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PubMed2002

ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination.

The development of a germinating embryo into an autotrophic seedling is arrested under conditions of water deficit. This ABA-mediated developmental checkpoint requires the bZIP transcription factor ABI5. Here, we used abi3-1, which is also unable to execute this checkpoint, to investigate the relative role of ABI3 and ABI5 in this process. In wild-type Arabidopsis plants, ABI3 expression and activity parallel those described for ABI5 following stratification. During this process, transcript levels of late embryogenesis genes such as AtEm1 and AtEm6 are also re-induced, which might be responsible for the acquired osmotic tolerance in germinated embryos whose growth is arrested. ABI5 expression is greatly reduced in abi3-1 mutants, which has low AtEm1 or AtEm6 expression. Cross complementation experiments showed that 35S-ABI5 could complement abi3-1, whereas 35S-ABI3 cannot complement abi5-4. These results indicate that ABI5 acts downstream of ABI3 to reactivate late embryogenesis programmes and to arrest growth of germinating embryos. Although ABI5 is consistently located in the nucleus, chromosomal immunoprecipitation (ChIP) experiments revealed that ABA increases ABI5 occupancy on the AtEm6 promoter.

Abscisic Acid↗

PubMedDate not supplied

Carbon budgets of temperate forest ecosystems.

A summary of carbon-budget data from 30 forest stands is presented together with information on both above- and belowground ecosystem components. Only 10 of the stands had complete biomass data, 21 had complete productivity data and six had heterotrophic, or autotrophic respiration data, or both. The most comprehensive stand-level data have been collected for Pinus spp., Pseudotsuga menziesii, Abies amabilis and Liriodendron tulipifera. Only incomplete carbon budgets are available for most ecosystems studied, because measurements have been limited to one or several ecosystem processes (e.g., decay, productivity, storage). Based on the few complete C-budget studies that have been published, it is concluded that tree species differ in annual turnover of tissues.

Journal Article↗

PubMed1981

In vivo inactivation of soluble hydrogenase of Alcaligenes eutrophus.

The soluble, NAD+-reducing hydrogenase in intact cells of Alcaligenes eutrophus was inactivated by oxygen when electron donors such as hydrogen or pyruvate were available. The sole presence of either oxygen or oxidizable substrates did not lead to inactivation of the enzyme. Inactivation occurred similarly under autotrophic growth conditions with hydrogen, oxygen and carbon dioxide. The inactivation followed first order reaction kinetics, and the half-life of the enzyme in cells exposed to a gas atmosphere of hydrogen and oxygen (8:2, v/v) at 30 degrees C was 1.5h. The process of inactivation did not require ATP-synthesis. There was no experimental evidence that the inactivation is a reversible process catalyzed by a regulatory protein. The possibility is discussed that the inactivation is due to superoxide radical anions (O2-) produced by the hydrogenase itself.

Adenosine Triphosphate↗

PubMed2001

Microbial influences on local carbon isotopic ratios and their preservation in carbonate.

Analysis of the carbon isotopic composition of carbonates is a valuable tool for studying microbial processes and looking for evidence of life. Microbial fixation of CO2 and conversion of organic carbon to CO2 can produce measurable delta 13C shifts in a microbial mat environment. Diffusion modeling demonstrates that substantial isotopic shifts can develop within the mat and in the diffusion boundary layer in the fluid when CO2 fixation is rapid and prolonged for several hours. Carbonates that precipitate during rapid CO2 fixation can preserve these microbially produced isotopic shifts. However, continued precipitation during intervals when respiration dominates or after the cessation of active microbial growth commonly dilutes autotrophic isotopic signatures. Thus, preserved isotopic signatures rarely reflect the magnitude of isotopic shifts within the mat. Interpretation of observed isotopic shifts in microbial mat carbonate depends on fully characterizing ambient delta 13C and eliminating other origins for isotopic shifts. The carbon isotopic composition of reservoirs can vary substantially, both on Earth and on other planets. Characterizing the reservoir composition and any changes through time is critical to evaluating microbially induced shifts. In addition, careful evaluation of non-microbial causes for shifts in isotopic composition is essential for a reliable interpretation. Complicating processes include recrystallization, calcite precipitation over extended periods of time, variable precipitation rates and water chemistry, and mixing of carbonates having different isotopic signatures.

Carbon Dioxide↗

PubMed1997

Whiting events: biogenic origin due to the photosynthetic activity of cyanobacterial picoplankton.

An annual whiting event occurs each year in late May to early June in Fayetteville Green Lake, New York. The initiation of this event correlates with exponential growth of the Synechococcus population within the lake. Synechococcus is the dominant (by approximately 4 orders of magnitude) autotrophic organism owing to the oligotrophic condition of the lake. The delta 13C values of the dissolved inorganic C range seasonally from -9.5% in winter to -6.2% in summer due to photosynthetic activity. Calcite precipitates principally in the microenvironment surrounding Synechococcus because of a photosynthetically driven alkalization process and the availability of the cells as nucleation sites. This calcite has a heavier delta 13C value (>4%) than does the dissolved inorganic C of the lake water owing to the cells' preferential uptake of 12C. A conceptual model suggests that photosynthetic activity and cell surface chemistry, together with the substantial surface area that arises from the great abundance of micron-sized cells, allow Synechococcus to dominate the annual whiting events in Fayetteville Green Lake.

Calcium Carbonate↗

PubMed2001

Pyrolytic characteristics of microalgae as renewable energy source determined by thermogravimetric analysis.

Two kinds of autotrophic microalgae, Spirulina platensis (SP) and Chlorella protothecoides (CP) were pyrolyzed at the heating rates of 15, 40, 60 and 80 degrees C/min up to 800 degrees C in a thermogravimetric analyzer to investigate their pyrolytic characteristics. Three stages (dehydration, devolatilization and solid decomposition) appeared in the pyrolysis process. SP and CP mainly devolatilized at 190-560 degrees C and 150-540 degrees C, respectively. A total volatile yield of about 71% was achieved from each microalga. As the heating rate increased, a lateral shift to higher temperatures was observed in their thermograms, and the instantaneous maximum and average reaction rates in the devolatilization stage were increased while the activation energy was decreased. The value of activation energy for CP pyrolysis was 4.22-5.25 x 10(4), lower than that of SP (7.62-9.70 x 10(4)), and the char in final residue of CP was 14.00-15.14%, less than that of SP by 2-3%. This indicated that CP is preferable for pyrolysis over SP. The experimental results may provide useful data for the design of pyrolytic processing systems using planktonic microalgae as feedstock.

Bioelectric Energy Sources↗

PubMed2006

Modeling of extracellular polymeric substances and soluble microbial products production in a submerged membrane bioreactor at various SRTs.

Extracelluar polymeric substances (EPSs) and soluble microbial products (SMPs) produced by microbial cultures involved in membrane biofouling have been widely investigated. A mathematical model of EPS and SMP formation and degradation was established based on the activated sludge model no. 1 (ASM1) and was applied to the membrane bioreactor sludge with different sludge retention times (SRTs). The unified theory that the distinct products from the EPS and SMP overlapped each other was integrated into the ASM1. Two components, five processes and eight parameters were newly added to set up the model. To increase the accuracy of model simulation, microbial kinetic parameters were determined by respirometry method and applied to the model instead of microbial kinetic constant offered in ASM1. From the respirometry result, both of heterotroph and autotroph showed different yield value, growth rate and decay rate from activated sludge. There was no significant effect of SRT on SMP production and the experimental results showed good agreement with the predicted values by the model simulation. With the developed unified EPS and SMP model, EPS and SMP production could be simulated so well that it can be applied for the membrane biofouling control.

Bioreactors↗

PubMed2002

SEP-1 - a subtilisin-like serine endopeptidase from germinated seeds of Hordeum vulgare L. cv. Morex.

Proteolysis is crucial for all living cells. It regulates protein processing, intracellular protein levels and removes abnormal or damaged proteins from the cell, working as a cellular housekeeper. By means of proteolysis, cells can control the short-lived regulatory proteins that affect processes such as signal transduction and reception, transcription, division and cellular growth. Proteolysis also furnishes amino acids for the de novo synthesis of proteins. In germinating seeds, its main role is to degrade storage proteins into small peptides and amino acids that can be used by the embryo during autotrophic growth. We have isolated and purified a serine endopeptidase, one of the many proteolytic enzymes that occur in germinated barley seeds (green malt), using chromatofocusing and DEAE-, CM-, and size-exclusion chromatographies. The enzyme, named SEP-1, has a molecular weight of 70 kDa, as estimated by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size-exclusion chromatography. SEP-1 was detected and measured by its ability to digest gelatin in gels and to hydrolyze the synthetic substrate N-succinyl Ala-Ala-Pro-Leu p-nitroanilide. The hydrolysis of the synthetic substrate was optimal at pH 6.5 and 50 degrees C with a K(m) of 2.6 mM. The enzyme was inhibited by phenylmethylsulfonyl fluoride and p-amidinophenyl methanesulfonyl fluoride but not by any other class-specific inhibitor, suggesting it was a serine endopeptidase. Its amino acid sequence was similar to those of other plant subtilisin-like serine peptidases (EC 3.4.21), especially to the cucumisin-like group. SEP-1 was present in resting seeds, and its activity increased during germination in all of the malted barley tissues except for the endosperm, where it never occurred, suggesting that the enzyme is not likely involved in storage-protein degradation.

Amino Acid Sequence↗

PubMed1984

Photo- and Metabolite Regulation of the Synthesis of Ribulose Bisphosphate Carboxylase/Oxygenase and the Phycobiliproteins in the Alga Cyanidium caldarium.

In the eukaryotic and unicellular alga Cyanidium caldarium the synthesis of the plastid enzyme ribulose bisphosphate carboxylase/oxygenase (RuBPCase) and the light gathering proteins phycocyanin (PC) and allophycocyanin (APC) is under the control of light and glucose, which is a metabolizable carbon source for this organism. Light promotes the synthesis of these proteins while glucose has a strong inhibitory effect on this process. All subunits of the proteins mentioned above are in vitro translation products of poly (A)(-)-RNA (Steinmüller, Kaling, Zetsche 1983 Planta 159: 308-313). Both factors-light and glucose-exert their effects mainly by modulation of the level of translatable messenger RNA for these proteins. Under autotrophic growth conditions the level of translatable RuBPCase-, PC-, and APC-messenger RNA is high, whereas in the presence of glucose the level of these mRNAs is low or not detectable at all.

Journal Article↗

PubMed1986

Stability of the determined state.

During development parts of plants become determined for specific fates which can persist in populations of dividing cells. Students of plant development have tended to favour the view that the determined state is stabilized at the supracellular level. We provide evidence for the alternative view that determination can be inherited at the cellular level. This conclusion is based on the observation that cultured cells derived from the leaf lamina and cortex of the stem of tobacco plants inherit different states of cytokinin requirement. Plant regeneration experiments show that the cytokinin-requiring (C-) state characteristic of leaf cells and the cytokinin autotrophic (C+) state characteristic of cortex cells are stable but not permanent. Progeny of both cell types can give rise to complete plants with tissues exhibiting the cytokinin requirement of comparable tissues of seed grown plants. Pith cells can shift from the C- to the C+ state by a process known as habituation. Evidence is presented that this epigenetic change is stabilized by a positive-feedback mechanism in which cytokinins appear to promote their own biosynthesis. A single dominant, Mendelian gene, H1-2, controls expression of the C- and C+ phenotypes. There are hints that this gene changes state in cultured cells at rates expected for epigenetic modifications. This suggests that the C- and C+ state can also be stabilized by genetic mechanisms.

Cytokinins↗

PubMed2002

Production of gaseous nitrogen compounds in a novel process for ammonium removal.

The production of gaseous nitrogen compounds, particularly the greenhouse gas nitrous oxide, was investigated in a novel process for ammonium removal from wastewater. The process is based on the adsorption of ammonium on zeolite followed by bioregeneration. The zeolite serves the dual purpose of an ion exchanger and a physical carrier for nitrifying bacteria which bio-regenerate the ammonium saturated mineral. An analysis of the nitrifying population composition in the reactor fed with simulated secondary effluent (NH4+ = 50 mg/l) revealed that about half of the bacteria in the biofilm were common ammonium oxidizers Nitrosococcus mobilis and Nitrosomonas, while the other half were nitrite oxidizers. The amount of nitrogen losses, under different conditions, and the identification of the emitted gases (N2 or N2O) were investigated in two sets of experiments: (I) batch experiments using biomass originating from the ion exchange reactor with and without the addition of nitrite, and (II) continuous experiments using the ion exchange reactor with zeolite as the biomass carrier. In the batch experiments, nitrite and oxygen concentrations were determined as the major parameters responsible for the formation of gaseous nitrogen gas during ammonia oxidation by autotrophic bacteria. Continuous experiments showed that the major parameter significantly affecting nitrogen losses was the amount of ammonium adsorbed by the zeolite during the ion exchange phase. The amount of ammonium adsorbed determines the ammonium concentration during the initial period of bioregeneration, which in turn directly influences oxygen demand and the resulting concentrations of oxygen and nitrite. It was concluded that the formation of nitrogen gas compounds in the ion exchange/bioregeneration process can be eliminated by adjusting the operational regime to have a shorter adsorption phase resulting in smaller amounts of ammonium adsorbed per cycle.

Adsorption↗

PubMed2006

The membrane biofilm reactor: the natural partnership of membranes and biofilm.

Many exciting new technologies for water-quality control combine microbiological processes with adsorption, advanced oxidation, a membrane or an electrode to improve performance, address emerging contaminants or capture renewable energy. An excellent example is the H2-based membrane biofilm reactor (MBfR), which delivers H2 gas to a biofilm that naturally accumulates on the outer surface of a bubbleless membrane. Autotrophic bacteria in the biofilm oxidise the H2 and use the electrons to reduce NO3-, CIO4- and other oxidised contaminants. This natural partnership of membranes and biofilm makes it possible to gain many cost, performance and simplicity advantages from using H2 as the electron donor for microbially catalysed reductions. The MBfR has been demonstrated for denitrification in drinking water; reduction of perchlorate in groundwater; reduction of selenate, chromate, trichloroethene and other emerging contaminants; advanced N removal in wastewater treatment and autotrophic total-N removal.

Biofilms↗

PubMed2001

N-removal in a granular sludge sequencing batch airlift reactor.

The removal of N-compounds in the sequencing batch airlift reactor (SBAR) containing granular sludge was studied under conditions of decreased dissolved oxygen (DO). A simulation model was developed to describe and evaluate the effects of several process conditions in the SBAR on N-removal performance. The model described the experimental data reasonable well. It has been shown that nitrification, denitrification, and removal of chemical oxygen demand (COD) can occur simultaneously in a granular sludge SBR. It has also been shown that the exact location of the autotrophic biomass influences the net N-removal. The distribution of the autotrophic biomass is influenced by the DO in the reactor. The optimal DO value is expected to be around 40% air saturation. It was shown that storage and subsequent degradation of poly-beta-hydroxybutyrate (PHB) benefit the denitrification. In particular, PHB is stored in bacteria situated in deeper layers of the granules below where the autotrophic activity occurs, serves as a C-source for denitrification.

Aerobiosis↗

PubMed2004

Belowground carbon dynamics in loblolly pine (Pinus taeda) immediately following diammonium phosphate fertilization.

Forest soils store an immense quantity of labile carbon (C) and a may be a large potential sink for atmospheric C. Forest management practices such as fertilization may enhance overall C storage in soils, yet changes in physiological processes following nutrient amendments have not been widely investigated. We intensively monitored belowground C dynamics for nearly 200 days following diammonium phosphate fertilization of pot-grown loblolly pine (Pinus taeda L.) seedlings in an effort to examine the short-term effects of fertilization on processes involved in soil C sequestration. Soil respiration rates initially increased in fertilized pots relative to controls, followed by a brief reversal in this trend and then a final sustained pattern of elevated rates of soil respiration in the fertilized treatment. Patterns in soil respiration rates over time reflected changes in autotrophic (root) and heterotrophic (microbial) components of soil respiration. Root respiration rates were greater in the fertilized treatment 49 days following fertilization and returned to control rates by the end of the study. In contrast, microbial respiration rates and microbial activity per soil C concentration remained depressed over the same time period. Compared with control seedlings, total root biomass was 27% greater in fertilized seedlings harvested at the end of the study, indicating that the elevated soil respiration rates observed toward the end of the study were a result of increased respiring root biomass. We conclude that fertilization, at least over the short-term, may increase soil C sequestration by increasing belowground biomass production and reducing microbial driven C turnover.

Biomass↗

PubMed2001

Toxic effects of linear alkylbenzene sulfonate on metabolic activity, growth rate, and microcolony formation of Nitrosomonas and Nitrosospira strains.

Strong inhibitory effects of the anionic surfactant linear alkylbenzene sulfonate (LAS) on four strains of autotrophic ammonia-oxidizing bacteria (AOB) are reported. Two Nitrosospira strains were considerably more sensitive to LAS than two Nitrosomonas strains were. Interestingly, the two Nitrosospira strains showed a weak capacity to remove LAS from the medium. This could not be attributed to adsorption or any other known physical or chemical process, suggesting that biodegradation of LAS took place. In each strain, the metabolic activity (50% effective concentration [EC(50)], 6 to 38 mg liter(-1)) was affected much less by LAS than the growth rate and viability (EC(50), 3 to 14 mg liter(-1)) were. However, at LAS levels that inhibited growth, metabolic activity took place only for 1 to 5 days, after which metabolic activity also ceased. The potential for adaptation to LAS exposure was investigated with Nitrosomonas europaea grown at a sublethal LAS level (10 mg liter(-1)); compared to control cells, preexposed cells showed severely affected cell functions (cessation of growth, loss of viability, and reduced NH(4)(+) oxidation activity), demonstrating that long-term incubation at sublethal LAS levels was also detrimental. Our data strongly suggest that AOB are more sensitive to LAS than most heterotrophic bacteria are, and we hypothesize that thermodynamic constraints make AOB more susceptible to surfactant-induced stress than heterotrophic bacteria are. We further suggest that AOB may comprise a sensitive indicator group which can be used to determine the impact of LAS on microbial communities.

Alkanesulfonic Acids↗

PubMed2006

Cell biology of molybdenum.

The transition element molybdenum (Mo) is of essential importance for (nearly) all biological systems as it is required by enzymes catalyzing diverse key reactions in the global carbon, sulfur and nitrogen metabolism. The metal itself is biologically inactive unless it is complexed by a special cofactor. With the exception of bacterial nitrogenase, where Mo is a constituent of the FeMo-cofactor, Mo is bound to a pterin, thus forming the molybdenum cofactor (Moco) which is the active compound at the catalytic site of all other Mo-enzymes. In eukaryotes, the most prominent Mo-enzymes are (1) sulfite oxidase, which catalyzes the final step in the degradation of sulfur-containing amino acids and is involved in detoxifying excess sulfite, (2) xanthine dehydrogenase, which is involved in purine catabolism and reactive oxygen production, (3) aldehyde oxidase, which oxidizes a variety of aldehydes and is essential for the biosynthesis of the phytohormone abscisic acid, and in autotrophic organisms also (4) nitrate reductase, which catalyzes the key step in inorganic nitrogen assimilation. All Mo-enzymes, except plant sulfite oxidase, need at least one more redox active center, many of them involving iron in electron transfer. The biosynthesis of Moco involves the complex interaction of six proteins and is a process of four steps, which also includes iron as well as copper in an indispensable way. Moco as released after synthesis is likely to be distributed to the apoproteins of Mo-enzymes by putative Moco-carrier proteins. Xanthine dehydrogenase and aldehyde oxidase, but not sulfite oxidase and nitrate reductase, require the post-translational sulfuration of their Mo-site for becoming active. This final maturation step is catalyzed by a Moco-sulfurase enzyme, which mobilizes sulfur from l-cysteine in a pyridoxal phosphate-dependent manner as typical for cysteine desulfurases.

Aldehyde Oxidase↗

PubMed1997

Oxidative metabolism of inorganic sulfur compounds by bacteria.

The history of the elucidation of the microbiology and biochemistry of the oxidation of inorganic sulfur compounds in chemolithotrophic bacteria is briefly reviewed, and the contribution of Martinus Beijerinck to the study of sulfur-oxidizing bacteria highlighted. Recent developments in the biochemistry, enzymology and molecular biology of sulfur oxidation in obligately and facultatively lithotrophic bacteria are summarized, and the existence of at least two major pathways of thiosulfate (sulfur and sulfide) oxidation confirmed. These are identified as the 'Paracoccus sulfur oxidation' (or PSO) pathway and the 'S4intermediate' (or S4I) pathway respectively. The former occurs in organisms such as Paracoccus (Thiobacillus) versutus and P. denitrificans, and possibly in Thiobacillus novellus and Xanthobacter spp. The latter pathway is characteristic of the obligate chemolithotrophs (e.g. Thiobacillus tepidarius, T. neapolitanus, T. ferrooxidans, T. thiooxidans) and facultative species such as T. acidophilus and T. aquaesulis, all of which can produce or oxidize tetrathionate when grown on thiosulfate. The central problem, as yet incompletely resolved in all cases, is the enzymology of the conversion of sulfane-sulfur (as in the outer [S-] atom of thiosulfate [-S-SO3-]), or sulfur itself, to sulfate, and whether sulfite is involved as a free intermediate in this process in all, or only some, cases. The study of inorganic sulfur compound oxidation for energetic purposes in bacteria (i.e. chemolithotrophy and sulfur photolithotrophy) poses challenges for comparative biochemistry. It also provides evidence of convergent evolution among diverse bacterial groups to achieve the end of energy-yielding sulfur compound oxidation (to drive autotrophic growth on carbon dioxide) but using a variety of enzymological systems, which share some common features. Some new data are presented on the oxidation of 35S-thiosulfate, and on the effect of other anions (selenate, molybdate, tungstate, chromate, vanadate) on sulfur compound oxidation, including observations which relate to the roles of polythionates and elemental sulfur as intermediates.

Gram-Negative Aerobic Bacteria↗

PubMed2004

A comparison of the effects of carbon dioxide concentration and temperature on respiration, translocation and nitrate reduction in darkened soybean leaves.

BACKGROUND AND AIMS: Respiration of autotrophs is an important component of their carbon balance as well as the global carbon dioxide budget. How autotrophic respiration may respond to increasing carbon dioxide concentrations, [CO(2)], in the atmosphere remains uncertain. The existence of short-term responses of respiration rates of plant leaves to [CO(2)] is controversial. Short-term responses of respiration to temperature are not disputed. This work compared responses of dark respiration and two processes dependent on the energy and reductant supplied by dark respiration, translocation and nitrate reduction, to changes in [CO(2)] and temperature. METHODS: Mature soybean leaves were exposed for a single 8-h dark period to one of five combinations of air temperature and [CO(2)], and rates of respiration, translocation and nitrate reduction were determined for each treatment. KEY RESULTS: Low temperature and elevated [CO(2)] reduced rates of respiration, translocation and nitrate reduction, while increased temperature and low [CO(2)] increased rates of all three processes. A given change in the rate of respiration was accompanied by the same change in the rate of translocation or nitrate reduction, regardless of whether the altered respiration was caused by a change in temperature or by a change in [CO(2)]. CONCLUSIONS: These results make it highly unlikely that the observed responses of respiration rate to [CO(2)] were artefacts due to errors in the measurement of carbon dioxide exchange rates in this case, and indicate that elevated [CO(2)] at night can affect translocation and nitrate reduction through its effect on respiration.

Carbon Dioxide↗