Microbial degradation of xenobiotics in the environment

Biodegradation of naturally occurring organic compounds follows their synthesis. In contrast, man-made compounds, also known as xenobiotics, are often refractory to degradation. The main reason is that they cannot be recognized by naturally present organisms and therefore do not enter common metabolic pathways. The physical and chemical characteristics of the compounds, as well as environmental factors, may influence their biodegradability. Some compounds may be transformed only in the presence of another compound which appears as a carbon and energy source. Very often compounds are degraded sequentially through the activity of a series of different organisms. The main degraders in nature are microorganisms, mostly bacteria and some fungi. These organisms, due to their rapid rates of multiplication and great metabolic potential, are able to adapt to new substrates. Selection of degradative potent microorganisms and their successive adaptation to a naturally persistent compound might be a powerful means for environmental detoxification. Although numerous laboratory experiments have given positive results, very few are applicable on a large scale. It is necessary to select microorganisms or microbial communities capable of controlled degradation of persistent organic chemicals without their transformation to other, more hazardous compounds. Better understanding of metabolic pathways for the biodegradation of specific organic compounds as well as more thorough knowledge of degrading microorganisms will make purposeful application of biodegradation possible.     

矿区周边土壤的微生物研究进展

我国多数地区矿产资源的开发都会给生态系统造成严重的破坏,土壤中的微生物活性下降是矿区周边土壤遭到破坏的重要标志之一,同时也是矿区土壤微生物演变的重要因素之一。本文针对矿区周边土壤中解磷微生物的种类和解磷机制进行了综述,还讨论了其作为促进磷酸盐利用率所存在的问题。     

Sequential enrichment of microbial populations exhibiting enhanced biodegradation of crude oil

The distribution of oil-degrading bacteria in the coastal water and sediments of Hokkaido, Japan, was surveyed. The potential of mixed microbial populations to degrade weathered crude oil was not confined to any ecological components (water or sediment) nor to the sampling stations. One microbial culture that was stable during repeated subculturing degraded 45% of the saturates and 20% of the aromatics present in crude oil in 10 days during the initial screening. The residual hydrocarbons in this culture were extracted by chloroform and dispersed in a fresh seawater-based medium and subsequently inoculated with microorganisms from the first culture. After full growth of the second culture, the residual hydrocarbons were again extracted and dispersed in a fresh medium in which microorganisms from the second culture had been inoculated. This sequential process was carried out six times to enrich those microorganisms that grew on the recalcitrant components of crude oil. After repeated exposure of the residual crude oil to the enriched microorganisms, about 80% of the initially added crude oil was degraded. The cultures obtained after each enrichment cycle were kept, and the degradation of fresh crude oil by the enriched microorganisms was examined. The degradative activity of the enriched cultures increased as the number of enrichment cycles increased. A microbial population that had been selected six times on the residual crude oil could degrade 70% of the saturates and 30% of the aromatics of crude oil. Thus, growth of a microbial population on residual crude oil improved its ability to biodegrade crude oil.     

Importance of the iron cycle in biohydrometallurgy

After the discovery in the 1940s that acid mine drainage was mainly a consequence of the metabolism of chemolithoautotrophic microorganisms able to oxidize metal sulfides, mostly pyrite, much research has been performed to understand the ecology and the physiology of the microorganisms involved. At first, to prevent this environmental problem, and later to improve the efficiency of biohydrometallurgical processes. Until recently, bioenergetic considerations focused most of the attention on the sulfur oxidizing microorganisms. The demonstration that ferric iron was mainly responsible for the oxidation of pyrite has had profound implications not only on the comprehension of the phenomena but also on the microbial ecology of the correspondent systems. The Tinto River (Southwestern Spain) is an acidic environment with a high concentration of ferric iron generated by the metabolic activity of chemolithotrophic microorganisms growing in the rich complex sulfides of the Iberian Pyritic Belt (IPB). The use of conventional as well as molecular ecology tools identified the most representative members of the chemolithotrophic community of the Tinto Basin as prominent members of the iron cycle, highlighting the importance of this element in the oxidation of sulfides. Contrary to what was expected, the sulfur cycle seems to operate with rather low efficiency in the Tinto ecosystem. Interestingly enough, anaerobic geomicrobiology seems to play an important role in the system. All these observations strongly suggest that the iron cycle is extremely important for biohydrometallurgical processes in which sulfidic minerals are involved. An understanding of the properties of these versatile microorganisms and their ecology is essential to guarantee efficient and reliable biohydrometallurgical operations.     

Microorganisms in drugs and cosmetics - occurrence, harms and consequences in hygienic manufacturing (author's transl)

The quantity of pharmaceutical and cosmetic products with different composition and the diversity of contaminating microorganisms set up special problems for each product with its specific field of application. It is not exact to generalize the hazard of contaminating microorganisms to product cathegories. Some product cathegories however are more imperilled to be contaminated with microorganisms and they are more hazardous than other ones. The most important component of the living matter is water that decides on growth, multiplication and survival of microorganisms in drugs and cosmetics. Products with a high content of available water are the most problematic ones. The consequences of survival and multiplication of microorganisms in relation to metabolic activity, pathogenicity and route of administration can be harmless or fatal. The nutritive wants of many microorganisms are very small, even simple salt solutions do not exclude microbial growth. There scarcely exist substrates not used as energy source by any microorganism and so it does not wonder that desinfectants are also used. Added preservatives may be absorbed or inactivated by suspended anorganic components, swelling agents, solubilizers etc., the containers or its closing. In the water phase of emulsions, in which under special conditions smaller amounts of the preservative are available, microorganisms sometimes can multiply. Skin care products neither belonging to pharmaceuticals nor to cosmetics present special clinical problems. Many times creams and lotions contain ingredients metabolized by microorganisms. Ointments and oils can be overgrown only by highly specialized organisms but if there is condensed water as a film at boundary surfaces much more microorganism species can grow. When using cosmetics it must be considered that parts of them will get into the eye. The eye is really endangered by Pseudomonads, which can according to the composition multiply in shampoos and whose contact to the eye can not be excluded. Syrups and solutions contain sugar concentrations, which suppress growth of most microorganisms except osmotolerant germs. Because of their low water content powders normally are protected against microbial growth but they should be free from clostridial spores for a mixture of powder and sweat is a good nutrient medium to Clostridia and fungi. Powders for surgical use must be sterile. Tablets and dragees do not allow microbial multiplication because of their low water activity. Under bad storage conditions a local increase of water content may permit microbial growth at the surface, especially in hygroscopicity. Fortunately there is seen a trend of not using multi-dose-containers for injections because of the high risk of contamination. It is to develop single-dose-containers also for other groups of preparations especially for eye-preparations. Many products microbiologically unobjectionable produced are contaminated in use, they contain the spectrum of microorganisms of the area of application...     

Importance of microbial ecology in the development of new mineral technologies

The study of the microbial ecology of extremely acidic, metal-rich environments has provided the foundation from which mineral processing technologies have developed. Many of the microorganisms that are known to have direct or supportive roles in commercial operations were first identified in (and isolated from) environmental samples. Microbial life in this ‘extreme’ environment is now known to be extensively diverse, as new species and genera of acidophiles continue to be discovered. The study of how acidophilic microorganisms interact with each other (a major tenet in microbial ecology) has an important bearing on mineral technologies; microbial consortia rather than single organisms are invariably found in commercial-scale bioleaching operations. Ecologically based studies have also helped to shed new insight into the biogeochemical processes which occur in mineral leaching environments. The application of molecular techniques, particularly when used in conjunction with improved methodologies in more traditional approaches, is providing new insights into environmental and applied aspects of acidophilic microbiology.     

Collagen packing in the dogfish egg case wall

Gompertz and logistic models were fitted to experimental counts of microorganisms growing in beef stored at 0, 4, 7, 9 and 10 degrees C. Samples were packaged in polyethylene (high gaseous permeability) and in EVA/SARAN/EVA (low gaseous permeability) films, being EVA ethyl vinyl acetate and SARAN polyvinyl and polyvinylidene chloride copolymer. Lag phase duration (LPD) and specific growth rate (mu) were obtained as derived parameters for lactic acid bacteria, Enterobacteriaceae, Pseudomonas sp. and psychrotrophic microorganisms. The reciprocal of LPD was fitted to an Arrhenius type equation; LPD of lactic acid bacteria showed a marked dependence on temperature, with activation energy values (ELPD) of 222.2 and 216.9 kJ/mol for polyethylene and ESE respectively. The effect of initial microbial population at different storage temperatures on adaptation period was analyzed. As the initial microbial population increased, adaptation period decreased for all studied microorganisms and for both packaging films. The effect of temperature on specific growth rate was better interpreted by the Arrhenius model than by the linear or the square root equations. Psychrotrophic microorganisms in beef showed the highest activation energy values for specific growth rate (E mu) in both packaging films, being E mu 85.50 and 103.10 KJ/mol for polyethylene and ESE film respectively. In both films, Enterobacteriaceae showed the lowest E mu values, being 15.33 and 59.89 kJ/mol in ESE and polyethylene respectively. The final number of microorganisms (maximum population density) did not show significant changes with storage temperature.     

Three-dimensional strain-rate imaging

Siderophores are low-molecular-weight high specificity, ferric iron chelating agents. They are produced under iron starvation by most microorganisms. Systems such as siderophores, involved in the acquisition of iron under iron limited conditions, may play a major role in microbial interactions. Some siderophores are virulence factors in animal and in plant pathogens. Moreover, siderophores have been demonstrated to play a major role in plant disease suppression by some bacterial biocontrol agents which inhibit the growth or the activity of plant pathogens by sequestering iron. This latest type of mechanism has been extensively studied in bacteria. However, the role of these iron chelating compounds in disease suppression by fungal biocontrol agents has not been clearly determined.     

废弃铬渣厂土壤理化性质对微生物多样性的影响

以废弃铬渣厂及其周边表层土壤为研究对象,采集5个区域土壤样品,运用高通量测序技术,揭示了表层土壤微生物多样性及其环境主要影响因素之间的关系。结果表明,有机质（SOM）、总磷（TP）、速效磷（AP）、速效氮（AN）和铵态氮（NH4+-N）含量均在下游最高、车间最低。门水平上,Actinobacteria、Proteobacteria、Acidobacteria和Chloroflexi为优势菌种;纲水平上,Alphaproteobacteria、Actinobacteria、Vicinamibacteria、Gemmaproteobacteria和Chloroflexi为优势菌种。总体来看,在重金属与土壤环境因子共同作用下,微生物丰度更倾向于受土壤环境因子的影响,其中TP、硝态氮（NO3+-N）和大多数重金属元素是微生物变化的主要影响因素;Actinobacteria与大多数重金属具有趋同性,对重金属耐受能力最强;金属元素Pb对细菌的生长繁衍存在一定的选择性,即金属元素的不同对土壤细菌类群的影响有差异。综上,废弃厂区修复治理过程中应考虑营养元素的投入与优势菌种的选择。本文研究加深了对重金属污染土壤微生物的变化及其驱动因子的了解,为废弃铬渣厂受污染的土壤修复提供理论依据。     

Farm factors associated with the presence of Mycobacterium paratuberculosis infection in dairy herds on the New York State Paratuberculosis Control Program

An extensive questionnaire was developed and used to collect data from 33 herds that were on the New York State Paratuberculosis Control Program, to study farm factors associated with the presence of Mycobacterium paratuberculosis infection in dairy herds. The results of the last whole herd paratuberculosis fecal culture were used to indicate presence of infection in a herd, with herds having one or more animals positive classified as 'infected'. The average prevalence within herds was 5.2%. Fourteen herds were uninfected and 19 herds had prevalences ranging from 0.7%-28.2%. Data on 31 continuous and 67 categorical risk factors were collected by questionnaire. Ten factors were significantly associated with prevalence risk of infection in the univariable logistic regression. These factors were: the type of farm operation (commercial/registered or both); earlier diagnosis of the disease before entering the control program; number of clinical cases in the previous year; whether clinical cases were raised or purchased animals; typical signs in clinical cases; exposure of calves 0-6 weeks of age to feces of adult cows; contact of young stock with adult animal feces from using the same equipment to clean the housing for both groups of animals; spreading feces on fields from which forage is later harvested and fed to animals of any age group; what is done with animals that are suspected of having paratuberculosis or test positive on culture; and frequency of cleaning the cow barn. Stepwise logistic regression was used to determine the significance of each risk factor while controlling simultaneously for the effect of other factors. The significant factors were the type of farm operation, clinical signs, and exposure of calves to feces of adult cows. Commercial herds, presence of clinical signs typical of paratuberculosis in animals, and exposure of calves 0-6 weeks old to feces of adult cows all indicate a higher likelihood that a herd is infected with M. paratuberculosis.     

Antimicrobial activity of a compound isolated from an oil-macerated garlic extract

A compound showing antimicrobial activity was isolated from an oil-macerated garlic extract by silica gel column chromatography and preparative TLC. On basis of the results of NMR and MS analyses, it was identified as Z-4,5,9-trithiadeca-1,6-diene-9-oxide (Z-10-devinylajoene; Z-10-DA). Z-10-DA exhibited a broad spectrum of antimicrobial activity against such microorganisms as gram-positive and gram-negative bacteria and yeasts. The antimicrobial activity of Z-10-DA was comparable to that of Z-ajoene, but was superior to that of E-ajoene. Z-10-DA and Z-ajoene are different in respect of substitution of the allyl group by the methyl group flanking a sulfinyl group. This result suggests that substitution by the methyl group would also be effective for the inhibition of microbial growth.     

IMGT, the international ImMunoGeneTics database

Propofol emulsion supports bacterial growth. Extrinsic contamination of propofol has been implicated as an etiological event in postsurgical infections. When added to propofol, local anesthetics (e.g., lidocaine) alleviate the pain associated with injecting it. Because local anesthetics have antimicrobial activity, we determined whether lidocaine would inhibit microbial growth by comparing the growth of four microorganisms in propofol and in mixtures of propofol and lidocaine. Known quanta of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans were inoculated into solutions of 1% propofol, 0.2% lidocaine in propofol, 0.5% lidocaine in propofol, 0.5% lidocaine in isotonic sodium chloride solution, and 0.9% isotonic sodium chloride solution. All microorganisms were taken from stock cultures and incubated for 24 h. Growth of microorganisms in each solution was compared by counting the number of colony-forming units grown from a subculture of the solution at 0, 3, 6, 12 and 24 h. Propofol supported the growth of E. coli and C. albicans. Propofol maintained static levels of S. aureus and was bactericidal toward P. aeruginosa. The addition of 0.2% and 0.5% lidocaine to propofol failed to prevent the growth of the studied microorganisms. The effect of 0.5% lidocaine in isotonic sodium chloride solution did not differ from the effects of isotonic sodium chloride solution alone. We conclude that lidocaine, when added to propofol in clinically acceptable concentrations, does not exhibit antimicrobial properties. IMPLICATIONS: Local anesthetics such as lidocaine have antimicrobial activity. Propofol supports the growth of bacteria responsible for infection. Bacteria were added to propofol and propofol mixed with lidocaine. The addition of lidocaine to propofol in clinically relevant concentrations did not prevent the growth of bacteria. The addition of lidocaine to propofol cannot prevent infection from contaminated propofol.     

The characteristics of the causative agents of suppurative-inflammatory complications in hemophiliacs

Morphological-cultural and physiological-biochemical properties of 24 strains of microorganisms agents of pyo-inflammatory complications of different localization in patients with hemophilia have been studied. Microorganisms strains presented by the following species: Staphylococcus aureus, S. epidermidis, S. saprophyticus, Proteus vulgaris, P. morganii, Hafnia alvei, Serratia marcescens, have been identified. It was found out that in monoculture staphylococci prove to be the leading etiological agent (60.9%), gram-negative enterobacteria (52.2%) and bacterial associations (8.7%) occur more rarely. Special attention was paid to the study of resistance of antibiotics, circulation and pathogenicity factors that had a direct effect on the main disease severity. It was ascertained that high activity of enzymes and presence of pathogenicity factors were the peculiarities of microorganisms isolated from pyo-septic sites in patients with hemophilia. All the strains possessed multiple resistance to antibiotics.     

Comparative behavioral effects between synthetic 2,4,5-trimethylthiazoline (TMT) and the odor of natural fox (Vulpes vulpes) feces in mice.

Synthetic 2,4,5-trimethylthiazoline (TMT)--a component of red fox (Vulpes vulpes) feces--is frequently used to induce unconditioned fear in rodents. Surprisingly, direct comparison between TMT and natural fox feces odor is almost nonexistent. In this study, Experiment 1 compared the avoidance in relation to TMT concentration, natural fox feces, and gender of fox and mice. Results show that the avoidance is (a) higher with either pure or 50% TMT as compared to natural fox feces, whereas the difference is slight with 10% TMT, and (b) significantly higher for the female mouse group compared to the male mouse group with TMT as well as natural fox feces. In addition, no clear difference in effect was observed between male and female fox feces. Experiment 2 compared behavioral parameters recorded as an index of fear and anxiety, general activity, and avoidance in elevated plus-maze and open-field chamber between 10% TMT and natural fox feces in relation to the estrus cycle of the mice. Results show no cycle period effect--except for the avoidance parameter "distance to odorant"--and no different effects between 10% TMT and natural fox feces except for freezing. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

An intestinal mucin is the target substrate for a baculovirus enhancin

An invertebrate intestinal mucin (IIM) was identified from a lepidopterous insect, Trichoplusia ni. The IIM is a major protein constituent of the peritrophic membrane that facilitates the digestive process, as well as protecting invertebrate digestive tracts from microbial infections. The IIM demonstrated biochemical characteristics similar to vertebrate mucins, but exhibited strong association with the chitin-containing peritrophic membrane matrix. We have demonstrated that a baculovirus enhancin, which is encoded and carried by specific baculoviruses, has mucin-degrading activity both in vitro and in vivo. The in vivo degradation of IIM by enhancin was correlated with the enhancement of baculovirus infections in insects. These findings have shown that viruses have evolved a novel strategy to overcome intestinal mucinous barriers against microorganisms by utilizing a mucin-degrading enzyme.     

Development of a method to assay the microbial population in heap bioleaching operations

Heap bioleaching is an economically viable approach to the mining of low-grade ores. Oxidation is microbially assisted, involving a consortium of microorganisms that together span the mesophilic to extreme thermophilic range of temperatures (25–80 °C). Temperatures inside the heap are not externally regulated, making the microbial interactions difficult to predict. In order to gain insight into these interactions, a qualitative and quantitative assay of the microorganisms that colonise the ore surface or are present in the liquid phase between the ore clusters at different levels within a heap has been developed. This method was developed using crude ore and liquid samples obtained from the GeoBiotics temperature controlled mesophilic heap operation at the Agnes Gold Mine in Barberton, South Africa, and the high temperature test columns at SGS Lakefield Research, Johannesburg, South Africa. This method of sample analysis may be applied to bioheap leach operations with and without temperature control. Ease of application, reproducibility and turn around time influenced technique design in order to provide a useful assay for commercial bioleaching operations.Following microbial removal from the solid phase using successive washes with detergent and acidified water, the cells were enumerated and genetic DNA was isolated. Microbial identification was achieved via restriction endonuclease analysis of the 16S rRNA genes, as well as 16S rRNA gene sequencing where necessary. Quantification was achieved using species-and genus-specific probes through fluorescent in situ hybridisation (FISH).     

Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage

The occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. However, these fatty acids can also be used as indicators of substrate usage. For this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. We grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratios of fatty acids of different lipid fractions. A comparison of the differences of delta13C values of palmitic acid (C16:0) with the delta13C values of the substrates revealed that the isotope ratio is independent of the growth stage and that most microorganisms showed enrichment of C16:0 with 13C when growing on glycerol. With the exception of Burkholderia gladioli, all microorganism showed depletion of 13C in C16:0 while incorporating the carbons of glucose, and most of them were enriched with 13C from mannose, with the exception of Pseudomonas fluorescens and the Zygomycotina. Usually, the glycolipid fractions are depleted in 13C compared to the phospholipid fractions. The delta13C pattern was not uniform within the different fatty acids of a given microbial species. Generally, tetradecanoic acid (C14:0) was depleted of 13C compared to palmitic acid (C16:0) while octadecanoic acid (C18:0) was enriched. These results are important for the calibration of a new method in which delta13C values of fatty acids from the environment delineate the use of bacterial substrates in an ecosystem.     

Model to Quantify Removal and Inactivation of Microorganisms Occluded in Effluent Wastewater Particles Using Filtration and Disinfection Systems

A model is presented to quantify microbial occlusion in effluent particles and improve understanding of the removal and inactivation of occluded microorganisms in filtration and disinfection systems. Microbial occlusion in particles is described in the model as a function of the particle size distribution, the microbial density (N1), which is the average quantity of target microorganisms within the subset of particles that contain microorganisms, and the frequency of association (N2), which is the ratio of particles that contain at least one target microorganism. To demonstrate the model, undisinfected secondary effluent samples were collected from an extended aeration treatment facility and analyzed to determine values for the model variables, N1 and N2 for heterotrophic bacteria and aerobic endospores and N2 for total coliform bacteria. Heterotrophic bacteria were present in most effluent particles (73–100%) at high densities (7–93 per particle), whereas aerobic endospores and total coliform bacteria were only present in a small percentage of effluent particles (0.1–6%) and the density of aerobic endospores in effluent particles was not appreciably higher than one per particle.