Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700

Microbial Evolution in Artisanal Pecorino-like Cheeses Produced from Two Farms Managing Two Different Breeds of Sheep (Comisana and Lacaune)

"Pecorino" is a typical semi-hard cheese obtained with raw or heat-treated sheep milk using procedures to valorize the raw material's chemical and microbiological properties. In the present study, using a high-throughput method of 16S rRNA gene sequencing, we assessed the evolution of the microbiome composition from milk to Pecorino-like cheese in artisanal processes using milk from Comisana and Lacaune sheep breeds. The comparative analysis of the bacterial community composition revealed significant differences in the presence and abundance of specific taxa in the milk microbiomes of the Comisana and Lacaune breeds. Next-Generation Sequencing (NGS) analysis also revealed differences in the curd microbiomes related to dairy farming practices, which have a relevant effect on the final structure of the Pecorino cheese microbiome.

Genome Analysis and Physiology of Pseudomonas sp. Strain OVF7 Degrading Naphthalene and n-Dodecane

The complete genome of the naphthalene- and n-alkane-degrading strain Pseudomonas sp. strain OVF7 was collected and analyzed. Clusters of genes encoding enzymes for the degradation of naphthalene and n-alkanes are localized on the chromosome. Based on the Average Nucleotide Identity and digital DNA-DNA Hybridization compared with type strains of the group of fluorescent pseudomonads, the bacterium studied probably belongs to a new species. Using light, fluorescent, and scanning electron microscopy, the ability of the studied bacterium to form biofilms of different architectures when cultured in liquid mineral medium with different carbon sources, including naphthalene and n-dodecane, was demonstrated. When grown on a mixture of naphthalene and n-dodecane, the strain first consumed naphthalene and then n-dodecane. Cultivation of the strain on n-dodecane was characterized by a long adaptation phase, in contrast to cultivation on naphthalene and a mixture of naphthalene and n-dodecane.

Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm

Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l-1. The results indicated that most probably diclofenac biodegrading cultures consisted of members of genera Ferrovibrio, Hydrocarboniphaga, Zavarzinia, and Sphingopyxis, while in ibuprofen biodegradation Nocardioides and Starkeya, and in carbamazepine biodegradation Nocardioides, Pseudonocardia, and Sphingopyxis might be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. Except Starkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation. Stenotrophomonas humi DIC_5 and Rhizobium daejeonense IBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l-1) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.

Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance

Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) -like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.

Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production

While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. In this work, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.

Together Is Better: The Rumen Microbial Community as Biological Toolbox for Degradation of Synthetic Polyesters

Identfication of plastics degradation and microbial community analysis of Rumen.

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Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

MetA (Rv3341) from Mycobacterium tuberculosis H37Rv strain exhibits substrate dependent dual role of transferase and hydrolase activity

The metA (Rv3341) gene from Mycobacterium tuberculosis H37Rv strain encodes a homoserine-acetyltransferase (HAT) enzyme, also called MetA. This enzyme plays a key role in the biosynthetic pathway of methionine and is a potential target for the development of antimicrobial drugs. Purified MetA showed 40 kDa molecular mass on SDS-PAGE. Manual docking was performed with substrates acetyl-CoA, l-homoserine, and p-nitrophenylacetate using crystal structure coordinates of MetA (PDB ID 6PUX) from M. tuberculosis. Multiple sequence alignment indicated that catalytic triad residues Ser157, Asp320, His350 were conserved across species in acetyltransferases, esterases, and hydrolases. As a conserved pentapeptide, GXSMG belongs to α/β hydrolase superfamily and it shares similarity with esterases and hydrolases from different sources. Hydrolase activity of MetA was tested using (PNPA), N-acetylglycine, N-acetylmethionine and Phe-Gly as substrate. LC-MS confirmed that MetA possessed HAT activity, but no homoserine-succinyltransferase (HST) and serine-acetyltransferase (SAT) activities. Replacing acetyl-CoA with PNPA as acetyl group donor showed a drastic reduction in transferase activity, arising due to the interaction of R227 of the enzyme with PNPA. This could prevent the binding of the second substrate in the right orientation and results in the preferential transfer of the acetyl group to water, thus exhibiting hydrolase rather than transferase activity. In this paper, we report that MetA has both transferase and hydrolase activity depending on the correct orientation of the second substrate and the availability of the amino acids involved in enzyme-substrate interaction.

Mentholation triggers brand-specific shifts in the bacterial microbiota of commercial cigarette products

Bacterial communities are integral constituents of tobacco products. They originate from tobacco plants and are acquired during manufacturing processes, where they play a role in the production of tobacco-specific nitrosamines. In addition, tobacco bacterial constituents may play an important role in the development of infectious and chronic diseases among users. Nevertheless, tobacco bacterial communities have been largely unexplored, and the influence of tobacco flavor additives such as menthol (a natural antimicrobial) on tobacco bacterial communities is unclear. To bridge this knowledge gap, time series experiments including 5 mentholated and non-mentholated commercially available cigarettes-Marlboro red (non-menthol), Marlboro menthol, Newport menthol box, Newport menthol gold, and Newport non-menthol-were conducted. Each brand was stored under three different temperature and relative humidity conditions. To characterize bacterial communities, total DNA was extracted on days 0 and 14. Resulting DNA was purified and subjected to PCR of the V3V4 region of the 16S rRNA gene, followed by sequencing on the Illumina HiSeq platform and analysis using the QIIME, phyloseq, metagenomeSeq, and DESeq software packages. Ordination analyses showed that the bacterial community composition of Marlboro cigarettes was different from that of Newport cigarettes. Additionally, bacterial profiles significantly differed between mentholated and non-mentholated Newports. Independently of storage conditions, tobacco brands were dominated by Proteobacteria, with the most dominant bacterial genera being Pseudomonas, unclassified Enterobacteriaceae, Bacillus, Erwinia, Sphingomonas, Acinetobacter, Agrobacterium, Staphylococcus, and Terribacillus. These data suggest that the bacterial communities of tobacco products differ across brands and that mentholation of tobacco can alter bacterial community composition of select brands. KEY POINTS: • Bacterial composition differed between the two brands of cigarettes. • Mentholation impacts cigarette microbiota. • Pseudomonas and Bacillus dominated the commercial cigarettes. Graphical abstract.

Microbiome characterization of poultry products based on the poultry part and production label

Poultry is one of the most consumed meats worldwide and there are many different types of poultry products available on the market for consumers. Many poultry producers provide a variety of labeled meats based on rearing system such as organic, free-range and antibiotic-free. However, these labels often can be misleading by implying organic products are better in safety and quality compared to poultry products without additional labels. In this study, the microbiological profiles of commercial poultry products were characterized via a next generation sequencing. A variety of poultry products including whole carcass, leg, breast and thigh were purchased from local markets and subdivided by labels indicating organic, non-antibiotic, free range and no-label. According to the microbiome analysis based on the 16S rRNA gene, similar level of species richness were observed in comparison by labels, however, different parts and producers exhibited significant differences. Also, microbial similarities among groups were measured and most samples showed relatively close clustering based on the poultry part and the producer. The results emphasize potential contamination routes and the importance of the control strategy during the pre-harvest step of poultry products. The results also envision potential opportunities to improve current production procedure being utilized by industries.

Isolation and characterization of 2-butoxyethanol degrading bacterial strains

A total of 11 bacterial strains capable of completely degrading 2-butoxyethanol (2-BE) were isolated from forest soil, a biotrickling filter, a bioscrubber, and activated sludge, and identified by 16S rRNA gene sequence analysis. Eight of these strains belong to the genus Pseudomonas; the remaining three strains are Hydrogenophaga pseudoflava BOE3, Gordonia terrae BOE5, and Cupriavidus oxalaticus BOE300. In addition to 2-BE, all isolated strains were able to grow on 2-ethoxyethanol and 2-propoxyethanol, ethanol, n-hexanol, ethyl acetate, 2-butoxyacetic acid (2-BAA), glyoxylic acid, and n-butanol. Apart from the only gram-positive strain isolated, BOE5, none of the strains were able to grow on the nonpolar ethers diethyl ether, di-n-butyl ether, n-butyl vinyl ether, and dibenzyl ether, as well as on 1-butoxy-2-propanol. Strains H. pseudoflava BOE3 and two of the isolated pseudomonads, Pseudomonas putida BOE100 and P. vancouverensis BOE200, were studied in more detail. The maximum growth rates of strains BOE3, BOE100, and BOE200 at 30 °C were 0.204 h-1 at 4 mM, 0.645 h-1 at 5 mM, and 0.395 h-1 at 6 mM 2-BE, respectively. 2-BAA, n-butanol, and butanoic acid were detected as potential metabolites during the degradation of 2-BE. These findings indicate that the degradation of 2-BE by the isolated gram-negative strains proceeds via oxidation to 2-BAA with subsequent cleavage of the ether bond yielding glyoxylate and n-butanol. Since Gordonia terrae BOE5 was the only strain able to degrade nonpolar ethers like diethyl ether, the degradation pathway of 2-BE may be different for this strain.

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

Spatial Environmental Heterogeneity Determines Young Biofilm Assemblages on Microplastics in Baltic Sea Mesocosms

Microplastics in aquatic environments provide novel habitats for surface-colonizing microorganisms. Given the continuing debate on whether substrate-specific properties or environmental factors prevail in shaping biofilm assemblages on microplastics, we examined the influence of substrate vs. spatial factors in the development of bacterial assemblages on polyethylene (PE), polystyrene (PS), wood, and seston and in the free-living fraction. Further, the selective colonization of microplastics by potential pathogens was investigated because among the bacterial species found in microplastic-associated biofilms are potentially pathogenic Vibrio spp. Due to their persistence and great dispersal potential, microplastics could act as vectors for these potential pathogens and for biofilm assemblages in general. Incubation experiments with these substrates were conducted for 7 days during a summer cruise along the eastern Baltic Sea coastline in waters covering a salinity gradient of 4.5-9 PSU. Bacterial assemblages were analyzed using 16S rRNA-gene amplicon sequencing, distance-based redundancy analyses, and the linear discriminant analysis effect size method to identify taxa that were significantly more abundant on the plastics. The results showed that the sample type was the most important factor structuring bacterial assemblages overall. Surface properties were less significant in differentiating attached biofilms on PE, PS, and wood; instead, environmental factors, mainly salinity, prevailed. A potential role for inorganic-nutrient limitations in surface-specific attachment was identified as well. Alphaproteobacteria (Sphingomonadaceae, Devosiaceae, and Rhodobacteraceae) and Gammaproteobacteria (Alteromonadaceae and Pseudomonas) were distinctive for the PE- and PS-associated biofilms. Vibrio was more abundant on the PE and PS biofilms than on seston, but its abundances were highest on wood and positively correlated with salinity. These results corroborate earlier findings that microplastics constitute a habitat for biofilm-forming microorganisms distinct from seston, but less from wood. In contrast to earlier reports of low Vibrio numbers on microplastics, these results also suggest that vibrios are early colonizers of surfaces in general. Spatial as well as temporal dynamics should therefore be considered when assessing the potential of microplastics to serve as vectors for bacterial assemblages and putative pathogens, as these parameters are major drivers of biofilm diversity.

Microbial bioremediation of oil contaminated seawater: A survey of patent deposits and the characterization of the top genera applied

Petroleum has been the world's major source of energy since the middle of the twentieth century, leading to positive changes but also social, political, and environmental problems worldwide. Oil contamination affects all ecosystems, and the remediation of polluted sites using environmentally friendly strategies is crucial. Here, we report an analysis of the patent documents of potential petroleum bioremediation techniques that use microbes to clean seawater. The patent search was performed using Orbit Intelligence®, SciFinder® and the Derwent World Patents Index®. A group of 500 patent documents were validated according to the search objective and carefully studied. Increases in patent deposits coincide with periods following widely reported oil spills, suggesting a relationship between media disclosure and stimulation of innovation activities. China leads the list of countries with patent applications in bioremediation with 152 deposits, followed by Russia with 133 and the US with 48. These three countries have completely different temporal deposit profiles, influenced by their historical, political, and economic scenarios. A total of 368 patents described degradation of the oil compounds exclusively by bacteria, 24 by fungi and yeasts, 1 by Archaea, 1 using a microalgal strain, and 32 by mixed consortia. The leading microbial genera found in the patents are Pseudomonas (114 patents), Bacillus (75), and Rhodococcus (60). In the top-10 list of microbial strains mostly cited/claimed, no genera are obligate hydrocarbonoclastic bacteria. This fact, together with the broad pattern found in the main International Patent Classification (IPC) codes, suggest that most of the documents are general bioremediation approaches and not focused on oil-polluted seawater. This work highlights the importance of stimulating the development of innovative environmentally friendly strategies focused on the degradation of oil hydrocarbons in marine ecosystems.

Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake

In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, "LNA," "high nucleic acid (HNA)-Small," and "HNA-Large," were classified through flow cytometric fingerprint, among which the "HNA-Small" group was possibly in the proliferation stage of the "LNA" group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.

Profiles of bacterial assemblages from microplastics of tropical coastal environments

Plastic waste is a global issue of an increasing concern in aquatic ecosystems. Microplastics form a large proportion of plastic pollution in marine environments. Although microplastics are prevalent, their distribution along the coasts of tropical regions is not well studied. Microplastic pieces (1-5 mm) were collected from two distinct regions along the coastlines of Singapore, from the northern coast in the Johor Strait and the southern coast in the Singapore Strait. Microplastics were present in concentrations ranging from 9.20-59.9 particles per kg of dry sand sediment. The majority of microplastics identified were foam particles (55%) and fragments (35%). Microplastics were significantly more abundant on heavily populated beaches compared to pristine beaches. High throughput sequencing was used to profile the communities of bacteria on the surfaces of microplastic particles. The structure of the microbial communities was primarily characterised by Proteobacteria and Bacteroidetes and were distinct across sites. Hydrocarbon-degrading genera such as Erythrobacter were dominant in areas with heavy shipping and pollution. Potential pathogenic genera such as Vibrio and Pseudomonas were also identified. This study highlights the diverse bacterial assemblages present on marine microplastic surfaces and the importance of understanding the bacterial plastisphere.

Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds

Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Discovery of Two Native Baeyer-Villiger Monooxygenases for Asymmetric Synthesis of Bulky Chiral Sulfoxides

Two Baeyer-Villiger monooxygenases (BVMOs), designated BoBVMO and AmBVMO, were discovered from Bradyrhizobium oligotrophicum and Aeromicrobium marinum, respectively. Both monooxygenases displayed novel features for catalyzing the asymmetric sulfoxidation of bulky and pharmaceutically relevant thioethers. Evolutionary relationship and sequence analysis revealed that the two BVMOs belong to the family of typical type I BVMOs and the subtype ethionamide monooxygenase. Both BVMOs are active toward medium- and long-chain aliphatic ketones as well as various thioether substrates but are ineffective toward cyclohexanone, aromatic ketones, and other typical BVMO substrates. BoBVMO and AmBVMO showed the highest activities (0.117 and 0.025 U/mg protein, respectively) toward thioanisole among the tested substrates. Furthermore, these BVMOs exhibited distinct activity and excellent stereoselectivity toward bulky and prochiral prazole thioethers, which is a unique feature of this family of BVMOs. No native enzyme has been reported for the asymmetric sulfoxidation of bulky prazole thioethers into chiral sulfoxides. The identification of BoBVMO and AmBVMO provides an important scaffold for discovering enzymes capable of asymmetrically oxidizing bulky thioether substrates by genome mining.IMPORTANCE Baeyer-Villiger monooxygenases (BVMOs) are valuable enzyme catalysts that are an alternative to the chemical Baeyer-Villiger oxidation reaction. Although BVMOs display broad substrate ranges, no native enzymes were reported to have activity toward the asymmetric oxidation of bulky prazole-like thioether substrates. Herein, we report the discovery of two type I BVMOs from Bradyrhizobium oligotrophicum (BoBVMO) and Aeromicrobium marinum (AmBVMO) which are able to catalyze the asymmetric sulfoxidation of bulky prazole thioethers (proton pump inhibitors [PPIs], a group of drugs whose main action is a pronounced and long-lasting reduction of gastric acid production). Efficient catalysis of omeprazole oxidation by BoBVMO was developed, indicating that this enzyme is a promising biocatalyst for the synthesis of bulky and pharmaceutically relevant chiral sulfoxide drugs. These results demonstrate that the newly identified enzymes are suitable templates for the discovery of more and better thioether-converting BVMOs.

Rapid identification of unknown carboxyl esterase activity in Corynebacterium glutamicum using RNA-guided CRISPR interference

RNA-guided genome engineering technologies have been developed for the advanced metabolic engineering of microbial cells to enhance production of value-added chemicals in Corynebacterium glutamicum as an industrial host. In this study, the RNA-guided CRISPR interference (CRISPRi) was applied to rapidly identify of unknown genes for native esterase activity in C. glutamicum. Combining with the carboxyl esterase (MekB) protein sequence alignment, two target genes (the cg0961 and cg0754) were selected for the CRISPRi application to investigate the possible native esterase in C. glutamicum. The recombinant strain with repressed expression of the cg0961 gene exhibited almost no capability on degradation of methyl acetate as a substrate of carboxyl esterase. This result was also confirmed in the cg0961 gene deletion mutant. Thus, we concluded that Cg0961 plays a major role of the native carboxyl esterase activity in C. glutamicum. In addition, CRISPRi demonstrated an application for gene identification and its function as another genetic tool for metabolic engineering in C. glutamicum.

Characterization of the 3-methyl-4-nitrophenol degradation pathway and genes of Pseudomonas sp. strain TSN1

3-Methyl-4-nitrophenol (3M4NP) is formed in soil as a hydrolysis product of fenitrothion, one of the major organophosphorus pesticides. A Pseudomonas strain was isolated as a 3M4NP degrader from a crop soil and designated TSN1. This strain utilized 3M4NP as a sole carbon and energy source. To elucidate the biodegradation pathway, we performed transposon mutagenesis with pCro2a (mini-Tn5495) and obtained three mutants accumulating a dark pink compound(s) from 3M4NP. Rescue cloning and sequence analysis revealed that in all mutants, the transposon disrupted an identical aromatic compound meta-cleaving dioxygenase gene, and a monooxygenase gene was located just downstream of the dioxygenase gene. These two genes were designated mnpC and mnpB, respectively. The gene products showed high identity with the methylhydroquinone (MHQ) monooxygenase (58%) and the 3-methylcatechol 2,3-dioxygenase (54%) of a different 3M4NP degrader Burkholderia sp. NF100. The transposon mutants converted 3M4NP or MHQ into two identical metabolites, one of which was identified as 2-hydroxy-5-methyl-1,4-benzoquinone (2H5MBQ) by GC/MS analysis. Furthermore, two additional genes (named mnpA1 and mnpA2), almost identical to the p-nitrophenol monooxygenase and the p-benzoquinone reductase genes of Pseudomonas sp. WBC-3, were isolated from the total DNA of strain TSN1. Disruption of mnpA1 resulted in the complete loss of the 3M4NP degradation activity, demonstrating that mnpA1 encodes the initial monooxygenase for 3M4NP degradation. The purified mnpA2 gene product could efficiently reduce methyl p-benzoquinone (MBQ) into MHQ. These results suggest that strain TSN1 degrades 3M4NP via MBQ, MHQ, and 2H5MBQ in combination with mnpA1A2 and mnpCB, existing at different loci on the genome.

Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions

Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene’s function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.

A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity

Microbial esterases play important roles in deep-sea organic carbon degradation and cycling. Although they have similar catalytic triads and oxyanion holes, esterases are hydrolases and homoserine transacetylases (HTAs) are transferases. Because two HTA homologs were identified as acetyl esterases, the HTA family was recently divided into the bona fide acetyltransferase subfamily and the acetyl esterase subfamily. Here, we identified and characterized a novel HTA-like esterase, Est22, from a deep-sea sedimentary metagenomic library. Est22 could efficiently hydrolyze esters with acyl lengths of up to six carbon atoms but had no transacetylase activity, which is different from HTAs and HTA-like acetyl esterases. Phylogenetic analysis also showed that Est22 and its homologs form a separate branch of the HTA family. We solved the structures of Est22 and its L374D mutant and modeled the structure of the L374D mutant with p-nitrophenyl butyrate. Based on structural, mutational, and biochemical analyses, Phe⁷¹ and Met¹⁷⁶ in the oxyanion hole and Arg²⁹⁴ were revealed to be the key substrate-binding residues. A detailed structural comparison indicated that differences in their catalytic tunnels lead to the different substrate specificities of Est22 and the other two HTA subfamilies. Biochemical and sequence analyses suggested that Est22 homologs may have the same substrate recognition and catalysis mechanisms as Est22. Due to the significant differences in sequences, structures, and substrate specificities between Est22 (and its homologs) and the other two HTA subfamilies, we suggest that Est22 and its homologs represent a new subfamily in the HTA family.IMPORTANCE Microbial esterases play important roles in the turnover of organic carbon in the deep sea. Esterases and HTAs represent two groups of α/β hydrolases. Esterases catalyze the hydrolysis of simple esters and are widely used in the pharmaceutical and agrochemical industries, while HTAs catalyze the transfer of an acetyl group from acetyl-coenzyme A (CoA) to homoserine and are essential for microbial growth. Here, we report on a novel HTA-like esterase, Est22, from a deep-sea sediment. Because of the significant differences in sequences, structures, and substrate specificities of HTAs and HTA-like acetyl esterases, Est22 and its homologs represent a new subfamily in the HTA family. This study offers new knowledge regarding marine esterases.

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L-1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase

Coenzyme A (CoA)-transferases catalyze the reversible transfer of CoA from acyl-CoA thioesters to free carboxylates. Class I CoA-transferases produce acylglutamyl anhydride intermediates that undergo attack by CoA thiolate on either the internal or external carbonyl carbon atoms, forming distinct tetrahedral intermediates <3 Å apart. In this study, crystal structures of succinyl-CoA:acetate CoA-transferase (AarC) from Acetobacter aceti are used to examine how the Asn347 carboxamide stabilizes the internal oxyanion intermediate. A structure of the active mutant AarC-N347A bound to CoA revealed both solvent replacement of the missing contact and displacement of the adjacent Glu294, indicating that Asn347 both polarizes and orients the essential glutamate. AarC was crystallized with the nonhydrolyzable acetyl-CoA (AcCoA) analog dethiaacetyl-CoA (1a) in an attempt to trap a closed enzyme complex containing a stable analog of the external oxyanion intermediate. One active site contained an acetylglutamyl anhydride adduct and truncated 1a, an unexpected result hinting at an unprecedented cleavage of the ketone moiety in 1a. Solution studies confirmed that 1a decomposition is accompanied by production of near-stoichiometric acetate, in a process that seems to depend on microbial contamination but not AarC. A crystal structure of AarC bound to the postulated 1a truncation product (2a) showed complete closure of one active site per dimer but no acetylglutamyl anhydride, even with acetate added. These findings suggest that an activated acetyl donor forms during 1a decomposition; a working hypothesis involving ketone oxidation is offered. The ability of 2a to induce full active site closure furthermore suggests that it subverts a system used to impede inappropriate active site closure on unacylated CoA.

Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome

Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.

A novel esterase subfamily with α/β-hydrolase fold suggested by structures of two bacterial enzymes homologous to L-homoserine O-acetyl transferases

MekB from Pseudomonas veronii and CgHle from Corynebacteriumglutamicum belong to the superfamily of α/β-hydrolase fold proteins. Based on sequence comparisons, they are annotated as homoserine transacetylases in popular databases like UNIPROT, PFAM or ESTHER. However, experimentally, MekB and CgHle were shown to be esterases that hydrolyse preferentially acetic acid esters. We describe the x-ray structures of these enzymes solved to high resolution. The overall structures confirm the close relatedness to experimentally validated homoserine acetyl transferases, but simultaneously the structures exclude the ability of MekB and CgHle to bind homoserine and acetyl-CoA. Insofar the MekB and CgHle structures suggest dividing the homoserine transacetylase family into subfamilies, namely genuine acetyl transferases and acetyl esterases with MekB and CgHle as constituting members of the latter.

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR.

Catalytic function of the mycobacterial binuclear iron monooxygenase in acetone metabolism

Mycobacteria such as Mycobacterium smegmatis strain mc(2)155 and Mycobacterium goodii strain 12523 are able to grow on acetone and use it as a source of carbon and energy. We previously demonstrated by gene deletion analysis that the mimABCD gene cluster, which encodes a binuclear iron monooxygenase, plays an essential role in acetone metabolism in these mycobacteria. In the present study, we determined the catalytic function of MimABCD in acetone metabolism. Whole-cell assays were performed using Escherichia coli cells expressing the MimABCD complex. When the recombinant E. coli cells were incubated with acetone, a product was detected by gas chromatography (GC) analysis. Based on the retention time and the gas chromatography-mass spectrometry (GC-MS) spectrum, the reaction product was identified as acetol (hydroxyacetone). The recombinant E. coli cells produced 1.02 mM of acetol from acetone within 24 h. Furthermore, we demonstrated that MimABCD also was able to convert methylethylketone (2-butanone) to 1-hydroxy-2-butanone. Although it has long been known that microorganisms such as mycobacteria metabolize acetone via acetol, this study provides the first biochemical evidence for the existence of a microbial enzyme that catalyses the conversion of acetone to acetol.

Degradation of toluene by ortho cleavage enzymes in Burkholderia fungorum FLU100

Burkholderia fungorum FLU100 simultaneously oxidized any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100%. Further metabolism occurred via enzymes of ortho cleavage pathways with complete mineralization. During the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ML) accumulated transiently, being further mineralized only after a lag phase of 2 h in case of cells pre-grown on benzene or mono-halogen benzenes. No lag phase, however, occurred after growth on toluene. Cultures inhibited by chloramphenicol after growth on benzene or mono-halogen benzenes were unable to metabolize 2-ML supplied externally, even after prolonged incubation. A control culture grown with toluene did not show any lag phase and used 2-ML as a substrate. This means that 2-ML is an intermediate of toluene degradation and converted by specific enzymes. The conversion of 4-methylcatechol as a very minor by-product of toluene degradation in strain FLU100 resulted in the accumulation of 4-carboxymethyl-4-methylbut-2-en-4-olide (4-methyl-2-enelactone, 4-ML) as a dead-end product, excluding its nature as a possible intermediate. Thus, 3-methylcyclohexa-3,5-diene-1,2-diol, 3-methylcatechol, 2-methyl muconate and 2-ML were identified as central intermediates of productive ortho cleavage pathways for toluene metabolism in B. fungorum FLU100.

Hyaluronic acid production with Corynebacterium glutamicum: effect of media composition on yield and molecular weight

AIMS

Corynebacterium glutamicum was tested as an alternative host for heterologous production of hyaluronic acid (HA).

METHODS AND RESULTS

A set of expression vectors containing hasA, encoding HA synthase from Streptococcus equi subsp. zooepidemicus, alone or in combination with genes encoding enzymes for HA precursor production (hasB, hasC, glmU from Pseudomonas putida KT2440) or bacterial haemoglobin (vgb from Vitreoscilla sp.) was constructed. Recombinant Coryne. glutamicum strains were cultivated in two different minimal media, CGXII and MEK700. HA was isolated from the culture broth by ethanol precipitation or ultrafiltration. Analyses of the isolated HA revealed that overall production was higher in CGXII medium (1241 mg l(-1)) than in MEK700 medium (363 mg l(-1)), but molecular weight of the product was higher in MEK700 (>1·4 MDa) than in CGXII (<270 kDa). Coexpression of hasB, hasC or glmU had no effect on HA yield and did not improve molecular weight of the product. Coexpression of vgb lowered HA yield about 1·5-fold and did not affect molecular weight of the product. Microscopy of negative-stained cultures revealed that Coryne. glutamicum produces no distinct HA capsule.

CONCLUSIONS

Regulation of cell growth and gene expression level of hasA are reasonable starting points for controlling the molecular weight of HA produced by Coryne. glutamicum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Corynebacterium glutamicum has a great potential as an alternative production host for HA. The fact that Coryne. glutamicum produces no distinct HA capsule facilitates HA isolation and improves overall yield.

Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation

Here, we present the complete genome of Rhodococcus pyridinivorans SB3094, a methyl-ethyl-ketone (MEK)-degrading strain used for bioaugmentation relating to the treatment of wastewater contamination with petrochemical hydrocarbons. The genome highlights important features for bioaugmentation, including the genes involved in the degradation of MEK.

Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons

Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and might be a useful agent to stimulate bioremediation of hydrocarbons in contaminated soils.

Elucidation of the upper pathway of alicyclic musk Romandolide degradation in OECD screening tests with activated sludge

The degradation of Romandolide ([1-(3',3'-dimethyl-1'-cyclohexyl)ethoxycarbonyl] methyl propanoate), a synthetic alicyclic musk, by activated sludge inocula was investigated using both the manometric respirometry test OECD 301F and the CO₂ evolution test. In addition to measuring its biodegradability, key steps of the upper part of the metabolic pathway responsible for Romandolide degradation were identified using extracts at different time points of incubation. Early metabolism of Romandolide yielded ester hydrolysis products, including Cyclademol (1-(3,3-dimethylcyclohexyl)ethanol). The principal metabolites after 31 days were identified as 3,3-dimethyl cyclohexanone and 3,3-dimethyl cyclohexyl acetate. Formation of 3,3-dimethyl cyclohexanone from Cyclademol by sludge was confirmed in subsequent experiments using Cyclademol as a substrate, indicating the involvement of an oxygen insertion reminiscent of a Baeyer-Villiger oxidation. Further mineralization of 3,3-dimethyl cyclohexanone was also confirmed in subsequent studies. Three steps were thus required for complete biodegradation of the alicyclic musk: (1) successive ester hydrolyses leading to the formation of Cyclademol with concomitant degradation of the resulting acids, (2) conversion of Cyclademol into 3,3-dimethyl cyclohexanone, and (3) further mineralization via ring cleavage.

Functional characterization and application of a tightly regulated MekR/P mekA expression system in Escherichia coli and Pseudomonas putida

A methyl ethyl ketone (MEK)-inducible system based on the broad-host-range plasmid pBBR1MCS2 and on the P mekA promoter region of the MEK degradation operon of Pseudomonas veronii MEK700 was characterized in Escherichia coli JM109 and Pseudomonas putida KT2440. For validation, β-galactosidase (lacZ) was used as a reporter. The novel system, which is positively regulated by MekR, a member of the AraC/XylS family of regulators, was shown to be subject to carbon catabolite repression by glucose, which, however, could not be attributed to the single action of the global regulators Crc and PtsN. An advantage is its extremely tight regulation accompanied with three magnitudes of fold increase of gene expression after treatment with MEK. The transcriptional start site of P mekA was identified by primer extension, thereby revealing a potential stem-loop structure at the 5' end of the mRNA. Since MekR was highly insoluble, its putative binding site was identified through sequence analysis. The operator seems to be composed of a 15-bp tandem repeat (CACCN5CTTCAA) separated by a 6-bp spacer region, which resembles known binding patterns of other members of the AraC/XylS family. Subsequent mutational modifications of the putative operator region confirmed its importance for transcriptional activation. As the -35 promoter element seems to be overlapped by the putative operator, a class II activation mechanism is assumed.

Genome sequence of Pseudomonas aeruginosa DQ8, an efficient degrader of n-alkanes and polycyclic aromatic hydrocarbons

Pseudomonas aeruginosa DQ8, which was isolated from the crude oil polluted soil in the Daqing oilfield of China, can efficiently degrade diesel, crude oil, n-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Here, we present a 6.8-Mb assembly of its genome sequence. We have annotated 23 coding sequences (CDSs) responsible for catabolism of n-alkanes and PAHs.

Genome sequence of Pseudomonas sp. strain PAMC 25886, isolated from alpine glacial cryoconite

Pseudomonas spp. have shown characteristics of efficiently metabolizing environmental pollutants and also producing exopolysaccharides known as biofilms. Here we present the draft genome sequence of Pseudomonas sp. strain PAMC 25886, which was isolated from glacier cryoconite in the Alps mountain permafrost region and which may provide further insight into biodegradative and/or biofilm-producing mechanisms in a cold environment.

Pyrimidine biosynthesis in Pseudomonas veronii and its regulation by pyrimidines

Pyrimidine biosynthesis in the nutritionally versatile bacterium Pseudomonas veronii ATCC 700474 appeared to be controlled by pyrimidines. When wild type cells were grown on glucose in the presence of uracil, four enzyme activities were depressed while all five enzyme activities increased in succinate-grown cells supplemented with uracil. Independent of carbon source, orotic acid-grown cells elevated aspartate transcarbamoylase, dihydroorotase, orotate phosphoribosyltransferase or OMP decarboxylase activity. Pyrimidine limitation of glucose-grown pyrimidine auxotrophic cells lacking OMP decarboxylase activity resulted in at least a doubling of the enzyme activities relative to their activities in uracil-grown cells. Less derepression of the enzyme activities was observed after pyrimidine limitation of succinate-grown mutant cells possibly due to catabolite repression. Aspartate transcarbamoylase activity in Ps. veronii was regulated at the level of enzyme activity since the enzyme was strongly inhibited by pyrophosphate, UDP, UTP, ADP, ATP and GTP. Overall, the regulation of pyrimidine biosynthesis in Ps. veronii could be used to differentiate it from other taxonomically related species of Pseudomonas.