Volatile-mediated killing of Arabidopsis thaliana by bacteria is mainly due to hydrogen cyanide

The volatile-mediated impact of bacteria on plant growth is well documented, and contrasting effects have been reported ranging from 6-fold plant promotion to plant killing. However, very little is known about the identity of the compounds responsible for these effects or the mechanisms involved in plant growth alteration. We hypothesized that hydrogen cyanide (HCN) is a major factor accounting for the observed volatile-mediated toxicity of some strains. Using a collection of environmental and clinical strains differing in cyanogenesis, as well as a defined HCN-negative mutant, we demonstrate that bacterial HCN accounts to a significant extent for the deleterious effects observed when growing Arabidopsis thaliana in the presence of certain bacterial volatiles. The environmental strain Pseudomonas aeruginosa PUPa3 was less cyanogenic and less plant growth inhibiting than the clinical strain P. aeruginosa PAO1. Quorum-sensing deficient mutants of C. violaceum CV0, P. aeruginosa PAO1, and P. aeruginosa PUPa3 showed not only diminished HCN production but also strongly reduced volatile-mediated phytotoxicity. The double treatment of providing plants with reactive oxygen species scavenging compounds and overexpressing the alternative oxidase AOX1a led to a significant reduction of volatile-mediated toxicity. This indicates that oxidative stress is a key process in the physiological changes leading to plant death upon exposure to toxic bacterial volatiles.     

Ralstonia solanacearum ��PGI-1 Strain KZR-5 Is Affected in Growth, Response to Cold Stress and Invasion of Tomato

The survival and persistence of Ralstonia solanacearum biovar 2 in temperate climates is still poorly understood. To assess whether genomic variants of the organism show adaptation to local conditions, we compared the behaviour of environmental strain KZR-5, which underwent a deletion of the 17.6?kb genomic island PGI-1, with that of environmental strain KZR-1 and potato-derived strains 1609 and 715. PGI-1 harbours two genes of potential ecological relevance, i.e. one encoding a hypothetical protein with a RelA/SpoT domain and one a putative cellobiohydrolase. We thus assessed bacterial fate under conditions of amino acid starvation, during growth, upon incubation at low temperature and invasion of tomato plants. In contrast to the other strains, environmental strain KZR-5 did not grow on media that induce amino acid starvation. In addition, its maximum growth rate at 28°C in rich medium was significantly reduced. On the other hand, long-term survival at 4°C was significantly enhanced as compared to that of strains 1609, 715 and KZR-1. Although strain KZR-5 showed growth rates (at 28°C) in two different media, which were similar to those of strains 1609 and 715, its ability to compete with these strains under these conditions was reduced. In singly inoculated tomato plants, no significant differences in invasiveness were observed among strains KZR-5, KZR-1, 1609 and 715. However, reduced competitiveness of strain KZR-5 was found in experiments on tomato plant colonisation and wilting when using 1:1 or 5:1 mixtures of strains. The potential role of PGI-1 in plant invasion, response to stress and growth in competition at high and moderate temperatures is discussed.     

The effect of area on local and regional elevational patterns of species richness

Aim To calculate the degree to which differences between local and regional elevational species richness patterns can be accounted for by the effects of regional area. Location Five elevational transects in Costa Rica, Ecuador, La Réunion, Mexico and Tanzania. Methods We sampled ferns in standardized field plots and collated regional species lists based on herbarium and literature data. We then used the Arrhenius function S = cA^z to correct regional species richness (S) for the effect of area (A) using three slightly different approaches, and compared the concordance of local and regional patterns prior to and after accounting for the effect of area on regional richness using linear regression analyses. Results We found a better concordance between local and regional elevational species richness after including the effect of area in the majority of cases. In several cases, local and regional patterns are very similar after accounting for area. In most of the cases, the maximum regional richness shifted to a higher elevation after accounting for area. Different approaches to correct for area resulted in qualitatively similar results. Main conclusions The differences between local and regional elevational richness patterns can at least partly be accounted for by area effects, suggesting that the underlying causes of elevational richness patterns might be the same at both spatial scales. Values used to account for the effect of area differ among the different study locations, showing that there is no generally applicable elevational species–area relationship.     

Accelerated methanogenesis from aliphatic and aromatic hydrocarbons under iron- and sulfate-reducing conditions

The impact of four electron acceptors on hydrocarbon-induced methanogenesis was studied. Methanogenesis from residual hydrocarbons may enhance the exploitation of oil reservoirs and may improve bioremediation. The conditions to drive the rate-limiting first hydrocarbon-oxidizing steps for the conversion of hydrocarbons into methanogenic substrates are crucial. Thus, the electron acceptors ferrihydrite, manganese dioxide, nitrate or sulfate were added to sediment microcosms acquired from two brackish water locations. Hexadecane, ethylbenzene or 1-(13)C-naphthalene were used as model hydrocarbons. Methane was released most rapidly from incubations amended with ferrihydrite and hexadecane. Ferrihydrite enhanced only hexadecane-dependent methanogenesis. The rates of methanogenesis were negatively affected by sulfate and nitrate at concentrations of more than 5 and 1 mM, respectively. Metal-reducing Geobacteraceae and potential sulfate reducers as well as Methanosarcina were present in situ and in vitro. Ferrihydrite addition triggered the growth of Methanosarcina-related methanogens. Additionally, methane was removed concomitantly by anaerobic methanotrophy. ANME-1 and -2 methyl coenzyme M reductase genes were detected, indicating anaerobic methanotrophy as an accompanying process [Correction added 16 December after online publication: 'methyl coenzyme A' changed to 'methyl coenzyme M' in this sentence]. The experiments presented here demonstrate the feasibility of enhancing methanogenic alkane degradation by ferrihydrite or sulfate addition in different geological settings.     

Exercise limits the production of endothelin in the coronary vasculature

We previously demonstrated that endothelin (ET)-mediated coronary vasoconstriction wanes with increasing exercise intensity via a nitric oxide- and prostacyclin-dependent mechanism (Ref. 23). Therefore, we hypothesized that the waning of ET coronary vasoconstriction during exercise is the result of decreased production of ET and/or decreased ET receptor sensitivity. We investigated coronary ET receptor sensitivity using intravenous infusion of ET and coronary ET production using intravenous infusion of the ET precursor Big ET, at rest and during continuous treadmill exercise at 3 km/h in 16 chronically instrumented swine. In the systemic vasculature, Big ET and ET induced similar changes in hemodynamic parameters at rest and during continuous exercise at 3 km/h, indicating that exercise does not alter ET production or receptor sensitivity in the systemic vasculature. In the coronary vasculature, infusion of ET resulted in similar dose-dependent decreases in coronary blood flow and coronary venous oxygen tension and saturation at rest and during exercise. In contrast, administration of Big ET resulted in dose-dependent decreases in coronary blood flow, as well as coronary venous oxygen tension and saturation at rest. These effects of Big ET were significantly reduced during exercise. Altogether, our data indicate that continuous exercise at 3 km/h attenuates ET-mediated coronary vasoconstriction through reduced production of ET from Big ET rather than through reduced ET sensitivity of the coronary vasculature. The decreased ET production during exercise likely contributes to metabolic coronary vasodilation.     

Improvement of pesticide mineralization in on-farm biopurification systems by bioaugmentation with pesticide-primed soil

Microcosms were used to examine whether pesticide-primed soils could be preferentially used over nonprimed soils for bioaugmentation of on-farm biopurification systems (BPS) to improve pesticide mineralization. Microcosms containing a mixture of peat, straw and either linuron-primed soil or nonprimed soil were irrigated with clean or linuron-contaminated water. The lag time of linuron mineralization, recorded for microcosm samples, was indicative of the dynamics of the linuron-mineralizing biomass in the system. Bioaugmentation with linuron-primed soil immediately resulted in the establishment of a linuron-mineralizing capacity, which increased in size when fed with the pesticide. Also, microcosms containing nonprimed soil developed a linuron-mineralizing population, but after extended linuron feeding. Additional experiments showed that linuron-mineralization only developed with some nonprimed soils. Concomitant with the increase in linuron degradation capacity, targeted PCR-denaturing gradient gel electrophoresis showed the proliferation of a Variovorax phylotype related to the linuron-degrading Variovorax sp. SRS16 in microcosms containing linuron-primed soil, suggesting the involvement of Variovorax in linuron degradation. The correlation between the appearance of specific Variovorax phylotypes and linuron mineralization capacity was less clear in microcosms containing nonprimed soil. The data indicate that supplementation of pesticide-primed soil results in the establishment of pesticide-mineralizing populations in a BPS matrix with more certainty and more rapidly than the addition of nonprimed soil.     

Verrucomicrobia subdivision 1 strains display a difference in the colonization of the leek (Allium porrum) rhizosphere

Strains CHC12 and CHC8, belonging to, respectively, Luteolibacter and Candidatus genus Rhizospheria (Verrucomicrobia subdivision 1), were recently isolated from the leek rhizosphere. The key question addressed in this study was: does attraction to and colonization of the rhizosphere occur in the same way for both strains? Therefore, the fate of the two strains was studied near in vitro-grown leek roots and in soil zones proximate to and at a further distance from roots in a model plant-soil microcosm set-up. Quantitative PCR detection with specific primers was used, as the cultivation of these bacteria from soil is extremely fastidious. The data indicated that natural populations of Luteolibacter (akin to strain CHC12) had lower numbers in the rhizosphere than in the corresponding bulk soil. On the other hand, the populations of Candidatus genus Rhizospheria, i.e. strain CHC8, showed higher numbers in the rhizosphere than in the bulk soil. Increased strain CHC8 cell-equivalent numbers in the rhizosphere were not only the result of in situ cell multiplication, but also of the migration of cells towards the roots. Luteolibacter and Candidatus genus Rhizospheria cells displayed differences in attraction to the rhizosphere and colonization thereof, irrespective of the fact that both belonged to Verrucomicrobia subdivision 1.     

Seasonal variations in the diversity and abundance of diazotrophic communities across soils

The nitrogen (N)-fixing community is a key functional community in soil, as it replenishes the pool of biologically available N that is lost to the atmosphere via anaerobic ammonium oxidation and denitrification. We characterized the structure and dynamic changes in diazotrophic communities, based on the nifH gene, across eight different representative Dutch soils during one complete growing season, to evaluate the amplitude of the natural variation in abundance and diversity, and identify possible relationships with abiotic factors. Overall, our results indicate that soil type is the main factor influencing the N-fixing communities, which were more abundant and diverse in the clay soils (n=4) than in the sandy soils (n=4). On average, the amplitude of variation in community size as well as the range-weighted richness were also found to be higher in the clay soils. These results indicate that N-fixing communities associated with sandy and clay soil show a distinct amplitude of variation under field conditions, and suggest that the diazotrophic communities associated with clay soil might be more sensitive to fluctuations associated with the season and agricultural practices. Moreover, soil characteristics such as ammonium content, pH and texture most strongly correlated with the variations observed in the diversity, size and structure of N-fixing communities, whose relative importance was determined across a temporal and spatial scale.     

The mitochondrial contact site complex, a determinant of mitochondrial architecture

Mitochondria are organelles with a complex architecture. They are bounded by an envelope consisting of the outer membrane and the inner boundary membrane (IBM). Narrow crista junctions (CJs) link the IBM to the cristae. OMs and IBMs are firmly connected by contact sites (CS). The molecular nature of the CS remained unknown. Using quantitative high-resolution mass spectrometry we identified a novel complex, the mitochondrial contact site (MICOS) complex, formed by a set of mitochondrial membrane proteins that is essential for the formation of CS. MICOS is preferentially located at the CJs. Upon loss of one of the MICOS subunits, CJs disappear completely or are impaired, showing that CJs require the presence of CS to form a superstructure that links the IBM to the cristae. Loss of MICOS subunits results in loss of respiratory competence and altered inheritance of mitochondrial DNA.