Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp

PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation

The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type they are reported to degrade. Each protein structure has been predicted in silico and can be visualized or downloaded for further investigation. In addition to standard database functionalities, such as searching, filtering and retrieving database records, we implemented several analytical tools that accept inputs, including gene, genome, metagenome, transcriptomes, metatranscriptomes and taxa table data. Users can now analyze their datasets for the presence of putative plastic-degrading species and potential plastic-degrading proteins and pathways from those species. Database URL:http://plasticdb.org.

Mastication of polyolefins alters the microbial composition in Galleria mellonella

Recent studies have indicated that Galleria mellonella larvae ingest polyethylene films and the degradation mechanism could inspire biotechnological exploitation for degrading plastic to eliminate global pollution from plastic waste. In this study, we tested the chemical compositions of masticated and ingested different plastic types by G. mellonella. High throughput sequencing of 16S rRNA gene was used to characterize the alteration of the microbial communities derived from salivary glands, gut contents and whole G. mellonella larvae. Our results indicated that G. mellonella is able to masticate polyethylene (PE), expanded polystyrene (EPS) and polypropylene (PP) and convert it to small particles with very large and chemically modified surfaces. The characteristics of the polymer affect the rate of damage. Formation of functional carbonyl groups on the appearance of oxidized metabolic intermediates of polyolefins in the frass samples observed. We found that the mastication of EPS, PP or PE could significantly alter the microbial composition in the gut content while it did not appear to influence the salivary glands microbial community. Representatives of Desulfovibrio vulgaris and Enterobacter grew with the PE diet while mastication of polystyrene and polypropylene increased the abundance of Enterococcus. The evaluation of bacterial communities in whole larvae confirmed the obtained result and additionally showed that the abundance of Paenibacillus, Corynebacterium and Commamonadaceae increased by Styrofoam (EPS) consumption.

Removal of polyethylene glycols from wastewater: A comparison of different approaches

Physicochemical methods such as adsorption on activated carbon, oxidation with either ozone or Fenton reagent, and chemical precipitation (coagulation), were assessed for the removal of polyethylene glycol (PEG) from wastewater. This contaminant is rarely investigated due to its low toxicity, although its presence limits the use of large water resources. The experimental tests showed that adsorption on activated carbon is well approximated by a Langmuir isotherm, and influenced by contact time, PEG molecular weight, pH, temperature, and initial PEG concentration. Ozonation allowed fragmenting the polymeric chains but was unable to remove completely the PEG, while about 85% of the total organic carbon (TOC) was removed by Fenton oxidation reaction by using a ratio between H₂O₂ and Fe^II close to 4. Coagulation did not produce results worthy of note, most likely because the uncharged PEG molecule does not interact with the iron hydroxide flocs. However, when performed after the Fenton oxidation (i.e., by simply raising the pH to values > 8), it allowed a further reduction of the residual TOC, up to 96% of the total, in the best case. Based on the resources used by each process studied and in consideration of the effectiveness of each of them, a semi-quantitative comparison on the sustainability of the different approaches is proposed.

Nrf2 contributes to the weight gain of mice during space travel

Space flight produces an extreme environment with unique stressors, but little is known about how our body responds to these stresses. While there are many intractable limitations for in-flight space research, some can be overcome by utilizing gene knockout-disease model mice. Here, we report how deletion of Nrf2, a master regulator of stress defense pathways, affects the health of mice transported for a stay in the International Space Station (ISS). After 31 days in the ISS, all flight mice returned safely to Earth. Transcriptome and metabolome analyses revealed that the stresses of space travel evoked ageing-like changes of plasma metabolites and activated the Nrf2 signaling pathway. Especially, Nrf2 was found to be important for maintaining homeostasis of white adipose tissues. This study opens approaches for future space research utilizing murine gene knockout-disease models, and provides insights into mitigating space-induced stresses that limit the further exploration of space by humans.

Using Nrf2 knockout mice, Suzuki, Uruno, Yumoto et al. show that space travel activates Nrf2 signaling, which contributes to the weight gain of mice by regulating fat metabolism of white adipose tissues. This study provides insights into potential interventions to mitigate stresses that accompany space travels.

2H and 13C isotope fractionation analysis of organophosphorus compounds for characterizing transformation reactions in biogas slurry: Potential for anaerobic treatment of contaminated biomass

The ability of anaerobic digestion (AD) to eliminate organophosphorus model compounds (OPs) with structural elements of phosphate, phosphorothioate and phosphorodithioate esters was studied. The enzymatic mechanism of the first irreversible degradation reaction was characterized using metabolite pattern and kinetic ²H/¹³C-isotope effect in original, cell-free and heat sterilized biogas slurry. The isotope fractionation study suggests different modes of degradation reactions. Representatives for phosphate ester, tris(2-chloroethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate, were hydrolyzed in biogas slurry without carbon or hydrogen isotope fractionation. Representatives for phosphorodithioate, Dimethoate and Malathion, were degraded in original slurry yielding carbon enrichment factor (ε_C) of -0.6 ± 0.1‰ and -5.5 ± 0.1‰ (-0.9 ± 0.1‰ and -7.2 ± 0.5‰ in cell-free slurry), without hydrogen isotope fractionation. Phosphorothioate degradation represented by Parathion and Parathion-methyl yielded surprisingly different ε_C (-0.7 ± 0.2 and -3.6 ± 0.4‰) and ε_H (-33 ± 5 and -5 ± 1‰) in original slurry compared to cell-free slurry (ε_C = -2.5 ± 0.5 and -8.6 ± 1.4‰; ε_H = -61 ± 10 and -10 ± 3‰) suggesting H-C bond cleavage. Degradation of Parathion and Parathion-methyl in sterilized slurry gave carbon but not hydrogen fractionation implying relative thermostable enzymatic activity with different mechanism. The correlation of ²H and ¹³C stable isotope fractionation of Parathion in biogas slurry showed distinct pattern (Λ_original = 31 ± 11, Λ_cell-free = 20 ± 2), indicating different mechanism from chemical hydrolysis. Overall, AD can be a potential treatment for OPs contaminated biomass or contaminated organic waste material.

Degradation of polyethylene glycols and polypropylene glycols in microcosms simulating a spill of produced water in shallow groundwater

Polyethylene glycols (PEGs) and polypropylene glycols (PPGs) are frequently used in hydraulic fracturing fluids and have been detected in water returning to the surface from hydraulically fractured oil and gas wells in multiple basins. We identified degradation pathways and kinetics for PEGs and PPGs under conditions simulating a spill of produced water to shallow groundwater. Sediment-groundwater microcosm experiments were conducted using four produced water samples from two Denver-Julesburg Basin wells at early and late production. High-resolution mass spectrometry was used to identify the formation of mono- and di-carboxylated PEGs and mono-carboxylated PPGs, which are products of PEG and PPG biodegradation, respectively. Under oxic conditions, first-order half-lives were more rapid for PEGs (<0.4-1.1 d) compared to PPGs (2.5-14 d). PEG and PPG degradation corresponded to increased relative abundance of primary alcohol dehydrogenase genes predicted from metagenome analysis of the 16S rRNA gene. Further degradation was not observed under anoxic conditions. Our results provide insight into the differences between the degradation rates and pathways of PEGs and PPGs, which may be utilized to better characterize shallow groundwater contamination following a release of produced water.

Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors

To determine whether the addition of conductive materials could enhance methane production by direct interspecies electron transfer (DIET), we operated three anaerobic reactors amended with non-conductive (ceramic) or conductive materials (anthracite and granular activated carbon (GAC)). Throughout eight months of operation, ethanol was consistently detected as the major fermentation product. The specific yield in the anthracite and GAC-added reactors increased by 31.5% and 43.3%, respectively, compared to the ceramic-added reactor. 16S rRNA gene sequencing results indicated Geobacter was dominant (up to 55% of total sequences), whereas acids-degrading syntrophic bacteria were low in abundance (<2%). Using metagenomic analysis, the draft genome of the dominant Geobacter population (bin GAC1) was reconstructed and observed to possess genetic abilities of ethanol oxidation, hydrogen production, and extracellular electron transfer, and represented a phylogenetically novel Geobacter species. While Methanosaeta was the dominant methanogen, reactors containing conductive materials harbored more diverse and abundant archaeal populations, as revealed by FISH, qPCR, and metagenomics. Our findings suggested that a novel Geobacter population could oxidize ethanol and employed both hydrogen transfer and DIET depending on the accessibility of conductive materials. Thermodynamic advantages of DIET over hydrogen production could lead to enhanced methane production in reactors with conductive materials.

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.

Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin-resistant Staphylococcus aureus

Recent creation of a Unified Microbiome Initiative (UMI) has the aim of understanding how microbes interact with each other and with us. When pathogenic Staphylococcus aureus infects the skin, the interplay between S. aureus and skin commensal bacteria occurs. Our previous data revealed that skin commensal bacteria can mediate fermentation against the growth of USA300, a community-acquired methicillin-resistant S. aureus MRSA. By using a fermentation process with solid media on a small scale, we define poly(ethylene glycol) dimethacrylate (PEG-DMA) as a selective fermentation initiator which can specifically intensify the probiotic ability of skin commensal Staphylococcus epidermidis bacteria. At least five short-chain fatty acids including acetic, butyric and propionic acids with anti-USA300 activities are produced by PEG-DMA fermentation of S. epidermidis. Furthermore, the S. epidermidis-laden PEG-DMA hydrogels effectively decolonized USA300 in skin wounds in mice. The PEG-DMA and its derivatives may become novel biomaterials to specifically tailor the human skin microbiome against invading pathogens.

Effects of Aqueous Film-Forming Foams (AFFFs) on Trichloroethene (TCE) Dechlorination by a Dehalococcoides mccartyi-Containing Microbial Community

The application of aqueous film-forming foams (AFFFs) to extinguish chlorinated solvent-fueled fires has led to the co-contamination of poly- and perfluoroalkyl substances (PFASs) and trichloroethene (TCE) in groundwater and soil. Although reductive dechlorination of TCE by Dehalococcoides mccartyi is a frequently used remediation strategy, the effects of AFFF and PFASs on TCE dechlorination are not well-understood. Various AFFF formulations, PFASs, and ethylene glycols were amended to the growth medium of a D. mccartyi-containing enrichment culture to determine the impact on dechlorination, fermentation, and methanogenesis. The community was capable of fermenting organics (e.g., diethylene glycol butyl ether) in all AFFF formulations to hydrogen and acetate, but the product concentrations varied significantly according to formulation. TCE was dechlorinated in the presence of an AFFF formulation manufactured by 3M but was not dechlorinated in the presence of formulations from two other manufacturers. Experiments amended with AFFF-derived PFASs and perfluoroalkyl acids (PFAAs) indicated that dechlorination could be inhibited by PFASs but that the inhibition depends on surfactant concentration and structure. This study revealed that the fermentable components of AFFF can stimulate TCE dechlorination, while some of the fluorinated compounds in certain AFFF formulations can inhibit dechlorination.

Anaerobic degradation of alcohol ethoxylates and polyethylene glycols in marine sediments

This research is focused on alcohol polyethoxylates (AEOs), nonionic surfactants used in a wide variety of products such as household cleaners and detergents. Our main objective in this work was to study the anaerobic degradation of these compounds and their main aerobic degradation products and precursors (polyethylene glycols, PEGs, which are also used for many other applications) in marine sediments, providing the first data available on this topic. First, we observed that average AEO sediment-water partition coefficients (Kd) increased towards those homologs having longer alkyl chains (from 257 L/kg for C12 to 5772 L/kg for C18),which were less susceptible to undergo biodegradation. Overall, AEO and PEG removal percentages reached up to 99.7 and 93%, respectively, after 169 days of incubation using anaerobic conditions in sediments ([O2] = 0 ppm, Eh = -170 to -380 mV and T = 30 °C). Average half-life was estimated to be in a range from 10 to 15 days for AEO homologs (C12AEO8-C18AEO8), and 18 days for PEGEO8.Methanogenic activity proved to be intense during the experiment, confirming the occurrence of anaerobic conditions. This is the first study showing that AEOs and PEGs can be degraded in absence of oxygen in marine sediments, so this new information should be taken into account for future environmental risk assessments on these chemicals.

Microbial community analysis of anaerobic reactors treating soft drink wastewater

The anaerobic packed-bed (AP) and hybrid packed-bed (HP) reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG) and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95%) after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs). Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR) increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR.

Microbial bioavailability of covalently bound polymer coatings on model engineered nanomaterials

By controlling nanoparticle flocculation and deposition, polymer coatings strongly affect nanoparticle fate, transport, and subsequent biological impact in the environment. Biodegradation is a potential route to coating breakdown, but it is unknown whether surface-bound polymers are bioavailable. Here we demonstrate, for the first time, that polymer coatings covalently bound to nanomaterials are bioavailable. Model poly(ethylene oxide) (PEO) brush-coated nanoparticles (densely cross-linked bottle brush copolymers) with hydrophobic divinyl benzene cross-linked cores and hydrophilic PEO brush shells, having ~ 30 nm hydrodynamic radii, were synthesized to obtain a nanomaterial in which biodegradation was the only available coating breakdown mechanism. PEO-degrading enrichment cultures were supplied with either PEO homopolymer or PEO brush nanoparticles as the sole carbon source, and protein and CO₂ production were monitored as a measure of biological conversion. Protein production after 90 h corresponded to 14% and 8% of the total carbon available in the PEO homopolymer and PEO brush nanoparticle cultures, respectively, and CO₂ production corresponded to 37% and 3.8% of the carbon added to the respective system. These results indicate that the PEO in the brush is bioavailable. Brush biodegradation resulted in particle aggregation, pointing to the need to understand biologically mediated transformations of nanoparticle coatings in order to understand the fate and transport of nanoparticles in the environment.

The effect of vinyl acetate in acetoclastic methanogenesis

The influence of vinyl acetate (VA) in the methanogenesis was evaluated, by using an upflow anaerobic sludge blanket reactor of 1.5L. The reactor was operated at 33.5 g/L volatile suspended solids to 30±2 °C, a hydraulic residence time of 1 day, an organic loading rate of 1 kgCOD/m3/d of two different mixtures of VA and glucose. The VA was methanized to 81% when its proportion was of 10% into reactor loading rate, when VA proportion increased to 25%, the methane production rate decreased to 62% and the acetate production rate increased almost 8 times. These results indicated that VA was only hydrolyzed and glucose was not used as a co-substrate. The effect of glucose on VA methanogenic degradation was evaluated through batch reactors of 60 mL, concluding that the glucose supported the methanogenesis without favoring the VA elimination. On the other hand, the results of the sludge from the reactor in the presence of VA demonstrated that VA caused an irreversibly inhibition of acetoclastic methanogenesis when the anaerobic sludge was exposed to this compound.

Aerobic biodegradation of polyethylene glycols of different molecular weights in wastewater and seawater

In order to distinguish between aerobic biodegradation of synthetic polymers in fresh and seawater, polyethylene glycols (PEGs) were systematically and comparatively investigated in inocula from municipal wastewater and seawater aquarium filters for the first time. The molecular weight (MW) of the PEGs, (HO(CH(2)CH(2)O)(n)H, n=3-1350) as representatives of water-soluble polymers, ranged from 250 to 57,800Da. The biodegradation was observed by removal of dissolved organic carbon and carbon dioxide production by applying standardized ISO and OECD test methods. Specific analyses using liquid chromatography mass spectrometry (LC-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) were performed. All PEGs selected were completely biodegradable in freshwater media within 65d. PEGs with an MW up to 14,600Da have a similar degradation pathway which is characterized by gradual splitting of C(2)-units off the chain resulting in formation of short-chain PEGs. In artificial seawater media, full biodegradation of PEGs up to 7400Da required more time than in freshwater. PEGs with MW 10,300 and 14,600Da were only partially degraded whereas PEGs with MW 26,600 and 57,800Da were not degraded for a period of 135d. The biodegradation pathway of PEG 250 and PEG 970 in seawater is similar to that for freshwater. For PEGs having an MW from 2000 to 10,300Da, the degradation pathway in seawater differs from the pathway of the shorter PEGs.

Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors

The microbial communities established in mesophilic and thermophilic expanded granular sludge bed reactors operated with sulfate as the electron acceptor were analyzed using 16S rRNA targeted molecular methods, including denaturing gradient gel electrophoresis, cloning, and phylogenetic analysis. Bacterial and archaeal communities were examined over 450 days of operation treating ethanol (thermophilic reactor) or ethanol and later a simulated semiconductor manufacturing wastewater containing citrate, isopropanol, and polyethylene glycol 300 (mesophilic reactor), with and without the addition of copper(II). Analysis, of PCR-amplified 16S rRNA gene fragments using denaturing gradient gel electrophoresis revealed a defined shift in microbial diversity in both reactors following a change in substrate composition (mesophilic reactor) and in temperature of operation from 30 degrees C to 55 degrees C (thermophilic reactor). The addition of copper(II) to the influent of both reactors did not noticeably affect the composition of the bacterial or archaeal communities, which is in agreement with the very low soluble copper concentrations (3-310 microg l(-1)) present in the reactor contents as a consequence of extensive precipitation of copper with biogenic sulfides. Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrates.

Biodegradation of poly(propylene glycol)s under the conditions of the OECD screening test

Two poly(propylene glycol)s (PPGs): PPG 425 and PPG 725 were tested under the conditions of the OECD Screening Test with activated sludge as inoculum. Tested PPG were the sole source of organic carbon in the test. Quantitative determination of the biodegradation progress was performed by the HPLC with fluorescence detection after derivatisation of PPG with naphthyl isocyanate. The liquid chromatography-mass spectrometry technique was used for identification and semiquantitative determination of metabolites. Separation of PPG and metabolites from the water matrix was performed by liquid-liquid extraction with chloroform. It was found that the shorter PPG 425 is biodegraded significantly worse than the longer PPG 725 and that biodegradation occurs without shortening of the PPG chain for both PPG. PPG molecules are oxidised to ketones and/or aldehydes during the aerobic biodegradation process.

Anaerobic biodegradability and methanogenic toxicity of key constituents in copper chemical mechanical planarization effluents of the semiconductor industry

Copper chemical mechanical planarization (CMP) effluents can account for 30-40% of the water discharge in semiconductor manufacturing. CMP effluents contain high concentrations of soluble copper and a complex mixture of organic constituents. The aim of this study is to perform a preliminary assessment of the treatability of CMP effluents in anaerobic sulfidogenic bioreactors inoculated with anaerobic granular sludge by testing individual compounds expected in the CMP effluents. Of all the compounds tested (copper (II), benzotriazoles, polyethylene glycol (M(n) 300), polyethylene glycol (M(n) 860) monooleate, perfluoro-1-octane sulfonate, citric acid, oxalic acid and isopropanol) only copper was found to be inhibitory to methanogenic activity at the concentrations tested. Most of the organic compounds tested were biodegradable with the exception of perfluoro-1-octane sulfonate and benzotriazoles under sulfate reducing conditions and with the exception of the same compounds as well as Triton X-100 under methanogenic conditions. The susceptibility of key components in CMP effluents to anaerobic biodegradation combined with their low microbial inhibition suggest that CMP effluents should be amenable to biological treatment in sulfate reducing bioreactors.

Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov

Deep subsurface sandstones in the area of Berlin (Germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. The in situ temperatures at the sampling sites ranged from 37 to 45 degrees C. Investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. Seven strains were isolated from porewater brines in the porous sandstone. Three of them were obtained with methanol (strains H1M, H3M, and B1M), three strains with triethylene glycol (strains H1T, B1T, and B2T) and one strain with a mixture of lactate, acetate and butyrate (strain H1-13). Due to phenotypic properties six isolates could be identified as members of the genus Desulfovibrio, and strain B2T as a Desulfotomaculum. The salt tolerance and temperature range for growth indicated that the isolates originated from the indigenous deep subsurface sandstones. They grew in mineral media reflecting the in situ ionic composition of the different brines, which contained 1.5 to 190 g NaCl x l(-1) and high calcium and magnesium concentrations. The Desulfovibrio strains grew at temperatures between 20 and 50 degrees C, while the Desulfotomaculum strain was thermophilic and grew between 30 and 65 degrees C. The strains utilized a broad spectrum of electron donors and acceptors. They grew with carbon compounds like lactate, pyruvate, formate, n-alcohols (C1-C5), glycerol, ethylene glycol, malate, succinate, and fumarate. Some strains even utilized glucose as electron donor and carbon source. All strains were able to use sulfate, sulfite and nitrate as electron acceptors. Additionally, three Desulfovibrio strains reduced manganese oxide, the Desulfotomaculum strain reduced manganese oxide, iron oxide, and elemental sulfur. The 16S rRNA analysis revealed that the isolates belong to three different species. The strains H1T, H3M and B1M could be identified as Desulfovibrio indonesiensis, and strain B2T as Desulfotomaculum geothermicum. The other Desulfovibrio strains (H1M, H1-13, and B1T) showed identical 16S rDNA sequences and similarities as low as 93% to their closest relative, Desulfovibrio aminophilusT. Therefore, these isolates were assigned to a new species, Desulfovibrio cavernae sp. nov., with strain H1M as the type strain.

Involvement of a quinoprotein (PQQ-containing) alcohol dehydrogenase in the degradation of polypropylene glycols by the bacterium Stenotrophomonas maltophilia

Previous work has shown that when the bacterium Stenotrophomonas maltophilia is grown on polypropylene glycol, different dye-linked polypropylene glycol dehydrogenase (PPG-DH) activities are induced during growth. Here the purification and characterization of the dehydrogenase activity induced in the stationary phase, and present in the periplasmic space, is described. The homogeneous enzyme preparation obtained consists of a homodimeric protein with a molecular mass of about 123 kDa and an isoelectric point of 5.9. The cofactor of the enzyme appeared to be pyrroloquinoline quinone (PQQ), no heme c was present, and holo-enzyme contained two PQQ molecules per enzyme molecule. In these respects, PPG-DH described here is similar to already known quinoprotein alcohol dehydrogenases, but in other respects, it is different. Therefore, it is suggested that PPG-DH could be a new type of quinoprotein alcohol dehydrogenase. Based on its strong preference for polyols, PPG-DH seems well fitted to carry out the first step in the degradation of PPGs, synthetic polymers containing a variety of hydroxyl groups.

Ether-bond scission in the biodegradation of alcohol ethoxylate nonionic surfactants by Pseudomonas sp. strain SC25A

Pseudomonas sp. strain SC25A, previously isolated for its ability to grow on alcohol ethoxylates (PEG dodecyl ethers) as sole source of carbon and energy, was shown to be capable of growth on the dodecyl ethers of mono-, di, tri- and octaethylene glycols. Comparative growth yields for this series of alcohol ethoxylate nonionic surfactants indicated that, whereas all of the carbon of monoethylene glycol dodecyl ether (MEGDE) was assimilable, only the alkyl chains were assimilated from the higher ethoxamers. These results are interpreted in terms of a primary biodegradation mechanism in which the scission of the dodecyl-ether bond is the first step. In the case of MEGDE this step separates the dodecyl chain from a C2 fragment, both of which are readily assimilable; for the higher ethoxamers, the assimilable dodecyl chain is accompanied by an ether-containing PEG derivative which would require further rounds of either scission before assimilation. Whole cells and cell extracts converted [1-14C]MEGDE initially and very rapidly to radiolabelled dodecanol. Disappearance of [14C]dodecaol was accompanied by production of [14C]dodecanal. [14C]Dodecanoic acid was present at relatively low concentrations throughout the incubation periods. [14C]Dodecan-1, 12-dioic acid was produced in significant quantities (up to 25% radiolabel), and the onset of its production coincided with the peak concentration of dodecanal, the disappearance of which mirrored the appearance of the dioic acid. Under anaerobic conditions in the presence of cell extracts, dodecanol (55% of radiolabel) and dodecanal (22%) accumulated rapidly from MEGDE, but there was little subsequent conversion to mono- or dicarboxylic acids. These results are interpreted in terms of a pathway initiated by dodecyl-ether cleavage to produce dodecanol, which is subsequently oxidized to dodecanal and dodecanoic acid. The formation of dodecan-1, 12-dioic acid, probably from dodecanal, may represent a means of harbouring carbon under non-growing conditions.

Breakdown of plastics and polymers by microorganisms

The interest in environmental issues is still growing and there are increasing demands to develop materials which do not burden the environment significantly. Awareness of the waste problem and its impact on the environment has awakened new interest in the area of degradable polymers. Biodegradation is necessary for water-soluble or water-miscible polymers because they eventually enter streams which can neither be recycled nor incinerated. It is important to consider the microbial degradation of natural and synthetic polymers in order to understand what is necessary for biodegradation and the mechanisms involved. This requires both biochemical insight and understanding of the interactions between materials and microorganisms. It is now widely requested that polymeric materials come from renewable resources instead of petrochemical sources. The microbial production of polymeric and oligomeric materials is also described.

Degradation of alkylphenol ethoxylates by Pseudomonas sp. strain TR01

An alkylphenol ethoxylate-degrading bacterium was isolated from activated sludge of a municipal sewage treatment plant by enrichment culture. This organism was found to belong to the genus Pseudomonas; since no corresponding species was identified, we designated it as Pseudomonas sp. strain TR01. This strain had an optimal temperature and pH of 30 degrees C and 7, respectively, for both growth and the degradation of Triton N-101 (a nonylphenol ethoxylate in which the average number of ethylene oxide [EO] units is 9.5). The strain was unable to mineralize Triton N-101 but was able to degrade its EO chain exclusively. The resulting dominant intermediate was identified by normal-phase high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry as a nonylphenol ethoxylate with 2 mol of EO units. A carboxylated metabolite, [(nonylphenoxy)ethoxy]acetic acid, was detected by gas chromatography-mass spectrometry. This bacterium also metabolized alcohol ethoxylates with various numbers of EO units but not polyethylene glycols whatever their degree of polymerization. By oxygen consumption assay, the alkyl group or arene corresponding to the hydrophobic part of alcohol ethoxylates or alkylphenol ethoxylates was shown to contribute to the induction of the metabolic system of the EO chain of Triton N-101, instead of the EO chain itself, which corresponds to its hydrophilic part. Thus, the isolated pseudomonad bacterium has unique substrate assimilability: it metabolizes the EO chain only when the chain linked to bulky hydrophobic groups.

Corrinoid-Dependent Methyl Transfer Reactions Are Involved in Methanol and 3,4-Dimethoxybenzoate Metabolism by Sporomusa ovata

Washed and air-oxidized proteins from Sporomusa ovata cleaved the C-O bond of methanol or methoxyaromatics and transferred the methyl to dl -tetrahydrofolate. The reactions strictly required a reductive activation by titanium citrate, catalytic amounts of ATP, and the addition of dl -tetrahydrofolate. Methylcorrinoid-containing proteins carried the methanol methyl, which was transferred to dl -tetrahydrofolate at a specific rate of 120 nmol h -1 mg of protein -1 . Tetrahydrofolate methylation diminished after the addition of 1-iodopropane or when the methyl donor methanol was replaced by 3,4-dimethoxybenzoate. However, whole Sporomusa cells utilize the methoxyl groups of 3,4-dimethoxybenzoate as a carbon source by a sequential O demethylation to 4-hydroxy-3-methoxybenzoate and 3,4-dihydroxybenzoate. The in vitro O demethylation of 3,4-[4- methoxyl - 14 C]dimethoxybenzoate proceeded via two distinct corrinoid-containing proteins to form 5-[ 14 C]methyltetrahydrofolate at a specific rate of 200 nmol h -1 mg of protein -1 . Proteins from 3,4-dimethoxybenzoate-grown cells efficiently used methoxybenzoates with vicinal substituents only, but they were unable to activate methanol. These results emphasized that specific enzymes are involved in methanol activation as well as in the activation of various methoxybenzoates and that similar corrinoid-dependent methyl transfer pathways are employed in 5-methyl-tetrahydrofolate formation from these substrates. Methyl-tetrahydrofolate could be demethylated by a distinct methyl transferase. That enzyme activity was present in washed and air-oxidized cell extracts from methanol-grown cells and from 3,4-dimethoxybenzoate-grown cells. It used cob(I)alamin as the methyl acceptor in vitro, which was methylated at a rate of 48 nmol min -1 mg of protein -1 even when ATP was omitted from the assay mixture. This methyl-cob(III)alamin formation made possible a spectrophotometric quantification of the preceding methyl transfers from methanol or methoxybenzoates to dl -tetrahydrofolate.

Role of electron-donating cosubstrates in the anaerobic biotransformation of chlorophenoxyacetates to chlorophenols by a bacterial consortium enriched on phenoxyacetate

A bacterial consortium that anaerobically mineralized phenoxyacetate, with transient production of phenol as an intermediate, was obtained from a methanogenic aquifer site near the Norman, OK municipal landfill. This consortium was able to convert the eight halogenated chlorophenoxyacetates tested to the corresponding chlorophenols. The chlorophenols were not subsequently metabolized. The addition of reduced substrates increased the rate of degradation of all chlorophenoxyacetates, with 78% of mono- and di-chlorinated substrates being transformed to chlorophenols in butyrate-amended cultures, compared to less than 37% transformed in unsupplemented cultures. Butyrate increased the transformation of 2,4,5-trichlorophenoxyacetate from 10% to 20%. An experiment evaluating the effects of several compounds on the side-chain cleavage reaction of 3-chlorophenoxyacetate showed that addition of compounds which readily act as hydrogen donors (butyrate, crotonate, ethanol, propionate, and hydrogen) resulted in 2 to 5 times the amount of 3-chlorophenoxyacetate transformed compared to controls with no amendment, formate had a slight stimulatory effect, and acetate and methanol had no effect. Butyrate addition also increased the rate of phenoxyacetate degradation, resulting in transient phenol accumulation not observed in butyrate-unamended controls. These results support the hypothesis that the side-chain cleavage of phenoxyacetate is a reductive process that is stimulated by the oxidation of reduced cosubstrates.

Anaerobic degradation of 1,2-propanediol by a new Desulfovibrio strain and D. alcoholovorans

A sulfate-reducing bacterium, strain HDv, was isolated from the anoxic soil of a ricefield using lactate as electron donor. Cells were gram-negative, motile, nonsporulating curved rods, with single polar flagella. Substrates were incompletely oxidized to acetate and included glycerol, 1,2- and 1,3-propanediol. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, maleate, and malate were utilized as electron acceptors. Pyruvate, fumarate, maleate, malate and dihydroxyacetone were fermented. Desulfoviridin and c-type cytochromes were present. The DNA base composition was 66.6 +/- 0.3 mol% G+C. The isolate was identified as a Desulfovibrio sp.; its metabolic properties were somewhat different from those of previously described Desulfovibrio species. Comparative biochemical study of 1,2-propanediol dissimilation by the new isolate and Desulfovibrio alcoholovorans showed that NAD-dependent dehydrogenases play a key role in the catabolism of this substrate. The hypothetical pathways of 1,2-propanediol degradation by Desulfovibrio spp. are presented.

Enzymes Involved in Anaerobic Polyethylene Glycol Degradation by Pelobacter venetianus and Bacteroides Strain PG1

In extracts of polyethylene glycol (PEG)-grown cells of the strictly anaerobically fermenting bacterium Pelobacter venetianus , two different enzyme activities were detected, a diol dehydratase and a PEG-degrading enzyme which was characterized as a PEG acetaldehyde lyase. Both enzymes were oxygen sensitive and depended on a reductant, such as titanium citrate or sulfhydryl compounds, for optimal activity. The diol dehydratase was inhibited by various corrinoids (adenosylcobalamin, cyanocobalamin, hydroxocobalamin, and methylcobalamin) by up to 37% at a concentration of 100 μM. Changes in ionic strength and the K + ion concentration had only limited effects on this enzyme activity; glycerol inhibited the enzyme by 95%. The PEG-degrading enzyme activity was stimulated by the same corrinoids by up to 80%, exhibited optimal activity in 0.75 M potassium phosphate buffer or in the presence of 4 M KCI, and was only slightly affected by glycerol. Both enzymes were located in the cytoplasmic space. Also, another PEG-degrading bacterium, Bacteroides strain PG1, contained a PEG acetaldehyde lyase activity analogous to the corresponding enzyme of P. venetianus but no diol dehydratase. Our results confirm that corrinoid-influenced PEG degradation analogous to a diol dehydratase reaction is a common strategy among several different strictly anaerobic PEG-degrading bacteria.

Efficient biodegradation of high-molecular-weight polyethylene glycols by pure cultures of Pseudomonas stutzeri

Biodegradation of polyethylene glycols (PEGs) of up to 13,000 to 14,000 molecular weight has been shown to be performed by a river water bacterial isolate (strain JA1001) identified as Pseudomonas stutzeri. A pure culture of strain JA1001 grew on PEG 1000 or PEG 10000 at 0.2% (wt/vol) as a sole source of carbon and energy with a doubling time of 135 or 150 min, respectively. Cultures metabolized 2 g of polymer per liter in less than 24 h and 10 g/liter in less than 72 h. The limit of 13,500 molecular weight in the size of the PEG sustaining growth and the presence of a PEG-oxidative activity in the periplasmic space indicated that PEGs cross the outer membrane and are subsequently metabolized in the periplasm. PEG oxidation was found to be catalyzed by PEG dehydrogenase, an enzyme that has been shown to be a single polypeptide. Characterization of PEG dehydrogenase revealed glyoxylic acid as the product of the PEG-oxidative cleavage. Glyoxylate supported growth by entering the cell and introducing its carbons in the general metabolism via the dicarboxylic acid cycle, as indicated by the ability of strain JA1001 to grow on this compound and the presence of malate synthase, the first enzyme in the pathway, in extracts of PEG-grown cells.

Ether-cleaving enzyme and diol dehydratase involved in anaerobic polyethylene glycol degradation by a new Acetobacterium sp

A strictly anaerobic, homoacetogenic bacterium was enriched and isolated from anoxic sewage sludge with polyethylene glycol (PEG) 1000 as sole source of carbon and energy, and was assigned to the genus Acetobacterium on the basis of morphological and physiological properties. The new isolate fermented ethylene glycol and PEG's with molecular masses of 106 to 1000 to acetate and small amounts of ethanol. The PEG-degrading activity was not destroyed by proteinase K treatment of whole cells. In cell-free extracts, a diol dehydratase and a PEG-degrading (ether-cleaving) enzyme activity were detected which both formed acetaldehyde as reaction product. The diol dehydratase enzyme was oxygen-sensitive and was stimulated 10-14 fold by added adenosylcobalamine. This enzyme was found mainly in the cytoplasmic fraction (65%) and to some extent (35%) in the membrane fraction. The ether-cleaving enzyme activity reacted with PEG's of molecular masses of 106 to more than 20000. The enzyme was measurable optimally in buffers of high ionic strength (4.0), was extremely oxygen-sensitive, and was inhibited by various corrinoids (adenosylcobalamine, cyanocobalamine, hydroxocobalamine, methylcobalamine). This enzyme was found exclusively in the cytoplasmic fraction. It is concluded that PEG is degraded by this bacterium inside the cytoplasm by a hydroxyl shift reaction, analogous to a diol dehydratase reaction, to form an unstable hemiacetal intermediate. The name polyethylene glycol acetaldehyde lyase is suggested for the responsible enzyme.