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PubMed2006

Ancient genes in contemporary persistent microbial pathogens.

Autotrophs, the earliest prokaryotes, use CO(2) as the sole or the key source in the reductive citric acid cycle for carbon fixation. This pathway, also known as the reductive tricarboxylic acid (rTCA) cycle, has as its center the Krebs cycle running in the reductive direction, using reduced cofactors for energy. During the infection process, persistent pathogenic bacteria like Mycobacterium tuberculosis, Helicobacter pylori, and Salmonella typhi experience diverse and hostile environments both intracellularly (in macrophages) and extracellularly. M. tuberculosis, for example, must adapt to nutrient-deprived, hypoxic conditions in the granuloma. Genomic annotations reveal the presence of the key enzymes of the rTCA cycle--citrate lyase (Enzyme Commission number EC 4.1.3.6) and 2-oxoglutarate synthase (EC 1.2.7.3)--along with the rest of the TCA cycle enzymes. It is possible that there is a metabolic switch to anaerobic respiration in which a complete or a partial TCA cycle may operate in the reductive mode. This switch would both facilitate carbon fixation and restore the balance of oxidative and reductive reactions during environmental transitions, thus enabling the pathogen to survive, grow, and persist. Verification of enzyme function by biochemical investigations and validation of gene essentiality by knockout studies may reveal these enzymes to be rational drug targets for treatment of persistent microbial infections in mechanism-based drug discovery processes.

Archaea↗

PubMed2005

Phytochrome evolution in green and nongreen plants.

Photoreceptors are critical molecules that function at the interface between organism and environment. Plants use specific light signals to determine their place in time and space, allowing them to synchronize their growth, metabolism, and development to the environments in which they occur. Thus, innovation in light sensing mechanisms is expected to coincide with adaptation and diversification. Three studies involving the well-characterized phytochrome photoreceptor system in plants indicate that much work is yet needed to test this expectation. In early diverging flowering plants, episodic positive selection influenced the evolution of phytochrome A, but little of the functional data needed to link molecular adaptation with a change in gene function are available. In the model plant Arabidopsis thaliana, known functional differences between a recently duplicated gene pair remain difficult to characterize at the sequence level. In parasitic plants, patterns of development that in autotrophs are under the control of light signals are highly modified, suggesting that phytochromes and other photoreceptors function differently in nonphotosynthetic plants. Analyses of phytochrome A coding sequences indicate that they are evolving under relaxed constraints in nonphotosynthetic Orobanchaceae, consistent with the expectation of functional change. Further work is needed to determine which of the processes mediated by phyA may have been altered, a line of investigation that may improve our understanding of divergence points in downstream signaling pathways.

Arabidopsis↗

PubMed2001

The effects of the flow pattern on organic oxidation and nitrification in aerated submerged biofilters.

Previous research has shown that a submerged biofilter is effective in removing organic matter and total organic nitrogen. Upflow and downflow biofilters were set up to investigate the different oxidative efficiencies on organic matter and ammonia nitrogen of different biofilter positions and to compare the biological activities of the upflow and downflow patterns. A comparison of the operational characteristics of the two types of biofilters is discussed. The main COD removal zone is 0-20 cm in the upflow biofilter, but in the downflow biofilter it occurs in the submerged zone. The nitrification process is dependent on the HRT and the residual COD. In the downflow biofilter, the efficiency of the nitrification increases with the HRT. The growth of nitrifying bacteria has a tendency to take place in higher zones in the downflow biofilter, especially for a longer HRT. Batch tests measured the biological activity of heterotrophs and nitrifying autotrophs with decomposition rates. In the upflow biofilter, the nitrification rates increased while the COD oxidative rates decreased with the height of the biofilter, so the effect of the HRT on the activity of the nitrifying autotrophs is significant. However, in the down biofilter, the activity of the nitrifying autotrophs was similar at different heights in the same HRT runs with the maximum nitrifying autotrophs activity being at an HRT of 6 hours.

Bacteria↗

PubMed1997

Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11.

The dissociation of the soluble NAD-reducing hydrogenase of Rhodococcus opacus MR11 into two dimeric proteins with different catalytic activities and cofactor composition is unique among the NAD-reducing hydrogenases studied so far. The genes of the soluble hydrogenase were localized on a 7.4 kbp Asnl fragment of the linear plasmid pHG201 via heterologous hybridization. Analysis of the nucleotide sequence of this fragment revealed the seven open reading frames ORF1, hoxF, -U, -Y, -H, -W and ORF7. The six latter ORFs belong to the gene cluster of the soluble hydrogenase. Their gene products are highly homologous to those of the NAD-reducing enzyme of Alcaligenes eutrophus H16. The genes hoxF, -U, -Y and -H encode the subunits alpha, gamma, delta and beta, respectively. The gene hoxW encodes a putative protease, which may be essential for C-terminal processing of the beta subunit. Finally, ORF7 encodes a protein which has similarities to cAMP- and cGMP-binding protein kinases, but its function is not known. ORF1, which lies upstream of the hydrogenase gene cluster, encodes a putative transposase found in IS elements of other bacteria. Northern hybridizations and primer extensions using total RNA of autotrophically and heterotrophically grown cells of R. opacus MR11 indicated that the hydrogenase genes are under control of a delta 70-like promoter located at the right end of ORF1 and are even transcribed under heterotrophic conditions at a low level. Furthermore, this promoter was shown to be active in the recombinant Escherichia coli strain LHY1 harbouring the 7.4 kbp Asnl fragment, resulting in overexpression of the hydrogenase genes. Although all four subunits of the soluble hydrogenase were shown via Western immunoblots to be synthesized in E. coli, no active enzyme was detectable.

Amino Acid Sequence↗

PubMed2006

Nitrogen dynamics in an Australian semiarid grassland soil.

We conducted a four-week laboratory incubation of soil from a Themeda triandra Forsskal grassland to clarify mechanisms of nitrogen (N) cycling processes in relation to carbon (C) and N availability in a hot, semiarid environment. Variation in soil C and N availability was achieved by collecting soil from either under tussocks or the bare soil between tussocks, and by amending soil with Themeda litter. We measured N cycling by monitoring: dissolved organic nitrogen (DON), ammonium (NH4+), and nitrate (NO3-) contents, gross rates of N mineralization and microbial re-mineralization, NH4+ and NO3- immobilization, and autotrophic and heterotrophic nitrification. We monitored C availability by measuring cumulative soil respiration and dissolved organic C (DOC). Litter-amended soil had cumulative respiration that was eightfold greater than non-amended soil (2000 compared with 250 microg C/g soil) and almost twice the DOC content (54 compared with 28 microg C/g soil). However, litter-amended soils had only half as much DON accumulation as non-amended soils (9 compared with 17 microg N/g soil) and lower gross N rates (1-4 compared with 13-26 microg N x [g soil](-1) x d(-1)) and NO3- accumulation (0.5 compared with 22 microg N/g soil). Unamended soil from under tussocks had almost twice the soil respiration as soil from between tussocks (300 compared with 175 microg C/g soil), and greater DOC content (33 compared with 24 microg C/g soil). However, unamended soil from under tussocks had lower gross N rates (3-20 compared with 17-31 microg N x [g soil](-1) d(-1)) and NO3- accumulation (18 compared with 25 microg N/g soil) relative to soil from between tussocks. We conclude that N cycling in this grassland is mediated by both C and N limitations that arise from the patchiness of tussocks and seasonal variability in Themeda litterfall. Heterotrophic nitrification rate explained >50% of total nitrification, but this percentage was not affected by proximity to tussocks or litter amendment. A conceptual model that considers DON as central to N cycling processes provided a useful initial framework to explain results of our study. However, to fully explain N cycling in this semiarid grassland soil, the production of NO3- from organic N sources must be included in this model.

Carbon↗

PubMed1996

Metabolite channeling in the origin of life.

A central question in the origin of life concerns whether primitive metabolites and catalysts interacted randomly in solution, as often envisaged, or whether they were arranged from the start in ordered metabolic complexes. The latter possibility would be consistent with the hypothesis of metabolite channeling in extant cells, which holds that intermediates in many pathways are transferred directly, without diffusion, between pathway enzymes. A model on this basis is proposed in which life originated autotrophically de novo in metabolic complexes organized on FeS2 (pyrite) mineral surfaces. Because metabolites and catalysts arose at specific sites in these complexes, they could interact specifically with neighbouring species in evolving pathways prior to the existence of protein enzymes with precise substrate binding sites. In successive stages, RNA catalysts and protein enzymes could be incorporated in these arrays. The overall process may be viewed as a molecular analogue of embryonic development, with the formation and positioning of each new component continuously transforming the whole. A corollary of the hypothesis relates to the evolution of translation and the genetic code. By virtue of channeling, biosynthetically related amino acids (e.g., aspartic acid and threonine) would have arisen close together in the complex. A second premise is that tRNAs with similar base sequences, and thus similar anticodons, were also clustered together in the complex and channeled to adjacent sites. As a result of these combined effects, tRNAs with similar anticodons would necessarily have been positioned close to, and thus more likely to have been charged with, metabolically related amino acids. This mechanism affords a new rationale for the observed codon structure of the genetic code, in which biosynthetically related amino acids possess similar codons.

Animals↗

PubMed2003

A simplified method to assess structurally identifiable parameters in Monod-based activated sludge models.

The first step in the estimation of parameters of models applied for data interpretation should always be an investigation of the identifiability of the model parameters. In this study the structural identifiability of the model parameters of Monod-based activated sludge models (ASM) was studied. In an illustrative example it was assumed that respirometric (dissolved oxygen or oxygen uptake rates) and titrimetric (cumulative proton production) measurements were available for the characterisation of nitrification. Two model structures, including the presence and absence of significant growth for description of long- and short-term experiments, respectively, were considered. The structural identifiability was studied via the series expansion methods. It was proven that the autotrophic yield becomes uniquely identifiable when combined respirometric and titrimetric data are assumed for the characterisation of nitrification. The most remarkable result of the study was, however, that the identifiability results could be generalised by applying a set of ASM1 matrix based generalisation rules. It appeared that the identifiable parameter combinations could be predicted directly based on the knowledge of the process model under study (in ASM1-like matrix representation), the measured variables and the biodegradable substrate considered. This generalisation reduces the time-consuming task of deriving the structurally identifiable model parameters significantly and helps the user to obtain these directly without the necessity to go too deeply into the mathematical background of structural identifiability.

Bacteria↗

PubMed2002

Oxygen-limited nitrification and denitrification in a lab-scale rotating biological contactor.

Rotating Biological Contactors (RBC) treating highly nitrogenous wastewaters are known to give rise to nitrogen losses, generally assumed to be due to concomitant nitrification and denitrification. In this study, a lab-scale nitrifying RBC reactor was shown to bring about losses of nitrogen of the order of 10 to 20% at ammonium loading rates of up to 2129 mg N m(-2) d(-1), when no extra carbon source was added. These higher removal values could be due to Oxygen-Limited Autotrophic Nitrification and Denitrification (OLAND), because the reactor was operated at oxygen limitation. When methanol was added as a soluble organic carbon source to further diminish oxygen transfer into the deeper parts of the biofilm, the RBC achieved 84% nitrogen removal (loading rate 2300 mg N m(-2) d(-1)) at a COD/N ratio of 3.1. The latter also suggests that the process was occurring parallel to conventional denitrification.

Bioreactors↗

PubMed2002

Oxygen-limited nitrogen removal in a lab-scale rotating biological contactor treating an ammonium-rich wastewater.

A lab-scale Rotating Biological Contactor (RBC) was operated with the purpose of oxygen-limited (autotrophic) nitrification-denitrification of an ammonium-rich synthetic wastewater without Chemical Oxygen Demand (COD). Based on the field observations that RBCs receiving anaerobic effluents come to anoxic ammonium removal, the RBC was inoculated with methanogenic sludge. Some 100 days after the addition of the anaerobic sludge to the reactor as a possible means of a rapid initiation of the nitrogen (N) removal process, a maximum ammonium removal of 1,550 mg N m(-2) d(-1) was achieved. Batch tests with 15N labeled ammonium and nitrite indicated that a large part of that N was removed via oxygen-limited oxidation of ammonium with nitrite as the electron acceptor. The other part was removed via conventional denitrification, presumably with COD released from lysis of cells. Species identification of the most abundant microorganisms revealed that Nitrosomonas spp. were the dominant ammonium-oxidizers in the sludge. Thus far, the molecular characterization of the sludge could not show the presence of Planctomycetes among the most dominant species. Overall this experiment confirms the property of the RBC system to remove ammonium to nitrogen gas without the use of heterotrophic carbon source.

Bacteria, Anaerobic↗

PubMed1998

Polyunsaturated membranes are required for photosynthetic competence in a mutant of Arabidopsis.

High levels of polyunsaturation are characteristic of all the membranes of plant and animal cells. For example, the chloroplasts of leaf cells contain about 75-80% polyunsaturated fatty acids. For the extra-chloroplast membranes in leaf cells and the membranes of non-photosynthetic tissues, values of 60-65% are typical. We report here the production of Arabidopsis double mutants that contain negligible levels of polyunsaturated fatty acids. The mutants were not capable of autotrophic growth and produced extremely chlorotic cotyledons and leaves. However, on sucrose media, the double mutants were robust plants showing strong leaf and root development. These observations indicate that the vast majority of receptor-mediated and transport-related membrane functions required to sustain the organism and induce proper development are adequately supported in the absence of polyunsaturated lipids. By contrast, photosynthesis is one process that does require high levels of membrane polyunsaturation.

Arabidopsis↗

PubMed2004

EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts.

When we think of extremophiles, organisms adapted to extreme environments, prokaryotes come to mind first. However, the unicellular red micro-alga Galdieria sulphuraria (Cyanidiales) is a eukaryote that can represent up to 90% of the biomass in extreme habitats such as hot sulfur springs with pH values of 0-4 and temperatures of up to 56 degrees C. This red alga thrives autotrophically as well as heterotrophically on more than 50 different carbon sources, including a number of rare sugars and sugar alcohols. This biochemical versatility suggests a large repertoire of metabolic enzymes, rivaled by few organisms and a potentially rich source of thermo-stable enzymes for biotechnology. The temperatures under which this organism carries out photosynthesis are at the high end of the range for this process, making G. sulphuraria a valuable model for physical studies on the photosynthetic apparatus. In addition, the gene sequences of this living fossil reveal much about the evolution of modern eukaryotes. Finally, the alga tolerates high concentrations of toxic metal ions such as cadmium, mercury, aluminum, and nickel, suggesting potential application in bioremediation. To begin to explore the unique biology of G. sulphuraria , 5270 expressed sequence tags from two different cDNA libraries have been sequenced and annotated. Particular emphasis has been placed on the reconstruction of metabolic pathways present in this organism. For example, we provide evidence for (i) a complete pathway for lipid A biosynthesis; (ii) export of triose-phosphates from rhodoplasts; (iii) and absence of eukaryotic hexokinases. Sequence data and additional information are available at http://genomics.msu.edu/galdieria.

Algal Proteins↗

PubMed2006

Effects of shallow-water hydrothermal venting on biological communities of coastal marine ecosystems of the western Pacific.

This review is based on integrated studies of the composition, structure and function of shallow-water ecosystems in the western Pacific that are influenced by underwater gas-hydrothermal activity. Most of the data were collected from 1985 to 1997 by the Institute of Marine Biology of the Far East Branch of the Russian Academy of Science during expeditions to zones of modern volcanism. Gas-hydrothermal activity of volcanoes has a great influence on the physicochemical characteristics of the water column and plankton, and of bottom sediment and benthic communities. The abundance of nutrients (SiO(3)(2-), PO(4)(3-), NO(3)(-)), gases (CO(2), CH(4), H(2), H(2)S) and other reduced compounds (C(n)H(n), S(0), S(2)O(3)(2-), NH(4)(+)) in zones of shallow-water hydrothermal vents provides conditions for the use of two energy sources for primary production: sunlight (photosynthesis) and the oxidation of reduced compounds (bacterial chemosynthesis). In areas of shallow-water volcanic activity, chemosynthesis occurs not only in the immediate vicinity of venting fluid release but also in the surface layer of the water column, where it occurs together with intense photosynthesis. This surface photosynthesis is found below the layer of chemosynthesis, which is related to the distribution of hydrothermal fluids at the water surface. The contribution of each of these processes to total primary production depends on the physical and chemical conditions created by the vents and on the range and adaptation potential of the organisms. On the seabed in zones of shallow-water venting, microorganisms form mats that consist of bacteria of various physiological groups, microalgae, the products of their metabolism and sedimentary particles. Oxygenic photosynthesis of benthic diatoms, bacterial photosynthesis (anoxygenic photosynthesis) and autotrophic chemosynthesis in algobacterial and bacterial mats generate organic matter additional to that produced in the water column. The high rates of primary production, abundance of organic matter in the water column and intense development of benthic microflora ensure the formation of an abundant benthic fauna. In Kraternaya Bight, Matupi Harbour and Bay of Plenty, the macrozoobenthos has low species diversity. The taxonomic composition of the populations is determined by geographical region (temperate or tropical), by the character of the seabed (hard or soft bottoms, rigid lava flows or hydrothermal structures), by the temperature of bottom sediments and of volcanic fluids and lastly by the chemical composition of the vent fluid (sulfide or nonsulfide). In most of the surveyed areas the fauna is derived from locally common species or from opportunistic species that can form high-density populations in eutrophic waters. The benthic communities of shallow-water venting areas have many characteristics in common with communities subject to anthropogenic impact (thermal, residential or industrial) or to changes resulting from a sharp deterioration of the marine environment. In contrast to the fauna of deeper water hydrothermal communities (i.e., those that exist below 200 m), shallow-water venting communities lack obligate hydrothermal species. The structure and function of the pelagic and benthic communities in areas of shallow-water venting can be regarded as transitional between those of deep-water vent communities and the normal communities of the coast.

Animals↗

PubMed2005

Localized hormone fluxes and early haustorium development in the hemiparasitic plant Triphysaria versicolor.

Perhaps the most obvious phenotypes associated with chemical signaling between plants are manifested by parasitic species of Orobanchaceae. The development of haustoria, invasive root structures that allow hemiparasitic plants to transition from autotrophic to heterotrophic growth, is rapid, highly synchronous, and readily observed in vitro. Haustorium development is initiated in aseptic roots of the facultative parasite Triphysaria versicolor when exposed to phenolic molecules associated with host root exudates and rhizosphere bioactivity. Morphological features of early haustorium ontogeny include rapid cessation of root elongation, expansion, and differentiation of epidermal cells into haustorial hairs, and cortical cell expansion. These developmental processes were stimulated in aseptic T. versicolor seedlings by the application of exogenous phytohormones and inhibited by the application of hormone antagonists. Surgically dissected root tips formed haustoria if the root was exposed to haustorial-inducing factors prior to dissection. In contrast, root tips that were dissected prior to inducing-factor treatment were unable to form haustoria unless supplemented with indole-3-acetic acid. A transient transformation assay demonstrated that auxin and ethylene-responsive promoters were up-regulated when T. versicolor was exposed to either exogenous hormones or purified haustoria-inducing factors. These experiments demonstrate that localized auxin and ethylene accumulation are early events in haustorium development and that parasitic plants recruit established plant developmental mechanisms to realize parasite-specific functions.

Arabidopsis↗

PubMed2001

Odour removal with a trickling filter at a small WWTP strongly influenced by the tourism season.

Etaples-Le Touquet's wastewater treatment plant (WWTP) is based on a coastal area of the Artois-Picardie region. The pollution load can vary from 20,000 p.e. to 60,000 p.e. over a weekend or in summer. The Collectivity and the Water Agency decided to cover and ventilate the main odour source points of the plant. The foul air was directed to a 2,500 m3/h inorganic bed biofilter (Alizair) for odour control. An odour monitoring took place during the first year of operation taking into account cold and warm seasons, high and low tourism seasons. The Alizair biofilter appeared an appropriate odour control process for small sized wastewater treatment plants, easy to operate and efficient even in areas where tourism seasons have a great impact on the pollution load arriving at the plant. The neighbourhood did not complain about odours any more and the operator was very confident with such a simple and effective system. The local Authorities and the Water Agency agreed to recommend Alizair biofilters with an autotrophic biomass adapted in the case of an old WWTP that cannot be up graded any more or for large pumping stations and wastewater storage prior treatment.

Bacteria↗

PubMed2002

Denitrification of groundwater with elemental sulfur.

Autotrophic denitrification was studied in laboratory columns packed with granular elemental sulfur only and operated in an upflow mode. Soluble inorganic carbon, sodium bicarbonate, was supplied as source of carbon for microbial growth. Denitrification rates of up to 0.20 kg N removed m(-3) d(-1) were obtained at a hydraulic retention time of I h, and a nitrate loading of 0.24 kg N m(-3) d(-1). The process is extremely simple, stable and easy to maintain.

Biodegradation, Environmental↗

PubMed2005

Feasibility of using ultrasonic irradiation to recover active biomass from waste activated sludge.

Under typical operating conditions, the microbial fraction of activated sludge flocs is approximately 40% by weight. The objective of this research is to evaluate the feasibility of using ultrasonic irradiation to disrupt activated sludge flocs allowing for the subsequent separation of active and inactive fractions. If separation of floc components is possible, then methods may be incorporated into wastewater treatment plant operations whereby only the inactive fraction of floc is wasted (i.e., of waste activated sludge, WAS), which in turn could increase the overall effective biological solids retention time, leading to increased process robustness with no net increase in reactor size. The results indicate that ultrasonic irradiation of WAS at 800 Wl(-1) followed by 30 min of settling can produce a supernatant with heterotrophic specific oxygen uptake rates (SOURs) of over two times the SOUR measured in the bulk mixed liquor. Under these conditions 26% of the initial heterotrophic activity was recovered within only 11% of the initial volatile mass. Similarly, autotrophic analysis revealed that nitrifying organisms, while sensitive to the effects of ultrasonic irradiation, can be separated from the activated sludge floc and recovered. An irradiation density of 200 Wl(-1) with an exposure time between 1 and 2 min produced a supernatant with a specific ammonia removal rate of over two times the initial mixed liquor rate.

Bacteria↗

PubMedDate not supplied

[Morphogenesis and the fine structure of Stibiobacter senarmontii].

The morphogenesis and fine structure of Stibiobacter senarmontii were studied during its cultivation in the autotrophic conditions of growth in a mineral medium as well as in a medium containing yeast extract. The morphology of the organism was shown to be variable. A young culture was represented mainly by rods with three flagella. Coccoid, club-shaped and branching forms were observed during aging of the culture. The cells multiplied by irregular division and by breaking along the partition of the parent cell. The latter process yielded cell aggregates looking like rings and hieroglyphs. Electronograms revealed a complex membrane apparatus, polyribosomes, large electron-transparent inclusions, and unknown electron-dense inclusions in the nuclear zone. The cell wall looked on cross-sections as a three-layer structure. The assignment of St. senarmontii to Gram-positive bacteria is discussed. The morphogenesis of this organism suggests that it is related to the coryneform group of bacteria.

Bacteria↗

PubMed1992

The initiation of biological processes on Earth: summary of empirical evidence.

With the currently available geological record at band, the existence of life on this planet as from at least 3.8 Gyr ago seems so firmly established as to be virtually unassailable. Specifically, various disparate lines of evidence have merged to indicate (1) that the surface of the Archaean Earth had hosted prolific microbial ecosystems as is testified by a quasi-continuous record of microbialites ("stromatolites") and associated microfossils of prokaryotic affinity over 3.5, if not 3.8 Gyr of geological history, and (2) that the sedimentary carbon record has preserved the isotopic signature of autotrophic (notably photosynthetic) carbon fixation over the same time span. With the observed enrichment of isotopically light carbon in sedimentary organic matter largely consonant with the bias in favor of 12C during photosynthesis, the mainstream of the carbon isotope record can be best explained as geochemical manifestation of the isotope discriminating properties of the ribulose-1,5-bisphosphate (RuBP) carboxylase reaction of the Calvin cycle suggesting an extreme degree of evolutionary conservatism in the biochemistry of autotrophic carbon fixation. As a consequence, partial biological control of the geochemical carbon cycle was established already during Early Archaean times and fully operative by the time of formation of the Earth's earliest sediments.

Carbon↗