Actinomycetes as agents of biodegradation in the environment--a review

Crystallization and preliminary X-ray crystallographic analysis of BxlE, a xylobiose transporter from Streptomyces thermoviolaceus OPC-520

Together with the integral membrane proteins BxlF and BxlG, BxlE isolated from Streptomyces thermoviolaceus OPC-520 forms an ATP-binding cassette (ABC) transport system that mediates the uptake of xylan. To clarify the structural basis of sugar binding by BxlE at the atomic level, recombinant BxlE was crystallized using the hanging-drop vapour-diffusion method at 290 K. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 44.63, b = 63.27, c = 66.40 A, beta = 103.05 degrees, and contained one 48 kDa molecule per asymmetric unit (V(M) = 1.96 A3 Da(-1)). Diffraction data collected to a resolution of 1.65 A using a rotating-anode X-ray source gave a data set with an overall R(merge) of 2.6% and a completeness of 91.3%. A data set from a platinum derivative is being used for phasing by the SAD method.

The genus Amycolatopsis: Indigenous plasmids, cloning vectors and gene transfer systems

The genus Amycolatopsis is a member of the phylogenetic group nocardioform actinomycetes. Most of the members of the genus Amycolatopsis are known to produce antibiotics. Additionally, members of this genus have been reported to metabolize aromatic compounds as the sole sources of carbon and energy. Development of genetic manipulation in Amycolatopsis has progressed slowly due to paucity of genetic tools and methods. The occurrence of indigenous plasmids in different species of Amycolatopsis is not very common. Till date, only three indigenous plasmids viz., pMEA100, pMEA300 and pA387 have been reported in Amycolatopsis species. Various vectors based on the indigenous plasmids, pMEA100, pMEA300 and pA387, have been constructed. These vectors have proved useful for molecular genetics studies of actinomycetes. Molecular genetic work with Amycolatopsis strains is not easy, since transformation methods have to be developed, or at least optimized, for each particular strain. Nonetheless, methods for efficient transformation (polyethyleneglycol (PEG) induced protoplast transformation, transformation by electroporation and direct transformation) have been developed and used successfully for the introduction of DNA into several Amycolatopsis species. The construction of plasmid cloning vectors and the development of gene transfer systems has opened up possibilities for studying the molecular genetics of these bacteria.

Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments

Microbial communities from riparian sediments contaminated with high levels of Ni and U were examined for metal-tolerant microorganisms. Isolation of four aerobic Ni-tolerant, Gram-positive heterotrophic bacteria indicated selection pressure from Ni. These isolates were identified as Arthrobacter oxydans NR-1, Streptomyces galbus NR-2, Streptomyces aureofaciens NR-3, and Kitasatospora cystarginea NR-4 based on partial 16S rDNA sequences. A functional gene microarray containing gene probes for functions associated with biogeochemical cycling, metal homeostasis, and organic contaminant degradation showed little overlap among the four isolates. Fifteen of the genes were detected in all four isolates with only two of these related to metal resistance, specifically to tellurium. Each of the four isolates also displayed resistance to at least one of six antibiotics tested, with resistance to kanamycin, gentamycin, and ciprofloxacin observed in at least two of the isolates. Further characterization of S. aureofaciens NR-3 and K. cystarginea NR-4 demonstrated that both isolates expressed Ni tolerance constitutively. In addition, both were able to grow in higher concentrations of Ni at pH 6 as compared with pH 7 (42.6 and 8.5 mM Ni at pH 6 and 7, respectively). Tolerance to Cd, Co, and Zn was also examined in these two isolates; a similar pH-dependent metal tolerance was observed when grown with Co and Zn. Neither isolate was tolerant to Cd. These findings suggest that Ni is exerting a selection pressure at this site for metal-resistant actinomycetes.

Eisenia fetida (Oligochaeta, Lumbricidae) activates fungal growth, triggering cellulose decomposition during vermicomposting

Cellulose is the most abundant polymer in nature and constitutes a large pool of carbon for microorganisms, the main agents responsible for soil organic matter decomposition. Cellulolysis occurs as the result of the combined action of fungi and bacteria with different requirements. Earthworms influence decomposition indirectly by affecting microbial population structure and dynamics and also directly because the guts of some species possess cellulolytic activity. Here we assess whether the earthworm Eisenia fetida (Savigny 1826) digests cellulose directly (i.e., with its associated gut microbiota) and also whether the effects of E. fetida on microbial biomass and activity lead to a change in the equilibrium between fungi and bacteria. By enhancing fungal communities, E. fetida would presumably trigger more efficient cellulose decomposition. To evaluate the role of E. fetida in cellulose decomposition, we carried out an experiment in which pig slurry, a microbial-rich substrate, was treated in small-scale vermireactors with and without earthworms. The presence of earthworms in vermireactors significantly increased the rate of cellulose decomposition (0.43 and 0.26% cellulose loss day(-1), with and without earthworms, respectively). However, the direct contribution of E. fetida to degradation of cellulose was not significant, although its presence increased microbial biomass (C(mic)) and enzyme activity (cellulase and beta-glucosidase). Surprisingly, as fungi may be part of the diet of earthworms, the activity of E. fetida triggered fungal growth during vermicomposting. We suggest that this activation is a key step leading to more intense and efficient cellulolysis during vermicomposting of organic wastes.

Catenulispora acidiphila gen. nov., sp. nov., a novel, mycelium-forming actinomycete, and proposal of Catenulisporaceae fam. nov

A novel, Gram-positive bacterial strain was isolated from forest soil. Among species with validly published names, the 16S rRNA gene sequence is related most closely (approx. 93 % similarity) to that of Sporichthya polymorpha DSM 43042T. However, differently from this species, it forms both vegetative and aerial mycelia. The aerial hyphae are straight to slightly flexuous, starting to septate to form chains of more than 20 cylindrical spores with a rugose surface. The strain is acidophilic, with a pH range for robust growth between 4.3 and 6.8 and an optimum around 6.0. The peptidoglycan type is A3γ ll-Dpm–Gly. The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. Predominant menaquinones are MK-9(H6) and -9(H4), and iso- and anteiso-branched C16 : 0 and C17 : 0 are the main cellular fatty acids. The DNA G+C content is 71.9 mol%. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics justify the proposal of Catenulispora gen. nov., with the type species Catenulispora acidiphila sp. nov. (type strain, ID139908T =DSM 44928T=NRRL B-24433T). Catenulisporaceae fam. nov. is also proposed.

Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177

Nocardioides aromaticivorans IC177 is a gram-positive carbazole degrader. The genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. The car genes were clustered into the carAaCBaBbAcAd and carDFE gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme A, respectively. The conserved amino acid motifs proposed to bind the Rieske-type [2Fe-2S] cluster and mononuclear iron, the Rieske-type [2Fe-2S] cluster, and flavin adenine dinucleotide were found in the deduced amino acid sequences of carAa, carAc, and carAd, respectively, which showed similarities with CarAa from Sphingomonas sp. strain KA1 (49% identity), CarAc from Pseudomonas resinovorans CA10 (31% identity), and AhdA4 from Sphingomonas sp. strain P2 (37% identity), respectively. Escherichia coli cells expressing CarAaAcAd exhibited major carbazole 1,9a-dioxygenase (CARDO) activity. These data showed that the IC177 CARDO is classified into class IIB, while gram-negative CARDOs are classified into class III or IIA, indicating that the respective CARDOs have diverse types of electron transfer components and high similarities of the terminal oxygenase. Reverse transcription-PCR (RT-PCR) experiments showed that the carAaCBaBbAcAd and carDFE gene clusters are operonic. The results of quantitative RT-PCR experiments indicated that transcription of both operons is induced by carbazole or its metabolite, whereas anthranilate is not an inducer. Biotransformation analysis showed that the IC177 CARDO exhibits significant activities for naphthalene, carbazole, and dibenzo-p-dioxin but less activity for dibenzofuran and biphenyl.

Root controls on soil microbial community structure in forest soils

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes

Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.

Pathways in the Degradation of Hydrolyzed Alcohols of Butyl Benzyl Phthalate in Metabolically Diverse Gordonia sp.Strain MTCC 4818

In the present study, the metabolic pathways involved in the degradation of benzyl alcohol and 1-butanol, the hydrolyzed products of butyl benzyl phthalate, were investigated by the Gordonia sp. strain MTCC 4818. The strain can utilize both benzyl alcohol and 1-butanol individually as sole carbon sources, where benzyl alcohol was found to be metabolized via benzaldehyde, benzoic acid and catechol, which was further degraded by ortho-cleavage dioxygenase to cis,cis-muconic acid and subsequently to muconolactone leading to tricarboxylic acid cycle. On the other hand, 1-butanol was metabolized via butyraldehyde and butyric acid, which was channeled into the tricarboxylic acid cycle via the beta-oxidation pathway. Numbers of dehydrogenases, both NAD+-dependent and NAD+-independent, were found to be involved in the degradation of benzyl alcohol and 1-butanol, where several dehydrogenases exhibited relaxed substrate specificity. Both 2,3- and 3,4-dihydroxybenzoic acids were utilized by the test organism for growth and metabolized by the ortho-cleavage pathway by the cell-free extract of benzoate-grown cells, similar to catechol, suggesting possible broad substrate specificity of the ring cleavage dioxygenase. Moreover, the test organism can utilize various primary and secondary alcohols, aliphatic aldehydes and acids in the C2-C5 range besides n-hexadecane, 1,4-butanediol and cyclohexanol individually as the sole carbon sources indicating metabolic diversity in the Gordonia sp. strain MTCC 4818.

Actinomycetes isolated from lichens: evaluation of their diversity and detection of biosynthetic gene sequences

Actinomycetes, one of the major communities of the microbial population present in soil, can also be found inhabiting a wide diversity of ecological sources. We have explored the use of lichens as an alternative source for the isolation of novel actinomycetes. Lichens are symbiotic mixtures of fungi, green algae and/or cyanobacteria and whereas these symbiotic components have been extensively described, the microbial community inhabiting this niche has not been well characterized. We studied the diversity of the actinomycete population isolated from lichens collected in tropical areas from the Hawaii and Reunion islands and in cold areas from Alaska. The diversity of the microbial population was evaluated using fatty acid analysis and molecular fingerprinting. A PCR approach to screen the isolates for genes associated with secondary metabolite production was applied to evaluate the biosynthetic potential of these strains; profiles obtained for each isolate were compared to the antimicrobial activity exhibited by these isolates in laboratory conditions. Our results demonstrate that lichens represent an extremely rich reservoir for the isolation of a wide diversity of actinomycetes many of them representing still today a rich untapped source of secondary metabolites.

Pseudonocardia dioxanivorans sp. nov., a novel actinomycete that grows on 1,4-dioxane

An actinomycete strain (CB1190T) was previously isolated from industrial sludge contaminated with 1,4-dioxane. The cells of this culture are Gram-positive and exhibit branching aerial and vegetative mycelium. Analysis of the 16S rRNA gene sequence indicates that the strain belongs to the genus Pseudonocardia, closely related to Pseudonocardia hydrocarbonoxydans, P. sulfidoxydans and P. halophobica. Physiological and biochemical characteristics of CB1190T are different from those of other known Pseudonocardia species. The novel organism described here is distinguished by its ability to grow on 1,4-dioxane, which is a probable human carcinogen. This culture can also grow on tetrahydrofuran, gasoline aromatics and several other toxic environmental contaminants. Strain CB1190T is capable of fixing dinitrogen. The predominant fatty acids are 16 : 0 iso, 16 : 1 iso cis9 and 17 : 1 iso cis9. The major phospholipid fatty acids are 16 : 0 iso, 16 : 0 10-Me and 17 : 0 10-Me. The peptidoglycan belongs to type A1γ, meso-diaminopimelic acid. The major menaquinone is MK-8 (H4). Mycolic acids are absent. The G+C content is 74 mol%. Based on morphological, physiological, chemotaxonomic and phylogenetic evidence, it is proposed that strain CB1190T (=ATCC 55486T=DSM 44775T) be classified as the type strain of a novel species, Pseudonocardia dioxanivorans sp. nov. Further studies with this organism will provide insights into metabolic pathways, responsible enzymes, kinetics and the fate of 1,4-dioxane in the environment.

Isolation and characterization of alachlor-degrading actinomycetes from soil

Alachlor (2-cloro-N-(methoxymethyl)-N-(2,6-diethylphenyl)-acetamide) is an extremely toxic and highly mobile herbicide that is widely used for pre-emergence control of grasses and weeds in many commercial crops in Brazil. In order to select soil actinomycetes able to degrade this herbicide, fifty-three actinomycete strains were isolated from soil treated with alachlor using selective conditions and subjected to in vitro degradation assays. Sixteen isolates were shown to be tolerant to high concentrations of the herbicide (up to 720 mg L(-1)), and six of these were able to grow and degrade >/= 50 alachlor (72 mg L(-1)) in mineral salts medium. Morphological and phylogenetic analysis enabled the assignment of the alachlor-degrading strains to the genus Streptomyces. Strain LS151 was related to the type strains of Streptomyces capoamus/Streptomyces galbus, whereas strains LS143 and LS153 were related to Streptomyces bikiniensis. The remaining strains, LS166, LS177 and LS182, were similar in morphological features and recovered in a single cluster based on 16S rDNA sequence analysis, but shown to be distinct on the basis of genomic fingerprint data (rep-PCR). Though a definitive taxonomic assignment of alachlor-degrading strains was not possible, these data indicate that ability to degrade this pesticide was detected in different Streptomyces taxa.

Living in a fungal world: impact of fungi on soil bacterial niche development

The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.

Optimization of extracellular endoxylanase, endoglucanase and peroxidase production by Streptomyces sp. F2621 isolated in Turkey

AIMS

To determine the effect of environmental conditions on the production of extracellular lignocellulose-degrading enzymes by Streptomyces sp. F2621 and to assess the potential use of these enzymes in the hydrolysis of lignocellulose material.

METHODS AND RESULTS

The production of extracellular lignocellulose-degrading enzymes, endoxylanase, endoglucanase and peroxidase during the growth of Streptomyces sp. F2621 in basal salts-yeast extract medium containing different carbon sources and the effect of a number of environmental parameters (e.g. carbon sources and concentrations, pH and temperature) were investigated. The highest endoxylanase (22.41 U ml(-1)) and peroxidase (0.58 U ml(-1)) activities were obtained after 2-4 days of incubation at 30 degrees C in a basal salts medium containing 0.4% (w/v) oat spelt xylan and 0.6% (w/v) yeast extract, corresponding to C : N ratio of 6 : 1. Cell-free extracellular enzyme preparations from the strain were capable of releasing both sugar and aromatic compounds during incubation with eucalyptus paper pulp, straw and xylan. Overall, 9.3% hydrolysis of xylan occurred after 24-h incubation. However the rates of hydrolysis of paper pulp and straw were approximately twofold less than xylan hydrolysis, although the total percentage hydrolysis of available substrate (24.5% and 16.3%, respectively) was greater than xylan hydrolysis.

CONCLUSIONS

The high levels of enzyme production achieved under batch cultivation conditions, coupled with no significant production of endoglucanase during the growth phase of organism and the release of both sugar and aromatic compounds from paper pulp and straw signify the suitability for these enzymes for industrial applications such as pulp and paper production.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results highlight the environmental conditions for the production of extracellular lignocellulose-degrading enzymes by Streptomyces sp. F2621 and suggest the use of streptomycetes and/or their enzymes in industrial processes.

Microbial population dynamics during fed-batch operation of commercially available garbage composters

Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste. All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93%. The core temperature in the reactors fluctuated between 31 degrees C and 58 degrees C due to self-heating. The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage. The moisture content was 48-63% early in the process and 30-40% at the steady state. Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state. Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II. This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period. The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period. But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage.

Molecular characterization of a high-affinity xylobiose transporter of Streptomyces thermoviolaceus OPC-520 and its transcriptional regulation

Streptomyces thermoviolaceus OPC-520 secretes two types of xylanases (StxI and StxII), an acetyl xylan esterase (StxIII), and an alpha-L-arabinofuranosidase (StxIV) in the presence of xylan. Xylan degradation products (mainly xylobiose) produced by the action of these enzymes entered the cell and were then degraded to xylose by an intracellular beta-xylosidase (BxlA). A gene cluster involved in xylanolytic system of the strain was cloned and sequenced upstream of and including a BxlA-encoding gene (bxlA). The gene cluster consisted of four different open reading frames organized in the order bxlE, bxlF, bxlG, and bxlA. Reverse transcriptase PCR analysis revealed that the gene cluster is transcribed as polycistronic mRNA. The deduced gene products, comprising BxlE (a sugar-binding lipoprotein), BxlF (an integral membrane protein), and BxlG (an integral membrane protein), showed similarity to components of the bacterial ATP-binding cassette (ABC) transport system; however, the gene for the ATP binding protein was not linked to the bxl operon. The soluble recombinant BxlE protein was analyzed for its binding activity for xylooligosaccharides. The protein showed high-level affinity for xylobiose (K(d) = 8.75 x 10(-9) M) and for xylotriose (K(d) = 8.42 x 10(-8) M). Antibodies raised against the recombinant BxlE recognized the detergent-soluble BxlE isolated from S. thermoviolaceus membranes. The deduced BxlF and BxlG proteins are predicted to be integral membrane proteins. These proteins contained the conserved EAA loop (between the fourth and the fifth membrane-spanning segments) which is characteristic of membrane proteins from binding-protein-dependent ABC transporters. In addition, the bxlR gene located upstream of the bxl operon was cloned and expressed in Escherichia coli. The bxlR gene encoded a 343-residue polypeptide that is highly homologous to members of the GalR/LacI family of bacterial transcriptional regulators. The purified BxlR protein specifically bound to a 4-bp inverted sequence overlapping the -10 region of the bxl operon. The binding of BxlR to the site was inhibited specifically by low concentrations of xylobiose. This site was also present in the region located between stxI and stxIV and in the upstream region of stxII. BxlR specifically bound to the regions containing the inverted sequence. These results suggest that BxlR might act as a repressor of the genes involved not only in the uptake system of xylan degradation products but also in xylan degradation of S. thermoviolaceus OPC-520.

Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity

AIMS

To evaluate the patterns of the production of antimicrobial compounds by diverse collection of actinomycetes isolated from different geographies under alternative conditions of pH and salinity in the media.

METHODS AND RESULTS

Actinomycetes were grouped based on their method of isolation and their phenotype diversity was determined by total fatty acid analysis. A total of 335 representative isolates, including 235 Streptomyces species and 100 actinomycetes from other taxa, were screened for the production of antimicrobial activities against a panel of bacteria, filamentous fungi and yeasts, including some of clinical relevance. Production of antimicrobial activities was detected in 230 strains. In the case of the genus Streptomyces, 181 antimicrobial activities (77% of the tested isolates) were recorded. The activities observed among the other actinomycetes taxa were lower (49% of the tested isolates).

CONCLUSIONS

The results of this study support the idea that species of actinomycetes isolated in alternative selective conditions of pH and salinity present a significant capacity to produce compounds with antibacterial or antifungal activity. The best group of isolates in terms of production of active secondary metabolites was the one isolated in saline conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results demonstrate that these actinomycetes strains isolated in alternative selective conditions of pH and salinity and collected from diverse geographical locations present a significant capacity to produce compounds with antibacterial or antifungal activity.

Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load

Bioaugmentation of bioreactors focuses on the removal of xenobiotics, with little attention typically paid to the recovery of disrupted reactor functions such as ammonium-nitrogen removal. Chloroanilines are widely used in industry as a precursor to a variety of products and are occasionally released into wastewater streams. This work evaluated the effects on activated-sludge reactor functions of a 3-chloroaniline (3-CA) pulse and bioaugmentation by inoculation with the 3-CA-degrading strain Comamonas testosteroni I2 gfp. Changes in functions such as nitrification, carbon removal, and sludge compaction were studied in relation to the sludge community structure, in particular the nitrifying populations. Denaturing gradient gel electrophoresis (DGGE), real-time PCR, and fluorescent in situ hybridization (FISH) were used to characterize and enumerate the ammonia-oxidizing microbial community immediately after a 3-CA shock load. Two days after the 3-CA shock, ammonium accumulated, and the nitrification activity did not recover over a 12-day period in the nonbioaugmented reactors. In contrast, nitrification in the bioaugmented reactor started to recover on day 4. The DGGE patterns and the FISH and real-time PCR data showed that the ammonia-oxidizing microbial community of the bioaugmented reactor recovered in structure, activity, and abundance, while the number of ribosomes of the ammonia oxidizers in the nonbioaugmented reactor decreased drastically and the community composition changed and did not recover. The settleability of the activated sludge was negatively influenced by the 3-CA addition, with the sludge volume index increasing by a factor of 2.3. Two days after the 3-CA shock in the nonbioaugmented reactor, chemical oxygen demand (COD) removal efficiency decreased by 36% but recovered fully by day 4. In contrast, in the bioaugmented reactor, no decrease of the COD removal efficiency was observed. This study demonstrates that bioaugmentation of wastewater reactors to accelerate the degradation of toxic chlorinated organics such as 3-CA protected the nitrifying bacterial community, thereby allowing faster recovery from toxic shocks.

Characterization of chitinase genes from an alkaliphilic actinomycete, Nocardiopsis prasina OPC-131

An alkaliphilic actinomycete, Nocardiopsis prasina OPC-131, secretes chitinases, ChiA, ChiB, and ChiB Delta, in the presence of chitin. The genes encoding ChiA and ChiB were cloned and sequenced. The open reading frame (ORF) of chiA encoded a protein of 336 amino acids with a calculated molecular mass of 35,257 Da. ChiA consisted of only a catalytic domain and showed a significant homology with family 18 chitinases. The chiB ORF encoded a protein of 296 amino acids with a calculated molecular mass of 31,500 Da. ChiB is a modular enzyme consisting of a chitin-binding domain type 3 (ChtBD type 3) and a catalytic domain. The catalytic domain of ChiB showed significant similarity to Streptomyces family 19 chitinases. ChiB Delta was the truncated form of ChiB lacking ChtBD type 3. Expression plasmids coding for ChiA, ChiB, and ChiB Delta were constructed to investigate the biochemical properties of these recombinant proteins. These enzymes showed pHs and temperature optima similar to those of native enzymes. ChiB showed more efficient hydrolysis of chitin and stronger antifungal activity than ChiB Delta, indicating that the ChtBD type 3 of ChiB plays an important role in the efficient hydrolysis of chitin and in antifungal activity. Furthermore, the finding of family 19 chitinase in N. prasina OPC-131 suggests that family 19 chitinases are distributed widely in actinomycetes other than the genus Streptomyces.

Induction of PAH-catabolism in mushroom compost and its use in the biodegradation of soil-associated phenanthrene

This paper describes the induction of phenanthrene-catabolism within Phase II mushroom compost resulting from its incubation with (1) phenanthrene, and (2) PAH-contaminated soil. Respirometers measuring mineralization of freshly added 14C-9-phenanthere were used to evaluate induction of phenanthrene-catabolism. Where pure phenanthrene (spiked at a concentration of 400 mg kg(-1) wet wt.) was used to induce phenanthrene-catabolism in compost, induction was measurable, with maximal mineralization observed after 7 weeks phenanthrene-compost contact time. Where PAH-contaminated soil was used to induce phenanthrene-catabolism in un-induced compost, induction was observed after 5 weeks soil-compost contact time. Microcosm-scale amelioration of soil contaminated with 14C-phenanthrene (aged in soil for 516 days prior to incubation with compost) indicated that both induced (using pure phenanthrene) and uninduced Phase II mushroom composts were equally able to promote degradation of this soil-associated contaminant. After 111 days incubation time, 42.7 +/- 6.3% loss of soil-associated phenanthrene was observed in the induced-compost soil mixture, while 36.7 +/- 2.9% loss of soil-associated phenanthrene was observed in the uninduced-compost soil mixture. These results are notable as they indicate that while pre-induction of phenanthrene-catabolism within compost is possible, it does not significantly increase the extent of degradation when the compost is used to ameliorate phenanthrene-contaminated soil. Thus, compost could be used directly in the amelioration of contaminated land i.e. without pre-induction of catabolism.

Cloning and expression of the benzoate dioxygenase genes from Rhodococcus sp. strain 19070

The bopXYZ genes from the gram-positive bacterium Rhodococcus sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled Escherichia coli to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic cis-diol or catechol, respectively. This expression system also rapidly transformed m-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in Rhodococcus sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both meta- and ortho-cleavage degradative pathways, which are associated in pseudomonads with the xyl and ben genes, respectively. Open reading frames downstream of bopXYZ, designated bopL and bopK, resembled genes encoding cis-diol dehydrogenases and benzoate transporters, respectively. The bop genes were in the same order as the chromosomal ben genes of P. putida PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in E. coli yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome c reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences.

Biodegradation of aliphatic-aromatic copolyesters: evaluation of the final biodegradability and ecotoxicological impact of degradation intermediates

The biological degradation behaviour of the aliphatic-aromatic copolyester Ecoflex was investigated with regard to the degree of degradation and the intermediates formed during the degradation process. The individual thermophilic strain Thermomonospora fusca, isolated from compost material, was used for the degradation experiments in a defined synthetic medium at 55 degrees C. After 22 days of degradation more than 99.9% of the polymer had depolymerized and with regard to the degradation of the diacid and diol components of Ecoflex only the monomers of the copolyesters (1,4-butanediol, terephthalate and adipate) could be detected by gas chromatography/mass spectroscopy (GC-MS) measurements in the medium. In interrupted degradation experiments predominantly the monoesters of adipic acid and terephthalic acid with 1,4-butanediol were observed in addition to the monomers. In toxicological tests with Daphnia magna and Photobacterium phosphoreum no significant toxicological effect was observed, neither for the monomeric intermediates nor for the oligomeric intermediates. From a risk assessment it can be concluded that there is no indication for an environmental risk when aliphatic-aromatic copolyesters of the Ecoflex-type are introduced into composting processes.

Thatch biodegradation and antifungal activities of two lignocellulolytic Streptomyces strains in laboratory cultures and in golf green turfgrass

The use of lignocellulolytic Streptomyces spp. as biological agents, to enhance thatch degradation in turf and to slow its rate of accumulation while controlling fungal growth in the thatch layer, was studied. In flask scale studies, two lignocellulolytic Streptomyces violaceusniger (= hygroscopicus) strains (YCED9 and WYE53) decomposed thatch (> 30% dry weight) over a 12-week incubation period. Biodegradation was accompanied by production of extracellular cellulases, xylanases, and peroxidases. The accumulation of the polymeric, water-soluble lignin degradation intermediate acid, precipitable polymeric lignin (APPL), was also observed. Residual thatch from 12-week-old cultures had an increased lignin-to-carbohydrate ratio, an indication that although lignin was metabolized, carbohydrates were preferential carbon sources for these actinomycetes. A spore-containing soluble dry powder formulation was used as an inoculum in an in situ field experiment. This formulation was maintained in storage at 4 degrees C for over two years without viability loss. Results from the golf green experiment showed that although treated thatch layers in established greens were not appreciably reduced over the course of one summer, the Streptomyces were active and maintained their populations within the thatch, while fungal growth was suppressed as compared to controls. The results show that treatment of turfgrass with these Streptomyces may be useful for the long-term control of fungal populations within the thatch. Longer field studies are required to assess the long-term potential for also controlling thatch build-up and fungal pathogens.

Analysis of a ptsH homologue from Streptomyces coelicolor A3(2)

A ptsH homologue of Streptomyces coelicolor A3(2) was identified in the emerging genome sequence, cloned in Escherichia coli and the S. coelicolor HPr over-produced and purified. The protein was phosphorylated in vitro in a phosphoenolpyruvate (PEP)-dependent manner by purified enzyme I (EI) from Bacillus subtilis, and much less efficiently in an ATP-dependent manner by purified HPr kinase, also from B. subtilis. There was no indication of ATP-dependent phosphorylation of the purified protein by cell extracts of either S. coelicolor or Streptomyces lividans. Deletion of the ptsH homologue from the S. coelicolor and S. lividans chromosomes had no effect on growth when fructose was supplied as sole carbon source, and in S. coelicolor it had no effect on glucose repression of agarase and galactokinase synthesis, suggesting that the HPr encoded by this gene does not play an essential role in fructose transport nor a general role in carbon catabolite repression.

Cloning, characterization and expression of beta-N-acetylglucosaminidase gene from Streptomyces thermoviolaceus OPC-520(1)

The nagB gene encoding beta-N-acetylglucosaminidase from S. thermoviolaceus OPC-520 was cloned and sequenced. The nagB gene could encode a protein of 541 amino acids with a calculated molecular mass of 58274. NagB revealed significant similarities to beta-N-acetylhexosaminidases and chitobiases from bacteria, which are classified into family 20 glycosyl hydrolases. NagB effectively hydrolyzed all of the chitin oligosaccharides from dimer to hexamer.

A novel beta-N-acetylglucosaminidase from Streptomyces thermoviolaceus OPC-520: gene cloning, expression, and assignment to family 3 of the glycosyl hydrolases

A beta-N-acetylglucosaminidase gene (nagA) of Streptomyces thermoviolaceus OPC-520 was cloned in Streptomyces lividans 66. The nucleotide sequence of the gene, which encodes NagA, revealed an open reading frame of 1,896 bp, encoding a protein with an Mr of 66, 329. The deduced primary structure of NagA was confirmed by comparison with the N-terminal amino acid sequence of the cloned beta-N-acetylglucosaminidase expressed by S. lividans. The enzyme shares no sequence similarity with the classical beta-N-acetylglucosaminidases belonging to family 20. However, NagA, which showed no detectable beta-glucosidase activity, revealed homology with microbial beta-glucosidases belonging to family 3; in particular, striking homology with the active-site regions of beta-glucosidases was observed. Thus, the above-mentioned results indicate that NagA from S. thermoviolaceus OPC-520 is classified as a family 3 glycosyl hydrolase. The enzyme activity was optimal at 60 degreesC and pH 5.0, and the apparent Km and Vmax values for p-nitrophenyl-beta-N-acetylglucosamine were 425.7 microM and 24.8 micromol min-1 mg of protein-1, respectively.

Hazard to man and the environment posed by the use of urban waste compost: a review

This review presents the current state of knowledge on the relationship between the environment and the use of municipal waste compost in terms of health risk assessment. The hazards stem from chemical and microbiological agents whose nature and magnitude depend heavily on the degree of sorting and on the composting methods. Three main routes of exposure can be determined and are quantified in the literature: (i) The ingestion of soil/compost mixtures by children, mostly in cases of pica, can be a threat because of the amount of lead, chromium, cadmium, PCDD/F and fecal streptococci that can be absorbed. (ii) Though concern about contamination through the food chain is weak when compost is used in agriculture, some authors anticipate accumulation of pollutants after several years of disposal, which might lead to future hazards. (iii) Exposure is also associated with atmospheric dispersion of compost organic dust that convey microorganisms and toxicants. Data on hazard posed by organic dust from municipal composts to the farmer or the private user is scarce. To date, microorganisms are only measured at composting plants, thus raising the issue of extrapolation to environmental situations. Lung damage and allergies may occur because of organic dust, Gram negative bacteria, actinomycetes and fungi. Further research is needed on the risk related to inhalation of chemical compounds.

Properties of a novel glucose-enhanced beta-glucosidase purified from Streptomyces sp. (ATCC 11238)

An inducible intracellular beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. QM-B814 (ATCC 11238) has been purified and characterized. The purified polypeptide is monomeric with a relative molecular mass of 62 kDa by SDS-PAGE and 42 kDa by size-exclusion chromatography; its isoelectric point is 4.2. The difference in the molecular mass values can be attributed to the glycosylated nature of the protein. The purified enzyme has a pH optimum of 6.0-6.5. The temperature optimum for activity is 50 degrees C; at this temperature the enzyme is stable for 1 h. The enzyme hydrolyzes mainly aryl-beta-glucosides but also presents significant activity against beta-linked disaccharides and maltose. The enzyme displays an unusual kinetic behavior and biphasic Lineweaver-Burk and Eadie-Hofstee plots for p-nitrophenyl-beta-D-glucoside and cellobiose were obtained. The enzyme presents beta-glycosyltransferase activity and an exoglycosidase-type action on cellodextrins. It is inhibited by delta-gluconolactone (Ki 0.44 mM) but, remarkably, glucose in the range 25-200 mM enhances the rate of p-nitrophenyl-beta-D-glucoside hydrolysis.

Characterization and sequence analysis of a Streptomyces rochei A2 endoglucanase-encoding gene

A 7-kb fragment of Streptomyces rochei A2 chromosomal DNA was cloned into pAT153 and shown to confer endoglucanase (EglS) activity on Escherichia coli cells. In E. coli clones, the EglS was secreted into the periplasm. Deletion analysis revealed that an 827-bp fragment was enough for the enzymatic activity. Sequence analysis showed that the 827-bp fragment codes for the catalytic domain of the enzyme. The complete sequence of the gene (eglS) is 1149-bp long. A signal peptide, a catalytic domain and a cellulose-binding domain were identified from the nucleotide sequence, and the EglS found to belong to the family H of cellulase catalytic domains. These conclusions were substantiated by determination of the N-terminal sequence of the purified protein and zymogram analysis, which revealed protein species with a molecular mass equal to that deduced from the nt sequence analysis.