The Contribution of Actinobacteria to the Degradation of Chlorinated Compounds: Variations in the Activity of Key Degradation Enzymes.

Bacteria make a huge contribution to the purification of the environment from toxic stable pollutants of anthropogenic and natural origin due to the diversity of their enzyme systems. For example, the ability to decompose 3-chlorobenzoate (3CBA) by the four representative genera of Actinobacteria, such as Rhodococcus, Gordonia, Microbacterium, and Arthrobacter, was studied. In most cases, the formation of 4-chlorocatechol as the only key intermediate during the decomposition of 3CBA was observed. However, Rhodococcus opacus strain 1CP was an exception, whose cells decomposed 3CBA via both 3-chloro- and 4-chlorocatechol. The enzyme 3-Chlorobenzoate 1,2-dioxygenase (3CBDO) induced during the growth of these bacteria in the presence of 3CBA differed significantly in substrate specificity from the benzoate dioxygenases induced upon growth in the presence of benzoate. The R. opacus 6a strain was found to contain genes encoding chlorocatechol 1,2-dioxygenase, chloromuconate cycloisomerase, and dienelactone hydrolase, whose nucleotide sequence was 100% consistent with the sequences of the corresponding genes encoding the enzymes of the modified 4-chlorocatechol ortho-cleavage pathway of the strain R. opacus 1CP. However, the gene encoding chloromuconolactone dehalogenase (clcF) was not found in the representatives of the actinomycete genera, including Gordonia and Arthrobacter. A linear mega-plasmid carrying 3-chlorocatechol degradation genes remained stable after maintaining the R. opacus 1CP strain on an agar-rich medium for 25 years. In general, a similar plasmid was absent in actinobacteria of other genera, as well as in closely related species of R. opacus 6a.

Degradability of commercial mixtures of polychlorobiphenyls by three Rhodococcus strains.

Biodegradative characteristics were investigated for the commercially available mixtures of polychlorinated biphenyls (PCBs) Trikhlorbifenil and Sovol degraded by the Rhodococcus wratislaviensis КT112-7, Rhodococcus wratislaviensis CH628 and Rhodococcus ruber P25 strains isolated from the natural habitats. For bioutilization of the Trikhlorbifenil, all three strains were found to have a high biodegrading potential: the complete destruction was achieved in 10-14 days. For the mixture Sovol, the bioutilization parameters were found to be of lower values: the degradation of the PCBs congeners was 96-98% after 14 days. For the tested polychlorobiphenyl mixtures, the structural specificities of congeners are discussed, the genes encoding monooxygenases are revealed, and explanation is given to the differences in biodegradative characteristics of the Rhodococcus strains towards di-, tri-, tetra-, penta-, hexa- and heptachlorobiphenyls. The presented data are highly relevant for environmental remediation of objects polluted with the extremely hazardous polychlorobiphenyls.

Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia.

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.

Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated Biphenyl Degrader.

We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a soil polluted with halogenated aromatic compounds in the city of Perm, Russia. The strain degrades polychlorinated biphenyls and a broad range of aromatic compounds. It possesses genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and monoaromatic compounds.

Chloromuconolactone dehalogenase ClcF of actinobacteria.

This work investigated the distribution of the clcF gene in actinobacteria isolated from different ecotopes. The gene encodes chloromuconolactone dehalogenase (CMLD) ClcF, the enzyme found to date in only one representative of Gram-positive bacteria, Rhodococcus opacus 1CP, adapted to 2-chlorophenol (2CP). Using primers specific to the clcF gene, from the DNA matrix of rhodococcal strains closely related to species Rhodococcus wratislaviensis (P1, P12, P13, P20, G10, KT112, KT723, BO1) we obtained PCR products whose nucleotide sequences were 100% identical to that of the clcF gene from strain R. opacus 1CP. CMLDs isolated from the biomass of strains Rhodococcus spp. G10 and P1 grown on 2CP did not differ by their subunit molecular mass deduced from the known amino acid sequence of the clcF gene from the ClcF of strain R. opacus 1CP. Matrix-assisted laser dissociation/ionization time-of-flight mass spectrometry showed the presence of a peak with m/z 11,194-11,196 Da both in whole cells and in protein solutions with a ClcF activity. Thus, we have first time shown the distribution of ClcF among actinobacteria isolated from geographically distant habitats.

Naphthalene-degrading bacteria of the genus Rhodococcus from the Verkhnekamsk salt mining region of Russia.

Eight moderately halotolerant naphthalene-degrading strains of the genus Rhodococcus isolated from soil samples and slime pit bottom sediment of the Verkhnekamsk salt mining region of Russia were characterized by PCR amplification of repetitive bacterial DNA elements (rep-PCR) and identified by 16S ribosomal RNA gene sequence analysis. The diversity of their dioxygenase (nar-like) genes was investigated as these genes are known to be involved in naphthalene-degradation. The analysis of the nar-like genes identified revealed their heterogeneity in the strains under study and identity to the known sequences of nar-like genes of previously characterized from members of the genus Rhodococcus.

Variability of enzyme system of Nocardioform bacteria as a basis of their metabolic activity.

The present review describes some aspects of organization of biodegradative pathways of Nocardioform microorganisms, first of all, with respect to their ability to degrade aromatic compounds, mostly methylbenzoate, chlorosubstituted phenols, and chlorinated biphenyls and the intermediates of their transformation: 4-chlorobenzoate and para-hydroxybenzoate. Various enzyme systems induced during degradation processes are defined. The ability of microorganisms to induce a few key enzymes under the influence of xenobiotics is described. This ability may increase the biodegradative potential of strains allowing them to survive in the changing environment or demonstrate to some extent the unspecific response of microorganisms to the effect of toxicants. Nocardioform microorganisms responsible for degradation of such persistent compounds as polychlorinated biphenyls, polyaromatic hydrocarbons, chlorinated benzoates and phenols and other xenobiotics are characterized. The possibility of using Nocardioform microorganisms in some aspects of biotechnology due to their ability to produce some compounds important for industry is also estimated.