Nitrate elimination by denitrification in hardwood forest soils of the Upper Rhine floodplain – correlation with redox potential and organic matter

Denitrification in floodplains is a major issue for river- and groundwater quality. In the Upper Rhine valley, floodplain forests are about to be restored to serve as flood retention areas (polders). Besides flood attenuation in downstream areas, improvement of water quality became recently a major goal for polder construction. Redox potential monitoring was suggested as a means to support assessment of nitrogen elimination in future floodplains by denitrification during controlled flooding. To elucidate the relationship between redox potential and denitrification, experiments with floodplain soils and in situ measurements were done. Floodplain soil of two depth profiles from a hardwood forest of the Upper Rhine valley was incubated anaerobically with continuous nitrate supply. Reduction of nitrate was followed and compared with redox potential and organic matter content. The redox potential under denitrifying conditions ranged from 10 to 300 mV. Redox potential values decreased with increasing nitrate reduction rates and increasing organic matter content. Furthermore, a narrow correlation between organicmatter and nitrate reduction was observed. Experiments were intended to help interpreting redox potentials generated under in situ conditions as exemplified by in situ observations for the year 1999. Results obtained by experiments and in situ observations showed that monitoring of redox potential could support management of the flooding regime to optimize nitrogen retention by denitrification in future flood retention areas

Influence of carbon availability on dentrification in the central Baltic Sea

Denitrification was investigated in the Baltic proper at two stations with different conditions in the deep water. The Gotland Deep was examined as an example of a basin with anoxic, H2S‐containing deep water and station T was taken as an example of low‐oxygen (<0.2 ml liter−1), sulfide‐free deep water. Denitrification was measured by the acetylene blockage method; in addition, N2O reduction was followed in samples without acetylene. To shed light on the factors limiting denitrification, we compared in situ rates to denitrification after adding nitrate or electron donors. Denitrification was restricted to the layer of the oxic‐anoxic interface in the Gotland Deep and to the water layer near the sediment of station T. For both stations it could be shown that denitrification was not limited by nitrate availability. A lack of available organic C seemed to limit denitrification rates and growth of denitrifiers. As a result of C limitation in the water column, denitrification was restricted to energy‐rich interfaces. In the low‐oxygen water away from energy‐rich interfaces, the less C‐demanding nitrification‐denitrification coupling (NH4+ → N2O → N2) seemed to be favored. Denitrification in the water of the central Baltic seems to be subjected to strong variability due to changing C supply during the course of the year. However, limitation by C availability can be assumed for most of the year and should be taken into account in calculating the N budget of the Baltic

Développement de techniques optiques pour la caractérisation de brouillards de gouttes dans les foyers aéronautiques

The optimization of combustion chambers is generally carried out using numerical simulation tools. When fuel is injected in liquid form, the simulation quality depends on the boundary conditions imposed to this phase close to the injector (diameter, velocity and volume flux of the droplets, slip velocity between phases). These boundary conditions are usually set from an experimental analysis under realistic conditions of injection, which in the best case uses Phase Doppler Anemo-granulometry (PDA). However, this point measurement technique is time consuming for an overall injector characterization and provides a measurement of the volume flux with some limitations. It is also difficult to access variables such as the velocity of the gas phase in the presence of droplets. To address this problem, it seems appropriate to implement spatially resolved optical diagnostic techniques.This study consists in the development of optical field techniques which combine approaches based on Mie scattering, fluorescent emission from droplets or tracers and use PIV algorithms to characterize simultaneously and quantitatively size, velocity and volume flux of the dispersed phase, and velocity of the continuous phase in droplet sprays in a realistic configuration of aeronautical injector. A particular attention is given to the study of the measurement accuracy. Thus, comparisons are carried out with complete databases obtained with the PDA. The analysis of these results is faced withphysical optics models governing phenomena of fluorescence and light scattering by particles using simulations. This approach allows us to effectively interpret the results obtained by direct imaging and define acquisition and processing parameters ensuring optimum accuracy.L’optimisation des chambres de combustion est généralement réalisée à l'aide d’outils de simulation numérique. Lorsque le carburant est injecté sous forme liquide, la qualité des simulations dépend en partie de la définition des conditions aux limites imposées pour cette phase à proximité de l'injecteur (diamètre, vitesse et flux volumique des gouttes, vitesse de glissement entre phases). Ces conditions aux limites sont généralement définies à partir d'une analyse expérimentale dans des conditions réalistes d’injection, qui fait appel, dans le meilleur des cas, à l’utilisation del’Anémogranulomètre Phase Doppler (PDA). Cependant, cette technique ponctuelle est coûteuse en temps pour une caractérisation globale de l’injecteur et fournit une mesure des flux volumiques avec des limitations. Il est également difficile d’accéder à des grandeurs telles que la vitesse de la phase gazeuse en présence des gouttes. Pour répondre à cette problématique, il paraît judicieux de mettre en oeuvre des techniques de diagnostic optique spatialement résolues.Cette étude consiste à développer des techniques optiques de champ couplant des approches basées sur la diffusion de Mie, sur l'émission fluorescente des gouttes ou de traceurs et utilisant des algorithmes de type PIV, pour caractériser de manière simultanée et quantitative la granulométrie, la vitesse et le flux volumique de la phase dispersée, ainsi que la vitesse de la phase continue dans les brouillards de gouttes au sein d’une configuration réaliste de foyer aéronautique. Une attention particulière est portée à l'étude de la précision de la mesure. Ainsi, des comparaisons sont effectuées avec des bases de données complètes obtenues à l’aide du PDA. L'analyse de ces résultats estconfrontée aux modèles de l'optique physique régissant les phénomènes de fluorescence et de diffusion de la lumière par des particules à l’aide de simulations. Cette démarche nous permet d'interpréter efficacement les résultats obtenus par imagerie directe et de définir les paramètres d'acquisition et de traitement assurant une précision optimale des mesures

Divergence in Gene Regulation Contributes to Sympatric Speciation of \u3ci\u3eShewanella baltica\u3c/i\u3e Strains

Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185—the strain isolated from a nitrate-rich environment—upregulated nearly twice the number of shared genes upregulated by OS195—the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations

Whole-genome enrichment provides deep insights into Vibrio cholerae metagenome from an African river

The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (&lt;50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on a Illumina MiSeq platform. Up to 1.8X107 bp (4.5x mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices this study provides a \u201cproof of concept\u201d on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments

Cytotoxicity, Intracellular Replication, and Contact-Dependent Pore Formation of Genotyped Environmental Legionella pneumophila Isolates from HospitalWater Systems in the West Bank, Palestine

Legionella pneumophila is the causative agent of Legionnaires’ disease. Due to the hot climate and intermittent water supply, the West Bank, Palestine, can be considered a high-risk area for this often fatal atypical pneumonia. L. pneumophila occurs in biofilms of natural and man-made freshwater environments, where it infects and replicates intracellularly within protozoa. To correlate the genetic diversity of the bacteria in the environment with their virulence properties for protozoan and mammalian host cells, 60 genotyped isolates from hospital water systems in the West Bank were analyzed. The L. pneumophila isolates were previously genotyped by high resolution Multi Locus Variable Number of Tandem Repeat Analysis (MLVA-8(12)) and sorted according to their relationship in clonal complexes (VACC). Strains of relevant genotypes and VACCs were compared according to their capacity to infect Acanthamoeba castellanii and THP-1 macrophages, and to mediate poreforming cytotoxicity in sheep red blood cells (sRBCs). Based on a previous detailed analysis of the biogeographic distribution and abundance of the MLVA-8(12)-genotypes, the focus of the study was on the most abundant L. pneumophila- genotypes Gt4(17), Gt6 (18) and Gt10(93) and the four relevant clonal complexes [VACC1, VACC2, VACC5 and VACC11]. The highly abundant genotypes Gt4(17) and Gt6(18) are affiliated with VACC1 and sequence type (ST)1 (comprising L. pneumophila str. Paris), and displayed seroroup (Sg)1. Isolates of these two genotypes exhibited significantly higher virulence potentials compared to other genotypes and clonal complexes in theWest Bank. Endemic for theWest Bank was the clonal complex VACC11 (affiliated with ST461) represented by three relevant genotypes that all displayed Sg6. These genotypes unique for the West Bank showed a lower infectivity and cytotoxicity compared to all other clonal complexes and their affiliated genotypes. Interestingly, the L. pneumophila serotypes ST1 and ST461 were previously identified by in situ-sequence based typing (SBT) as main causative agents of Legionnaires’ disease (LD) in the West Bank at a comparable level. Overall, this study demonstrates the site-specific regional diversity of L. pneumophila genotypes in theWest Bank and suggests that a combination of MLVA, cellular infection assays and hierarchical agglomerative cluster analysis allows an improved genotype-based risk assessment

Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus level

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 77 (2011): 5352-5360, doi:10.1128/AEM.00097-11.The use of comparative genomics among different microbiological species has increased substantially as sequence technologies become more affordable. However, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at the time. In this study, we provide a high throughput alternative to this limiting step by coupling comparative genomics to phenotype arrays for five sequenced Shewanella strains. Positive phenotypes were obtained for 441 nutrients (C, N, P, and S sources), with N-based compounds being the most utilized for all strains. Many genes and pathways predicted by genome analyses were confirmed with the comparative phenotype assay, and three degradation pathways believed to be missing in Shewanella were confirmed. A number of previously unknown gene products were predicted to be part of pathways or to have a function, expanding the number of gene targets for future genetic analyses. Ecologically, the comparative high throughput phenotype analysis provided insights into niche specialization within the five different strains. For example, Shewanella amazonensis strain SB2B, isolated from the Amazon River delta, was capable of utilizing 60 C compounds, whereas Shewanella sp. strain W3-18-1, from the deep marine sediment, utilized only 25 of them. In spite of the large number of nutrient sources yielding positive results, our study indicated that except for the N-sources they were not sufficiently informative to predict growth phenotypes from increasing evolutionary distances. Our results indicate the importance of phenotypic evaluation for confirming genome predictions. This strategy will accelerate the functional discovery of genes and provide an ecological framework for microbial genome sequencing projects.The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract numbers DE-AC02-05CH11231 and DE-FG02-08ER64511

Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae)

<p>Abstract</p> <p>Background</p> <p>The explosion in availability of whole genome data provides the opportunity to build phylogenetic hypotheses based on these data as well as the ability to learn more about the genomes themselves. The biological history of genes and genomes can be investigated based on the taxomonic history provided by the phylogeny. A phylogenetic hypothesis based on complete genome data is presented for the genus <it>Shewanella </it>(Gammaproteobacteria: Alteromonadales: Shewanellaceae). Nineteen taxa from <it>Shewanella </it>(16 species and 3 additional strains of one species) as well as three outgroup species representing the genera <it>Aeromonas </it>(Gammaproteobacteria: Aeromonadales: Aeromonadaceae), <it>Alteromonas </it>(Gammaproteobacteria: Alteromonadales: Alteromonadaceae) and <it>Colwellia </it>(Gammaproteobacteria: Alteromonadales: Colwelliaceae) are included for a total of 22 taxa.</p> <p>Results</p> <p>Putatively homologous regions were found across unannotated genomes and tested with a phylogenetic analysis. Two genome-wide data-sets are considered, one including only those genomic regions for which all taxa are represented, which included 3,361,015 aligned nucleotide base-pairs (bp) and a second that additionally includes those regions present in only subsets of taxa, which totaled 12,456,624 aligned bp. Alignment columns in these large data-sets were then randomly sampled to create smaller data-sets. After the phylogenetic hypothesis was generated, genome annotations were projected onto the DNA sequence alignment to compare the historical hypothesis generated by the phylogeny with the functional hypothesis posited by annotation.</p> <p>Conclusions</p> <p>Individual phylogenetic analyses of the 243 locally co-linear genome regions all failed to recover the genome topology, but the smaller data-sets that were random samplings of the large concatenated alignments all produced the genome topology. It is shown that there is not a single orthologous copy of 16S rRNA across the taxon sampling included in this study and that the relationships among the multiple copies are consistent with 16S rRNA undergoing concerted evolution. Unannotated whole genome data can provide excellent raw material for generating hypotheses of historical homology, which can be tested with phylogenetic analysis and compared with hypotheses of gene function.</p