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Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. The Medinaut Shipboard Scientific Party.

Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible Nautile. Geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in (13)C (delta(13)C values are as low as -95 per thousand). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of (13)C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, our results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings is the predominant microbiological process.

Anaerobiosis↗

Modeling acidogenic and sulfate-reducing processes for the determination of fermentable fractions in wastewater.

The biochemical acidogenic potential (BAP) of a wastewater is the maximum concentration of volatile fatty acids (VFAs) that can be measured at the end of an anaerobic fermentation test. A model was constructed to describe the acidogenic reactions occurring during BAP tests and to divide the BAP into organic fractions. The model was calibrated with a set of specific experiments highlighting the role of sulfate-reducing bacteria on acidogenic processes, which description was necessary for correct parameter identification. The model could describe acidogenic fermentation processes, with or without sulfate reduction, at 20 degrees C, for 13 wastewaters of different origin, composition, and settleability using the same optimized parameters. A simplified version of the model, without sulfate reduction, was able to describe VFA production by the adjustment of only three variables: readily fermentable organic matter (Sf), anaerobically hydrolyzable organic matter (Xf), and heterotrophic acidogenic biomass (Xha), which proved to be coherent with the experimental BAP value. The combination of the BAP test and the model developed in this study resulted in a new reliable tool to characterize wastewater under anaerobic conditions. As VFAs are the main substrates for phosphate-accumulating organisms (PAOs), the use of organic fractions VFA, Sf, Xf, and Xha in wastewater treatment plant modeling could improve the predictability and optimization of enhanced biological phosphorus removal (EBPR) processes.

Bacteria, Anaerobic↗

Isotopic biogeochemistry of the Oxford Clay Formation (Jurassic), UK.

A total of 165 samples was obtained from the Oxford Clay Formation at seven different sites. Nearly all were from the Peterborough Member (Lower Oxford Clay), but seven were from the Stewartby and Weymouth Members (Middle and Upper Oxford Clay respectively). Five samples from the underlying Kellaways Formation were also examined. Stratigraphic relationships were estimated on the basis of ammonite subzones and results from all locations can be placed along a single stratigraphic scale. The following were determined for all samples: abundance and isotopic composition of organic carbon, abundances of carbonate carbon and total sulphur, and the Rock-Eval pyrolysis parameters hydrogen index, oxygen index and Tmax. For a subset of eight samples selected to be representative of geochemical and apparent palaeoenvironmental variations, soluble organic compounds were extracted and the isotopic composition of pristane, phytane, and long-chain n-alkanes determined by isotope-ratio-monitoring gas chromatograph mass spectrometry. Concentrations of organic carbon in samples from the Peterborough Member ranged from 0.5 to 16.6 % and delta values of total organic carbon (TOC) ranged from -27.7 to -23.1% v. PDB. Shales dominated by epifaunal bivalve assemblages have high concentrations of TOC and values of H index approaching 800, indicating preservation of hydrogen-rich organic material. Conversely, shell beds and calcareous and silty clay beds have lower abundances of TOC and values of H index dropping below 100, indicating extensive oxidation of the organic matter. Isotopic composition of pristane and phytane in the Peterborough and Stewartby Members average -31.7%, those in the Weymouth Member average -29.8. Values of delta for long-chain n-alkanes average -28%. Together these results indicate delta values for primary inputs as follows: terrestrial vascular plants, -23.5%; Peterborough Member algae, -28.2; Stewartby Member algae, -29.1%; Weymouth Member algae, -26.6% Comparison of primary delta values to those of TOC indicates that in some cases secondary processes enriched TOC relative to primary inputs by as much as 4%. Paleontological evidence in these same beds indicates development of extensive food-webs and supports attribution of this isotopic enrichment to heterotrophic reworking.

Alkanes↗

Mass balance of a wastewater loaded canal system: case study of Bangkok.

A dynamic water quality model was applied in order to investigate self-purification processes in highly loaded canals in the centre of Bangkok, capital city of Thailand. Oxygen production by aquatic plants induces a significant diurnal variation of the dissolved oxygen concentration. The corresponding profiles of heterotrophic growth and BOD5 concentration demonstrate the limiting impact of oxygen shortage during night time. Both self-purification mechanisms--biological degradation and settling--are considered and water-sediment interactions are calculated. Simulation results and measurement data are summarized by mass balance schemes which offer a telling characterization of the complex system.

Biodegradation, Environmental↗

[Role of exogenous carbon dioxide in the metabolism of methane-oxidizing bacteria].

The object of this work was to study the ability of methane oxidizing bacteria to use CO2 as an acceptor of electrons liberated in methane oxidation and the role of CO2 fixation in the constructive metabolism of the bacteria. All of the studied methane oxidizing bacterial cultures were found to be capable of fixing the 14C of hydrocarbonate. The activity of the process was shown to be similar in different strains. Up to 30% of the carbon in the biomass composition could originate from the carbon of HCO3-. Methane oxidizing bacteria that assimilated C1-compounds via the hexulose phosphate and serine pathways had the same level of HCO3- fixation. No differences were found among strains of the same species, among species, or among genera. The assimilation of HCO3- was catalyzed by PEP-carboxylase (i. e. in a heterotrophous way) or, in some cultures, by ribulose-1,5-diphosphate carboxylase, the key enzyme in the autotrophous pathway of CO2 assimilation. The enzymological mechanisms of HCO3- assimilation are discussed. The biological role of CO2 fixation in the metabolism of methane oxidizing bacteria that use the hexulose phosphate and serine pathways of methane assimilation may be different. The process can either play the role of anapleurotic reactions in the tricarboxylic acid cycle, or be an element of the serine pathway of methane assimilation. Calculations have shown that the extent to which a substrate to be metabolized is reduced seems to determine the activity of exogenous CO2 fixation. The contribution made by HCO3- fixation into the carbon metabolism of methane oxidizing bacteria confirms that they are related to lithotrophous organisms.

Bicarbonates↗

Concentrations and tracking of listeria monocytogenes strains in a seafood-processing environment using a most-probable-number enrichment procedure and randomly amplified polymorphic DNA analysis.

Concentrations of environmental microflora and Listeria monocytogenes were monitored at multiple environmental locations within a seafood-processing facility over the course of 6 months. Concentrations of L. monocytogenes were determined using a most-probable-number (MPN) enrichment procedure. Two floor drains had persistent low concentrations of L. monocytogenes (0.03 to >1,100 MPN/cm2). In comparison, concentrations of the other organisms in the drain were much higher (heterotrophic plate count range of 10(5) to 10(8) CFU/cm2). Concentrations of environmental organisms (heterotrophic aerobic plate counts and counts of pseudomonads, Shewanella spp., Aeromonas hydrophila, and coliforms) were not correlated with concentrations of L. monocytogenes. The 178 confirmed L. monocytogenes isolates from the MPN procedure were further characterized by randomly amplified polymorphic DNA analysis. Sixteen different banding patterns were identified, and nine of the patterns were identified from samples collected on two or more collection dates. From all locations, banding type A was observed in 98 confirmed isolates (55%). Although present, L. monocytogenes was a relatively minor component in the ecosystem of the floor drains in this seafood-processing facility.

Animals↗

Assimilable organic carbon (AOC) and biodegradable dissolved organic carbon (BDOC): complementary measurements.

The objective of this study was to evaluate the necessity of measuring both assimilable organic carbon (AOC) and biodegradable dissolved organic carbon (BDOC) as indicators of bacterial regrowth potential. AOC and BDOC have often been measured separately as indicators of bacterial regrowth, or together as indicators of bacterial regrowth and disinfection by-product formation potential, respectively. However, this study proposes that both AOC and BDOC should be used as complementary measurements of bacterial regrowth potential. In monitoring of full-scale membrane filtration, it was determined that nanofiltration (NF) removed over 90% of the BDOC while allowing the majority of the AOC through. Heterotrophic plate counts (HPC) remained low during the entire period of monitoring due to high additions of disinfectant residual. In a two-year monitoring of a water treatment plant that switched its treatment process from chlorination to chlorination and ozonation, it was observed that the plant effluent AOC increased by 127% while BDOC increased by 49% after the introduction of ozone. Even though AOC is a fraction of BDOC, measuring only one of these parameters can potentially under- or overestimate the bacterial regrowth potential of the water.

Biodegradation, Environmental↗

The role of cell hydrophobicity in the formation of aerobic granules.

Cell hydrophobicity is an important affinity force in cell self-immobilization and attachment processes. The role of cell hydrophobicity in the formation of aerobic granules has not been clear. Therefore, two series of experiments were conducted to investigate the role of cell hydrophobicity in the formation of aerobic heterotrophic and nitrifying granules in sequencing batch reactors, while the effects of shear strength, hydraulic selection pressure, and organic loading rate on the cell hydrophobicity were also studied. Results showed that the formations of heterotrophic and nitrifying granules were associated very closely with the cell hydrophobicity. The hydrophobicity of granular sludge was nearly twofold higher than that of conventional bioflocs. A high shear force or hydraulic selection pressure imposed on microorganisms resulted in a significant increase in the cell hydrophobicity, while the cell hydrophobicity seemed not to be sensitive to the changes in the organic loading rates in the range studied. In conclusion, the cell hydrophobicity could induce and further strengthen cell-cell interaction, and might be a main triggering force to initiate the granulation of heterotrophic and nitrifying bacteria.

Aerobiosis↗

The impact of floc size on respiration inhibition by soluble toxicants--a comparative investigation.

Activated sludge facilities are susceptible to upset by shock loads of toxic compounds. We hypothesized that floc size plays an important role in determining the sensitivity of mixed liquor to shock by cadmium and 2,4-dinitrophenol (DNP). To test this hypothesis, heterotrophic respiration inhibition experiments were conducted using mixed liquor from a pilot-scale membrane bioreactor (MBR) and full-scale activated sludge (FSAS) facility with gravity settling secondary clarifiers that were operated under similar process conditions. MBR mixed liquor flocs were both 41% smaller and 2 and 1.25 times more sensitive to equivalent soluble cadmium and DNP concentrations, respectively, compared to FSAS mixed liquor flocs. Similarly, FSAS mixed liquor that had been sheared (resulting in a smaller average floc diameter) was 1.5 times more sensitive to soluble cadmium than non-sheared FSAS mixed liquor. These results suggest that activated sludge process conditions that create smaller floc particles, such as the use of membranes for liquid-solid separation, are more susceptible to upset events caused by shock loads of cadmium and DNP. The particle size distribution (PSD) and average floc diameter of a mixed liquor suspension should be measured and reported when stating the inhibition concentration of a specific toxicant.

2,4-Dinitrophenol↗

Integrated system for the treatment of oxides of nitrogen from flue gases.

A novel and effective system was developed for the complete treatment of NOx from flue gases. The system consisted of photocatalytic or ozone oxidation of NOx, followed by scrubbing and biological denitrification. Maximum photocatalytic oxidation of NOx was achieved while using powdered TiO2 at a catalytic loading rate of 10 g/h, relative humidity of 50%, and a space time of 10 s. The used catalyst was regenerated and reused. A total of 72% of oxidized NO was recovered as HNO3/HNO2 in the regeneration process. Stoichiometrically, 10% excess ozone was able to affect 100% oxidation of NO to NO2. Presence of SO2 adversely influenced the oxidation of NO by ozone. The scrubbing of NO was effective with distilled water. Heterotrophic denitrifiers were able to denitrify the leachate with an efficiency of 90%, using sewage (COD 450 mg/L) as electron donor. The new integrated treatment system seems to be a promising alternative for complete treatment of NOx from flue gases.

Air Pollution↗

Sucrose cycling in heterotrophic plant cell metabolism: first step towards an experimental model.

Sucrose is the cornerstone of higher plant metabolism. Produced by photosynthesis, sucrose is the main substrate for respiration and biosynthesis. The emerging idea is that sucrose may act as regulator of its own metabolism, characterized in particular by a permanent process of degradation and formation. This sucrose turnover may control several important physiological functions. Of particular concern is an energy dependent cycle involving the hexokinase. This report presents an experimental approach to define quantitatively physiological states of suspension-cultured plant cells wih reference to their sucrose content and respiration rate. Sucrose depletion of normal cells incubated in a medium devoid of sugar is measured in vivo using 13C and respiration is simultaneously recorded. Results obtained with sucrose-storing cells and Arabidopsis thaliana show that respiration rate is closely linked to the available sucrose. Sucrose-depleted cells offer a stable model to study the bioenergetics of the process.

Acer↗

Sucrose-inducible endocytosis as a mechanism for nutrient uptake in heterotrophic plant cells.

The capacity of plant heterotrophic organs to transport and accumulate incoming nutrients (mostly in the form of sucrose) directly impacts their final size, crop productivity and nutritional value. Endocytosis as a mechanism for nutrient uptake in heterotrophic cells was investigated using suspension culture cells of sycamore (Acer pseudoplatanus L.) and the endocytic inhibitors wortmannin and LY294002. Time course analysis of sucrose uptake in intact walled cells revealed a two-phase process involving an initial 90 min wortmannin- and LY294002-insensitive sucrose uptake period, followed by a prolonged phase of rapid sucrose accumulation which was greatly inhibited by the two endocytic inhibitors. Walled cells were assessed for their capacity to incorporate the fluorescent endocytosis marker lucifer yellow-CH (LY) in the presence or absence of sucrose. Rates of sucrose and LY accumulation were virtually identical, as was their response to wortmannin. In addition, LY incorporation increased as a function of external sucrose concentration. When sucrose was substituted by other sugars or amino acids, uptake of LY greatly diminished, indicating that sucrose itself is the primary signal of endocytosis. Microscopic observations revealed the formation of vesicles containing LY and its eventual accumulation on the vacuole when sucrose was present in the incubation medium. These results demonstrate the existence of a sucrose-inducible endocytic process as a viable mechanism for solute transport into the vacuole of storage cells.

Acer↗

Nitrification at Low pH by Aggregated Chemolithotrophic Bacteria.

A study was performed to gain insight into the mechanism of acid-tolerant, chemolithotrophic nitrification. Microorganisms that nitrified at pH 4 were enriched from two Dutch acid soils. Nitrate production in the enrichment cultures was indicated to be of a chemolithoautotrophic nature as it was (i) completely inhibited by acetylene at a concentration as low as 1 mumol/liter and (ii) strongly retarded under conditions of carbon dioxide limitation. Electron microscopy of the enrichment cultures showed the presence of bacteria that were morphologically similar to strains of known chemolithotrophic nitrifying genera. Many of the enriched bacteria, in particular those that were identified as ammonium oxidizers, were aggregated. Filtration experiments indicated that aggregated cells were able to nitrify at low pH, whereas single cells were not. It is hypothesized that cells inside the aggregates are protected against the toxicity of nitrous acid. Nitrification by aggregated chemolithoautotrophic bacteria may be the dominating process of nitrate formation in many acid soils as it does not appear to depend on the existence of microsites of high pH (acid-sensitive autotrophic nitrification) or on the availability of organic carbon (heterotrophic nitrification).

Journal Article↗

Occurrence of legionellae in hot water distribution systems of Finnish apartment buildings.

The occurrence of legionellae in the hot water distribution systems of 67 buildings located in different parts of Finland was studied. Most of the buildings were apartment buildings. They had different hot water temperatures, and some received their cold potable water from surface water plants and some from ground water plants. Hot water samples were taken from taps, showers, and water mains just before and after the heat exchanger. Legionella pneumophila was isolated from 30% of the distribution systems. In the legionella-positive samples the legionella concentration varied from < 50 to 3.2 x 10(5) colony-forming units (cfu)/L (mean 2.7 x 10(3) cfu/L). The highest concentration of legionellae was found in the shower water. Legionellae appeared more often and with higher concentrations in hot water systems using cold water processed in surface water plants than in hot water systems associated with ground water plants. A high organic matter content in surface waters might favor the occurrence of legionellae and also the growth of other heterotrophic microbes. Mean water temperature just after heating was slightly higher in the legionella-negative systems than in the legionella-positive systems (53.5 vs. 51.5 degrees C).

Finland↗

A simple method for chloroplast transformation in Chlamydomonas reinhardtii.

Photosystem (PS)I is a multi-subunit pigment-protein complex that uses light energy to transfer electrons from plastocyanin to ferredoxin. Application of genetic engineering to photo-synthetic reaction center proteins has led to a significant advancement in our understanding of primary electron transfer events and the role of the protein environment in modulating these processes. Chlamydomonas reinhardtii provides a system particularly amenable to analyze the structure-function relationship of PSI. Chlamydomonas reinhardtii is also a favorable organism for chloroplast transformation because it contains a single chloroplast and grows heterotrophically when supplemented with acetate. Chlamydomonas has served as a model organism for the development of chloroplast transformation procedures and the study of photosynthetic mutants generated using this method. Exogenous cloned cpDNA can be introduced into the chloroplast by using this biolistic gene gun method. DNA-coated tungsten or gold particles are bombarded onto cells. Upon its entry into chloroplasts, the transforming DNA is released from the particles and integrated into the chloroplast genome through homologous recombination. The most versatile chloroplast selectable marker is aminoglycoside adenyl transferase (aadA), which can be expressed in the chloroplast to confer resistance to spectinomycin or streptomycin. This chapter describes the procedures for chloroplast transformation.

Animals↗

The transient-state, multiple-species biofilm model for biofiltration processes.

We describe the transient-state, multiple-species biofilm model (TSMSBM), which is a novel synthesis of key modeling features needed to describe multiple-species biofilms that experience time-varying conditions, particularly including periodic detachment by backwashing. The TSMSBM includes six features that are essential for describing multiple-species biofilms that undergo changes over time: (1) four biomass types: heterotrophs, ammonia oxidizers, nitrite oxidizers, and inert biomass; (2) seven chemical species: input biodegradable organic material (BOM), NH4(+)-N, NO2(-)-N, NO3(-)-N, utilization-associated products, biomass-associated products, and dissolved oxygen; (3) eight reactions that describe the rates of consumption or production of the different species, as well as the stoichiometric linkages among the rates; (4) reaction with diffusion of all the soluble species in the biofilm; (5) growth, decay, detachment, and flux of each biomass type by location in the biofilm; and (6) constant or periodic detachment of biofilm, both of which allow for protection of biomass deep inside the biofilm. The last two features of the TSMSBM provide novel additions to biofilm modeling, and the synthesis of all features is a unique advancement. A series of examples illustrates insights that the TSMSBM can provide about the transient development of multiple-species biofilms; the roles of soluble microbial products and detachment in controlling the distribution of biomass types and process performance; and how backwashing affects the biofilm in drinking-water biofiltration.

Biofilms↗

Temperature characteristics of photosynthetic and heterotrophic activities: seasonal variations in temperate microbial plankton.

The seasonal variation in temperature characteristics of photosynthetic and heterotrophic activities in the microbial plankton of Bedford Basin, Nova Scotia, was investigated. Measurements were made of the photosynthetic uptake of [C]bicarbonate and its incorporation into cellular protein as well as the heterotrophic uptake of H-labeled amino acids and their incorporation into cellular protein. Activity-temperature curves were analyzed objectively by nonlinear estimation of parameters from various mathematical models. Over the seasonal cycle, the cardinal temperatures and a parameter formally equivalent to the thermodynamic enthalpy of activation for most of the four processes measured were positively correlated with the water temperature. The temperature sensitivity of metabolic activity (i.e., change in activity per unit change in temperature) was indexed by the tangent to the activity-temperature curves. When this index was expressed in dimensionless form by normalization to the scaling factor of the activity-temperature curves, the resulting relative temperature sensitivity, evaluated at the prevailing temperature, proved to be statistically invariant throughout the year. During the height of the spring bloom, the water temperature (-0.3 degrees C) was not so low as to inhibit metabolic activity of either the phytoplankton or the bacterioplankton. The evidence suggests that heterotrophic utilization of products is not suppressed during the spring phytoplankton bloom.

Journal Article↗

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts.

A growing number of processes throughout biology are regulated by redox via thiol-disulfide exchange. This mechanism is particularly widespread in plants, where almost 200 proteins have been linked to thioredoxin (Trx), a widely distributed small regulatory disulfide protein. The current study extends regulation by Trx to amyloplasts, organelles prevalent in heterotrophic plant tissues that, among other biosynthetic activities, catalyze the synthesis and storage of copious amounts of starch. Using proteomics and immunological methods, we identified the components of the ferredoxin/Trx system (ferredoxin, ferredoxin-Trx reductase, and Trx), originally described for chloroplasts, in amyloplasts isolated from wheat starchy endosperm. Ferredoxin is reduced not by light, as in chloroplasts, but by metabolically generated NADPH via ferredoxin-NADP reductase. However, once reduced, ferredoxin appears to act as established for chloroplasts, i.e., via ferredoxin-Trx reductase and a Trx (m-type). A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter). The proteins function in a range of processes in addition to starch metabolism: biosynthesis of lipids, amino acids, and nucleotides; protein folding; and several miscellaneous reactions. The results suggest a mechanism whereby light is initially recognized as a thiol signal in chloroplasts, then as a sugar during transit to the sink, where it is converted again to a thiol signal. In this way, amyloplast reactions in the grain can be coordinated with photosynthesis taking place in leaves.

Amino Acids↗