Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps

Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites

The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanellaoneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O2 deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research

Calcium-(organo)aluminum-proton competition for adsorption to tomato root cell walls: Experimental data and exchange model calculations

Aluminum interacts with negatively charged surfaces in plant roots, causing inhibition of growth and nutrient uptake in plants growing on acid soils. Pectins in the root cell wall form the major cation adsorption surface, with Ca2+ as the main adsorbing cation. Adsorption of Al3+ and Ca2+ to isolated cell wall material of tomato (Lycopersicon esculentum L.) roots was examined at pH 3.00-4.25 and in the presence of the aluminum chelators citrate and malate. Al3+ displaced Ca2+ from its pectic binding sites in the cell wall to a large extent but apparently also bound to non-Ca binding groups, displacing protons. Aluminum adsorption depended on the pH of the solution, with little Al adsorbing to the cell wall material at very low pH (< 3.50). Under very acid conditions Al3+ replacing Ca2+ at pectic cross-links is therefore not expected to play a role in X toxicity. Equimolar concentrations of citrate decreased Al competition for Ca binding sites almost completely, whereas malate only had an intermediate effect. The competition of (organo) Al3+, Ca2+, and H+ for cell wall binding sites was described adequately using the Gaines-Thomas exchange model

Response of Bambara Groundnut (Vigna subterranea (l.) Verdc.) to Phosphorus Fertilisation in Botswana

Soils in Botswana are known to be poor in phosphorus. Information is lacking on the P requirements of bambara groundnut (Vigna subterranea) in Botswana soils and soil moisture can also limit P uptake. Elsewhere the response of bambara groundnut to P fertilization is contradictory. The effects of phosphorus (P) fertilization on growth and yield of bambara groundnut were studied in a pot and a field experiments using a low P loamy sand (P-Bray 6.2 mg P kg-1) at Sebele Botswana. In the pot experiment, the response to two bambara groundnut landraces ('Diphiri Cream' and 'Zimbabwe Red') to P fertilization (0-480 mg P pot-1) was investigated. In the field experiment, the response of 'Diphiri Cream' to P fertilization (0-80 kg P ha-1) was investigated under two different soil moisture regimes (unsupplemented rainfall and supplementary irrigation) with samples taken at 28, 49,78, 99, days after sowing (DAS) and the final harvest at 126 DAS. In the pot experiment, terminated at 51 DAS, there was a positive response of shoot dry matter (DM) to P fertilization while the two landraces did not differ significantly. Root DM, nodule fresh weight and shoot P and nitrogen (N) concentrations were not affected by P fertilization. In the field, P fertilization had no effect, while supplementary irrigation increased all plant growth parameters except root DM. Total seed yield was 2.8 t and 4.2 t ha-1 for unsupplemented rainfall and supplementary irrigation treatments, respectively. Shoot P and N concentrations were not affected by soil moisture level. The positive effect of P in the pot and not in the field experiment may be an indication of low P supply of plants in pots due to a small rooted soil volume. The response in the pot experiment may indicate a 'starter P effect', whereas lack of response in the field may indicate unavailability of applied P to bambara groundnut. These aspects are discussed in this paper. UNISWA Research Journal of Agriculture, Science and Technology Vol. 4 (2) 2000: pp 202-20

Hydrolysis and reduction of factor 390 by cell extracts of Methanobacterium thermoautotrophicum (strain delta H).

Cell extracts of Methanobacterium thermoautotrophicum (strain delta H) were found to perform a hydrogen-dependent reduction of factor 390 (F390), the 8-adenylyl derivative of coenzyme F420. Upon resolution of cell extracts, F390-reducing activity copurified with the coenzyme F420-dependent hydrogenase. This indicates that F390 serves as a substrate of that enzyme. Activity towards F390 was approximately 40-fold lower than that towards coenzyme F420 (0.12 and 5.2 mumol.min-1.mg of protein-1, respectively). In addition, cell extracts catalyzed the hydrolysis of F390 to AMP and coenzyme F420. This hydrolysis required the presence of thiols (6 mM) and much ionic strength (1 M KCl) and was reversibly inhibited by oxygen. The reaction proceeded optimally at pH 8.2 and was Mn dependent. Conditions for F390 hydrolysis in cell extracts are in many respects opposite to those previously described for F390 synthesis

Leaf area expansion and assimilate production in sunflower (Helianthus annuus L.) growing under low phosphorus conditions

Reductions in leaf area and plant growth as a consequence of phosphorus (P) limitations have been attributed both to direct effects of P shortage on leaf expansion rate and to a reduced production of assimilates required for growth. Canopy assimilation and leaf area expansion are closely interrelated processes. In this work we used experimental and simulation techniques to identify and study their importance in determining leaf area on sunflower (Helianthus annuus L.) growing under P-deficient conditions. Experiment 1 was done outdoors, in Buenos Aires, Argentina, and Experiment 2 in a glasshouse in Wageningen, The Netherlands. In both experiments we studied the effects of soil P addition on leaf appearance, leaf expansion, dry matter accumulation, and leaf photosynthesis of non-water stressed plants grown in pots containing a P-deficient soil. Before sowing the equivalent amounts of 0–600 kg of super phosphate ha-1 were added to the pots. Phosphorus deficiency delayed leaf appearance increasing the value of the phyllochron (PHY) up to 76%, the rate of leaf area expansion during the quasi-linear phase of leaf expansion (LER) was reduced by up to 74%, with respect to high P plants. Phosphorus deficiency reduced by up to 50% the rate of light saturated photosynthesis per unit of leaf area (AMAX) in recently expanded leaves, while at low levels of leaf insertion in the canopy, AMAX was reduced by up to 85%, when compared to that in high P plants. Phosphorus deficiency also reduced the duration of the quasi-linear phase of leaf expansion by up to eight days. The values of LER were related (r = 0.56, P < 0.05) to the mean concentration of P in all the leaves (Leaves P%) and not to the concentration of P in the individual leaf where LER was determined (r = 0.22, P < 0.4) suggesting that under P deficiency individual leaf expansion was not likely to be regulated by the total P concentration at leaf level. The values of AMAX of individual leaves were related (r = 0.79, P < 0.01) to the concentration of total P in the corresponding leaf (Leaf P%). LER showed a hyperbolic relationship with Leaves P% (R2 = 0.94, P < 0.01, n = 13) that saturate at 0.14%. AMAX showed a hyperbolic relationship with Leaf P% (R2 = 0.73, P < 0.01, n = 53) that saturated with values of Leaf P% higher than 0.22. A morphogenetic model of leaf area development and growth was developed to quantify the effect of assimilate supply at canopy level on total leaf area expansion, and to study the effects of model parameters on the growth of sunflower plants under P-deficient conditions. With this model we identified the existence of direct effects of P deficiency on individual leaf area expansion. However, we calculated that under mild P stress conditions up to 83% of the reduction in the observed leaf area was explained by the particular effects of P% on the rate of leaf appearance, on the duration of the linear period of leaf expansion, and on the value of AMAX. We also calculated that the effects of P deficiency on the value of AMAX alone, explained up to 41% of the observed reductions in total leaf area between the highest and the intermediate P level in Experiment 2. Possible mechanisms of action of the direct effects of P on individual leaf expansion are discussed in this paper