Anaerobic microbial associations degrading aromatic amino acids

Anaerobic microbial associations have been isolated that degrade aromatic amino acids to methane and carbon dioxide at high rates. Significant differences between the morphological, cytological, and physiological traits of cultures isolated from samples of adapted and unadapted sludge are shown. The effects of cultivation temperature, illumination, and presence of mineral nitrogen and bicarbonate in the medium upon adaptation of enrichment cultures to substrates and subsequent behavior of the anaerobic associations have been studied. Intermediate and final products of degradation of aminoaromatic compounds and the sequence of their formation in the cultures have been determined. We have also studied the effects of exogenous electron acceptors and additional carbon sources on the degradation of aminoaromatic compounds.     

Methanogenic degradation of (amino)aromatic compounds by anaerobic microbial communities

degradation of a range of aromatic substrates by anaerobic microbial communities was studied. Active methanogenic microbial communities decomposing aminoaromatic acids and azo dyes into CH₄ and CO₂ were isolated. Products of primary conversion were found to be 2-hydroxybenzyl and benzyl alcohols gradually transforming into benzoate. It was shown that isolated microbial communities are capable of converting the initial substrates—benzyl alcohol, benzoate, salicylic acid, and azo dye Acid Orange 6—into biogas without a lag-phase but with different velocities. Aromatic and linear intermediates of biodegradation of aromatic amines by obtained enrichment cultures were determined for the first time. Selective effect of aromatic substrates on a microbial community that was expressed in decrease in diversity and gradual change of dominant morphotypes was revealed.     

Carbon Metabolism of Filamentous Anoxygenic Phototrophic Bacteria of the Family Oscillochloridaceae

The carbon metabolism of representatives of the family Oscillochloridaceae (Oscillochloris trichoides DG6 and the recent isolates Oscillochloris sp. R, KR, and BM) has been studied. Based on data from an inhibitory analysis of autotrophic CO₂ assimilation and measurements of the activities of the enzymes involved in this process, it is concluded that, in all Oscillochloris strains, CO₂ fixation occurs via the operation of the Calvin cycle. Phosphoenolpyruvate (PEP), which is formed in this cycle, can be involved in the metabolism via the following reaction sequence: PEP (+CO₂) å oxalacetate å malate å fumarate å succinate å succinyl-CoA (+CO₂) å 2-oxoglutarate. Acetate, utilized as an additional carbon source, can be carboxylated to pyruvate by pyruvate synthase and further involved in the metabolism via the above reaction sequence. Propionyl-CoA synthase and malonyl-CoA reductase, the key enzymes of the 3-hydroxypropionate cycle, have not been detected in Oscillochloris representatives.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 305–312.Original Russian Text Copyright © 2005 by Berg, Keppen, Krasil’nikova, Ugol’kova, Ivanovsky.     

Autophagic degradation in rat liver after vinblastine treatment

Mechanisms of autophagic proteolysis in the liver have been studied using vinblastine. Vinblastine stimulated degradation by induced autophagy in a dose-related fashion [1, 2]. Insulin partially inhibits the increased rate of degradation and the formation of autophagosomes as well as the lysosomal fragility induced by vinblastine. Insulin has little effect, however, on basal, non-induced degradation rates. Vinblastine-induced autophagy enhances the degradation of both ‘old’ and ‘newly’ synthesized proteins and is therefore in that sense a random process. The administration of high doses of colchicine also augments proteolysis. This effect is attributed to increase in autophagy. The very nascent vinblastine-induced autophagosomes appear to lack hydrolytic enzymes and acquire them only after fusion with lysosomes. The autophagolysosomal population induced by vinblastine is heterogeneous with respect to shape, size, content and density. Isolated secondary lysosomes (‘residual bodies’) lacking morphologically recognizable sequestered membranes (degradable substrate) show no release of degradation products. Autophagosomes fuse with secretory vesicles originating from the Golgi apparatus.     

The Marriage Migration Characteristics of the Rostov Oblast Population

Marriage records have been used to study the marriage migration structure of five raions of the Rostov oblast. The mean ethnic marriage assortativeness in the Russian and Ukrainian rural populations are 1.16 and 1.6, respectively. The endogamy index of the urban population varies from 0.19 to 0.34; and that of the rural population, from 0.21 to 0.54. Malecot’s isolation by distance parameters have been calculated. Genetic landscapes have been constructed.__________Translated from Genetika, Vol. 41, No. 7, 2005, pp. 981–985.Original Russian Text Copyright © 2005 by Kriventsova, El’chinova, Amelina, Zinchenko.     

Microbial consortia for the aerobic degradation of aromatic compounds in olive oil mill effluent

Aerobic consortia that grow on olive oil mill effluent (OOME) were obtained by enrichment. Several cultures were capable of metabolizing monoaromatic compounds, supplied as the sole carbon source at 2 g L^–1. Some consortia degraded mixtures of seven aromatics (4 g L^–1) after 1 week of incubation at 32°C. The consortia were also active against monoaromatics of the undiluted OOME. This reduced the inhibitory effect of phenolic compounds prior to the anaerobic digestion of OOME at batch scale. No inhibition of the anaerobic microbial populations was noticed with treated OOME. From the most active consortium, nine different bacterial strains were isolated and shown to grow on simple aromatic compounds. Removal of 50% of the initial chemical oxygen demand and degradation of almost all of the simple aromatics in undiluted OOME was obtained with reconstituted bacterial mixtures. A slight reduction in colouration was due to adsorption of coloured compounds to bacterial cells. Presumably, the consortia could not reduce and degrade the coloured compounds in OOME.     

Cell cycle variation associated with feeder effects in cultures of Chinese hamster fibroblasts

Sub-confluent monolayer cultures of an established line of Chinese hamster fibroblast (Don) are shown to exhibit a density-dependent stimulation of growth. Evidence is presented that both long and short range ‘feeder effects’ are involved. Using the technique of autoradiography, cell cycle parameters have been studied in sub-confluent cultures seeded at different densities to identify the source of this density-dependent variation in growth rate. The durations of S phase, G2, and mitosis are constant as indicated by “percentage labelled mitoses” curves. A simple procedure has been developed for measurement of the fraction of a cell population in the G1 state, and this fraction is shown to be inversely related to the density of the culture. It is concluded that regulation of cell growth associated with feeder effects in cultured Don cells occurs within the G1 state. The data obtained from “percentage labelled mitoses” curves are shown to be highly consistent with the predictions of the Transition Probability model for cell cycle regulation.     

The effects of cell-cell contact on the spreading of pigmented retina epithelial cells in culture

The behaviour of chick embryo pigmented retina epithelial (PRE) cells has been studied in living and fixed cultures. Isolated PRE cells lacking contacts with other cells were characteristically only poorly spread upon the substrate, blebbed vigorously and lacked leading lamellae. PRE cells incorporated into islands or sheets of cells were extensively spread upon the substrate, lacked blebs and displayed typical leading lamellae if marginally positioned in an island. Observations of living cultures demonstrated that within 3 h of establishing contact with an island of cells a previously isolated PRE cell lost the morphology characteristic of isolated cells and became indistinguishable from its neighbours in the island. Measurements of the area of substrate occupied by single cells and cells in 2-cell islands suggests that similar changes occur as two cells make contact to form a 2-cell island. The evidence suggests that these changes are a direct response to the establishment of a cell-cell contact and I propose that the phenomenon be termed ‘contact-induced spreading’.Contact-induced spreading is not an ‘all or none’ phenomenon since isolated PRE cells can spread extensively and cease blebbing in the absence of cell contact. However a given isolated PRE cell spends only a very small proportion of its time displaying this well spread morphology and therefore at any time the majority of isolated PRE cells display the poorly spread morphology.The possible relationship between contact-induced spreading and other cellular interactions known to be dependent on cell-cell contact is discussed.     

Stable,position-related responses to retinoic acid by chick limb-bud mesenchymal cells in serum-free cultures

Summary Retinoic acid (RA) has dramatic effects on limb-skeletal patterning in vivo and may well play a pivotal role in normal limb morphogenesis. RA’s effects on the expression of pattern-related genes in the developing limb are probably mediated by cytoplasmic RA-binding proteins and nuclear RA-receptors. Little is known, however, about how RA modifies specific cellular behaviors required for skeletal morphogenesis. Earlier studies supported a role for regional differences in RA concentration in generating the region-specific cell behaviors that lead to pattern formation. The present study explores the possibility that position-related, cell-autonomous differences in the way limb mesenchymal cells respond to RA might have a role in generating pattern-related cell behavior. Mesenchymal cells from different proximodistal regions of stage 21–22 and 23–24 chick wing-buds were grown in chemically defined medium and exposed to 5 or 50 ng/ml of RA for 4 days in high-density microtiter cultures. The effects of RA on chondrogenesis in these cultures clearly differed depending on the limb region from which the cells were isolated. Regional differences in RA’s effects on growth over 4 days in these cultures were less striking. The region-dependent responses of these cells to RA proved relatively stable in culture despite ongoing cytodifferentiation. This serum-free culture model will be useful in exploring the mechanisms underlying the region-dependent responsiveness of these cells to RA.     

Microbial degradation of tannins – A current perspective

Tannins are water-soluble polyphenolic compounds having wide prevalence in plants. Hydrolysable and condensed tannins are the two major classes of tannins. These compounds have a range of effects on various organisms – from toxic effects on animals to growth inhibition of microorganisms. Some microbes are, however, resistant to tannins, and have developed various mechanisms and pathways for tannin degradation in their natural milieu. The microbial degradation of condensed tannins is, however, less than hydrolysable tannins in both aerobic and anaerobic environments. A number of microbes have also been isolated from the gastrointestinal tract of animals, which have the ability to break tannin-protein complexes and degrade tannins, especially hydrolysable tannins. Tannase, a key enzyme in the degradation of hydrolysable tannins, is present in a diverse group of microorganisms, including rumen bacteria. This enzyme is being increasingly used in a number of processes. Presently, there is a need for increased understanding of the biodegradation of condensed tannins, particularly in ruminants.     

Degradation of chlorinated nitroaromatic compounds

Chlorinated nitroaromatic compounds (CNAs) are persistent environmental pollutants that have been introduced into the environment due to the anthropogenic activities. Bacteria that utilize CNAs as the sole sources of carbon and energy have been isolated from different contaminated and non-contaminated sites. Microbial metabolism of CNAs has been studied, and several metabolic pathways for degradation of CNAs have been proposed. Detoxification and biotransformation of CNAs have also been studied in various fungi, actinomycetes and bacteria. Several physicochemical methods have been used for treatment of wastewater containing CNAs; however, these methods are not suitable for in situ bioremediation. This review describes the current scenario of the degradation of CNAs.     

Naphthalene Degradation and Incorporation of Naphthalene-Derived Carbon into Biomass by the Thermophile Bacillus thermoleovorans

The thermophilic aerobic bacterium Bacillus thermoleovorans Hamburg 2 grows at 60°C on naphthalene as the sole source of carbon and energy. In batch cultures, an effective substrate degradation was observed. The carbon balance, including naphthalene, metabolites, biomass, and CO₂, was determined by the application of [1-¹³C]naphthalene. The incorporation of naphthalene-derived carbon into the bulk biomass as well as into specified biomass fractions such as fatty acids and amino acids was confirmed by coupled gas chromatography-mass spectrometry (GC-MS) and isotope analyses. Metabolites were characterized by GC-MS; the established structures allow tracing the degradation pathway under thermophilic conditions. Apart from typical metabolites of naphthalene degradation known from mesophiles, intermediates such as 2,3-dihydroxynaphthalene, 2-carboxycinnamic acid, and phthalic and benzoic acid were identified for the pathway of this bacterium. These compounds indicate that naphthalene degradation by the thermophilic B. thermoleovorans differs from the known pathways found for mesophilic bacteria.     

Desulfonation and Degradation of the Disulfodiphenylethercarboxylates from Linear Alkyldiphenyletherdisulfonate Surfactants

Earlier work showed that the biodegradation of a commercial linear monoalkyldiphenyletherdisulfonate surfactant as a carbon source for microbial growth leads to the quantitative formation of corresponding disulfodiphenylether carboxylates (DSDPECs), which were not degraded. α-Proteobacterium strain DS-1 (DSM 13023) catalyzes these reactions. These DSDPECs have now been characterized by high-pressure liquid chromatography coupled via an electrospray interface to a mass spectrometer. DSDPECs were a complex mixture of compounds which indicated catabolism via ω-oxygenation and β-oxidation. DSDPECs were subject to quantitative desulfonation in bacterial cultures in which they served as sole sulfur sources for bacterial growth. On average, one sulfonate group per DSDPEC species was removed, and the organism responsible for this desulfonation was isolated and identified as Rhodococcus opacus ISO-5. The products were largely monosulfodiphenylether carboxylate-phenols (MSDPEC-phenols). MSDPEC-phenols were subject to extensive dissimilation by bacteria from activated sludge.     

Engineering role models: do non-human species have the answers?

A shift from traditional engineering approaches to ecologically-based techniques will require changing societal values regarding ‘how and what’ is defined as engineering and design. Non-human species offer many ecological engineering examples that are often beneficial to ecosystem function and other biota. For example, organisms known as ‘ecosystem engineers’ build, modify, and destroy habitat in their quest for food and survival. Similarly, ‘keystone species’ have greater impacts on community or ecosystem function than would be predicted from their abundance. The capacity of these types of organisms to affect ecosystems is great. They exert controlling influences over ecosystems and communities by altering resource allocation, creating habitats and modifying relative competitive advantages.Species’ effects in ecosystems, although context-dependent, can be evaluated as ‘beneficial’ or ‘detrimental’. The evaluation depends on whether effects on other species or ecosystem function are more or less desirable from a given perspective. Organisms with beneficial impacts facilitate the presence of other species, employ efficient nutrient cycling, and are sometimes characterized by specific mutualisms. In contrast, many cases of detrimental engineering are found from introduced (i.e., exotic) species and are characterized by a loss of species richness, a lack of nutrient retention and the degradation of ecosystem integrity. Species’ impacts on ecosystems and community traits have been quantified in ecological studies and can be used similarly to understand, design and model human engineering structures and impacts on the landscape. Emulation of species with beneficial impacts on ecosystems can provide powerful guidance to the goals of ecological engineering. Using role model organisms that have desirable effects on species diversity and ecosystem function will be important in developing alternatives to traditional engineering practices.     

DNA replication in macronuclei of Tetrahymena pyriformis GL

DNA replication in macronuclei of Tetrahymena pyriformis GL has been studied to discriminate between hypotheses developed for the interpretation of intraclonal differentiation in ciliated protozoa (the diploid subnuclear, and the ‘master’-‘slave’ hypotheses). Tetrahymena cells were grown in a heavy ¹⁵N-³H medium and then transferred to a light ¹⁴N-¹⁴C medium. DNA was isolated after various periods following this transfer and studied in equilibrium CsCl density gradient centrifugation. Time-related changes in the DNA buoyant density pattern were investigated. The data obtained are interpreted to mean that all DNA in macronuclei of asynchronously growing Tetrahymena at exponential phase replicates semiconservatively once in a cell cycle. These data are in good agreement with the findings of Andersen & Zeuthen obtained on synchronous Tetrahymena cultures in the presence of BUdR.These results are not consistent with the ‘master’-‘slave’ hypothesis. The diploid subnuclear hypothesis is not in accord with other experimental evidence. An alternative hypothesis has been proposed concerning the nature of the macronuclear units and the process of determination. The two main points of this hypothesis are: (a) macronuclear units are diploid genome fragments (‘nucleosomes’); (b) determination is a process of haploidization by ‘allelic splitting’ at a definite macronuclear fission. Consistency with experimental data is discussed and some predictions of the hypothesis are given.     

Anaerobic degradation of 2-aminobenzoate (anthranilic acid) by denitrifying bacteria

In the presence of oxygen many aminoaromatic compounds polymerize to form recalcitrant macromolecules. To circumvent undesirable oxidation reactions, the anaerobic biodegradation of a simple member of this class of compounds was investigated. Two strains of bacteria were isolated which degrade 2-aminobenzoate anaerobically under denitrifying conditions, with nitrate as the terminal electron acceptor. Both organisms, which were assigned to the genus Pseudomonas, oxidized 2-aminobenzoate completely to CO2 and NH4+. Nitrate was reduced to nitrite. When nitrate was deplete from the growth medium the accumulated nitrite was reduced to nitrogen. The results establish a model system for the anaerobic, rapid, and complete oxidation of an aminoaromatic compound.     

Carbon Isotope Fractionation during Anaerobic Degradation of Methyl tert-Butyl Ether under Sulfate-Reducing and Methanogenic Conditions

Methyl tert-butyl ether (MTBE), an octane enhancer and a fuel oxygenate in reformulated gasoline, has received increasing public attention after it was detected as a major contaminant of water resources. Although several techniques have been developed to remediate MTBE-contaminated sites, the fate of MTBE is mainly dependent upon natural degradation processes. Compound-specific stable isotope analysis has been proposed as a tool to distinguish the loss of MTBE due to biodegradation from other physical processes. Although MTBE is highly recalcitrant, anaerobic degradation has been demonstrated under different anoxic conditions and may be an important process. To accurately assess in situ MTBE degradation through carbon isotope analysis, carbon isotope fractionation during MTBE degradation by different cultures under different electron-accepting conditions needs to be investigated. In this study, carbon isotope fractionation during MTBE degradation under sulfate-reducing and methanogenic conditions was studied in anaerobic cultures enriched from two different sediments. Significant enrichment of ¹³C in residual MTBE during anaerobic biotransformation was observed under both sulfate-reducing and methanogenic conditions. The isotopic enrichment factors () estimated for each enrichment were almost identical (−13.4 to −14.6; r² = 0.89 to 0.99). A value of −14.4 ± 0.7 was obtained from regression analysis (r² = 0.97, n = 55, 95% confidence interval), when all data from our MTBE-transforming anaerobic cultures were combined. The similar magnitude of carbon isotope fractionation in all enrichments regardless of culture or electron-accepting condition suggests that the terminal electron-accepting process may not significantly affect carbon isotope fractionation during anaerobic MTBE degradation.     

Cobalt(II) ion as a promoter of hydroxyl radical and possible ‘crypto-hydroxyl’ radical formation under physiological conditions. Differential effects of hydroxyl radical scavengers

Co(II) ions react with hydrogen peroxide under physiological conditions to form a ‘reactive species’ that can hydroxylate aromatic compounds (phenol and salicylate) and degrade deoxyribose to thiobarbituric-acid-reactive material. Catalase decreases the formation of this species but superoxide dismutase or low concentrations of ascorbic acid have little effect. EDTA, present in excess over the Co(II), can accelerate deoxyribose degradation and aromatic hydroxylation. In the presence of EDTA, deoxyribose degradation by the reactive species is inhibited competitively by scavengers of the hydroxyl radical (OH), their effectiveness being related to their second-order rate constants for reaction with OH. In the absence of EDTA the scavengers inhibit only at much higher concentrations and their order of effectiveness is changed. It is suggested that, in the presence of EDTA, hydroxyl radical is formed ‘in free solution’ and attacks deoxyribose or an aromatic molecule. In the absence of EDTA, OH radical is formed in a ‘site-specific’ manner and is difficult to intercept by OH scavengers. The relationship of these results to the proposed ‘crypto OH’ radical is discussed.     

Biodegradation of methyl t-butyl ether by pure bacterial cultures

Three pure bacterial cultures degrading methyl t-butyl ether (MTBE) were isolated from activated sludge and fruit of the Gingko tree. They have been classified as belonging to the genuses Methylobacterium, Rhodococcus, and Arthrobacter. These cultures degraded 60 ppm MTBE in 1–2 weeks of incubation at 23–25 °C. The growth of the isolates on MTBE as sole carbon source is very slow compared with growth on nutrient-rich medium. Uniformly-labeled [¹⁴C]MTBE was used to determine ¹⁴CO₂ evolution. Within 7 days of incubation, about 8% of the initial radioactivity was evolved as ¹⁴CO₂. These strains also grow on t-butanol, butyl formate, isopropanol, acetone and pyruvate as carbon sources. The presence of these compounds in combination with MTBE decreased the degradation of MTBE. The cultures pregrown on pyruvate resulted in a reduction in ¹⁴CO₂ evolution from [¹⁴C]MTBE. The availability of pure cultures will allow the determination of the pathway intermediates and the rate-limiting steps in the degradation of MTBE. Received: 8 December 1995 / Received last revision: 5 August 1996 / Accepted: 12 August 1996