Isolation and characterization of thermophilic bacteria capable of degrading dehydroabietic acid

Detoxification of Plant Aromatic Abietanoids via Cleavage of the Benzene Ring into 11,12-Seco-diterpene Polyenes by a Specialist Insect of Leucosceptrum canum

Leaves of Leucosceptrum canum harbor abundant toxic aromatic abietanoids, and they are rarely attacked by insect herbivores, except for the larvae of Nacna malachitis. The excrements of the insect that fed on L. canum leaves were investigated, leading to the isolation and identification of two unprecedented 11,12-seco-abietane diterpene polyenes: nacnabietanins A (1) and B (2). This discovery heralds a unique detoxification mechanism of plant aromatic abietanoids by insects through enzymatic cleavage of stable benzene rings into more easily degraded polyenes.

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.

Bioconversion of ecotoxic dehydroabietic acid using Rhodococcus actinobacteria

Actinobactrial strains Rhodococcus erythropolis IEGM 267 and R. rhodochrous IEGM 107 were used to study biodegradation of dehydroabietic acid (DHA), a toxic tricyclic diterpenoid. The experiments were carried out in batch cultures of pre-grown rhodococci in the presence of 0.1% (v/v) n-hexadecane under aerobic conditions for 7 days. It was shown that R. erythropolis IEGM 267 and R. rhodochrous IEGM 107 partially and completely degraded DHA (500 mg/L), respectively. Characteristic physicochemical (reduced zeta potential) and morphological-physiological (increased average size of single cells and cell aggregates, increased root-mean-square roughness) changes in DHA-exposed actinobacteria were revealed. Products of DHA bioconversion by R. erythropolis IEGM 267 were analyzed and exhibited a previously unidentified metabolite 5α-hydroxy-abieta-8,11,13-triene-18-oat. The obtained experimental data widen the knowledge on the catalytic activity of rhodococci and their possible contribution to decontamination of natural ecosystems from pollutants.

Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring

A moderately thermophilic bacterial strain designated wcf1T, isolated from a hot spring located in the Tainan area, southern Taiwan, was characterized using a polyphasic approach. The cells were Gram-negative, non-pigmented, rod-shaped, non-spore-forming and motile. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Schlegelella; its only close neighbour was the type strain of Schlegelella thermodepolymerans, K14T (97.8 %). The isolate was clearly distinguishable from other strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It was evident from the genotypic and phenotypic data that strain wcf1T represents a novel species in the genus Schlegelella, for which the name Schlegelella aquatica sp. nov. is proposed, with the type strain wcf1T (=BCRC 17557T=LMG 23380T).

Tepidimonas thermarum sp. nov., a new slightly thermophilic betaproteobacterium isolated from the Elisenquelle in Aachen and emended description of the genus Tepidimonas

Several non-pigmented bacterial isolates, with an optimum growth temperature of about 50-55 degrees C, were recovered from the Elisenquelle at Aachen, Germany. Phylogenetic analysis of the 16S rRNA gene sequence of strains AA-1(T) and AA-2 indicated that these organisms represent a new species of the genus Tepidimonas. The major fatty acids of strains AA-1(T) and AA-2 are 16:0 and 16:1 omega7c. Ubiquinone 8 is the major respiratory quinone, the major polar lipids are phosphotidylethanolamine and phosphotidylglycerol. The new isolates are aerobic; thiosulfate is oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains AA-1(T) (=LMG 23094(T); =CIP 108777(T)) and AA-2 (=LMG 23095; =CIP 108778) represents a new species for which we recommend the name Tepidimonas thermarum.

Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections

The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as Alcaligenes faecalis, Comamonas terrigena, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection, Alkanindiges illinoisensis, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.

Effects of pulp and paper mill effluents on the microplankton and microbial self-purification capabilities of the Biobío River, Chile

Most studies focus on the ecotoxicity of pulp and paper mill effluents, rather than on how they affect the physicochemical and biological structure and the intrinsic ecological capabilities of the receiving watercourses. We investigated the impact of such effluents on the water quality, microplankton system and microbial self-purification capacity (degradation of polymeric organic compounds via extracellular enzymes) of the Biobío River in Chile. The physicochemical impact on the water quality was indicated by raised conductivity, by the pollution of the water body with nitrate, nitrite and soluble reactive phosphorus, by the appearance of tannin and lignin, and by the steady accumulation of inorganic and organic suspended matter (SPM) along the river. From the biological structure of the microplankton system, very low and declining concentrations of chlorophyll a and heterotrophic flagellate densities were determined. The pulp and paper mill effluents introduced high bacterial abundances and biomass concentrations into the river water. This reflects the effective use made of the abundantly available inorganic and organic nutrients within this industrial and municipal process water by bacteria adapted to these extreme environments, additionally supported by concomitant low grazing pressure derivable from low heterotrophic flagellate abundances. Indeed, in one section of the river affected by a pulp mill, the plant was found to significantly contribute to the self-cleaning capacity of the river. However, this elevated degradation capacity was not enough to compensate for the additionally discharged organic material which, together with the toxic effects of the paper plant effluents, significantly interferes with the ecological status of the Biobío River.

Tepidimonas arfidensis Sp. Nov., a Novel Gram-negative and thermophilic bacterium isolated from the bone marrow of a patient with leukemia in Korea

A Gram-negative bacillus, SMC-6271(T), which was isolated from the bone marrow of a patient with leukemia but could not be identified by a conventional microbiologic method, was characterized by a genotypic analysis of 16S rRNA gene. Sequences of the 16S rRNA gene revealed that this bacterium was closely related to Tepidimonas ignava and other slightly thermophilic isolates but diverged distinctly from them. Analyses of cellular fatty acid composition and performance of biochemical tests confirmed that this bacterium is a distinct species from the other Tepidimonas species. Based on the evaluated phenotypic and genotypic characteristics, it is proposed that SMC-6271T (=ABB 0301T =KCTC 12412T =JCM 13232T) should be classified as a new species, namely Tepidimonas arfidensis sp. nov.

Caenibacterium thermophilum is a later synonym of Schlegelella thermodepolymerans

Recently, two strains of Schlegelella thermodepolymerans Elbanna et al. 2003 and an independently isolated bacterium, Caenibacterium thermophilum Manaia et al. 2003, were described in parallel as gen. nov., sp. nov. Analysis of the 16S rRNA genes revealed similarity between C. thermophilum and the two strains of S. thermodepolymerans of 99.8 and 99.6 %, respectively. DNA-DNA hybridization experiments revealed mean DNA reassociation levels of 97-98 % among C. thermophilum and the two strains of S. thermodepolymerans, thereby confirming the close relationship and indicating that C. thermophilum is a later synonym of S. thermodepolymerans.

Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge

A bacterial strain, N2-680(T) (=DSM 15264(T)=LMG 21760(T)), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-beta-hydroxybutyrate and had an optimal growth temperature of about 47 degrees C. Strain N2-680(T) was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 degrees C, the major components in fatty acid methyl ester analysis were C(16 : 0) and cyclo-C(17 : 0). The highest 16S rDNA sequence identity of isolate N2-680(T) was to Leptothrix mobilis and Ideonella dechloratans (95.7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95.6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93.6 and 94.7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680(T) represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed.

Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate)

A novel thermophilic bacterium, strain K14T, capable of degrading poly(3-hydroxybutyrate) as well as copolymers containing 3-hydroxybutyrate and 3-mercaptopropionate linked by thioester bonds, was isolated. 16S rDNA sequence analysis showed that strain DhA-71, a dehydroabietic acid-degrading bacterium, was the nearest phylogenetic neighbour and that both strains should be placed as members of a newly created genus, Schlegelella gen. nov., in the Rubrivivax subgroup of the beta-Proteobacteria. Strain K14T (= LMG 21644T = DSM 15344T) is proposed as the type strain of Schlegelella thermodepolymerans gen. nov., sp. nov. Its phylogenetic, morphological, biochemical and chemotaxonomic characteristics are described in detail.

Examination of environmental quality of raw and composting de-inking paper sludge

Paper sludges were traditionally landfilled or burned. Over the years, the use of paper sludges on soils has increased, as well as the concerns about their environmental effects. Therefore, the chemical characterization of paper sludges and their young (immature) compost needed to be investigated, and over 150 inorganic and organic chemicals were analyzed in de-inking paper sludge (DPS). In general, nitrogen, phosphorus and potassium contents were low but variable in raw DPS and its young compost. The contents of arsenic, boron, cadmium, cobalt, chromium, manganese, mercury, molybdenum, nickel, lead, selenium, and zinc were also low and showed low variability. However, the copper contents were above the Canadian compost regulation for unrestricted use and required a follow-up. The fatty- and resin acids, and polycyclic aromatic hydrocarbons were the organic chemicals measured at the highest concentrations. For resinic acids, care should be taken to avoid that leachates reach aquatic life. For polycyclic aromatic hydrocarbons, naphthalene should be followed until soil content reaches 0.1 microg g(-1), the maximum allowed for soil use for agricultural purposes according to Canadian Environmental Quality Guidelines. In young compost, the concentration of these chemical families decreased over time and most compounds were below the detection limits after 24 weeks of composting. In raw DPS, among the phenol, halogenated and monoaromatic hydrocarbons, dioxin and furan, and polychlorinated biphenyl families, most compounds were below the detection limits. The raw DPS and its young compost do not represent a major threat for the environment but can require an environmental follow-up.

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.

Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing

We investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. For this investigation, we developed a composite method based on analyses of PCR amplicons containing the ribosomal intergenic spacer (RIS) and its flanking partial 16S rRNA gene. Community percent similarity was determined on the basis of RIS length polymorphism. A community succession was evident in the lagoon, indicated by a progressive community transition through seven sample locations. The most abrupt changes in community structure were associated with a temperature change from 39 to 35 degrees C and with increases in dissolved oxygen. The temporal differences in community structure, based on summer and winter samplings, were greater than the spatial differences during either season. Clone libraries of rDNA-RIS amplicons were constructed from each of three summer samples. Among 90 clones analyzed (30 clones from each sample), 56 phylotypes were distinguished by restriction fragment length polymorphism. Indices of phylotype richness, evenness, and diversity all increased in clone libraries from the beginning to the end of the lagoon. A representative clone of each phylotype was phylogenetically analyzed on the basis of its partial 16S rRNA gene sequence (ca. 450 bp). Phylogenetic analysis confirmed the increase in diversity and further indicated increasing richness of bacterial divisions. Pioneers in the community spatial succession appeared to include thermotolerant, microaerophilic methanol-oxidizing bacteria related to the genus Methylobacillus, as well as thermotolerant, microaerophilic nitrogen-fixing bacteria related to the genus Azospirillum.

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.