thauera terpenica 58Eu^T, than to genomes of the family Alcaligenaceae, which harbors the genus Castellaniella. A collection of 72 transposon mutants unable to grow on limonene contained 17 inactivated genes, with 46 mutants located in the two genes ctmAB (cyclic terpene metabolism). CtmA and ctmB were annotated as FAD-dependent oxidoreductases and clustered together with ctmE, a 2Fe-2S ferredoxin gene, and ctmF, coding for a NADH:ferredoxin oxidoreductase. Transposon mutants of ctmA, B or E did not grow aerobically or anaerobically on limonene, but on perillyl alcohol. The next steps in the pathway are catalyzed by the geraniol dehydrogenase GeoA and the geranial dehydrogenase GeoB, yielding perillic acid. Two transposon mutants had inactivated genes of the monoterpene ring cleavage (mrc) pathway. 2-Methylcitrate synthase and 2-methylcitrate dehydratase were also essential for the monoterpene metabolism but not for growth on acetate.

Conclusions

The genome of Castellaniella defragrans 65Phen is related to other genomes of Alcaligenaceae, but contains a genomic island with genes of the monoterpene metabolism. Castellaniella defragrans 65Phen degrades limonene via a limonene dehydrogenase and the oxidation of perillyl alcohol. The initial oxidation at the primary methyl group is independent of molecular oxygen.

Physiology of deletion mutants in the anaerobic β-myrcene degradation pathway in Castellaniella defragrans

BACKGROUND

Monoterpenes present a large and versatile group of unsaturated hydrocarbons of plant origin with widespread use in the fragrance as well as food industry. The anaerobic β-myrcene degradation pathway in Castellaniella defragrans strain 65Phen differs from well known aerobic, monooxygenase-containing pathways. The initial enzyme linalool dehydratase-isomerase ldi/LDI catalyzes the hydration of β-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/GaDH contribute to the formation of geranic acid.A genetic system was for the first time applied for the betaproteobacterium to prove in vivo the relevance of the linalool dehydratase-isomerase and the geraniol dehydrogenase. In-frame deletion cassettes were introduced by conjugation and two homologous recombination events.

RESULTS

Polar effects were absent in the in-frame deletion mutants C. defragrans Δldi and C. defragrans ΔgeoA. The physiological characterization of the strains demonstrated a requirement of the linalool dehydratase-isomerase for growth on acyclic monoterpenes, but not on cyclic monoterpenes. The deletion of geoA resulted in a phenotype with hampered growth rate on monoterpenes as sole carbon and energy source as well as reduced biomass yields. Enzyme assays revealed the presence of a second geraniol dehydrogenase. The deletion mutants were in trans complemented with the broad-host range expression vector pBBR1MCS-4ldi and pBBR1MCS-2geoA, restoring in both cases the wild type phenotype.

CONCLUSIONS

In-frame deletion mutants of genes in the anaerobic β-myrcene degradation revealed novel insights in the in vivo function. The deletion of a high-affinity geraniol dehydrogenase hampered, but did not preclude growth on monoterpenes. A second geraniol dehydrogenase activity was present that contributes to the β-myrcene degradation pathway. Growth on cyclic monoterpenes independent of the initial enzyme LDI suggests the presence of a second enzyme system activating unsaturated hydrocarbons.

Anaerobic oxidation of n-alkenes by sulphate-reducing bacteria from the genus Desulfatiferula: n-ketones as potential metabolites

Two alkene-degrading sulphate-reducing bacteria from the genus Desulfatiferula (Desulfatiferula olefinivorans strain LM2801(T) and Desulfatiferula sp. strain BE2801) were investigated for their 1-alkene metabolism. Their total cellular fatty acids were predominantly C-even when they were grown on C-even 1-alkene (1-hexadecene), whereas a mixture of fatty acids with C-odd or C-even carbon chains predominated when cells were grown on C-odd 1-alkene (1-pentadecene). This is consistent with the fatty acid composition of other sulphate-reducing strains previously reported to grow on n-alkenes. Linear and 3-OH-fatty acids appear to be the main fatty acids produced by the two Desulfatiferula strains. The analysis of their neutral lipids led to identifying several n-alkanols and n-ketones with the same number of carbon atoms as the alkene growth substrate and with functionality located between C-1 and C-5. Growth of strains LM2801(T) and BE2801 on (per) deuterated 1-alkenes provided direct evidence of their anaerobic transformation to corresponding 1-alkanols, n-ketones and linear (3-OH-) fatty acids. These results demonstrate that Desulfatiferula strains oxidize a 1-alkene by oxidation of the double bond at C-1, but also at C-2 to C-5 (after eventual isomerization of the double bond) yielding the corresponding C-2 to C-5 n-ketones (via the corresponding n-alkanols). The formation of specific 3-OH-fatty acids by elongation of shorter chain fatty acids was also demonstrated. Based on our observations, pathways for anaerobic 1-alkene metabolism in sulphate-reducing bacteria from the genus Desulfatiferula are proposed. They indicate that n-ketones can constitute new metabolites of the biodegradation of n-alkenes in anaerobic environments.

Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes

Castellaniella (ex Alcaligenes) defragrans strain 65Phen mineralizes monoterpenes in the absence of oxygen. Soluble cell extracts anaerobically catalyzed the isomerization of geraniol to linalool and the dehydration of linalool to myrcene. The linalool dehydratase was present in cells grown on monoterpenes, but not if grown on acetate. We purified the novel enzyme ∼1800-fold to complete homogeneity. The native enzyme had a molecular mass of 160 kDa. Denaturing gel electrophoresis revealed one single protein band with a molecular mass of 40 kDa, which indicated a homotetramer as native conformation. The aerobically purified enzyme was anaerobically activated in the presence of 2 mm DTT. The linalool dehydratase catalyzed in vitro two reactions in both directions depending on the thermodynamic driving forces: a water secession from the tertiary alcohol linalool to the corresponding acyclic monoterpene myrcene and an isomerization of the primary allylalcohol geraniol in its stereoisomer linalool. The specific activities (V(max)) were 140 nanokatals mg(-1) for the linalool dehydratase and 410 nanokatals mg(-1) for the geraniol isomerase, with apparent K(m) values of 750 μm and 500 μm, respectively. The corresponding open reading frame was identified and revealed a precursor protein with a signal peptide for a periplasmatic location. The amino acid sequence did not affiliate with any described enzymes. We suggest naming the enzyme linalool dehydratase-isomerase according to its bifunctionality and placing it as a member of a new protein family within the hydrolyases (EC 4.2.1.X).

Characterization of diverse heterocyclic amine-degrading denitrifying bacteria from various environments

Although, there have been many published bacterial strains aerobically degrading the heterocyclic amine compounds, only one strain to date has been reported to degrade pyrrolidine under denitrifying conditions. In this study, denitrifying bacteria degrading pyrrolidine and piperidine were isolated from diverse geological and ecological origins through selective enrichment procedures. Based on the comparative sequence results of 16S rRNA genes, 30 heterocyclic amine-degrading isolates were grouped into ten distinct phylotypes belonging to the genera Thauera, Castellaniella, Rhizobium, or Paracoccus of the phylum Proteobacteria. The representative isolates of individual phylotypes were characterized by phylogenetic, phenotypic and chemotaxonomical traits, and dissimilatory nitrite reductase gene (nirK and nirS). All isolates completely degraded pyrrolidine and piperidine under both aerobic and anaerobic conditions. The anaerobic degradations were coupled to nitrate reduction. A metabolic pathway for the anaerobic degradation of pyrrolidine was proposed on the basis of enzyme activities implicated in pyrrolidine metabolism from three isolates. The three key pyrrolidine-metabolizing enzymes pyrrolidine dehydrogenase, gamma-aminobutyrate/alpha-ketoglutarate aminotransferase, and succinic semialdehyde dehydrogenase, were induced by heterocyclic amines under denitrifying conditions. They were also induced in cells grown aerobically on heterocyclic amines, suggesting that the anaerobic degradation of pyrrolidine shares the pathway with aerobic degradation.

Biotransformation of terpenes

The main application of terpenes as fragrances and flavors depends on the absolute configuration of the compounds because enantiomers present different organoleptic properties. Biotransformations allow the production of regio- and stereoselective compounds under mild conditions. These products may be labeled as "natural". Commercially useful chemical building-blocks and pharmaceutical stereo isomers can also be produced by bioconversion of terpenes. Enzymes and extracts from bacteria, cyanobacteria, yeasts, microalgae, fungi, plants, and animal cells have been used for the production and/or bioconversion of terpenes. In addition, whole cell catalysis has also been used. A variety of media and reactors have been assessed for these biotransformations and have produced encouraging results, as discussed in this review.

Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate

Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the alpha, beta, delta, and gamma subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing delta-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the delta-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

Geranic acid formation, an initial reaction of anaerobic monoterpene metabolism in denitrifying Alcaligenes defragrans

Monoterpenes with an unsaturated hydrocarbon structure are mineralized anaerobically by the denitrifying beta-proteobacterium Alcaligenes defragrans. Organic acids occurring in cells of A. defragrans and culture medium were characterized to identify potential products of the monoterpene activation reaction. Geranic acid (E,E-3,7-dimethyl-2,6-octadienoic acid) accumulated to 0.5 mM in cells grown on alpha-phellandrene under nitrate limitation. Cell suspensions of A. defragrans 65Phen synthesized geranic acid in the presence of beta-myrcene, alpha-phellandrene, limonene, or alpha-pinene. Myrcene yielded the highest transformation rates. The alicyclic acid was consumed by cell suspensions during carbon limitation. Heat-labile substances present in cytosolic extracts catalyzed the formation of geranic acid from myrcene. These results indicated that a novel monoterpene degradation pathway must be present in A. defragrans.

Biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems

Isoprenoic compounds play a major part in the global carbon cycle. Biosynthesis and mineralization by aerobic bacteria have been intensively studied. This review describes our knowledge on the anaerobic metabolism of isoprenoids, mainly by denitrifying and fermentative bacteria. Nitrate-reducing beta-Proteobacteria were isolated on monoterpenes as sole carbon source and electron donor. Thauera spp. were obtained on the oxygen-containing monoterpenes linalool, menthol, and eucalyptol. Several strains of Alcaligenes defragrans were isolated on unsaturated monoterpenes as growth substrates. A novel denitrifying beta-Proteobacterium, strain 72Chol, mineralizes cholesterol completely to carbon dioxide. Physiological studies showed the presence of several oxidative pathways in these microorganisms. Investigations by organic geochemists indicate possible contributions of anaerobes to early diagenetic processes. One example, the formation of p-cymene from monoterpenes, could indeed be detected in methanogenic enrichment cultures. In man, cholic acid (CA) and chenodeoxycholic acid (CDCA), are synthesized in the liver from cholesterol. During their enterohepatic circulation, bile acids are biotransformed by the intestinal microflora into a variety of metabolites. Known bacterial biotranformations of conjugated bile acids include: deconjugation, oxidation of hydroxy groups at C-3, C-7 and C-12 with formation of oxo bile acids and reduction of these oxo groups to either alpha- or beta-configuration. Quantitatively, the most important bacterial biotransformation is the 7 alpha-dehydroxylation of CA and CDCA yielding deoxycholic acid and lithocholic acid, respectively. The 7 alpha-dehydroxylation of CA occurs via a novel six-step biochemical pathway. The genes encoding several enzymes that either transport bile acids or catalyze various reactions in the 7 alpha-dehydroxylation pathway of Eubacterium sp. strain VPI 12708 have been cloned, expressed in Escherichia coli, purified, and characterized.