Genome sequences of Burkholderia sp. Strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil.

The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil, isolated from legume nodules, are reported. Their gene contents in relation to plant-microbe interactions and xenobiotic degradation are discussed

Influencia del ambiente edáfico y la fertilización nitrogenada, en cultivares de trigo diferenciados por su potencial

The purpose of the present study was to evaluate the effect of soil environment on yield and response of three wheat cultivars to fertilization with three doses (0, 40 and 120 kg.ha-1). The differences were analyzed with analysis of variance and Fisher's LSD test. Gross margins of each treatment were calculated. All four factors tested in this experiment (site, environment, cultivar and fertilization) had a significant influence on crop performance. Yield and fertilization response were related to water availability which differed among environments. The yield component that most affected yield was the number of grains per square meter, showing strong variability among treatments (5000 to 15000 g.m-2). These differences produced a wide range of variation in gross margins between environments, where a negative effect of fertilization in the more moisture limited environment could be observed, while in those with less moisture restrictions a positive contribution of fertilization to gross margin was found.El objetivo del trabajo fue evaluar el efecto del ambiente edáfico sobre el rendimiento y la respuesta de tres variedades de trigo a la fertilización nitrogenada a la siembra (dosis 0, 40 y 120 Kg N.ha-1). Las diferencias fueron evaluadas mediante ANOVA doble y LSD de Fisher. Se calcularon los márgenes brutos por tratamiento. Los cuatro factores considerados en el ensayo (sitio, ambiente, cultivar y fertilización) influenciaron significativamente sobre el cultivo. El rendimiento y la respuesta a la fertilización se relacionaron con la disponibilidad de agua que resultó contrastante entre ambientes. El número de granos m2 fue el componente con mayor incidencia sobre el rendimiento variando ampliamente entre tratamientos (desde 5000 a 15000 granos.m-2). Estas diferencias dieron lugar a un amplio rango de variación en los márgenes brutos entre ambientes, comprobándose un efecto negativo de la fertilización en el ambiente con mayores restricciones y una contribución positiva en el margen bruto en los ambientes con menores restricciones hídricas

Variability of BVOC emissions from a Mediterranean mixed forest in southern France with a focus on Quercus pubescens

International audienceWe aimed at quantifying biogenic volatile organic compound (BVOC) emissions in June from three Mediter-ranean species located at the O 3 HP site (southern France): Quercus pubescens, Acer monspessulanum and C. coggygria (for isoprene only). As Q. pubescens was shown to be the main BVOC emitter with isoprene representing ≈ 99 % of the carbon emitted as BVOC, we mainly focused on this species. C. coggygria was found to be a non-isoprene emitter (no other BVOCs were investigated). To fully understand both the canopy effect on Q. pubescens isoprene emissions and the inter-individual variability (tree to tree and within canopy), diurnal variations of isoprene were investigated from nine branches (seven branches located to the top of canopy at ≈ 4 m above ground level (a.g.l.), and two inside the canopy at ≈ 2 m a.g.l.). The Q. pubescens daily mean isoprene emission rate (ER d) fluctuated between 23 and 98 µgC g −1 DM h −1. Q. pubescens daily mean net assimilation (Pn) ranged between 5.4 and 13.8, and 2.8 and 6.4 µmol CO 2 m −2 s −1 for sunlit and shaded branches respectively. Both ER d and isoprene emission factors (Is), assessed according to Guenther et al. (1993) algorithm, varied by a factor of 4.3 among the sunlit branches. While sunlit branches ER d was clearly higher than for shaded branches, there was a non-significant variability of Is (59 to 77 µgC g −1 DM h −1). Diurnal variations of iso-prene emission rates (ERs) for sunlit branches were also investigated. ERs were detected at dawn 2 h after Pn became positive and were mostly exponentially dependent on Pn. Diurnal variations of ERs were not equally well described throughout the day by temperature (C T) and light (C L) parameters according to G93 algorithm. Temperature had more impact than photosynthetically active radiation (PAR) on the morning emissions increase, and ER was no longer correlated to C L × C T between solar noon (maximum ER) and mid-afternoon, possibly due to thermal stress of the plant. A comparison between measured and calculated emissions using two isoprene algorithms (G93 and MEGAN – Model of Emissions of Gases and Aerosols from Nature) highlighted the importance of isoprene emission factor Is value used, and some weakness in assessing isoprene emissions under Mediterranean climate conditions (drought) with current iso-prene models

Concentrations and fluxes of isoprene and oxygenated VOCs at a French Mediterranean oak forest

The CANOPEE project aims to better understand the biosphere–atmosphere exchanges of biogenic volatile organic compounds (BVOCs) in the case of Mediterranean ecosystems and the impact of in-canopy processes on the atmospheric chemical composition above the canopy. Based on an intensive field campaign, the objective of our work was to determine the chemical composition of the air inside a canopy as well as the net fluxes of reactive species between the canopy and the boundary layer. Measurements were carried out during spring 2012 at the field site of the Oak Observatory of the Observatoire de Haute Provence (O3HP) located in the southeast of France. The site is a forest ecosystem dominated by downy oak, Quercus pubescens Willd., a typical Mediterranean species which features large isoprene emission rates. Mixing ratios of isoprene, its degradation products methylvinylketone (MVK) and methacrolein (MACR) and several other oxygenated VOC (OxVOC) were measured above the canopy using an online proton transfer reaction mass spectrometer (PTR-MS), and fluxes were calculated by the disjunct eddy covariance approach. The O3HP site was found to be a very significant source of isoprene emissions, with daily maximum ambient concentrations ranging between 2–16 ppbv inside and 2–5 ppbv just above the top of the forest canopy. Significant isoprene fluxes were observed only during daytime, following diurnal cycles with midday net emission fluxes from the canopy ranging between 2.0 and 9.7 mg m−2 h1. Net isoprene normalized flux (at 30 °C, 1000 μmol quanta m−2 s−1) was estimated at 7.4 mg m−2 h−1. Evidence of direct emission of methanol was also found exhibiting maximum daytime fluxes ranging between 0.2 and 0.6 mg m−2 h−1, whereas flux values for monoterpenes and others OxVOC such as acetone and acetaldehyde were below the detection limit. The MVK+MACR-to-isoprene ratio provided useful information on the oxidation of isoprene, and is in agreement with recent findings proposing weak production yields of MVK and MACR, in remote forest regions where the NOx concentrations are low. In-canopy chemical oxidation of isoprene was found to be weak and did not seem to have a significant impact on isoprene concentrations and fluxes above the canopy

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean.

The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15. Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation and competitiveness

Caracterización del sistema de secreción de tipo VI en Rhizobium etli Mim1

La simbiosis rizobio-leguminosa es altamente específica. La translocación de proteínas denominadas efectores desde el citoplasma bacteriano a la célula vegetal es un elemento relacionado con dicha especificidad. Los efectores pueden ser translocados a través de diferentes sistemas de secreción. El análisis de genomas de rizobios ha permitido identificar en algunos la presencia de sistemas de secreción de tipo VI (T6SS). El T6SS tiene como componente principal una nanoestructura similar a las que utilizan los bacteriófagos1 para inyectar su ADN y que las bacterias usan para secretar proteínas. Los genes implicados en la formación de T6SS están agrupados y los que codifican para componentes estructurales del sistema presentan mayor grado de conservación entre rizobios y frente a otras bacterias en comparación a los genes que codifican para efectores y reguladores del sistema. En nuestro grupo se está estudiando el T6SS de Rhizobium etli bv mimosae Mim12 aislada de nódulos de Mimosa affinis y capaz de nodular además Phaseolus vulgaris y Leucaena leucocephala. La cepa Mim1 contiene una agrupación de 28 genes en el plásmido f no simbiótico, relacionados con la formación de un T6SS, presentando una organización similar a la descrita en Agrobacterium tumefaciens C583 que consiste en dos operones divergentes. Se ha descrito para varios microorganismos que cuando el T6SS está activo, las proteínas Hcp y VgrG que forman parte del aparato de secreción pueden detectarse en el medio extracelular3. Los genes que codifican proteínas estructurales en las dos bacterias presentan una gran similitud, así Hcp muestra un 94% de identidad entre ambas permitiendo que los anticuerpos que detectan Hcp de Agrobacterium3 también reaccionen con Hcp de Mim1. Utilizando anticuerpos contra Hcp de Agrobacterium se ha identificado esta proteína en el medio extracelular de cultivos de Mim1 en fase estacionaria y débilmente en fase exponencial. También se ha demostrado su presencia en nódulos de judía y en cultivos crecidos en presencia de exudados de L. leucocephala, P. vulgaris y Pisum sativum. Además, con el fin de conocer en qué condiciones se activa el T6SS de Mim1, se analizó una región de ADN presumiblemente promotora comprendida entre las dos agrupaciones de genes orientados de forma divergente de Mim1. Esta región se fusionó transcripcionalmente a un gen b-gal delator sin promotor del vector pMP220 en las dos posibles orientaciones, una de las orientaciones (P1) controlaría la expresión de genes como hcp y posibles efectores y la otra (P2) de otros genes estructurales. Los resultados mostraron que ambas orientaciones se expresaban a altas DO600 (0,8-1) aunque los valores de P1 fueron entre dos y tres veces superiores a los de P2. Sin embargo a bajas DO600 (0,1-0,2) la actividad de P1 ser redujo a la mitad y la de P2 a niveles del control sin promotor. Con el objetivo de conocer el papel del T6SS en simbiosis se han realizado 3 mutantes que afectan a genes estructurales del T6SS de Mim1, uno en el gen hcp, otro en tssM y el tercero es una deleción de todos los genes presumiblemente dependientes de P2. Se examinó el fenotipo producido en P. vulgaris y L. leucocephala y se observó que los tres mutantes produjeron nódulos blancos y plantas con un porte similar a plantas no inoculadas, con menor tamaño que las inoculadas con la cepa parental y con un color más amarillento. En este trabajo se ha mostrado por primera vez que la presencia de un T6SS en rizobios tiene un efecto beneficioso en la simbiosis con varios hospedadores. En estos momentos se esta trabajando en la caracterización de posibles efectores. Referencias. 1. Records AR. 2011 The type VI secretion system: a multipurpose delivery sustem with a phage-like machinery. Mol Plant Microbe Interact 24: 751-757. 2. Rogel MA et al. 2014. Genomic basis of symbiovar mimosae in Rhizobium etli. BMC Genomics 15: 575 3. Wu, HY et al. 2012. Acid-induced type VI secretion system is regulated by ExoR-ChvG/Chv

Characterization of type VI secretion systems (T6SS) of endosymbionts from mimosa or lupine

The T6SS is a nanosyringe that injects proteins into prokaryotic or eukaryotic cells, and it is encoded in the genomes of more than 25% of Gram-negative bacteria (1). We are studying the T6SS of Rhizobium etli Mim1 and Bradyrhizobium sp. LmicA16, symbionts of Phaseolus vulgaris/Leucaena leucocephala and Lupinus micranthus/Lupinus angustifolius/Spartium junceum, respectively. R. etli Mim1 contains a T6SS gene cluster organized in two divergent operons. When the T6SS is active, Hcp, a constituent of the secretory apparatus, can be detected in the extracellular medium (2). Hcp has been immunologically detected in the supernatant of Mim1 cultures. This protein was also detected in bean nodule extracts and in cultures grown in the presence of different legumes exudates. The putative divergent promoters located between the two T6SS gene clusters were analysed by ?- gal fusions. The results showed high levels of expression of the two promoters at high OD and low values at lower ODs. Mutants affected in structural genes induced white nodules with P. vulgaris and L. leucocephala. On the other hand, mutagenesis of T6SS structural genes from LmicA16 strain produced different symbiotic phenotypes. An LmicA16 tssC mutant showed reduced levels of nitrogen fixation on L. micranthus, whereas the same mutant induced the formation of few white, non-fixing nodules on L. angustifolius and S. junceum. (1) Ho et al. (2013) Cell Host Microbe 15:9-21. (2) Wu et al. (2012) PLoS Pathog. 8:1-18 Funded by grants BIO2013-43040-P (MINECO), CGL2011-26932 (MICINN) and AL16-PID-06 (UPM)

A comparison of three load-velocity based methods to estimate maximum overhead press performance in weightlifters

This study aimed to evaluate whether lifting velocity can be used to estimate the overhead press one repetition maximum (1RM) and to explore the differences in the accuracy of the 1RM between three velocity-based methods. Twenty-seven weightlifters (16 men and 11 women) participated. The first session was used to test the overhead press 1RM. The second session consisted of an incremental loading test during the overhead press. The mean velocity was registered using a transducer attached to the barbell. A 1-way repeated-measures analysis of variance (ANOVA) with Bonferroni post hoc corrections was applied to the absolute differences between the actual and predicted 1RMs. Raw differences with 95% limits of agreement and ordinary least-products regressions were used to test the concurrent validity of the 1RM prediction methods with respect to the actual 1RM. The ANOVA did not reveal significant differences for the absolute differences respect to the actual 1RM between the three 1RM prediction methods ( F = 3.2, p = .073). The absolute errors were moderate for the Multiple-Point (6.1 ± 3.7%), Two-Point45−75 (8.6 ± 6.2%), and Two-Point45−90 methods (5.7 ± 4.0%). The validity analysis showed that all the 1RM prediction methods underestimated the actual 1RM (1.0–2.2 kg), but ordinary least-products regressions failed to show fixed or proportional bias. These results suggest that the Multiple-Point and Two-Point45−90 velocity-based methods might be viable tools to predict the overhead press 1RM in weightlifters, but practitioners are encouraged to use the direct 1RM for a more accurate prescription of the training loads

Genomic analysis of three Bradyrhizobium geno(species) nodulating Lima bean (Phaseolus lunatus L.) in Peru

The Lima bean (Phaseolus lunatus), also known as pallar, ibes, garrofón or butter bean in Peru, México, Spain and USA, respectively, is the second most economically important species of Phaseolus. Peru is a centre of origin and domestication of Lima bean. This crop is cultivated mainly in the Central coast of Peru under a subtropical arid climate. In contrast to the common bean (Phaseolus vulgaris) which forms nodules with fast growing Rhizobium strains, the Lima bean forms nodules with slow growing bacteria of the Bradyrhizobium genus (López-López et al. 2013, Ormeño-Orrillo et al. 2006). We found strains of Bradyrhizobium yuanmingense and of three novel Bradyrhizobium genospecies inside P. lunatus nodules in Peru (Ormeño- Orrillo et al. 2006). Strains of the three novel genospecies were characterized by showing an extra-slow growing phenotype (generation time > 10 h-1) and strong alkali production in yeast extract mannitol medium. Two of the novel genospecies were recently named as Bradyrhizobium paxllaeri and Bradyrhizobium icense (Durán et al. 2014). B. paxllaeri strains dominate nodule occupancy followed by those of B. icense and then the third and yet-unnamed genospecies. With the aim to gain insights into this differential competitive ability, we sequenced the genome of one representative strain of each species. Sequencing was performed with the Illumina HiSeq or MiSeq platform and genome assembly with the SPAdes program. Gene prediction and automated annotation was performed with Prokka and RAST. Annotation of genes putatively involved in competitiveness was manually curated. Assemblies had from 55 to 175 contigs, with N50 sizes > 131 kb. Genome sizes of B. paxllaeri and B. icense were similar (8.2 Mb) and larger than that of the third genospecies (7.8 Mb). Preliminary analysis revealed differences between B. paxllaeri and the other two genospecies such as more genes for type IV pilus and two nodA genes. A comparative genomic analysis of P. lunatus symbionts will be presented at the meeting