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PubMed2001

Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria.

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.

Archaea↗

PubMed1977

Reversal of the neoplastic state in plants.

Crown-gall transformation involves the gradual and progressive activation of several biosynthetic capacities of the normal cell. These changes in cellular heredity, although extremely stable, are nonetheless potentially reversible and leave the cell totipotent. There is growing evidence that tumor-inducing principle is a self-replicating entity similar to a plasmid. Thus, it could be argued that tumor progression involves changes in the number or state of these entities in the cell. Studies of CDF habituation bear directly on this problem. Conversion of a cell division factor (CDF)-requiring normal cell to the CDF-autotrophic state is a key event in transformation. The fact that CDF habituation is progressive, occurs in the absence of agents of bacterial origin, and has an epigenetic basis indicates that it is not necessary to invoke either somatic mutation or the addition of foreign genes to account for tumor stability and progression in crown-gall. This conclusion provides further support for the hypothesis that, in the words of Braun,(78) "... the cancer problem is basically a problem of anomolous differentiation... Neoplastic growth, like developmental processes, stems from epigenetic modifications against a constant cellular genome."

Cell Differentiation↗

PubMed2006

Selective forces for the origin of the eukaryotic nucleus.

The origin of the eukaryotic cell nucleus and the selective forces that drove its evolution remain unknown and are a matter of controversy. Autogenous models state that both the nucleus and endoplasmic reticulum (ER) derived from the invagination of the plasma membrane, but most of them do not advance clear selective forces for this process. Alternative models proposing an endosymbiotic origin of the nucleus fail to provide a pathway fully compatible with our knowledge of cell biology. We propose here an evolutionary scenario that reconciles both an ancestral endosymbiotic origin of the eukaryotic nucleus (endosymbiosis of a methanogenic archaeon within a fermentative myxobacterium) with an autogenous generation of the contemporary nuclear membrane and ER from the bacterial membrane. We specifically state two selective forces that operated sequentially during its evolution: (1) metabolic compartmentation to avoid deleterious co-existence of anabolic (autotrophic synthesis by the methanogen) and catabolic (fermentation by the myxobacterium) pathways in the cell, and (2) avoidance of aberrant protein synthesis due to intron spreading in the ancient archaeal genome following mitochondrial acquisition and loss of methanogenesis.

Biological Evolution↗

PubMed1983

Biosynthetic mechanism of ribulose-1,5-bisphosphate carboxylase in the purple photosynthetic bacterium, Chromatium vinosum. III. Absence of extrachromosomal DNA.

Inducible formation of ribulose-1,5-bisphosphate (RuBP) carboxylase in the cells of Chromatium vinosum under autotrophic conditions was not affected by six different inhibitors of DNA synthesis. Photosynthetic CO2 fixation and RuBP carboxylase activities were not influenced by seven reagents known to eliminate plasmids. Plasmids were not detectable by agarose gel electrophoresis employing either the cleared lysate or alkaline sodium dodecyl sulfate method, nor were they detected by ethidium bromide-CsCl density gradient centrifugation. Overall experimental results tend to indicate that plasmids are absent in the Chromatium cells and that the induction of RuBP carboxylase is presumably not regulated in the DNA replication process.

Carboxy-Lyases↗

PubMed2005

Transparent exopolymeric particles' distribution in the northern Adriatic and their relation to microphytoplankton biomass and composition.

Transparent exopolymer particles (TEP) are generated during transformation processes within the non-living organic matter continuum in the seawater. Seasonal dynamics of TEP along the Po River Delta-Rovinj transect was followed during the 3-year period, using a spectrophotometric method of determination of TEP. Relationships between TEP and phytoplankton biomass (chlorophyll a), abundance and composition, as well as phaeophytin, were analysed. Microphytoplankton spring blooms are confirmed to be an important source of TEP, with some species more related to TEP concentration dynamics, such as Chaetoceros sp. and Skeletonema costatum. Notable spatial west to east gradient of autotrophic biomass and consequently of TEP was observed, as well as gradual decrease with depth. In addition, TEP concentration increments were observed up to 2 months before the mucilage events followed by the decrease of TEP concentration during the event itself. Pattern of TEP dynamics in the years with mucilage events was the most pronounced in 2002, when the event was spatially and temporally the most extended.

Biomass↗

PubMed2006

An examination of the carbon isotope effects associated with amino acid biosynthesis.

Stable carbon isotope ratios (delta(13)C) were determined for alanine, proline, phenylalanine, valine, leucine, isoleucine, aspartate (aspartic acid and asparagine), glutamate (glutamic acid and glutamine), lysine, serine, glycine, and threonine from metabolically diverse microorganisms. The microorganisms examined included fermenting bacteria, organotrophic, chemolithotrophic, phototrophic, methylotrophic, methanogenic, acetogenic, acetotrophic, and naturally occurring cryptoendolithic communities from the Dry Valleys of Antarctica. Here we demonstrated that reactions involved in amino acid biosynthesis can be used to distinguish amino acids formed by life from those formed by nonbiological processes. The unique patterns of delta(13)C imprinted by life on amino acids produced a biological bias. We also showed that, by applying discriminant function analysis to the delta(13)C value of a pool of amino acids formed by biological activity, it was possible to identify key aspects of intermediary carbon metabolism in the microbial world. In fact, microorganisms examined in this study could be placed within one of three metabolic groups: (1) heterotrophs that grow by oxidizing compounds containing three or more carbon-to-carbon bonds (fermenters and organotrophs), (2) autotrophs that grow by taking up carbon dioxide (chemolitotrophs and phototrophs), and (3) acetoclastic microbes that grow by assimilation of formaldehyde or acetate (methylotrophs, methanogens, acetogens, and acetotrophs). Furthermore, we demonstrated that cryptoendolithic communities from Antarctica grouped most closely with the autotrophs, which indicates that the dominant metabolic pathways in these communities are likely those utilized for CO(2 )fixation. We propose that this technique can be used to determine the dominant metabolic types in a community and reveal the overall flow of carbon in a complex ecosystem.

Amino Acids↗

PubMed2006

Feeding by larvae of intertidal invertebrates: assessing their position in pelagic food webs.

One of the leading determinants of the structure and dynamics of marine populations is the rate of arrival of new individuals to local sites. While physical transport processes play major roles in delivering larvae to the shore, these processes become most important after larvae have survived the perils of life in the plankton, where they usually suffer great mortality. The lack of information regarding larval feeding makes it difficult to assess the effects of food supply on larval survival, or the role larvae may play in nearshore food webs. Here, we examine the spectrum of food sizes and food types consumed by the larvae of two intertidal barnacle species and of the predatory gastropod Concholepas concholepas. We conducted replicated experiments in which larvae were exposed to the food size spectrum (phytoplankton, microprotozoan and autotrophic picoplankton) found in nearshore waters in central Chile. Results show that barnacle nauplii and gastropod veligers are omnivorous grazers, incorporating significant fractions of heterotrophs in their diets. In accordance with their feeding mechanisms and body size, barnacle nauplii were able to feed on autotrophic picoplankton (<5 microm) and did not consume the largest phytoplankton cells, which made the bulk of phytoplankton biomass in spring-summer blooms. Balanoid nauplii exhibited higher ingestion rates than the smaller-bodied chthamaloid larvae. Newly hatched C. concholepas larvae also consumed picoplankton cells, while competent larvae of this species ingested mostly the largest phytoplankton cells and heterotrophic protozoans. Results suggest that persistent changes in the structure of pelagic food webs can have important effects on the species-specific food availability for invertebrate larvae, which can result in large-scale differences in recruitment rates of a given species, and in the relative recruitment success of the different species that make up benthic communities.

Animals↗

PubMed1978

[Effect of growth conditions on the activity of the enzymes of cyclic 3':5'-AMP synthesis and decay in phototrophic bacteria].

Activity, ratio and summary content of cyclic AMP enzymes, adenylate cyclase and phosphodiesterase varied depending on growth conditions of phototrophic bacteria (Rhodospirillum rubrum and Rhodopseudomonas palustris). It suggests, that membrane-bound and soluble enzymes carry different functions. The increase of adenylate cyclase under chaning growth conditions was usually accompanied by the increase of phosphodiesterase. Sharp increase of both enzymes activity was observed when bacteria were growth in aerobic conditions. The activity of both enzymes in chromatophores was 2.8-fold higher when bacteria were grown in the light in anaerobic conditions, than in chromatophores of bacteria grown under stationary aerobic conditions in the light. It is suggested that 3':5' AMP can participate in autotrophic carbon assimilation or in the synthesis of pigments and other components of bacterial photosynthetizing apparatus. Substitution of NH4+ into NO3- and glutamate under the growing of R. rubrum in anaerobic conditions in the light resulted in the increase of the enzymes activities, which is the evidence of possible role of 3':5' AMP in mineral nitrogen uptake and nitrogen fixation. Glutamate concentration of 4 g/l stimulated the enzymes both in vivo and in vitro. The data obtained suggest that 3':5' AMP can carry multiple functions, participating in regulation of a number of metabolic processes in photorophic bacteria.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2004

Are picoplankton responsible for calcite precipitation in lakes?

Deposits of lacustrine calcite are important records of environmental changes. In order to interpret these archives, knowledge about the origin of the calcite is essential. It has been accepted that calcite precipitation can be induced by bacteria and algae. However, the detailed mechanisms are still unclear. This review summarizes what is known about the interactions between calcite precipitation and the autotrophic picoplankton. We consider findings from both field and laboratory studies. Field studies show that calcite precipitation in oligotrophic lakes is strongly linked with picocyanobacteria blooms. Laboratory experiments led to the formulation of the mechanism of precipitation induced by microalga. Experiments also showed that precipitation induced by picocyanobacteria is influenced by various factors including the uptake of inorganic carbon and the structure of the cell walls. Recent studies indicate that the influence of environmental conditions like the composition of lake water has to be taken into account as well. We conclude that in situ observations of precipitation processes at picoplankton cells under controlled conditions are needed to improve our understanding of mineral bacteria interaction.

Calcium Carbonate↗

PubMed1998

Clinorotation affects mesophyll photosynthetic cells in leaves of pea seedlings.

Experiments with autotrophs in altered gravity condition have a grate significant for development of space biology. The main results of investigation in the photosynthetic apparatus state under microgravity condition have based on the experiments with maturity plants and their differentiated cells. The structural and functional organization of photosynthetic cells in seedlings is poor understandable still. Along with chloroplasts preserving a native membrane system in palisade parenchyma cells of the 29-day pea plant leaves in microgravity, chloroplasts with fribly packed or damaged granae, whose thylakoids appeared as vesicles with an electrontransparent content, were also observed. The investigation of preceding process induced these effects have a sense. That is why, the goal of our experiments was to perform the study of a structural organization of the photosynthetic cells of 3-d pair of pea seedlings leaves under the influence of clinorotation.

Chlorophyll↗

PubMed2003

Characterisation of aerobic bio treatment of meat plant effluent.

Primary treated meat processing plant effluent was characterised for the calibration of the ASM 2 model. The total COD of the wastewater was 500-2,000 mg L(-1). The wastewater contained 15-18% of RBCOD. RBCOD of the meat processing wastewater was from short chain fatty acids (SCFA). Acetic and iso-valeric acids contributed 50% of the total SCFA COD. The inert soluble and particulate COD fractions were each 4%. The COD exerted by carbohydrate was 5% of the total COD. Fat and protein contributed 51% and 44% of the total COD of the wastewater respectively. The average concentrations of ammonia, total phosphorus, total suspended solids and alkalinity were 75 mg L(-1), 34 mg L(-1), 450 mg L(-1) and 275 mg L(-1) CaCO3 respectively. Maximum specific growth rates of heterotrophs and autotrophs were between 1.2-2.5 day(-1) and 0.65-0.8 day(-1). The heterotrophs yield coefficient was 0.63 on a COD basis.

Bacteria, Aerobic↗

PubMed1996

hyp gene products in Alcaligenes eutrophus are part of a hydrogenase-maturation system.

In Alcaligenes eutrophus H16 the hyp gene complex consists of six open reading frames hypA1, B1, F1, C, D and E whose products are involved in maturation of the two NiFe hydrogenases: an NAD-reducing cytoplasmic enzyme (SH) and a membrane-bound electron-transport-coupled protein (MBH). hypB1 and hypF1 were originally considered to form a single open reading frame designated hypB [Dernedde, J., Eitinger, M. & Friedrich, B. (1993) Arch. Microbiol. 159, 545-553]. Re-examination of the relevant sequence identified hypB1 and hypF1 as two distinct genes. Non-polar in-frame deletions in the individual hyp genes were constructed in vitro and transferred via gene replacement to the wild-type strain. The resulting mutants fall into two classes. Deletions in hypC, D and E (class I) gave a clear negative phenotype, while hypA1, B1 and F1 deletion mutants (class II) were not impaired in hydrogen metabolism. Class I mutants were unable to grow on hydrogen under autotrophic conditions. The enzymatic activities of SH and MBH were disrupted in all three class I mutants. Immunoblot analysis showed the presence of the H2-activating SH subunit (HoxH) at levels comparable to those observed in the wild-type strain whereas the other three subunits (HoxF, U and Y) were only detectable in trace amounts, probably due to proteolytic degradation. Likewise, MBH was less stable in hypC, D and E deletion mutants and was not attached to the cytoplasmic membrane. In the wild-type strain, HoxH and the MBH large subunit (HoxG) undergo C-terminal proteolytic processing before attaining enzymatic activity. In class I mutants this maturation was blocked. 63Ni-incorporation experiments identified both hydrogenases as nickel-free apoproteins in these mutants. Although class II mutants bearing deletions in hypA1, B1 and F1 showed no alteration of the wild-type phenotype, a role for these genes in the incorporation of nickel and hence hydrogenase maturation cannot be excluded, since there is experimental evidence that this set of genes is duplicated in A. eutrophus.

Alcaligenes↗

PubMed2002

Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers.

Increased awareness of the metabolic diversity within autotrophic nitrifying bacteria has led to a re-evaluation of their role in the cycling of nitrogen in terrestrial and aquatic ecosystems. This has been accompanied by improvements in our ability to characterise natural populations of autotrophic ammonia oxidising bacteria through the application of molecular techniques. Molecular approaches indicate considerable diversity within natural populations and the association of different groups of ammonia oxidisers with different environments and changes in populations in response to environmental factors. To some extent, results from molecular approaches are consistent with those adopting laboratory enrichment and isolation strategies. Physiological studies on the latter demonstrate links between phylogenetic groups and possession of characteristics of relevance to ecological studies. Understanding of the significance of ammonia oxidiser species and functional diversity for global cycling of nitrogen require greater links between molecular analyses, physiological studies and measurements of nitrogen cycling processes. However, there is increasing evidence for physiological properties driving the environmental distribution of particular groups of ammonia oxidisers and for associations between nitrification process rates and ammonia oxidiser community structure.

Bacterial Typing Techniques↗

PubMed2003

Calorimetric assessment of activity in WWTP biomass.

A heat flux bench-scale calorimeter (Bio-RC1) has been used to assess the metabolic activity of microbial populations involved in wastewater treatment biological processes under aerobic, anoxic and anaerobic conditions. Under strictly aerobic conditions, a linear correlation was observed between oxygen uptake rate and heat flux for heterotrophic and nitrifying bacterial populations. Using the same calorimetric approach and the same apparatus, toxicity and biodegradability of a pesticides factory wastewater were investigated. The activity of heterotrophic and nitrifying aerobic communities was monitored considering both oxygen consumption and heat dissipation, whereas, under anoxic conditions, calorimetric data were compared to the traditional NUR (nitrate uptake rate) test. Heterotrophic activity was found to be 52% inhibited after toxic wastewater exposure under both aerobic and anoxic conditions and 30% inhibition was observed on autotrophic ammonia oxidation. Additionally, calorimetric measurements have been successfully applied to investigate anaerobic digestion. The thermal response of a mesophilic granular sludge to repetitive glucose pulses has been evaluated and a toxicity test has been performed by exposing the biomass to increasing concentrations of formaldehyde.

Ammonia↗

PubMedDate not supplied

Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis.

Methanococcus jannaschii is an autotrophic hyperthermophilic archaeon isolated from an oceanic hydrothermal vent. Its primary pathway for energy production is methanogenesis from H2 and CO2. High-throughput Multidimensional Protein Identification Technology based on microcapillary LC/LC/ MS/MS was used to investigate the proteome of M. jannaschii and the methanogenesis pathway in cells grown in complex medium with high H2 supply. A total of 963 proteins have been unambiguously identified. The identified proteins represent approximately 54% of the whole genome of M. jannaschii. About 44% of the identified proteins are either conserved hypothetical or hypothetical proteins. We identified 83-95% of the proteins predicted to be involved in amino acid biosynthesis, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, transcription, and purine, pyridine, nucleoside, and nucleotide synthesis. Over 40% of these proteins have better than 50% sequence coverage. Approximately 90% of the predicted methanogenesis proteins were detected. In contrast, only 27-37% of predicted hypothetical proteins, proteins involved in transport and binding, and proteins with regulatory functions were identified. High peptide number, spectrum count, and sequence coverage have been used as indicators of high expression levels and are in good agreement with codon bias analysis. Predicted intein peptides were detected in MJ1043 (DNA-directed RNA polymerase, subunit A"), MJ0542 (phosphoenolpyruvate synthase), MJ0782 (transcription initiation factor IIB), and MJ1422 (putative replication factor C subunit). New peptides created by protein splicing were detected in MJ0885 (DNA dependent DNA polymerase), MJ0542, and MJ0782. The methanogenesis pathway and the enzymes involved are also discussed.

Amino Acid Sequence↗

PubMedDate not supplied

[Biogeochemical processes of methane cycle in the soils, swamps and lakes of Western Siberia].

The biogeochemical processes of methane production and oxidation were studied in the upper horizons of tundra and taiga soils and of raised bogs and lake bottom sediments nearby the Tarkosalinsk gas field in western Siberia. Both in dry and water-logged soils, the total methane concentration (in soil particles and gaseous phase) was an order of magnitude higher than in the soil gaseous phase alone (22 and 1.1 nl/cm3, respectively). In bogs and lake bottom sediments, methane concentration was as high as 11 microliters/cm3. Acetate was the major precursor of the newly formed methane. The rate of aceticlastic methanogenesis reached 55 ng C/(cm3 day), whereas that of autotrophic methanogenesis was an order of magnitude lower. The most active methane production and oxidation were observed in bogs and lake sediments where the delta 13C values of CO2 were inversely related to the intensity of bacterial methane oxidation. Methane diffusing from bogs and lake bottom sediments showed delta 13C values ranging from -78 to -47@1000, whereas the delta 13C value of carbon dioxide ranged from -18 to -6@1000. In these ecosystems, methane emission comprised from 3 to 206 mg CH4/(m2 day). Conversely, the dry and water-logged soils of tundra and taiga took up atmospheric methane at a rate varying from 0.3 to 5.3 mg CH4/(m2 day). Methane consumption in soils was of biological rather than of adsorptive nature. This was confirmed by the radioisotopic method and chamber experiments, in which weighting of methane carbon was observed (the delta 13C value changed from -51 to -41@1000).

Bacteria↗

PubMed2005

Impact of different in vitro electron donor/acceptor conditions on potential chemolithoautotrophic communities from marine pelagic redoxclines.

Anaerobic or microaerophilic chemolithoautotrophic bacteria have been considered to be responsible for CO2 dark fixation in different pelagic redoxclines worldwide, but their involvement in redox processes is still not fully resolved. We investigated the impact of 17 different electron donor/acceptor combinations in water of pelagic redoxclines from the central Baltic Sea on the stimulation of bacterial CO2 dark fixation as well as on the development of chemolithoautotrophic populations. In situ, the highest CO2 dark fixation rates, ranging from 0.7 to 1.4 micromol liter(-1) day(-1), were measured directly below the redoxcline. In enrichment experiments, chemolithoautotrophic CO2 dark fixation was maximally stimulated by the addition of thiosulfate, reaching values of up to 9.7 micromol liter(-1) CO2 day(-1). Chemolithoautotrophic nitrate reduction proved to be an important process, with rates of up to 33.5 micromol liter(-1) NO3(-) day(-1). Reduction of Fe(III) or Mn(IV) was not detected; nevertheless, the presence of these potential electron acceptors influenced the development of stimulated microbial assemblages. Potential chemolithoautotrophic bacteria in the enrichment experiments were displayed on 16S ribosomal complementary DNA single-strand-conformation polymorphism fingerprints and identified by sequencing of excised bands. Sequences were closely related to chemolithoautotrophic Thiomicrospira psychrophila and Maorithyas hadalis gill symbiont (both Gammaproteobacteria) and to an uncultured nitrate-reducing Helicobacteraceae bacterium (Epsilonproteobacteria). Our data indicate that this Helicobacteraceae bacterium could be of general importance or even a key organism for autotrophic nitrate reduction in pelagic redoxclines.

Carbon Dioxide↗

PubMed2001

Autotrophic ammonia oxidation at low pH through urea hydrolysis.

Ammonia oxidation in laboratory liquid batch cultures of autotrophic ammonia oxidizers rarely occurs at pH values less than 7, due to ionization of ammonia and the requirement for ammonium transport rather than diffusion of ammonia. Nevertheless, there is strong evidence for autotrophic nitrification in acid soils, which may be carried out by ammonia oxidizers capable of using urea as a source of ammonia. To determine the mechanism of urea-linked ammonia oxidation, a ureolytic autotrophic ammonia oxidizer, Nitrosospira sp. strain NPAV, was grown in liquid batch culture at a range of pH values with either ammonium or urea as the sole nitrogen source. Growth and nitrite production from ammonium did not occur at pH values below 7. Growth on urea occurred at pH values in the range 4 to 7.5 but ceased when urea hydrolysis was complete, even though ammonia, released during urea hydrolysis, remained in the medium. The results support a mechanism whereby urea enters the cells by diffusion and intracellular urea hydrolysis and ammonia oxidation occur independently of extracellular pH in the range 4 to 7.5. A proportion of the ammonia produced during this process diffuses from the cell and is not subsequently available for growth if the extracellular pH is less than 7. Ureolysis therefore provides a mechanism for nitrification in acid soils, but a proportion of the ammonium produced is likely to be released from the cell and may be used by other soil organisms.

Ammonia↗