Isolation and characterization of isopimaric acid-degrading bacteria from a sequencing batch reactor

An Insight into the Roles of Dietary Tryptophan and Its Metabolites in Intestinal Inflammation and Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is complex, chronic, and relapsing gastrointestinal inflammatory disorders, which includes mainly two conditions, namely ulcerative colitis (UC) and Crohn's disease (CD). Development of IBD in any individual is closely related to his/her autoimmune regulation, gene-microbiota interactions, and dietary factors. Dietary tryptophan (Trp) is an essential amino acid for intestinal mucosal cells, and it is associated with the intestinal inflammation, epithelial barrier, and energy homeostasis of the host. According to recent studies, Trp and its three major metabolic pathways, namely kynurenine (KYN) pathway, indole pathway, and 5-hydroxytryptamine (5-HT) pathway, have vital roles in the regulation of intestinal inflammation by acting directly or indirectly on the pro/anti-inflammatory cytokines, functions of various immune cells, as well as the intestinal microbial composition and homeostasis. In this review, recent advances in Trp- and its metabolites-associated intestinal inflammation are summarized. It further discusses the complex mechanisms and interrelationships of the three major metabolic pathways of Trp in regulating inflammation, which could elucidate the value of dietary Trp to be used as a nutrient for IBD patients.

Microbial Conversion of Toxic Resin Acids

Organic wood extractives—resin acids—significantly contribute to an increase in the toxicity level of pulp and paper industry effluents. Entering open ecosystems, resin acids accumulate and have toxic effects on living organisms, which can lead to the ecological imbalance. Among the most effective methods applied to neutralize these ecotoxicants is enzymatic detoxification using microorganisms. A fundamental interest in the in-depth study of the oxidation mechanisms of resin acids and the search for their key biodegraders is increasing every year. Compounds from this group receive attention because of the need to develop highly effective procedures of resin acid removal from pulp and paper effluents and also the possibility to obtain their derivatives with pronounced pharmacological effects. Over the past fifteen years, this is the first report analyzing the data on distribution, the impacts on living organisms, and the microbial transformation of resin acids. Using the example of dehydroabietic acid—the dominant compound of resin acids in effluents—the review discusses the features of interactions between microorganisms and this pollutant and also highlights the pathways and main products of resin acid bioconversion.

Selecting microbial strains from pine tree resin: biotechnological applications from a terpene world

Resin is a chemical and physical defensive barrier secreted by many plants, especially coniferous trees, with insecticidal and antimicrobial properties. The degradation of terpenes, the main components accounting for the toxicity of resin, is highly relevant for a vast range of biotechnological processes, including bioremediation. In the present work, we used a resin-based selective medium in order to study the resin-tolerant microbial communities associated with the galls formed by the moth Retinia resinella; as well as resin from Pinus sylvestris forests, one of the largest ecosystems on Earth and a yet-unexplored source of terpene-degrading microorganisms. The taxonomic and functional diversity of the cultivated, resin-tolerant fraction of the whole microbiota were unveiled by high-throughput sequencing, which resulted in the detection of more than 40 bacterial genera among the terpene-degrading microorganisms, and a range of genes involved in the degradation of different terpene families. We further characterized through culture-based approaches and transcriptome sequencing selected microbial strains, including Pseudomonas sp., the most abundant species in both environmental resin and R. resinella resin-rich galls, and three fungal species, and experimentally confirmed their ability to degrade resin and also other terpene-based compounds and, thus, their potential use in biotechnological applications involving terpene catabolism.

Bacterial metabolism of chlorinated dehydroabietic acids occurring in pulp and paper mill effluents

Chlorinated dehydroabietic acids are formed during the chlorine bleaching of wood pulp and are very toxic to fish. Thus, destruction of these compounds is an important function of biological treatment systems for pulp and paper mill effluents. In this study, 12 strains of diverse, aerobic resin acid-degrading bacteria were screened for the ability to grow on chlorinated dehydroabietic acids as sole organic substrates. All seven strains of the class Proteobacteria able to use dehydroabietic acid were also able to use a mixture of 12- and 14-chlorodehydroabietic acid (Cl-DhA). None of the strains used 12,14-dichlorodehydroabietic acid. Sphingomonas sp. strain DhA-33 grew best on Cl-DhA and simultaneously removed both Cl-DhA isomers. Ralstonia sp. strain BKME-6 was typical of most of the strains tested, growing more slowly on Cl-DhA and leaving higher residual concentrations of Cl-DhA than DhA-33 did. Strains DhA-33 and BKME-6 mineralized (converted to CO(inf2) plus biomass) 32 and 43%, respectively, of carbon in Cl-DhA consumed. Strain DhA-33 produced a metabolite from Cl-DhA, tentatively identified as 3-oxo-14-chlorodehydroabietin, and both strains produced dissolved organic carbon which may include unidentified metabolites. Cl-DhA removal was inducible in both DhA-33 and BKME-6, and induced DhA-33 cells also removed 12,14-dichlorodehydroabietic acid. Based on activities of strains DhA-33 and BKME-6, chlorinated DhAs, and potentially toxic metabolite(s) of these compounds, are relatively persistent in biological treatment systems and in the environment.

Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

Three bacterial strains, designated MT1T, RW10Tand IpA-2T, had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genusPseudomonas. Analysis of the results of DNA–DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA–DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the namesPseudomonas reinekeisp. nov. (type strain MT1T=DSM 18361T=CCUG 53116T),Pseudomonas mooreisp. nov. (type strain RW10T=DSM 12647T=CCUG 53114T) andPseudomonas mohniisp. nov. (type strain IpA-2T=DSM 18327T=CCUG 53115T) are proposed.

Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples

Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic alpha-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.

Microbial degradation of the organophosphate pesticide, Ethion

The organophosphate pesticide, Ethion, remains a major environmental contaminant in rural Australia and poses a significant threat to environmental and public health. The aerobic degradation of Ethion by mesophilic bacteria isolated from contaminated soils surrounding disused cattle dip sites was investigated. Two isolates, identified as Pseudomonas and Azospirillum species, were capable of biodegrading Ethion when cultivated in minimal salts medium. The abiotic hydrolytic degradation products of Ethion such as Ethion Dioxon and O,O-diethylthiosphosphate were not detected. The data suggest the rapid degradation of Ethion to support microbial growth. The results have implications for the development of a bioremediation strategy.

Characterization of tdt genes for the degradation of tricyclic diterpenes by Pseudomonas diterpeniphila A19-6a

Resin acids are tricyclic diterpenes that are toxic to aquatic life when released in high concentrations in pulp mill effluents. These naturally formed organic acids are readily degraded by bacteria and fungi; nevertheless, many of the mechanisms involved are still unknown. We report the localization, cloning, and sequencing of genes for abietane degradation (9.18 kb; designated tdt (tricyclic diterpene) LRSABCD) from the gamma-Proteobacterium Pseudomonas diterpeniphila A19-6a. Using gene knockout mutants, we demonstrate that tdtL, encoding a putative CoA ligase, is required for growth on abietic and dehydroabietic acids. A second gene knockout in tdtD, encoding a putative cytochrome P450 monooxygenase, reduced the growth of strain A19-6a on abietic and dehydroabietic acids as sole sources of carbon and energy, but did not eliminate growth. The degree of homology between P450TdtD and P450TerpC, the closest known P450 homologue to TdtD, identifies TdtD as a new member of the P450 superfamily. Hybridization of six of the tdt genes to genomic DNA of a related resin acid degrading bacterium Pseudomonas abietaniphila BKME-9 identified tdt homologues in this strain that utilizes aromatic ring dioxygenase genes (dit) to open the ring structure of abietic and dehydroabietic acids. These results suggest the tdt and dit genes may function in concert to allow these Pseudomonas strains to degrade resin acids. Homologues of several of the tdt genes were detected in resin acid degrading Ralstonia and Comamonas species within the beta- and gamma-Proteobacteria.

Apparent contradiction: psychrotolerant bacteria from hydrocarbon-contaminated arctic tundra soils that degrade diterpenoids synthesized by trees

Resin acids are tricyclic terpenoids occurring naturally in trees. We investigated the occurrence of resin acid-degrading bacteria on the Arctic tundra near the northern coast of Ellesmere Island (82 degrees N, 62 degrees W). According to most-probable-number assays, resin acid degraders were abundant (10(3) to 10(4) propagules/g of soil) in hydrocarbon-contaminated soils, but they were undetectable (<3 propagules/g of soil) in pristine soils from the nearby tundra. Plate counts indicated that the contaminated and the pristine soils had similar populations of heterotrophs (10(6) to 10(7) propagules/g of soil). Eleven resin acid-degrading bacteria belonging to four phylogenetically distinct groups were enriched and isolated from the contaminated soils, and representative isolates of each group were further characterized. Strains DhA-91, IpA-92, and IpA-93 are members of the genus Pseudomonas. Strain DhA-95 is a member of the genus Sphingomonas. All four strains are psychrotolerant, with growth temperature ranges of 4 degrees C to 30 degrees C (DhA-91 and DhA-95) or 4 degrees C to 22 degrees C (IpA-92 and IpA-93) and with optimum temperatures of 15 to 22 degrees C. Strains DhA-91 and DhA-95 grew on the abietanes, dehydroabietic and abietic acids, but not on the pimaranes, isopimaric and pimaric acids. Strains IpA-92 and IpA-93 grew on the pimaranes but not the abietanes. All four strains grew on either aliphatic or aromatic hydrocarbons, which is unusual for described resin acid degraders. Eleven mesophilic resin acid degraders did not use hydrocarbons, with the exception of two Mycobacterium sp. strains that used aliphatic hydrocarbons. We conclude that hydrocarbon contamination in Arctic tundra soil indirectly selected for resin acid degraders, selecting for hydrocarbon degraders that coincidentally use resin acids. Psychrotolerant resin acid degraders are likely important in the global carbon cycle and may have applications in biotreatment of pulp and paper mill effluents.

Isolation and characterization of thermophilic bacteria capable of degrading dehydroabietic acid

Using a semi-continuous enrichment method, we isolated two thermophilic bacterial strains, which could completely degrade abietane resin acids, including dehydroabietic acid (DhA). Strain DhA-73, isolated from a laboratory-scale bioreactor treating bleached kraft mill effluent at 55 degrees C, grew on DhA as sole carbon source; while DhA-71, isolated from municipal compost, required dilute tryptic soy broth for growth on DhA. DhA-71 grew on DhA from 30 degrees C to 60 degrees C with maximum growth at 50 degrees C; while, DhA-73 grew on DhA from 37 degrees C to 60 degrees C with maximum growth at 55 degrees C. At 55 degrees C, the doubling times for DhA-71 and DhA-73 were 3.3 and 3.7 h, respectively. DhA-71 and DhA-73 had growth yields of 0.26 and 0.19 g of protein per g of DhA, respectively. During growth on DhA, both strains converted DhA to CO2, biomass, and dissolved organic carbon. Analyses of the 16S-rDNA sequences of these two strains suggest that they belong to two new genera in the Rubrivivax subgroup of the beta subclass of the Proteobacteria. Strains DhA-71 and DhA-73 are the first two bacteria isolated and characterized that are capable of biodegradation of resin acids at high temperatures. This study provided direct evidence for biodegradation of resin acids and feasibility for biotreatment of pulp mill effluent at elevated temperatures.

Phylogeny, ribosomal RNA gene typing and relative abundance of new Pseudomonas species (sensu stricto) isolated from two pinyon-juniper woodland soils of the arid southwest U.S

Rhizosphere-inhabiting Pseudomonas species interact with plant roots and may be important for plant performance under stressful environmental conditions. A comparison was conducted of culturable Pseudomonas isolates associated with pinyon rhizosphere and between-tree interspace areas in a hot, dry, volcanic cinder field and an adjacent sandy loam soil, in order to identify Pseudomonas species which may be involved in pinyon pine survival under stressful conditions. From a collection of 800 isolates, eleven isolates exhibiting different colony morphology were selected for 16S ribosomal RNA gene sequencing. Phylogenetic analysis of rDNA sequences from the eleven field isolates, forty-six described Pseudomonas species, and thirty-four previously characterized environmental isolates indicated that the isolates from the cinders and sandy loam soil clustered into three groups. The field isolates were distinct from any of the named species or other environmental isolates. Oligonucleotide primer pairs that differentiated three field isolate groups were designed from the 16S rDNA sequences, and eight hundred Pseudomonas field isolates cultured from pinyon rhizospheres and interspaces in the cinders and sandy loam soils were typed into the three groups using PCR assays. The composition of Pseudomonas populations in four environments was significantly different. The relative abundance of the three rDNA-based groups appeared to be affected by both the soil type and the pinyon rhizosphere.

A novel aromatic-ring-hydroxylating dioxygenase from the diterpenoid-degrading bacterium Pseudomonas abietaniphila BKME-9

Pseudomonas abietaniphila BKME-9 is able to degrade dehydroabietic acid (DhA) via ring hydroxylation by a novel dioxygenase. The ditA1, ditA2, and ditA3 genes, which encode the alpha and beta subunits of the oxygenase and the ferredoxin of the diterpenoid dioxygenase, respectively, were isolated and sequenced. The ferredoxin gene is 9. 2 kb upstream of the oxygenase genes and 872 bp upstream of a putative meta ring cleavage dioxygenase gene, ditC. A Tn5 insertion in the alpha subunit gene, ditA1, resulted in the accumulation by the mutant strain BKME-941 of the pathway intermediate, 7-oxoDhA. Disruption of the ferredoxin gene, ditA3, in wild-type BKME-9 by mutant-allele exchange resulted in a strain (BKME-91) with a phenotype identical to that of the mutant strain BKME-941. Sequence analysis of the putative ferredoxin indicated that it is likely to be a [4Fe-4S]- or [3Fe-4S]-type ferredoxin and not a [2Fe-2S]-type ferredoxin, as found in all previously described ring-hydroxylating dioxygenases. Expression in Escherichia coli of ditA1A2A3, encoding the diterpenoid dioxygenase without its putative reductase component, resulted in a functional enzyme. The diterpenoid dioxygenase attacks 7-oxoDhA, and not DhA, at C-11 and C-12, producing 7-oxo-11, 12-dihydroxy-8,13-abietadien acid, which was identified by 1H nuclear magnetic resonance, UV-visible light, and high-resolution mass spectrometry. The organization of the genes encoding the various components of the diterpenoid dioxygenase, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual Fe-S cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.

Diversity of Pseudomonas strains isolated with King's B and Gould's S1 agar determined by repetitive extragenic palindromic-polymerase chain reaction, 16S rDNA sequencing and Fourier transform infrared spectroscopy characterisation

King's B and Gould's S1 agar were compared with regard to the isolation of Pseudomonas from four environmental samples. In all samples, King's B gave the highest number of colony-forming units, and in some environments, there were more fluorescent colony-forming units on King's B as well. However, almost all types grew on Gould's S1, which enabled us to isolate a greater variety of groups than with King's B, fluorescent as well as non-fluorescent members of Pseudomonas. The Pseudomonas isolates were comparatively typed by repetitive extragenic palindromic-polymerase chain reaction and Fourier transform infrared spectroscopy, not previously used for environmental Pseudomonas. The two typing methods were similar in resolution, thus Fourier transform infrared spectroscopy proved fast and reproducible and is a good method for discrimination at subspecies level. Representative strains were identified by partial 16S rDNA sequencing. Thus, we suggest Gould's S1 agar be used for isolation of Pseudomonas because the results are reproducible, specific and give the most diverse recovery and the least work.

Physiological and phylogenetic diversity of bacteria growing on resin acids

Resin acids are tricyclic diterpenes which are synthesized by trees and are a major cause of toxicity of pulp mill effluents. Bacterial strains isolated from three different sources and which grow on resin acids were physiologically characterized. Eleven strains, representating distinct groups, were further characterized physiologically and phylogenetically. The isolates had distinct specificities for use, as growth substrates, of the different resin acids tested. The isolates also used fatty acids but were generally limited in use of other diverse substrates tested. According to their 16S rDNA sequences, the representative isolates are related to members of the genera, Sphingomonas, Zoogloea, Ralstonia, Burkholderia, Pseudomonas and Mycobacterium. Analysis of whole-cell fatty acid profiles generally supported those phylogenetic relationships. However, most of the isolated did not have high similarities to reference strains in the Microbial Identification System database of fatty acid profiles or in the Biolog database of substrate oxidation patterns. Described species of Sphingomonas, Zoolgoea, Burkholderia Pseudomonas, most closely related to the isolates we characterized, failed to grow on, or degrade, resin acids. We propose recognition of Zoogloea resiniphila sp. nov., Pseudomonas vancouverensis sp. nov., P. abietaniphila sp. nov. and P. multiresinivorans sp. nov.

Psychrotolerant bacteria isolated from arctic soil that degrade polychlorinated biphenyls at low temperatures

Psychrotolerant polychlorinated biphenyl (PCB)-degrading bacteria were isolated at 7 degreesC from PCB-contaminated Arctic soil by using biphenyl as the sole organic carbon source. These isolates were distinguished from each other by differences in substrates that supported growth and substrates that were oxidized. 16S ribosomal DNA sequences suggest that these isolates are most closely related to the genus Pseudomonas. Total removal of Aroclor 1242, and rates of removal of selected PCB congeners, by cell suspensions of Arctic soil isolates and the mesophile Burkholderia cepacia LB400 were determined at 7, 37, and 50 degreesC. Total removal values of Aroclor 1242 at 7 degreesC by LB400 and most Arctic soil isolates were similar (between 2 and 3.5 &mgr;g of PCBs per mg of cell protein). However the rates of removal of some individual PCB congeners by Arctic isolates were up to 10 times higher than corresponding rates of removal by LB400. Total removal of Aroclor 1242 and the rates of removal of individual congeners by the Arctic soil bacteria were higher at 37 degreesC than at 7 degreesC but as much as 90% lower at 50 degreesC than at 37 degreesC. In contrast, rates of PCB removal by LB400 were higher at 50 degreesC than at 37 degreesC. In all cases, temperature did not affect the congener specificity of the bacteria. These observations suggest that the PCB-degrading enzyme systems of the bacteria isolated from Arctic soil are cold adapted.

Microbiology and biodegradation of resin acids in pulp mill effluents: a minireview

Resin acids, a group of diterpenoid carboxylic acids present mainly in softwood species, are present in many pulp mill effluents and toxic to fish in recipient waters. They are considered to be readily biodegradable. However, their removal across biological treatment systems has been shown to vary. Recent studies indicate that natural resin acids and transformation products may accumulate in sediments and pose acute and chronic toxicity to fish. Several resin acid biotransformation compounds have also been shown to bioaccumulate and to be more resistant to biodegradation than the original material. Until recently, the microbiology of resin-acid degradation has received only scant attention. Although wood-inhabiting fungi have been shown to decrease the level of resin present in wood, there is no conclusive evidence that fungi can completely degrade these compounds. In contrast, a number of bacterial isolates have recently been described which are able to utilize dehydroabietic or isopimaric acids as their sole carbon source. There appears to be an unusually high degree of substrate specificity with respect of the utilization of abietane congeners and the presence of substituents. Pimaranes do not appear to be attacked to the same extent as the abietanes. This paper reviews the occurrence, chemistry, toxicity, and biodegradation of resin acids in relation to the biological treatment of pulp and paper mill effluents.