Identification and analysis of the Shewanella oneidensis major oxygen-independent coproporphyrinogen III oxidase gene

Shewanella oneidenesis MR-1 is a facultative anaerobe that can use a large number of electron acceptors including metal oxides. During anaerobic respiration, S. oneidensis MR-1 synthesizes a large number of c cytochromes that give the organism its characteristic orange color. Using a modified mariner transposon, a number of S. oneidensis mutants deficient in anaerobic respiration were generated. One mutant, BG163, exhibited reduced pigmentation and was deficient in c cytochromes normally synthesized under anaerobic condition. The deficiencies in BG163 were due to insertional inactivation of hemN1, which exhibits a high degree of similarity to genes encoding anaerobic coproporphyrinogen III oxidases that are involved in heme biosynthesis. The ability of BG163 to synthesize c cytochromes under anaerobic conditions, and to grow anaerobically with different electron acceptors was restored by the introduction of hemN1 on a plasmid. Complementation of the mutant was also achieved by the addition of hemin to the growth medium. The genome sequence of S. oneidensis contains three putative anaerobic coproporphyrinogen III oxidase genes. The protein encoded by hemN1 appears to be the major enzyme that is involved in anaerobic heme synthesis of S. oneidensis. The other two putative anaerobic coproporphyrinogen III oxidase genes may play a minor role in this process.     

Improving retting of fibre through genetic modification of flax to express pectinases

Flax (Linum usitatissimum L.) is a raw material used for important industrial products. Linen has very high quality textile properties, such as its strength, water absorption, comfort and feel. However, it occupies less than 1% of the total textile market. The major reason for this is the long and difficult retting process by which linen fibres are obtained. In retting, bast fibre bundles are separated from the core, the epidermis and the cuticle. This is accomplished by the cleavage of pectins and hemicellulose in the flax cell wall, a process mainly carried out by plant pathogens like filamentous fungi. The remaining bast fibres are mainly composed of cellulose and lignin. The aim of this study was to generate plants that could be retted more efficiently. To accomplish this, we employed the novel approach of transgenic flax plant generation with increased polygalacturonase (PGI ) and rhamnogalacturonase (RHA) activities. The constitutive expression of Aspergillus aculeatus genes resulted in a significant reduction in the pectin content in tissue-cultured and field-grown plants. This pectin content reduction was accompanied by a significantly higher (more than 2-fold) retting efficiency of the transgenic plant fibres as measured by a modified Fried’s test. No alteration in the lignin or cellulose content was observed in the transgenic plants relative to the control. This indicates that the over-expression of the two enzymes does not affect flax fibre composition. The growth rate and soluble sugar and starch contents were in the range of the control levels. It is interesting to note that the RHA and PGI plants showed higher resistance to Fusarium culmorum and F. oxysporum attack, which correlates with the increased phenolic acid level. In this report, we demonstrate for the first time that over-expression of the A. aculeatus genes results in flax plants more readily usable for fibre production. The biochemical parameters of the cell wall components indicated that the fibre quality remains similar to that of wild-type plants, which is an important pre-requisite for industrial applications. Magdalena Musialak and Magdalena Wróbel-Kwiatkowska participated equally in the preparation of this paper     

3-Methylaspartate ammonia-lyase from a facultative anaerobe,strain YG-1002

3-Methylaspartase was purified 24-fold and crystallized from the crude extract of the cells of a facultative anaerobic bacterium from soil, strain YG-1002. The molecular mass of the native enzyme was about 84 kDa and that of the subunit was about 42 kDa. The pH optimum for the deamination reaction of (2S, 3S)-3-methylaspartic acid and those for the amination reaction of mesaconic acid were 9.7 and 8.5; its optimum temperature was 50°C. The enzyme was stable at pH 5.5–11.0 and up to 50°C. The enzyme required both divalent and monovalent cations such as Mg²⁺ and K⁺. The enzyme was inhibited by sulfhydryl reagents, metal-chelating reagents and some divalent cations. The enzyme catalyzed the reversible amination/deamination reactions between several 3-substituted (S)-aspartic acids and their corresponding fumaric acid derivatives. The enzyme preferentially acted on (2S, 3S)-3-methylaspartic acid and mesaconic acid in the deamination and the amination reactions respectively. The enzyme showed high similarities in several enzymological properties and N-terminal amino acid sequence with 3-methylaspartase from an obligate anaerobic bacteriumClostridium tetanomorphum.     

Metabolic Fate of O-Ethyl S,S-Diphenyl Phosphorodithiolate (Hinosan®) in Rice Plant

Metabolism and residual fate of O-ethyl S,S-diphenyl phosphorodithiolate (Hinosan®) applied on rice plant was examined by using ³⁵S-labeled or ³²P-labeled compound. Ion exchange chromatography, thin-layer chromatography and gas-liquid chromatography with flame thermionic detector or flame photometric detector were applied for identification of water soluble and toluene soluble metabolites of Hinosan. Degradation of Hinosan at the initial stage of metabolism was mainly the cleavage of P-S linkage, and a large portion of phenyl dihydrogen phosphorothiolate and a minor portion of O-ethyl S-phenyl hydrogen phosphorothiolate were found as water soluble metabolites. Phenylthio radical released on the production of the above mentioned metabolites was recovered as diphenyl disulfide, which was finally converted to sulfuric acid through benzenesulfonic acid. Triphenyl phosphorotrithiolate and O,O-diethyl S-phenyl phosphorothiolate were produced by transesterification between molecules of Hinosan at the initial stage of metabolism. Examination of metabolites in rice grains showed that sulfur and phosphorus atoms in Hinosan were incorporated into neutral or cationic substances probably after several steps of chemical transformation.     

Soil respiration is stimulated by elevated CO2 and reduced by summer drought: three years of measurements in a multifactor ecosystem manipulation experiment in a temperate heathland (CLIMAITE)

This study investigated the impact of predicted future climatic and atmospheric conditions on soil respiration (R_S) in a Danish Calluna‐Deschampsia‐heathland. A fully factorial in situ experiment with treatments of elevated atmospheric CO₂ (+130 ppm), raised soil temperature (+0.4 °C) and extended summer drought (5–8% precipitation exclusion) was established in 2005. The average R_S, observed in the control over 3 years of measurements (1.7 μmol CO₂ m^?2 sec^?1), increased 38% under elevated CO₂, irrespective of combination with the drought or temperature treatments. In contrast, extended summer drought decreased R_S by 14%, while elevated soil temperature did not affect R_S overall. A significant interaction between elevated temperature and drought resulted in further reduction of R_S when these treatments were combined. A detailed analysis of short‐term R_S dynamics associated with drought periods showed that R_S was reduced by ~50% and was strongly correlated with soil moisture during these events. Recovery of R_S to pre‐drought levels occurred within 2 weeks of rewetting; however, unexpected drought effects were observed several months after summer drought treatment in 2 of the 3 years, possibly due to reduced plant growth or changes in soil water holding capacity. An empirical model that predicts R_S from soil temperature, soil moisture and plant biomass was developed and accounted for 55% of the observed variability in R_S. The model predicted annual sums of R_S in 2006 and 2007, in the control, were 672 and 719 g C m^?2 y^?1, respectively. For the full treatment combination, i.e. the future climate scenario, the model predicted that soil respiratory C losses would increase by ~21% (140–150 g C m^?2 y^?1). Therefore, in the future climate, stimulation of C storage in plant biomass and litter must be in excess of 21% for this ecosystem to not suffer a reduction in net ecosystem exchange.     

The thermodynamic effects of exposing nucleic acid bases to water: solubility measurements in water and organic solvents

In order to examine the thermodynamic effects of exposing nucleic acid bases to water, we have measured the solubility of adenine, cytosine, and uracil in water and in organic solvents as a function of temperature. Transfer of a nucleic acid base from an organic environment into water is characterized by positive values for ΔH and for ΔS. We conclude from this result that the overall interaction between nucleic acid bases and water cannot be hydrophobic. If the effect we observe represents structure breaking in water by nucleic acid bases, this process would account for a major portion of the large, positive melting entropy of DNA, and would also contribute substantially to the melting enthalpy.     

Peptide Thioester Synthesis via an Auxiliary-Mediated N–S Acyl Shift Reaction in Solution

The 4,5-dimethoxy-2-mercaptobenzyl (Dmmb) group attached to a main chain amide in a peptide is easily transformed into an S-peptide via an intramolecular N–S acyl shift reaction under acidic conditions, and the S-peptide produces a peptide thioester through an intermolecular thiol–thioester exchange reaction. In order to develop a method for efficiently preparing peptide thioesters based on the N–S acyl shift reaction, the factors involved in this process were analyzed in detail. The general features of the transformation at the Dmmb group attached amide bond in a trifluoroacetic acid (TFA) solution and the generation of a peptide thioester were examined by ¹³C-NMR spectral measurements, reversed-phase (RP) HPLC analyses, mass measurements, and amino acid analyses. The methoxy group of the Dmmb group was not essential for the N–S acyl shift reaction, but played a role in stabilizing the thioester form. The addition of water to the TFA solution accelerated the N–S acyl shift reaction mediated by the Dmmb group and also suppressed the acid-catalyzed cleavage of the Dmmb group. A peptide thioester was produced from the S-peptide via an intermolecular thiol–thioester exchange reaction with minimal epimerization of the amino acid residue that constituted the thioester bond. Undesirable side reactions, such as the hydrolysis of the thioester bond and an S–N acyl shift reaction occurred during the synthetic process, which is a subject of further investigation.     

Use of Cellulose-Degrading Nitrogen-Fixing Bacteria in the Enrichment of Roughage with Protein

A new strain of acid-tolerant facultative anaerobic cellulose-degrading bacteria Bacillus cytaseus 21 (Mc Bethe ef Scales, 1912), which are capable to fixing atmospheric nitrogen, was isolated. This strain is intended for solid-phase fermentation and enrichment with protein of cellulose-containing waste of plant cultivation.     

Modelling the soil-plant-atmosphere continuum in a Quercus–Acer stand at Harvard Forest: the regulation of stomatal conductance by light, nitrogen and soil/plant hydraulic properties

Our objective is to describe a multi-layer model of C₃-canopy processes that effectively simulates hourly CO₂ and latent energy (LE) fluxes in a mixed deciduous Quercus-Acer (oak–maple) stand in central Massachusetts, USA. The key hypothesis governing the biological component of the model is that stomatal conductance (g_s) is varied so that daily carbon uptake per unit of foliar nitrogen is maximized within the limitations of canopy water availability. The hydraulic system is modelled as an analogue to simple electrical circuits in parallel, including a separate soil hydraulic resistance, plant resistance and plant capacitance for each canopy layer. Stomatal opening is initially controlled to conserve plant water stores and delay the onset of water stress. Stomatal closure at a threshold minimum leaf water potential prevents xylem cavitation and controls the maximum rate of water flux through the hydraulic system. We show a strong correlation between predicted hourly CO₂ exchange rate (r²= 0.86) and LE (r²= 0.87) with independent whole-forest measurements made by the eddy correlation method during the summer of 1992. Our theoretical derivation shows that observed relationships between CO₂ assimilation and LE flux can be explained on the basis of stomatal behaviour optimizing carbon gain, and provides an explicit link between canopy structure, soil properties, atmospheric conditions and stomatal conductance.     

The AtPP gene of the Brassica napus S locus region is specifically expressed in the stigma and encodes a protein similar to a methyltransferase involved in plant defense

Self-incompatibility (SI) in Brassica is controlled by the S locus. The specificity of the SI response is controlled on the stigma side by the S receptor kinase (SRK) and on the pollen side by the SCR (S locus cysteine-rich) protein, but other proteins might be involved in the process of self-pollen rejection. In this study, we show that the AtPP gene linked to the S locus of Brassica napus is expressed in the stigmas of SI lines. AtPP has a developmental pattern of expression similar to the SRK gene. The AtPP protein has similarity with members of an Arabidopsis protein family and with an S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, which is a plant defense-related protein of Clarkia breweri representing a new class of methyltransferases. A member of the AtPP gene family is present in the homeolog region of the S locus in Arabidopsis. Therefore, this gene might have co-evolved with S genes from an ancestral S locus of Brassicaceae. Possible functions of the AtPP protein in the self-recognition process are discussed. Received: 9 October 2000 / Revision accepted: 23 April 2001     

Humic substance mineralization in a tropical oxbow lake (São Paulo,Brazil)

We evaluated the mineralization rates of humic substances in Infernão oxbow lake (State of São Paulo, Brazil). Experiments were conducted under aerobic and anaerobic conditions using fulvic acid and humic acid from four sources: Scirpus cubensis and Cabomba piauhyensis leachate submitted to a 120-day degradation process, sediment, and dissolved organic matter from the lake water. A fixed amount of substrate was added to 450 ml of water from Infernão lake, filtered over glass wool. After adding substrate, the flasks were incubated at 21.0°C under aerobic and anaerobic conditions. The dissolved organic carbon was monitored during 95 days. The results were fitted to first-order kinetics model, which pointed to one labile and one refractory fraction. The refractory fractions predominated, ranging from 71.4 to 84.3% for fulvic acid and from 73.4 to 85.0% for humic acid. Mineralization rates of the labile fractions of dissolved organic carbon were higher under aerobic than anaerobic conditions, while the converse was true for the refractory fractions.     

Utilization of cathodic hydrogen by hydrogen-oxidizing bacteria

Summary Hydrogen is consumed by methanogenic, sulphate-reducing, and homoacetogenic bacteria and members of these bacterial groups are able to grow chemolithotrophically with hydrogen as sole energy source. Cathodic hydrogen consumption by sulphate-reducing bacteria has been proposed as one of the factors in the anaerobic corrosion of metals. Desulfovibrio spp. were able to utilize cathodic hydrogen from mild steel as the only source of energy for growth with sulphate or nitrate as terminal electron acceptor. Other hydrogen-oxidizing bacteria such as Methanospirillum hungatei, Acetobacterium woodii and Wolinella succinogenes were also able to utilize cathodic hydrogen from mild steel for energy generation and growth. Weight loss studies of mild steel coupons under different growth conditions of Desulfovibrio spp. indicated that hydrogen removal alone is not the cause of corrosion and the depolarization phenomenon probably plays a role only in the initiation of the anaerobic microbial corrosion process.     

Toward a plant-based proxy for the isotope ratio of atmospheric water vapor

Atmospheric water vapor is a major component of the global hydrological cycle, but the isotopic balance of vapor is largely unknown. Here, using models and observations, we show that the leaf water δ¹⁸O in the tropical Crassulacean acid metabolism (CAM) epiphyte Tillandsia usneoides is controlled by the δ¹⁸O of atmospheric water vapor in a predictable manner, irrespective of precipitation inputs. By taking the leaf‐water‐atmospheric signature as recorded in plant organic material, we have reconstructed the atmospheric water vapor δ¹⁸O signature for Miami, FL, USA between 1878 and 2005 using contemporary and herbarium specimens. T. usneoides ranges from Virginia, USA southwards through the tropics to Argentina, and the CAM epiphytic lifeform is widespread in other species. Therefore, there is significant potential for using epiphytes to reconstruct the isotope ratio of atmospheric water (both δ¹⁸O and δD) for spatial scales that span over 60° of latitude and temporal scales that cover the last century of global temperature increase.     

Bacterial corrosion of mild steel under the condition of simultaneous formation of ferrous and sulphide ions

Summary Corrosion of mild steel in cultures of a Pseudomonas species under the condition of simultaneous formation of Fe(II) and S^2- was initially inhibited by inhibiting the anodic reaction, but after long incubation the corrosion process was allowed to continue. When only S^2- was produced, the initial corrosion rate increased for up to 60 h but later declined, probably due to a protective FeS film formed on the metal. Cathodic reactions were affected in a similar fashion as the anode.Extensive pitting corrosion was observed when the mild steel coupons were immersed in bacterial culture producing Fe(IIO) and S^2-, but not in the uninoculated control.     

Survival, Gap Formation, and Recovery Dynamics in Grassland Ecosystems Exposed to Heat Extremes: The Role of Species Richness

A field experiment was performed in which the richness of perennial grasses (S) was varied in model ecosystems exposed to a simulated heat wave (free air temperature increase and drought). The proportion of individuals that survived the heat wave decreased with S, which could be ascribed to higher water consumption in the species-rich systems. Higher transpiration at high diversity was also observed in other studies using functional groups and could have originated from increased leaf area, less intense stomatal closure, or a combination of both. The increased tiller number per plant that we observed, while leaf area per tiller remained constant, suggests that an enhanced leaf area index was most likely responsible. However, competitive interactions also seemed to play a role in the influence of S on survival. Regrowth of the surviving individuals, expressed as leaf area per living plant after a recovery period following the heat wave, increased with S, most likely due to the dominance of productive species, which was facilitated by the additional space yielded by more intense gap formation at higher S (due to higher plant mortality). Species richness affected both the size and density of the gaps. Mean size increased exponentially with S, while density increased at low S but decreased at higher S when connectance of the gaps occurred. Size distribution of the gaps was not affected. Received 18 January 2000; accepted 31 May 2001.     

Biodegradation and corrosion behaviour of <Emphasis Type="Italic">Serratia marcescens</Emphasis> ACE2 isolated from an Indian diesel-transporting pipeline

A facultative anaerobic species Serratia marcescens ACE2 isolated from the corrosion products of a diesel-transporting pipeline in North West India was identified by 16S rDNA sequence analysis. The role of Serratia marcesens ACE2 on biodegradation of commercial corrosion inhibitor (CCI) and its influence on the corrosion of API 5LX steel has been enlightened. The degrading strain ACE2 is involved in the process of corrosion of steel API 5LX and also utilizes the inhibitor as organic source. The quantitative biodegradation efficiency of corrosion inhibitor was 58%, which was calculated by gas chromatography mass spectrum analysis. The effect of CCI on the growth of bacteria and its corrosion inhibition efficiency were investigated. Additionally, the role of this bacterium in corrosion of steel has been investigated by powder X-ray diffractometer (XRD) and scanning electron microscope studies. The presence of high-intensity ferric oxides and manganese oxides noticed from the XRD indicates that ACE2 enhances the corrosion process in presence of inhibitor as a carbon source. This basic study will be useful for the development of new approaches for the detection, monitoring and control of microbial corrosion in petroleum product pipelines.     

Optimization of process variables for minimization of byproduct formation during fermentation of blackstrap molasses to ethanol at industrial scale

Aims: To investigate the effect of molasses concentration, initial pH of molasses medium, and inoculum’s size to maximize ethanol and minimize methanol, fusel alcohols, acetic acid and aldehydes in the fermentation mash in industrial fermentors. Methods and Results: Initial studies to optimize temperature, nitrogen source, phosphorous source, sulfur supplement and minerals were performed. The essential nutrients were urea (2 kg in 60 m³), 0·5 l each of commercial phosphoric acid and sulfuric acid (for pH control) added at the inoculum preparation stage only. Yields of ethanol, methanol, fusel alcohols, total acids and aldehydes per 100‐l fermentation broth were monitored. Molasses at 29°Brix (degree of dissolved sugars in water), initial pH 4·5, inoculum size 30% (v/v) and anaerobic fermentation supported maximum ethanol (7·8%) with Y_P/S = 238 l ethanol per tonne molasses (96·5% yield) (8·2% increase in yield), and had significantly lower values of byproducts than those in control experiments. Conclusions: Optimization of process variables resulted in higher ethanol yield (8·2%) and reduced yield of methanol, fusel alcohols, acids and aldehydes. Significance and Impact of the Study: More than 5% substrate is converted into byproducts. Eliminating or reducing their formation can increase ethanol yield by Saccharomyces cerevisiae, decrease the overall cost of fermentation process and improve the quality of ethanol.     

Role of <Emphasis Type="Italic">Serratia marcescens</Emphasis> ACE2 on diesel degradation and its influence on corrosion

A facultative anaerobic species Serratia marcescens ACE2 isolated from the corrosion products of diesel transporting pipeline in North West, India was identified by 16S rDNA sequence analysis. The role of Serratia marcesens ACE2 on biodegradation of diesel and its influence on the corrosion of API 5LX steel has been elucidated. The degrading strain ACE2 is involved in the process of corrosion of steel API 5LX and also utilizes the diesel as an organic source. The quantitative biodegradation efficiency (BE) of diesel was 58%, calculated by gas-chromatography–mass spectrum analysis. On the basis of gas-chromatography–mass spectrum (GC–MS), Fourier Transform infrared spectroscopy (FTIR) and X-ray diffractometer (XRD), the involvement of Serratia marcescens on degradation and corrosion has been investigated. This basic study will be useful for the development of new approaches for detection, monitoring and control of microbial corrosion.     

Amino acid composition of fractions of ‘Kentucky-31’ tall fescue as affected by N fertilization and mild water stress

Summary Environmental and management factors can influence the protein concentration of forages, significantly altering specific amino acid content. Drought, high rates of fertilizer N and the presence of a fungal endophyte have been associated with significant alterations in plant N metabolites and animal performance problems on tall fescue. A controlled environment study was conducted to examine the influence of N fertilization (10 and 100 gN/g) and water regime (low and adequate soil water availability) upon the distribution and concentration of amino acids in endophyte infected tall fescue (Festuca arundinacea, Schreb.) herbage. Tall fescue tissue was collected from three replicates of each treatment, quick frozen in liquid N and lyophilized. Two insoluble (R_I, structural residue; R_II, membrane residue) and two soluble (S_I, soluble protein; S_II, low molecular weight N compounds) fractions were collected. Amino acid analyses of acid hydrolysates of fractions showed that application of 100 N significantly increased the concentration (per unit dry weight) of all amino acids in the entire plant, with an average increase of about 55%. Application of 110 N increased the concentrations of most amino acids in fractions R_I, R_II, and S_I, but only aspartate-asparagine, glutamate-glutamine, alanine, threonine, serine, valine and proline in fraction S_II. Fraction R_I contained about 65% of total amino acids under 10 N and 55% under 110 N even though N level did not alter dry matter distribution among fractions. While the amount of dry matter was least in S_I, amino acids in the fraction ranged from 8% (leucine, 10 N) to 20% (lysine, 110 N) of the total amount of specific amino acids recovered. Significant increases in proline, glutamate, aspartate, serine, valine, threonine, alanine and phenylalanine concentration occurred under low soil-water availability compared with adequate water conditions. Basic amino acids including histidine, arginine and lysine increased with increased N and with water stress at each N level. Application of N increased amounts, and water stress influenced distribution of amino acids among the fractions of tall fescue herhage. Nitrogenous components, such as non-protein amino acids which could influence plant nutritive quality, were increased in fraction S_II by increased N and water stress.     

CO2-forced evolution of plant gas exchange capacity and water-use efficiency over the Phanerozoic

The capacity of plants to fix carbon is ultimately constrained by two core plant attributes: photosynthetic biochemistry and the conductance to CO₂ diffusion from the atmosphere to sites of carboxylation in chloroplasts, predominantly stomatal conductance. Analysis of fossilized plant remains shows that stomatal density (number per unit area, D) and size (length by width, S) have fluctuated widely over the Phanerozoic Eon, indicating changes in maximum stomatal conductance. Parallel changes are likely to have taken place in leaf photosynthetic biochemistry, of which maximal rubisco carboxylation rate, V_cmax is a central element. We used measurements of S and D from fossilized plant remains spanning the last 400 Myr (most of the Phanerozoic), together with leaf gas exchange data and modeled Phanerozoic trends in atmospheric CO₂ concentration, [CO₂]_a, to calibrate a [CO₂]_a‐driven model of the long‐term environmental influences on S, D and V_cmax. We show that over the Phanerozoic large changes in [CO₂]_a forced S, D and V_cmax to co‐vary so as to reduce the impact of the change in [CO₂]_a on leaf CO₂ assimilation for minimal energetic cost and reduced nitrogen requirements. Underlying this is a general negative correlation between S and D, and a positive correlation between water‐use efficiency and [CO₂]_a. Furthermore, the calculated steady rise in stomatal conductance over the Phanerozoic is consistent with independent evidence for the evolution of plant hydraulic capacity, implying coordinated and sustained increase in gas exchange capacity and hydraulic capacity parallel long‐term increases in land plant diversity.