Population genomics of host specificity in Rhizobium leguminosarum bv. viciae

Legumes establish a root-nodule symbiosis with soil bacteria collectively known as rhizobia. This symbiosis allows legumes to benefit from the nitrogen fixation capabilities of rhizobia and thus to grow in the absence of any fixed nitrogen source. This is especially relevant for Agriculture, where intensive plant growth depletes soils of useable, fixed nitrogen sources. One of the main features of the root nodule symbiosis is its specificity. Different rhizobia are able to nodulate different legumes. Rhizobium leguminosarum bv. viciae is able to establish an effective symbiosis with four different plant genera (Pisum, Lens, Vicia, Lathyrus), and any given isolate will nodulate any of the four plant genera. A population genomics study with rhizobia isolated from P. sativum, L. culinaris, V. sativa or V. faba, all originating in the same soil, showed that plants select specific genotypes from those available in that soil. This was demonstrated at the genome-wide level, but also for specific genes. Accelerated mesocosm studies with successive plant cultures provided additional evidence on this plant selection and on the nature of the genotypes selected. Finally, representatives from the major rhizobial genotypes isolated from these plants allowed characterization of the size and nature of the respective pangenome and specific genome compartments. These were compared to the different genotypes ?symbiotic and non-symbiotic?present in rhizobial populations isolated directly from the soil without plant intervention

Biocontrol capabilities of the genus Serratia

This review focuses on the production of natural bioactive products and their biocontrol capabilities of the enterobacterial genus Serratia. Serratia represents a unique group of enterobacteria with a notable secondary metabolism, able to produce a wide range of natural bioactive products including the b-lactam antibiotic carbapenem or the antifungal compound oocydin A. However, until very recently, most of the Serratia isolates originated from human and animal infections, and a systematic approach to the isolation of Serratia from natural habitats has been missing. The paucity of environmental isolates has so far limited our understanding of the potential of Serratia to produce new natural bioactive products and their capacity to be used in sustainable agriculture as biocontrol agents. The ability to isolate Serratia from soils, together with the analytical capabilities 2 afforded by the democratization of genome sequencing methodologies, opens the door to the isolation and characterization of such novel biocontrol agents, hitherto inaccessible. Introduction In 1823, Bartolomeo Bizio, a pharmacist from Padua in Italy, described Serratia marcescens (Bizio 1823) representing the type species of the new genus. A remarkable characteristic of this bacterium was the production of a bright-red pigment called prodigiosin (Williams 1973). A miraculous bloody discolouration in polenta (corn mush) and bread drew the attention of Bizio. He identified a microorganism as the cause of this phenomenon that he named Serratia marcescens: Serratia in honour of an Italian physicist named Serafino Serrati, and marcescens from the Latin word for decaying, because the blood pigment was found to deteriorate quickly. The pigment responsible for the bloody discolouration was later on described and named prodigiosin. Members of the type species S. marcescens are prodigiosin producers and opportunistic nosocomial pathogens, and represent the most important human pathogens within the genus (Eisenstein 1990). Bacteria fromPeer reviewe

Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil

Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil

Characterisation of Non-symbiotic Rhizobial and Serratia Populations from Soil

El suelo representa unos de los ambientes más complejos a nivel microbiano y un gran reservorio de éstos. En este trabajo se han estudiado dos grupos diferentes de bacterias gram-negativas, los Rizobios y Serratia. Los Rizobios establecen endosimbiosis con plantas, fundamentalmente del grupo de las Fabaceae (leguminosas). En esta simbiosis, las leguminosas se alimentan del nitrógeno atmosférico fijado a amonio por los Rizobios. Como consecuencia las leguminosas se independizan de la necesidad de un suministro externo de nitrógeno fijado. Serratia es un género de bacterias de la familia Enterobacteriaceae que destaca por su metabolismo secundario, y algunos compuestos derivados de este metabolismo, como la prodigiosina o los carbapenemas, han sido extensamente estudiados. La utilización de medios semi-selectivos de crecimiento, junto con un cribado por PCR utilizando marcadores de género desarrollados en este trabajo o de especie, resultó en el aislamiento de rizobios de crecimiento rápido y lento de los géneros Neorhizobium, Ensifer y Bradyrhizobium, así como de enterobacterias del género Serratia, a partir de suelos donde nunca se habían cultivado leguminosas. Esta metodología, permitió el aislamiento y caracterización de Rizobios, en particular, de Rizobios que no contienen ni genes de nodulación ni de fijación de nitrógeno, denominados no simbióticos, que hasta este trabajo no habían sido descritos detalladamente, también de Serratia, cuyas poblaciones tampoco habían sido bien estudiadas, en ambos casos debido a la falta de metodología apropiada. La presencia y abundancia de Rizobios varió en los diferentes suelos estudiados. Las poblaciones de Rizobios no simbióticos fueron en todos los casos, mayores y más diversas que las de los simbióticos obtenidos por el método de planta trampa. Como resultado, se identificaron nuevas poblaciones de Rizobios no-simbioticos y se describió la primera especie de Neorhizobium no simbiótico. La comparación a nivel genómico de dos aislados de Ensifer de un mismo suelo, uno de ellos simbiótico y otro no simbiótico, muy parecidos filogenéticamente, puso de manifiesto la reorganización de los plásmidos simbióticos (pSyms), particularmente del pSymA que contiene los genes de nodulación y fijación. También se aislaron Rizobios del género de crecimiento lento Bradyrhizobium; esta población resultó ser muy diversa, conteniendo aislados tanto simbióticos, como no simbióticos o solamente fijadores de nitrógeno. Por otro lado, los aislamientos de Serratia obtenidos reproducen la diversidad de la totalidad del género Serratia. El cribado fenotípico de compuestos relacionados con el metabolismo secundario mostró un rango de producción muy interesante de compuestos, como por ejemplo antibióticos y antifúngicos. ----------ABSTRACT---------- Soil represents one of the most complex environments and a large bacterial reservoir. In this work, two groups of Gram-negative soil bacteria were studied, Rhizobia and Serratia. Rhizobia establish endosymbioses mainly with plants belonging to the Fabaceae (legumes) group. During this symbiosis, legume plants are able to feed from the atmospheric nitrogen fixed to ammonia by the Rhizobia, which makes them independent from any external fixed nitrogen supply. Serratia belong to a genus within the Enterobacteriaceae family; characteristic of these bacteria is their secondary metabolism, producing compounds such as prodigiosin or carbapenem that have been extensively studied. Semi-selective enrichment, followed by PCR screening with genus-specific markers developed in this work and species markers, resulted in the successful direct isolation of fast and slow-growing Rhizobia of the genera Neorhizobium, Ensifer and Bradyrhizobium, and of the enterobacterium Serratia, from different soils where no legumes had been cultivated. This methodology allowed the isolation and characterisation of Rhizobia, particularly of those lacking either nodulation or fixation genes, which, before these work, had never studied at this level and of Serratia, whose populations have also been poorly studied, in both cases due to the lack of appropriate methodology. Abundance and presence of Rhizobia varied among soils, but the rhizobial non-symbiotic populations were, in all cases, larger and more diverse than the symbiotic ones that were obtained using the trap plant method. This led to the identification of novel non-symbiotic Rhizobia populations and to the first non-symbiotic Neorhizobium species description. It also allowed the genomic comparison of two Ensifer isolates from the same soil, highly-related phylogenetically, one containing symbiotic genes and another one missing them altogether. Whole genome analyses and alignment showed pSyms reorganisation –particularly of pSymA that harbours the nodulation and fixation genes– between these strains. Slow-growing Bradyrhizobium were also isolated; our methodology uncovered a very diverse population consisting of symbiotic, non-symbiotic and nitrogenfixing isolates. Our Serratia soil isolates reproduced the diversity of the whole genus. Phenotypic screening of secondary metabolism related compounds, showed production of a full range of potentially interesting compounds, among them some with antibiotic or antifungal activities

Neorhizobium tomejilense sp. nov., first non-symbiotic Neorhizobium species isolated from a dryland agricultural soil in southern Spain

We describe for the first time a non-symbiotic species of the recently described genus Neorhizobium, lacking nodulation or nitrogen fixation genes. The strains were isolated from a dryland agricultural soil in Southern Spain where no record of legume cultivation is available, thus we propose the name Neorhizobium tomejilense sp. nov. (type strain T17_20T, LMG 30623T and CECT 9621T). N. tomejilense exhibit a clear distinct lineage from the other Neorhizobium species, N. galegae HAMBI 540T, N. alkalisoli DSM 21826T, N. huautlense DSM 21817T, based on polyphasic evidence. Phylogenetic marker analysis of 16S rDNA, atpD, glnII, recA, rpoB and thrC genes and genomic identity data derived from the draft genomic sequences showed that N. tomejilense strains clearly separated from the other Neorhizobium species and that N. galegae HAMBI 540T represents the closest type species to N. tomejilense with 90.1 % Average Nucleotide Identity (ANIb), well below the 95-96 % species circumscription threshold. Phenotypic characterisation of N. tomejilense also displayed differences with the other Neorhizobium species. Whole-cell matrix-assisted laser-desorption time-of-flight mass spectrometry (WC MALDI-TOF-MS) fingerprint analysis and the dendrogram derived from the fingerprint profiles, showed a clearly distinct group formed by the three N. tomejilense isolates (T17_20T, T20_22 and T11_12) from the other Neorhizobium especies.We thank Francisco Temprano, Dulce Rodríguez-Navarro, and Francisco Perea, from IFAPA “Las Torres-Tomejil,” for generously facilitating our soil sampling in the Tomejil experimental farm. We are grateful to Aidan Parte for expert advice on bacterial nomenclature.Peer reviewe

Multiple jobholding and path-dependent employment regimes Answering the qualification and protection needs of multiple job holders

'The flexibilisation of labour markets is called for by most political and economic and firms as the sesame towards economic competitiveness. But do employment systems and social protection regimes provide the workforce with the adequate social incentives - in the form of secured, qualifying and acknowledged transitions between or combinations of occupations, that would at the same time facilitate and legitimize this labour flexibility? To answer this question from a very empirical point of view and in a diagnosis form, this study takes a particular form of non-standard employment - multiple jobholding -and explores first, on the basis of the scarce data available in the OECD, the differentiated occupational profiles it is hiding, from post-modern employment forms to archaic and 'bad jobs'. It concentrates then, through a single French case-study, on the training and social policy issues at stake in making multiple jobholding a qualifying and secured form of employment. The French case appears as a negative yardstick to measure the inertia of employment systems in departing from the norm of 'normal' employment understood as full-time monooccupational male employment.' (author's abstract)'Die Flexibilisierung von Arbeitsmaerkten wird von den meisten politischen und oekonomischen Akteuren als ein Allheilmittel zur Steigerung der Wettbewerbsfaehigkeit betrachtet. Bieten jedoch die Beschaeftigungssysteme und sozialen Sicherungssysteme den Beschaeftigten die entsprechenden sozialen Anreize - d.h. abgesicherte, qualifizierende und anerkannte Uebergaenge zwischen (bzw. Kombinationen von) beruflichen Taetigkeiten - an, die gleichzeitig die Flexibilitaet des Arbeitsvermoegens erleichtern und legitimieren? Zur empirischen Beantwortung dieser Frage befasst sich diese Studie mit einer spezifischen Form der atypischen Beschaeftigung - der Mehrfachbeschaeftigung. In einem ersten Schritt werden auf der Basis von OECD-Daten, die verschiedenen beruflichen Profile, die sich hinter diesem Schlagwort verstecken, dargestellt - von sogenannten post-modernen Arbeitsformen bis hin zu archaischen und 'bad jobs'. Die Studie konzentriert sich dann in einem zweiten Schritt auf die weiterbildungs- und sozialpolitischen Fragen, die sich bei der Entwicklung von einer qualifizierenden und gesicherten Mehrfachbeschaeftigung stellen. Dies wird am Beispiel einer franzoesischen Fallstudie deutlich gemacht. Der franzoesische Fall liefert ein gutes Beispiel fuer die Traegheit von Beschaeftigungssystemen, die den Wandel von 'normaler' Beschaeftigung - d.h. von Vollzeitbeschaeftigung an einem Arbeitsplatz von Maennern -hin zu flexibleren Beschaeftigungsformen erschweren.' (Autorenreferat)German title: Mehrfachbeschaeftigung und spezifische Beschaeftigungssysteme: eine Antwort auf die Qualifikations- und Schutzbeduerfnisse von MehrfachbeschaeftigtenAvailable from <a href=http://skylla.wz-berlin.de/pdf/2002/i02-201.pdf target=NewWindow>http://skylla.wz-berlin.de/pdf/2002/i02-201.pdf</a> / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals

Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- l-ido-deoxynojirimycin (l-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of l-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. l-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species