Degradation of various chlorophenols under alkaline conditions by gram-negative bacteria closely related to Ochrobactrum anthropi

Nitrifying biomass can retain its acclimation to 2,4,6-trichlorophenol

Many municipal wastewater treatment plants in China receive industrial wastewater that contains inhibitory organic chemicals, such as chlorinated phenols. For the common aerobic biological treatment, nitrification is a key step, but nitrifying bacteria are notably sensitive to inhibition by chlorinated phenols. In this work, normal activated sludge (containing nitrifying biomass) was acclimated to 2,4,6-trichlorophenol (TCP). The acclimated biomass had more than 2-fold faster nitrification kinetics than normal biomass when exposed to TCP, and it also achieved effective TCP removal in parallel. When suddenly exposed to TCP after as much as two months without TCP input, the acclimated nitrifying biomass retained effective nitrification and TCP biodegradation: The nitrification rate and TCP removal rate were 0.325 mM/h and 0.049 mM/h for the acclimated biomass, compared to only 0.165 mM/h and 0.001 mM/h for normal biomass. Resistance to TCP inhibition also was retained for 5 generations of sub-culturing without TCP exposure. High-throughput sequencing confirmed that the acclimated biomass contained nitrifying bacteria and heterotrophic bacteria capable of degrading TCP, although the key genera changed during sub-culturing.

16S rRNA gene phylogeny and tfdA gene analysis of 2,4-D-degrading bacteria isolated in China

Twenty-two 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial isolates were collected from agricultural soils at three sites in China. Sequence analysis of the 16S rRNA genes indicated that the isolates were phylogenetically grouped into four categories: Ochrobactrum anthropi, in the Alpha- class of the phylum Proteobacteria (3 out of 22 isolates), Cupriavidus sp., of the Betaproteobacteria (3 out of 22), Pseudomonas sp. and Stenotrophomonas sp., which are Gammaproteobacteria (7 out of 22), and Bacillus sp., of the phylum Firmicutes (9 out of 22). Primers were designed to amplify the conserved domain of tfdA, which is known to be involved in the degradation of 2,4-D. Results showed that the tfdA genes of all 22 strains were most similar to that of Cupriavidus necator JMP134, which belongs to the 2,4-D/α-ketoglutarate dioxygenase TfdA protein family, indicating that the JMP134-type tfdA gene is likely to be almost universal among the 2,4-D-degrading bacteria isolated from China. Degradation abilities of these 22 strains were investigated in assays using 2,4-D as the sole source of carbon and energy. Thirteen strains degraded >60 % of the available 2,4-D (500 mg l(-1)) over a 1-week incubation period, while a further nine Bacillus sp. strains degraded 50-81 % of the available 2,4-D. None of these nine strains degraded other selected herbicides, such as mecoprop, 2-methyl-4-chlorophenoxyacetic acid, quizalofop, and fluroxypyr. This is the first report of 2,4-D-degradation by Bacilli.

Biodegradation kinetics of the nitramine explosive CL-20 in soil and microbial cultures

The cyclic nitramine explosive CL-20 (C(6)H(6)N(12)O(12), 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12 -hexaazaisowurtzitane) is a relatively new energetic compound which could be a persistent organic pollutant. To follow its biodegradation dynamics, CL-20 was added to soil alone or together with organic co-substrates and N-source and incubated under oxic and anoxic conditions. Without co-substrates, the CL-20 degradation was detectable only under anoxic conditions. The highest degradation rate was found under aerobic conditions and with the addition of co-substrates, succinate and pyruvate being more efficient than acetate, glucose, starch or yeast extract. When added to intact soil, CL-20 degradation was not affected by the N content, but in soil serially diluted with N-free succinate-mineral medium, the process became N-limited. About 40% of randomly selected bacterial colonies grown on succinate agar medium were able to decompose CL-20. Based on 16S rDNA gene sequence and cell morphology, they were affiliated to Pseudomonas, Rhodococcus, Ochrobactrum, Mycobacterium and Ralstonia. In the pure culture of Pseudomonas sp. MS-P grown on the succinate-mineral N(+) medium, the degradation kinetics were first order with the same apparent kinetic constant throughout growth and decline phases of the batch culture. The observed kinetics agreed with the model that supposes co-metabolic transformation of CL-20 uncoupled from cell growth, which can be carried out by several constitutive cellular enzymes with wide substrate specificity.

Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species

The internal 16S/23S rDNA (rrs/rrl) internal spacer region 1 (ITS1) of 54 Ochrobactrum strains and close relatives was analysed. Separation of ITS1 containing PCR products by gel-electrophoresis, DGGE, cloning and sequencing revealed ITS1 length and sequence heterogeneity. We found up to 5 different allelic ITS1 stretches within a single strain (Ochrobactrum intermedium LMG 3301T), and 2-3 different ITS1 alleles in O. tritici. Within ITS1, ITS1c, being part of the conserved double-stranded rrn processing stem dsPS1, produced the most reliable segment tree. The overall ITS1, ITS1c and rrs phylogenetic tree topologies were generally consistent, but there was evidence for horizontal rrn (segment) transfer in O. tritici LMG 2134 (formerly O. anthropi). Good correlations were found between ITS1, ITS1c and rrs sequence similarity and DNA-DNA hybridization values indicating that phylogenetic analysis of ITS1 and ITS1c both can be used to preliminarily deduce the phylogenetic affiliation if HGT was excluded. Strains sharing > 96.19% ITS1c (> 95.11% ITS1) similarity fell within a species, and < or = 68.42% ITS1c (< or = 70.33% ITS1) similarity outside a genus. Both ITS1 and ITS1c analysis resolved microdiversity more profoundly than rrs analysis and revealed clades (genomovars) within O. anthropi that were also produced in rep cluster analysis. There was no evidence for habitat-specific ITS1 genomovars within Ochrobactrum species. Diversity of Ochrobactrum was higher in soil than at the rhizoplane below and at the species level. Isolates from soil contained only 1 rrn type whereas isolates from human clinical, animal and rhizoplane specimens could contain more.

The effects of salinity and other factors on nitrite reduction by Ochrobactrum anthropi 49187

The nitrite reductase (NIR) gene was cloned from Ochrobactrum anthropi 49187 and found to contain an open reading frame of 1131 nucleotides, encoding a polypeptide of 376 amino acids. The O. anthropi NIR gene encodes a copper-type dissimilatory reductase based on sequence homology with other genes. The polypeptide product is predicted to form a trimeric holoenzyme of 37 kDa subunits based on molecular weight estimates of extracts in activity gels. Expression of the enzyme is up-regulated by nitrate, presumably through the intermediate nitrite, and its activity is influenced by inhibitors. Salinity enhances the activity of existing NIR enzyme, but appears to decrease the expression of new enzyme.

Analysis of bacterial DNA patterns—an approach for controlling biotechnological processes

Optimisation of biotechnological processes catalysed by microbial cells requires detailed information about operational limits of the single cells. Their performance is correlated with distinct physiological states. We related these states to cell cycle events, which were found to proceed extremely diversely in different bacterial strains. Characteristic DNA patterns were found flow cytometrically, depending on the type of strain, substrates and growth conditions involved; this information can be used for the development of control strategies of bioprocesses, although some skill is required. Four bacterial strains (the Gram-negative strains Acinetobacter calcoaceticus 69-V, Ralstonia eutropha JMP 134, Ochrobactrum anthropi K2-14 and the Gram-positive strain Rhodococcus erythropolis K2-3) were grown in mono- and mixed cultures on different substrates, and analysed regarding their proliferation behaviour. The resulting DNA distribution patterns provided three types of valuable information. First, correlation of proliferation activity with the appearance of a major part of cells within the C(2) stage of the cell cycle is a strain-specific feature. Second, bacteria usually maintain more than one chromosome under limiting growth conditions: DNA replication is completed in such cases, but cell division fails. Third, high growth rates are associated with uncoupled DNA synthesis. Its general initiation might be genetically determined in the first place, but it is promoted by optimal growth conditions and the presence of substrates that can be metabolised at high rates, thereby allowing substantial amounts of carbon, other nutrients and energy to be used exclusively for DNA synthesis.

Population analysis of a binary bacterial culture by multi-parametric flow cytometry

To study the degradation of a xenobiotic that requires a mixed culture it is essential to monitor the proportions and to control the population dynamics of the component strains. For these purposes fluorochromising techniques and multi-parametric flow cytometry were used to follow Rhodococcus erythropolis K2-3 and Ochrobactrum anthropi K2-14, both of which are needed to degrade 4-(2,4-dichlorophenoxy)butyric acid (2,4-DB). Although the two strains can grow in constant proportions in mixed cultures on other substrates, 2,4-DB could not be degraded as a sole substrate in a continuous process and R. erythropolis K2-3 was clearly impaired in the binary mixture. Addition of a second, easily assimilable substrate (xylitol) in appropriate concentrations (empirically determined) helped this strain survive, and thus facilitated complete degradation of the xenobiotic. This combination of substrates was found to stabilise the growth of R. erythropolis K2-3 and, consequently promoted the action of O. anthropi K2-14. Thus, the two organisms became established in constant proportions in a continuous process until reaching steady state. Consequently, multiplication and cell division activities of the two components of the binary culture were high and reached similar values to those attained when they are grown in pure culture.

Physiological and genetic characteristics of two bacterial strains utilizing phenoxypropionate and phenoxyacetate herbicides

Two strains, Rhodoferax sp. P230 and Delftia (Comamonas) acidovorans MCI, have previously been shown to carry activities for the degradation of the two enantiomers of (RS)-2-(2,4-dichlorophenoxy-)propionate (dichlorprop) and (RS)-2-(4-chloro-2-methylphenoxy-)propionate (mecoprop) and, in addition, are capable of degrading phenoxyacetate derivatives 2.4-dichlorophenoxyacetate (2,4-D) and 4-chloro-2-methylphenoxyacetate (MCPA). Metabolism of the herbicides is initiated by alpha-ketoglutarate-dependent dioxygenases for both enantiomers of the phenoxypropionate herbicides and for 2,4-D. These activities were constitutively expressed for both enantiomers of dichlorprop in strain MC1 and for the Renantiomer in strain P230. Enzyme activities for the complete degradation of phenoxyacetate and phenoxypropionate herbicides were induced during incubation on either of these herbicides. Strain MC1 has about threefold higher activities for the degradation of dichlorprop and for growth on this substrate (mumax = 0.15 h(-1)) than strain P230; the maximum growth rate on 2,4-D amounts to 0.045 h(-1) with strain MC1. Dichlorprop is utilized faster than mecoprop and the R-enantiomers are cleaved with higher rates than the S-enantiomers. The degradation of the chlorophenolic intermediates seems to proceed via the modified ortho cleavage pathway as indicated by activities of the respective enzymes. The enzymatic results were supported by genetic investigations by which the presence of the genes tfdB (encoding a dichlorophenol hydroxylase), tfdC (encoding a chlorocatechol 1,2-dioxygenase) and tfdD (encoding a chloromuconate cycloisomerase) could be demonstrated in both strains by PCR after application of respective primers. The presence of the tfdA gene (encoding a 2,4-D/alpha-ketoglutarate dioxygenase) was only shown for strain P230 but was lacking in strain MC1. Sequence analysis of the tfd gene fragments revealed high homology to the degradative genes of other proteobacterial strains degrading chloroaromatic compounds. Strain MC1 carries a plasmid of about 120 kb which apparently harbors herbicide degradative genes as concluded from deletion mutants which have lost 2,4-D[phenoxalkanoate]/alpha-ketoglutarate dioxygenase activities for cleavage of the R- and S-enantiomer, and of 2,4-D. For strain P230, no plasmid could be demonstrated; the activity was stably conserved in this strain during growth under nonselective conditions.

Ecology and evolution of bacterial microdiversity

Using high resolution molecular fingerprinting techniques like random amplification of polymorphic DNA, repetitive extragenic palindromic PCR and multilocus enzyme electrophoresis, a high bacterial diversity below the species and subspecies level (microdiversity) is revealed. It became apparent that bacteria of a certain species living in close association with different plants either as associated rhizosphere bacteria or as plant pathogens or symbiotic organisms, typically reflect this relationship in their genetic relatedness. The strain composition within a population of soil bacterial species at a given field site, which can be identified by these high resolution fingerprinting techniques, was markedly influenced by soil management and soil features. The observed bacterial microdiversity reflected the conditions of the habitat, which select for better adapted forms. In addition, influences of spatial separation on specific groupings of bacteria were found, which argue for the occurrence of isolated microevolution. In this review, examples are presented of bacterial microdiversity as influenced by different ecological factors, with the main emphasis on bacteria from the natural environment. In addition, information available from some of the first complete genome sequences of bacteria (Helicobacter pylori and Escherichia coli) was used to highlight possible mechanisms of molecular evolution through which mutations are created; these include mutator enzymes. Definitions of bacterial species and subspecies ranks are discussed in the light of detailed information from whole genome typing approaches.

A theoretical study on the metabolic requirements resulting from alpha-ketoglutarate-dependent cleavage of phenoxyalkanoates

The etherolytic cleavage of phenoxyalkanoic acids in various bacteria is catalyzed by an alpha-ketoglutarate-dependent dioxygenase. In this reaction, the electron acceptor is oxidatively decarboxylated to succinate, whereas the proper substrate is cleaved by forming the oxidized alkanoic acid and the phenolic intermediate. The necessity of regenerating alpha-ketoglutarate and the consequences for the overall metabolism were investigated in a theoretical study. It was found that the dioxygenase mechanism is accompanied by a significant loss of carbon amounting to up to 62.5% in the assimilatory branch, thus defining the upper limit of carbon conversion efficiency. This loss in carbon is almost compensated for in comparison to a monooxygenase-catalyzed initial step when the dissimilatory efforts of the entire metabolism are included: the yield coefficients become similar. The alpha-ketoglutarate-dependent dioxygenase mechanism has more drastic consequences for microorganisms which are restricted in their metabolism to the first step of phenoxyalkanoate degradation by excreting the phenolic intermediate as a dead-end product. In the case of phenoxyacetate derivatives, the cleavage reaction would quickly cease due to the exhaustion of alpha-ketoglutarate and no growth would be possible. With the cleavage products of phenoxypropionate and phenoxybutyrate herbicides, i.e., pyruvate and succinate(semialdehyde), respectively, as the possible products, the regeneration of alpha-ketoglutarate will be guaranteed for stoichiometric reasons. However, the maintenance of the cleavage reaction ought to be restricted due to physiological factors owing to the involvement of other metabolic reactions in the pool of metabolites. These effects are discussed in terms of a putative recalcitrance of these compounds.