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PubMed1967

Regulation of autotrophic and heterotrophic carbon dioxide fixation in Hydrogenomonas facilis.

After growth on various carbon sources, sonic extracts of Hydrogenomonas facilis contained ribulosediphosphate (RuDP) carboxylase and phosphoribulokinase (Ru5-P kinase). After very short sonic treatment, a reductive adenosine triphosphate (ATP)-dependent incorporation of (14)CO(2) was also detectable. Reduced nicotinamide adenine dinucleotide (NADH(2)) served as reductant 30-fold more effectively than reduced nicotinamide adenine dinucleotide phosphate (NADPH(2)). Adenosine 5'-phosphate (AMP) and adenosine 5'-pyrophosphate (ADP) inhibited Ru5-P kinase and NADH(2)-, ATP-dependent CO(2) fixation. The levels and duration of CO(2) fixation suggested that it is a cyclic process. The requirement of reduced pyridine nucleotide and ATP and the sensitivity of fixation to AMP and ADP support the conjecture that it occurs via the Calvin cycle. After thorough study of variables affecting catalysis, specific activities (millimicromoles of substrate disappearing per milligram of protein) at 30 C were determined for RuDP carboxylase (C), Ru5-P kinase (K) and ATP-, NADH(2)- dependent CO(2) fixation (CO(2) F) after growth autotrophically on fructose, glucose, ribose, glutamate, lactate, succinate, and acetate. Values for these growth modes were, respectively-for C: 67.3, 51.1, 51.4, 24.6, 2.05, 10.2, 2.25, 1.4; for K: 24.7, 24.0, 23.2, 14.2, 12.8, 12.9, 13.4, 2.8; and for CO(2) F: 4.54, 4.83, 3.10, 2.87, 0.85, 1.51, 0.24, 0.41. The qualitative parallel between values for RuDP carboxylase and CO(2) fixation suggests that one major control point in fixation is the step catalyzed by RuDP carboxylase.

Adenine Nucleotides↗

PubMed1991

Hormonal modulation of plant growth: the role of auxin perception.

The organisation of growth and development in vascular plants appears to be highly adapted to meet the specific demands of a sessile, autotrophic habit. Many of the characteristic features of plant development are associated with the activities of five groups of phytohormones. Each of the phytohormones has the ability to influence fundamentally a remarkable variety of developmental and physiological processes. This ability has been widely documented but remains to be explained. Here we describe how recent breakthroughs in the analysis and understanding of eucaryotic signal transduction are being applied, in conjunction with technical advances in molecular genetics, to elucidate the molecular basis of the phytohormonal properties of auxin. Both auxin concentration, and the sensitivity of plant cells to this phytohormone have been implicated as important parameters in auxin action. We describe recent molecular biological approaches to assess the contribution made by each of these parameters. Emphasis is given to a description of recent genetic and biochemical progress towards identification of the molecular targets of the auxin signal and the molecular components involved in its subsequent transduction.

Endoplasmic Reticulum↗

PubMed2005

Community level analysis: genetic and biogeochemical approaches to investigate community composition and function in aerobic ammonia oxidation.

Aerobic ammonia oxidation is the process that converts ammonium to nitrate and thus links the regeneration of organic nitrogen to fixed nitrogen loss by denitrification. It is performed by a phylogenetically restricted group of Proteobacteria (ammonia-oxidizing bacteria, AOB) that are autotrophic and obligately aerobic. This chapter describes methods for the measurement of ammonia oxidation in the environment, with a focus on seawater systems and stable isotopic tracer methods. It also summarizes the current state of molecular ecological approaches for detection of AOB in the environment and characterization of the composition of AOB assemblages.

Ammonia↗

PubMed2004

Thinking about the evolution of photosynthesis.

Photosynthesis is an ancient process on Earth. Chemical evidence and recent fossil finds indicate that cyanobacteria existed 2.5-2.6 billion years (Ga) ago, and these were certainly preceded by a variety of forms of anoxygenic photosynthetic bacteria. Carbon isotope data suggest autotrophic carbon fixation was taking place at least a billion years earlier. However, the nature of the earliest photosynthetic organisms is not well understood. The major elements of the photosynthetic apparatus are the reaction centers, antenna complexes, electron transfer complexes and carbon fixation machinery. These parts almost certainly have not had the same evolutionary history in all organisms, so that the photosynthetic apparatus is best viewed as a mosaic made up of a number of substructures each with its own unique evolutionary history. There are two schools of thought concerning the origin of reaction centers and photosynthesis. One school pictures the evolution of reaction centers beginning in the prebiotic phase while the other school sees reaction centers evolving later from cytochrome b in bacteria. Two models have been put forth for the subsequent evolution of reaction centers in proteobacteria, green filamentous (non-sulfur) bacteria, cyanobacteria, heliobacteria and green sulfur bacteria. In the selective loss model the most recent common ancestor of all subsequent photosynthetic systems is postulated to have contained both RC1 and RC2. The evolution of reaction centers in proteobacteria and green filamentous bacteria resulted from the loss of RC1, while the evolution of reaction centers in heliobacteria and green sulfur bacteria resulted from the loss of RC2. Both RC1 and RC2 were retained in the cyanobacteria. In the fusion model the most recent common ancestor is postulated to have given rise to two lines, one containing RC1 and the other containing RC2. The RC1 line gave rise to the reaction centers of heliobacteria and green sulfur bacteria, and the RC2 line led to the reaction centers of proteobacteria and green filamentous bacteria. The two reaction centers of cyanobacteria were the result of a genetic fusion of an organism containing RC1 and an organism containing RC2. The evolutionary histories of the various classes of antenna/light-harvesting complexes appear to be completely independent. The transition from anoxygenic to oxygenic photosynthesis took place when the cyanobacteria learned how to use water as an electron donor for carbon dioxide reduction. Before that time hydrogen peroxide may have served as a transitional donor, and before that, ferrous iron may have been the original source of reducing power.

Journal Article↗

PubMed1987

Autotrophic synthesis of activated acetic acid from CO2 in Methanobacterium thermoautotrophicum. Synthesis from tetrahydromethanopterin-bound C1 units and carbon monoxide.

The synthesis of acetyl-CoA from CO2, H2, and various C1 compounds was studied in vitro with extracts and with protein fractions of Methanobacterium thermoautotrophicum. Acetyl-CoA synthesis from CO2 and H2 by extracts required CO2 reduction to CH4 to proceed. Both processes were highly stimulated by formaldehyde which served as the carbon precursor of both CH4 and the CH3 group of acetate. Carbon monoxide in combination with formaldehyde dramatically stimulated the acetyl-CoA synthesis up to 150-fold. In this system, which did not require CO2 reduction to the formaldehyde and CO level, acetyl-CoA synthesis was no longer dependent on CH4 formation. The soluble (100,000 X g supernatant) cell protein was resolved into a protein fraction [45-60% (NH4)2SO4-fraction] which catalyzed acetyl-CoA synthesis at a specific rate of 15 nmol X min-1 X (equivalent of mg cell protein)-1 (60 degrees C). This oxygen-sensitive enzyme reaction required dithioerythritol for activity and was strictly dependent on coenzyme A, CO, and N5,N10-methylene tetrahydromethanopterin, N5-methyl tetrahydromethanopterin or formaldehyde plus tetrahydromethanopterin. The incorporation of formaldehyde is explained by the spontaneous formation of methylene tetrahydromethanopterin. The product of the reaction, acetyl-CoA, was quantitatively derived from CO (carboxyl of acetate) and a C1 derivative of tetrahydromethanopterin (methyl of acetate). The C1 derivative of tetrahydromethanopterin could not be replaced by a C1 derivative of tetrahydrofolate or by methyl-coenzyme M; ATP was not required. The active protein fraction contained CO dehydrogenase and at least on corrinoid protein. These results provide strong biochemical arguments for the proposed mechanism of autotrophic acetyl-CoA synthesis in Methanobacterium.

Acetyl Coenzyme A↗

PubMed1994

Metabolism of methanogens.

Methanogenic archaea convert a few simple compounds such as H2 + CO2, formate, methanol, methylamines, and acetate to methane. Methanogenesis from all these substrates requires a number of unique coenzymes, some of which are exclusively found in methanogens. H2-dependent CO2 reduction proceeds via carrier-bound C1 intermediates which become stepwise reduced to methane. Methane formation from methanol and methylamines involves the disproportionation of the methyl groups. Part of the methyl groups are oxidized to CO2, and the reducing equivalents thereby gained are subsequently used to reduce other methyl groups to methane. This process involves the same C1 intermediates that are formed during methanogenesis from CO2. Conversion of acetate to methane and carbon dioxide is preceded by its activation to acetyl-CoA. Cleavage of the latter compound yields a coenzyme-bound methyl moiety and an enzyme-bound carbonyl group. The reducing equivalents gained by oxidation of the carbonyl group to carbon dioxide are subsequently used to reduce the methyl moiety to methane. All these processes lead to the generation of transmembrane ion gradients which fuel ATP synthesis via one or two types of ATP synthases. The synthesis of cellular building blocks starts with the central anabolic intermediate acetyl-CoA which, in autotrophic methanogens, is synthesized from two molecules of CO2 in a linear pathway.

Acetates↗

PubMed2005

Ecological specialization of mixotrophic plankton in a mixed water column.

In recent years, the population dynamics of plankton in light- or nutrient-limited environments have been studied extensively. Their evolutionary dynamics, however, have received much less attention. Here, we used a modeling approach to study the evolutionary behavior of a population of plankton living in a mixed water column. Initially, the organisms are mixotrophic and thus have both autotrophic and heterotrophic abilities. Through evolution of their trophic preferences, however, they can specialize into separate autotrophs and heterotrophs. It was found that the light intensity gradient enables evolutionary branching and thus may result in the ecological specialization of the mixotrophs. By affecting the gradient, other environmental properties also acquire influence on this evolutionary process. Intermediate mixing intensities, large mixing depths, and high nutrient densities were found to facilitate evolutionary branching and thus specialization. Later results may explain why mixotrophs are often more dominant in oligotrophic systems while specialist strategies are associated with eutrophic systems.

Adaptation, Physiological↗

PubMed2002

Denitrification of industrial wastewater with sulfur and limestone packed column.

An autotrophic denitrification system was developed for nitrate contaminated industrial wastewater whose C/N ratio was very low. The microbes containing Thiobacillus denitrificans as a dominant species were attached on the surface of granular elemental sulfur packed in a column. Elemental sulfur was used as an electron donor for autotrophic denitrification. The granules of limestone were mixed with the granular sulfur to moderate the decrease of alkalinity during autotrophic denitrification. The stoichiometry and basic kinetics of denitrification were studied in column runs. The effects of minerals such as phosphorus on treatment performance were clarified. The wastewater from steel production plants was treated by the present biofilm process. Low extent of nitrogen removal was caused by the lack of minerals.

Acidithiobacillus thiooxidans↗

PubMed2003

[Biological processes of the human environment regeneration within the Martian crew life support systems].

Five ground-based experiments at RF SRC-IBMP had the purpose to make a thorough investigation of a model of the human-unicellular algae-mineralization life support system. The system measured 15 m3 and contained 45 liters of alga suspension; the dry alga density was 10 to 12 g/l and water volume (including the alga suspension) amounted to 59 l. More sophisticated LSS models where algae were substituted by higher plants (crop area in the greenhouse equaled 15 m2) were investigated in three experiments from 1.5 mos. to 2 mos. in duration. It was found that the alga containing LSS was able to fulfill not only the macrofunction (air and water regeneration) but also several additional functions (air purification, establishment of microbial cenosis etc.) providing an adequate human environment. This polyfunctionality of the biological regenerative processes is a weighty argument for their integration into space LSSs. Another important aspect is that the unicellular algae containing systems are highly reliable owing to a huge number of species-cells which will be quickly recovered in case of the death of a part of the population and, consequently, functionality of the LSS autotrophic component will be restored before long. For an extended period of time the Martian crew will have no communication with the Earth's biosphere which implies that LSS should be absolutely reliable and redundant. Redundancy can be achieved through installation aboard the vehicle of two systems constructed on different principles of regeneration, i.e. physical-chemical and biological. Each of the LSSs should have the power to satisfy all needs of the crew. The best option is when two systems are functioning in parallel sharing the responsibility for the human environment. Redundancy in this case will mean that in the event of failure or a drastic decrease in performance of one system the other one will make up for the loss by increasing its share in the overall regeneration process.

Biomass↗

PubMed1987

Light and acetate regulate a mitochondrial malate dehydrogenase.

A malate dehydrogenase was purified from the unicellular green alga Chlorogonium elongatum Dangeard. The enzyme was localized in the mitochondria by immunogold electron microscopy and was found to be present on the cristae. The concentration of the enzyme is regulated by acetate and light. In cells cultured heterotrophically with acetate as carbon source the activity and the concentration of the enzyme is 5- to 6-fold higher than in autotrophic cells. In mixotrophically cultured cells (light and acetate) the enzyme level attains only half of the value of that in heterotrophic cells. Acetate induces an increase of the enzyme concentration while light has an inhibitory effect on this process.

Journal Article↗

PubMedDate not supplied

[Role of carbonic acid and ammonium nitrogen in regulation of metabolism and physiological function in heterotrophic organisms].

The paper emphasizes common and distinctive features of carbonic acid fixation (carboxylation) in autotrophic and heterotrophic organisms as well as metabolic significance of the carboxylation reaction in the synthesis of lipids, amino acids, sugars, purine and pyrimidine nucleotides and in the functioning of a tricarboxylic cycle as an energy source in biosynthetic processes and of precursors of many vital metabolites in the organism. The paper also gives a short description of effective preparations created at the laboratory on the basis of a close dependence of biosynthetic processes in the organism on the carbonic acid fixation and the ways of their stimulation by intensifying carboxylation established by the author and his collaborators. The preparations are used for raising the productivity of farm animals, poultry and fish as well as for accelerating of blood regeneration with post-hemorrhagic and other anemias, regeneration of damaged soft and bone tissues.

Ammonia↗

PubMed2006

A quantitative measure of nitrifying bacterial growth.

Nitrifying bacteria convert ammonia (NH3) to nitrate (NO3-) in a nitrification reaction. Methods to quantitatively separate the growth rate of these important bacterial populations from that of the dominant heterotrophic bacteria are important to our understanding of the nitrification process. The changing concentration of ammonia is often used as an indirect measure of nitrification but ammonification processes generate ammonia and confound this approach while heterotrophs remove nitrate via denitrification. Molecular probe methods can tell us what proportion of the microbial community is nitrifying bacteria but not their growth rate. The technique proposed here was able to quantify the growth rate of the nitrifying bacterial populations amidst complex ecological processes. The method incubates [methyl-3H] thymidine with water samples in the presence and absence of an inhibitor of nitrification-thiourea. The radioactively labeled DNA in the growing bacteria was extracted. The rate of incorporation of the label into the dividing bacterial DNA was used to determine bacterial growth rate. Total bacterial community growth rates in full-scale and pilot-scale fixed-film nitrifying reactors and an activated sludge reactor were 2.1 x 10(8), 4.1 x 10(8) and 0.4 x 10(8)cell ml(-1)d(-1), respectively; the growth rate of autotrophic-nitrifying bacteria was 0.7 x 10(8), 2.6 x 10(8) and 0.01 x 10(8)cell ml(-1)d(-1), respectively. Autotrophic-nitrifying bacteria contributed 30% and 60% of the total bacterial community growth rate in the nitrifying reactors whereas only 2% was observed in the activated sludge reactor that was not designed to nitrify. The rates of ammonia loss from the nitrifying reactors corresponded to the rate of growth of the nitrifying bacteria. This method has the potential to more often identify factors that enhance or limit nitrifying processes in both engineered and natural aquatic environments.

Bacteria↗

PubMed1998

A novel, non-redox-regulated NAD-dependent malate dehydrogenase from chloroplasts of Arabidopsis thaliana L.

We report a novel plastidic NAD-dependent malate dehydrogenase (EC 1. 1.1.37), which is not redox-regulated in contrast to its NADP-specific counterpart (EC 1.1.1.82). Analysis of isoenzyme patterns revealed a single NAD-MDH associated with highly purified chloroplasts isolated from Arabidopsis and spinach. A cDNA clone encoding the novel enzyme was found in the Arabidopsis EST data base by sorting all putative clones for NAD-dependent malate dehydrogenase. A derived amino acid sequence is very similar to mitochondrial and peroxisomal NAD-MDHs within the region coding for the mature protein but possesses a 80-amino acid long N-terminal domain with typical characteristics of a chloroplast transit peptide. In vitro synthesized labeled precursor protein was imported into the stroma of spinach chloroplasts and processed to a mature enzyme subunit of 34 kDa. Expressed in Escherichia coli, the recombinant enzyme exhibited the same distinctive isoelectric point of 5.35 as the original enzyme from Arabidopsis chloroplasts. Northern analysis revealed that the protein is expressed in both autotrophic and heterotrophic tissues. The findings reported here indicate that the "malate valve" operates not only in the illuminated chloroplasts but also in dark chloroplasts and in heterotrophic plastids and is therefore a general mechanism to maintain the optimal ratio between ATP and reducing equivalents in plastids.

Amino Acid Sequence↗

PubMed1983

Use of carboxylic acids by Thiobacillus A2.

Thiobacillus A2 can grow on acetate, glycollate, succinate and citrate as sole carbon and energy sources. Results of growth and transport experiments indicated that separate transport systems existed for the four acids although acetate uptake by bacteria grown on glycollate was very rapid. Citrate was a potentially toxic substrate in that low concentrations had to be supplied to adapt organisms to growth on citrate following autotrophic culture on thiosulphate. Apparent Ks values for transport by whole organisms were around 10(-4) M. The effects of uncoupling agents, phosphate and arsenate, on acid uptake did not allow identification of the mechanisms of transport, but indicated energy-requiring processes possibly involving anion participation. The ratio of carbon assimilated from the -CH2- and the -COOH carbons of succinate was about 5:1, reflecting very rapid decarboxylation of succinate following uptake into the cell.

Acetates↗

PubMed2001

Fundamental processes within natural and constructed wetland ecosystems: short-term versus long-term objectives.

Use of wetland ecosystems for water pollution control consists essentially of sustained induced disturbances as pollutants are loaded to complex biological communities. Objectives are to maximize pollutant loading, incorporation, and retention while maintaining highest levels of community metabolism and minimal alteration of community structure. Several basic processes are emphasized: (a) macrophyte productivity in relation to shoot:root ratios, and nutrient availability; (b) macrophyte life history strategies, succession, and biodiversity under constant pollutant stress; (c) importance of standing dead and particulate detritus; (d) functions and controlling mechanisms of heterotrophic and autotrophic periphyton in pollutant retention and recycling; (e) coupling of microbial metabolism to macrophyte retention of pollutants; (f) gaseous losses to the atmosphere; (g) losses of dissolved organic matter and its utilization; and (h) water losses by evapotranspiration and effects on wetland efficacy. Short-term wetland removal efficiencies are confounded by massive variations in retentive capacities diurnally, seasonally, and spatially, in exceeding physiological tolerance levels, and in species succession. Problems of channelization, altered microhydrology, and assimilation/retention are major in natural and non-engineered ecosystems. Wetlands are highly ephemeral and variable in their capabilities for sequestering and retention of nutrients and other pollutants.

Ecosystem↗

PubMed2002

Active biomass in activated sludge mixed liquor.

The engineering and technology of the activated sludge system are reasonably well established, with systems implemented worldwide for the biological removal of C, N and/or P. Parallel to this development, significant advances have been made in the microbiological and biochemical areas of activated sludge. These advances have been driven by the development of new analytical techniques that allow microorganisms to be studied in situ in the activated sludge environment. However, there has been little cross-linking and overlap between the engineering and technology and microbiology and biochemistry paradigms. In particular, the information from the microbiology and biochemistry has not been integrated into the engineering and technology paradigm, to enable improved system design and optimization. One area that can form a starting point to build bridges between the two paradigm sets, is measurement of active biomass. The current design and simulation models invariably include active biomass for each organism group as fundamental parameters which define quantitatively the kinetic rates of the relevant biological processes. However, these parameters remain purely hypothetical because to date they have not been quantitatively measured; their acceptance is based on the consistency of model predicted results over a wide range of application. This paper describes developments in quantitative measurement of the heterotrophic and autotrophic active biomass concentrations within the engineering and technology paradigm, and the formulation of a multinational project which will attempt to link these measurements and the defined engineering environment to the new microbiological and biochemical analytical techniques. It is hoped that this project will facilitate integration of the two paradigms sets.

Bacteria↗

PubMed1999

Missing lithotroph identified as new planctomycete.

With the increased use of chemical fertilizers in agriculture, many densely populated countries face environmental problems associated with high ammonia emissions. The process of anaerobic ammonia oxidation ('anammox') is one of the most innovative technological advances in the removal of ammonia nitrogen from waste water. This new process combines ammonia and nitrite directly into dinitrogen gas. Until now, bacteria capable of anaerobically oxidizing ammonia had never been found and were known as "lithotrophs missing from nature". Here we report the discovery of this missing lithotroph and its identification as a new, autotrophic member of the order Planctomycetales, one of the major distinct divisions of the Bacteria. The new planctomycete grows extremely slowly, dividing only once every two weeks. At present, it cannot be cultivated by conventional microbiological techniques. The identification of this bacterium as the one responsible for anaerobic oxidation of ammonia makes an important contribution to the problem of unculturability.

Ammonia↗

PubMed1997

The hupC gene product is a component of the electron transport system for hydrogen oxidation in Pseudomonas hydrogenovora.

The hydrogenase gene cluster containing nine genes (hupSLCDFGHIJ) was identified by sequencing of an 8.8-kb DNA region from Pseudomonas hydrogenovora. To investigate the function of the hupC gene product, we isolated a hupC-null mutant (HID3) of P. hydrogenovora by introducing an in-frame deletion into the hupC. The mutant, HID3, could not grow autotrophically but retained half the level of hydrogenase activity of the wild-type strain. Results of the oxygen consumption test and Western blot analysis revealed that the hupC gene product is a b-type cytochrome but not involved in the hydrogenase maturation process.

Amino Acid Sequence↗