Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus

Lupinus mariae-josephi is a recently described endemic Lupinus species from a small area in Eastern Spain where it thrives in soils with active lime and high pH. The L. mariae-josephi root symbionts were shown to be very slow-growing bacteria with different phenotypic and symbiotic characteristics from those of Bradyrhizobium strains nodulating other Lupinus. Their phylogenetic status was examined by multilocus sequence analyses of four housekeeping genes (16S rRNA, glnII, recA, and atpD) and showed the existence of a distinct evolutionary lineage for L. mariae-josephi that also included Bradyrhizobium jicamae. Within this lineage, the tested isolates clustered in three different sub-groups that might correspond to novel sister Bradyrhizobium species. These core gene analyses consistently showed that all the endosymbiotic bacteria isolated from other Lupinus species of the Iberian Peninsula were related to strains of the B. canariense or B. japonicum lineages and were separate from the L. mariae-josephi isolates. Phylogenetic analysis based on nodC symbiotic gene sequences showed that L. mariae-josephi bacteria also constituted a new symbiotic lineage distant from those previously defined in the genus Bradyrhizobium. In contrast, the nodC genes of isolates from other Lupinus spp. from the Iberian Peninsula were again clearly related to the B. canariense and B. japonicum bv. genistearum lineages. Speciation of L. mariae-josephi bradyrhizobia may result from the colonization of a singular habitat by their unique legume host.

Análisis genómico y funcional de los sistemas de Quorum Sensing en Rhizobium leguminosarum

Rhizobium leguminosarum (Rl) es una alfa-proteobacteria capaz de establecer una simbiosis diazotrófica con distintas leguminosas. A pesar de la importancia de esta simbiosis en el balance global del ciclo del nitrógeno, muy pocos genomas de rhizobios han sido secuenciados, que aporten nuevos conocimientos relacionados con las características genéticas que contribuyen a importantes procesos simbióticos. Únicamente tres secuencias completas de Rl han sido publicadas: Rl bv. viciae 3841 y dos genomas de Rl bv. trifolii (WSM1325 y WSM2304), ambos simbiontes de trébol. La secuencia genómica de Rlv UPM791 se ha determinado por medio de secuenciación 454. Este genoma tiene un tamaño aproximado de 7.8 Mb, organizado en un cromosoma y 5 replicones extracromosómicos, que incluyen un plásmido simbiótico de 405 kb. Este nuevo genoma se ha analizado en relación a las funciones simbióticas y adaptativas en comparación con los genomas completos de Rlv 3841 y Rl bv. trifolii WSM1325 y WSM2304. Mientras que los plásmidos pUPM791a y b se encuentran conservados, el plásmido simbiótico pUPM791c exhibe un grado de conservación muy bajo comparado con aquellos descritos en las otras cepas de Rl. Uno de los factores implicados en el establecimiento de la simbiosis es el sistema de comunicación intercelular conocido como Quorum Sensing (QS). El análisis del genoma de Rlv UPM791 ha permitido la identificación de dos sistemas tipo LuxRI mediados por señales de tipo N-acyl-homoserina lactonas (AHLs). El análisis mediante HPLC-MS ha permitido asociar las señales C6-HSL, C7-HSL y C8-HSL al sistema rhiRI, codificado en el plásmido simbiótico; mientras que el sistema cinRI, localizado en el cromosoma, produce 3OH-C14:1-HSL. Se ha identificado una tercera sintasa (TraI) codificada en el plásmido simbiótico, pero su regulador correspondiente se encuentra truncado debido a un salto de fase. Adicionalmente, se han encontrado tres reguladores de tipo LuxR-orphan que no presentan una sintasa LuxI asociada. El efecto potencial de las señales tipo AHL se ha estudiado mediante una estrategia de quorum quenching, la cual interfiere con los sistemas de QS de la bacteria. Esta estrategia está basada en la introducción del gen aiiA de Bacillus subtilis, que expresa constitutivamente una enzima lactonasa degradadora de AHLs. Para llevar a cabo el análisis en condiciones simbióticas, se ha desarrollado un sistema de doble marcaje que permite la identificación basado en los marcadores gusA y celB, que codifican para una enzima β–glucuronidasa y una β–galactosidasa termoestable, respectivamente. Los resultados obtenidos indican que Rlv UPM791 predomina sobre la cepa Rlv 3841 para la formación de nódulos en plantas de guisante. La baja estabilidad del plásmido que codifica para aiiA, no ha permitido obtener una conclusión definitiva sobre el efecto de la lactonasa AiiA en competitividad. Con el fin de analizar el significado y la regulación de la producción de moléculas señal tipo AHL, se han generado mutantes defectivos en cada uno de los dos sistemas de QS. Se ha llevado a cabo un análisis detallado sobre la producción de AHLs, formación de biofilm y simbiosis con plantas de guisante, veza y lenteja. El efecto de las deleciones de los genes rhiI y rhiR en Rlv UPM791 es más drástico en ausencia del plásmido pUPM791d. Mutaciones en cinI o cinRIS muestran tanto ausencia de señales, como producción exclusivamente de las de bajo peso molecular, respectivamente, producidas por el sistema rhiRI. Estas mutaciones mostraron un efecto importante en simbiosis. El sistema rhiRI se necesita para un comportamiento simbiótico normal. Además, mutantes cinRIS generaron nódulos blancos e ineficientes, mientras que el mutante cinI fue incapaz de producir nódulos en ninguna de las leguminosas utilizadas. Dicha mutación resultó en la inestabilización del plasmido simbiótico por un mecanismo dependiente de cinI que no ha sido aclarado. En general, los resultados obtenidos indican la existencia de un modelo de regulación dependiente de QS significativamente distinto a los que se han descrito previamente en otras cepas de R. leguminosarum, en las cuales no se había observado ningún fenotipo relevante en simbiosis. La regulación de la producción de AHLs Rlv UPM791 es un proceso complejo que implica genes situados en los plásmidos UPM791c y UPM791d, además de la señal 3-OH-C14:1-HSL. Finalmente, se ha identificado un transportador de tipo RND, homologo a mexAB-oprM de P. aeruginosa e implicado en la extrusión de AHLs de cadena larga. La mutación he dicho transportador no tuvo efectos apreciables sobre la simbiosis. ABSTRACT Rhizobium leguminosarum (Rl) is a soil alpha-proteobacterium that establishes a diazotrophic symbiosis with different legumes. Despite the importance of this symbiosis to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far which provide new insights into the genetic features contributing to symbiotically relevant processes. Only three complete sequences of Rl strains have been published: Rl bv. viciae 3841, harboring six plasmids (7.75 Mb) and two Rl bv. trifolii (WSM1325 and WSM2304), both clover symbionts, harboring 5 and 4 plasmids, respectively (7.41 and 6.87 Mb). The genomic sequence of Rlv UPM791 was undertaken by means of 454 sequencing. Illumina and Sanger reads were used to improve the assembly, leading to 17 final contigs. This genome has an estimated size of 7.8 Mb organized in one chromosome and five extrachromosomal replicons, including a 405 kb symbiotic plasmid. Four of these plasmids are already closed, whereas there are still gaps in the smallest one (pUPM791d) due to the presence of insertion elements and repeated sequences, which difficult the assembly. The annotation has been carried out thanks to the Manatee pipeline. This new genome has been analyzed as regarding symbiotic and adaptive functions in comparison to the Rlv 3841 complete genome, and to those from Rl bv. trifolii strains WSM1325 and WSM2304. While plasmids pUPM791a and b are conserved, the symbiotic plasmid pUPM791c exhibited the lowest degree of conservation as compared to those from the other Rl strains. One of the factors involved in the symbiotic process is the intercellular communication system known as Quorum Sensing (QS). This mechanism allows bacteria to carry out diverse biological processes in a coordinate way through the production and detection of extracellular signals that regulate the transcription of different target genes. Analysis of the Rlv UPM791 genome allowed the identification of two LuxRI-like systems mediated by N-acyl-homoserine lactones (AHLs). HPLC-MS analysis allowed the adscription of C6-HSL, C7-HSL and C8-HSL signals to the rhiRI system, encoded in the symbiotic plasmid, whereas the cinRI system, located in the chromosome, produces 3OH-C14:1-HSL, previously described as “bacteriocin small”. A third synthase (TraI) is encoded also in the symbiotic plasmid, but its cognate regulator TraR is not functional due to a fameshift mutation. Three additional LuxR orphans were also found which no associated LuxI-type synthase. The potential effect of AHLs has been studied by means of a quorum quenching approach to interfere with the QS systems of the bacteria. This approach is based upon the introduction into the strains Rl UPM791 and Rl 3841 of the Bacillus subtilis gene aiiA expressing constitutively an AHL-degrading lactonase enzyme which led to virtual absence of AHL even when AiiA-expressing cells were a fraction of the total population. No significant effect of AiiA-mediated AHL removal on competitiveness for growth in solid surface was observed. For analysis under symbiotic conditions we have set up a two-label system to identify nodules produced by two different strains in pea roots, based on the markers gusA and celB, encoding a β–glucuronidase and a thermostable β–galactosidase enzymes, respectively. The results obtained show that Rlv UPM791 outcompetes Rlv 3841 for nodule formation in pea plants, and that the presence of the AiiA plasmid does not significantly affect the relative competitiveness of the two Rlv strains. However, the low stability of the pME6863 plasmid, encoding aiiA, did not lead to a clear conclusion about the AiiA lactonase effect on competitiveness. In order to further analyze the significance and regulation of the production of AHL signal molecules, mutants deficient in each of the two QS systems were constructed. A detailed analysis of the effect of these mutations on AHL production, biofilm formation and symbiosis with pea, vetch and lentil plants has been carried out. The effect of deletions on Rlv UPM791 rhiI and rhiR genes is more pronounced in the absence of plasmid pUPM791d, as no signal is detected in UPM791.1, lacking this plasmid. Mutations in cinI or cinRIS show either no signals, or only the small ones produced by the rhiRI system, suggesting that cinR might be regulating the rhiRI system. These mutations had a strong effect on symbiosis. Analysis of rhi mutants revealed that rhiRI system is required for normal symbiotic performance, as a drastic reduction of symbiotic fitness is observed when rhiI is deleted, and rhiR is essential for nitrogen fixation in the absence of plasmid pUPM791d. Furthermore, cinRIS mutants resulted in white and inefficient nodules, whereas cinI mutant was unable to form nodules on any legume tested. The latter mutation is associated to the instabilization of the symbiotic plasmid through a mechanism still uncovered. Overall, the results obtained indicate the existence of a model of QS-dependent regulation significantly different to that previously described in other R. leguminosarum strains, where no relevant symbiotic phenotype had been observed. The regulation of AHL production in Rlv UPM791 is a complex process involving the symbiotic plasmid (pUPM791c) and the smallest plasmid (pUPM791d), with a key role for the 3-OH-C14:1-HSL signal. Finally, we made a search for potential AHL transporters in Rlv UPM791 genome. These signals diffuse freely across membranes, but in the case of the long-chain AHLs an active efflux system might be required, as it has been described for C12-HSL in the case of Pseudomonas aeruginosa. We have identified a putative AHL transporter of the RND family homologous to P. aeruginosa mexAB-oprM. A mutant strain deficient in this transporter has been generated, and TLC analysis shows absence of 3OH-C14:1-HSL in its supernatant. This deficiency was complemented by the reintroduction of an intact copy of the genes via plasmid transfer. The mutation in mexAB genes had no significant effects on the symbiotic performance of R. leguminosarum bv. viciae.

Three functional luciferase domains in a single polypeptide chain

We report a unique case of a gene containing three homologous and contiguous repeat sequences, each of which, after excision, cloning, and expression in Escherichia coli, is shown to code for a peptide catalyzing the same reaction as the native protein, Gonyaulax polyedra luciferase (Mr = 137). This enzyme, which catalyzes the light-emitting oxidation of a linear tetrapyrrole (dinoflagellate luciferin), exhibits no sequence similarities to other luciferases in databases. Sequence analysis also reveals an unusual evolutionary feature of this gene: synonymous substitutions are strongly constrained in the central regions of each of the repeated coding sequences.

Rapid transition in the structure of a coral reef community: The effects of coral bleaching and physical disturbance

Coral reef communities are in a state of change throughout their geographical range. Factors contributing to this change include bleaching (the loss of algal symbionts), storm damage, disease, and increasing abundance of macroalgae. An additional factor for Caribbean reefs is the aftereffects of the epizootic that reduced the abundance of the herbivorous sea urchin, Diadema antillarum. Although coral reef communities have undergone phase shifts, there are few studies that document the details of such transitions. We report the results of a 40-month study that documents changes in a Caribbean reef community affected by bleaching, hurricane damage, and an increasing abundance of macroalgae. The study site was in a relatively pristine area of the reef surrounding the island of San Salvador in the Bahamas. Ten transects were sampled every 3–9 months from November 1994 to February 1998. During this period, the corals experienced a massive bleaching event resulting in a significant decline in coral abundance. Algae, especially macroalgae, increased in abundance until they effectively dominated the substrate. The direct impact of Hurricane Lili in October 1996 did not alter the developing community structure and may have facilitated increasing algal abundance. The results of this study document the rapid transition of this reef community from one in which corals and algae were codominant to a community dominated by macroalgae. The relatively brief time period required for this transition illustrates the dynamic nature of reef communities.

Conserved circadian elements in phylogenetically diverse algae

Circadian expression of the luciferin-binding protein (LBP) from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. A small interval in the lbp 3′-untranslated region, which contains seven UG-repeats, serves as a cis-acting element to which a trans-acting factor (CCTR) binds in a circadian manner. Its binding activity correlates negatively with the circadian expression of LBP. Here I report the identification of a protein in the green alga Chlamydomonas reinhardtii that represents a CCTR analog. It binds both specifically and under control of the circadian clock to the UG-repeat region. The data show for the first time that circadian cis-elements implicated in translational regulation have been conserved during evolution.

Defensive extrusive ectosymbionts of Euplotidium (Ciliophora) that contain microtubule-like structures are bacteria related to Verrucomicrobia

Epixenosomes, ectosymbionts on hypotrich ciliates (genus Euplotidium) defend their host against the ciliate predator Litonotus lamella. Although here only Euplotidium itoi and Euplotidium arenarium from tide pools along a rocky shore near Leghorn (Ligurian sea) were studied in detail, these epibionts are certainly present on specimens of E. itoi and on other Euplotidium species in similar north coastal habitats. The complex life history of epixenosomes has two main stages. In stage I, cells with typical prokaryotic structure divide by binary fission. Stage II cells show complex organization with different cytoplasmic compartments where an extrusive apparatus within a proteinaceous matrix, although not membrane-bounded, differs from the remaining cytoplasm. The ejection process is involved in defense; extrusive apparatus is surrounded by a basket consisting of bundles of tubules. These tubules, 22 ± 3 nm in diameter, delimited by a wall made up of globular structures, are sensitive to inhibitor of tubulin polymerization (nocodazole/4°C temperature) and react positively with different antitubulin antibodies, two of which are monoclonal. The prokaryotic vs. eukaryotic nature of epixenosomes was resolved by comparative sequence analysis of amplified small subunit rRNA genes and in situ hybridization with fluorescently labeled rRNA-targeted polynucleotide probes. These unique ectosymbionts are phylogenetically related to Verrucomicrobia. Epixenosomes represent marine symbionts in this recently discovered division of the Bacteria.

Establishment of an animal–bacterial association: Recruiting symbiotic vibrios from the environment

While most animal–bacterial symbioses are reestablished each successive generation, the mechanisms by which the host and its potential microbial partners ensure tissue colonization remain largely undescribed. We used the model association between the squid Euprymna scolopes and Vibrio fischeri to examine this process. This light organ symbiosis is initiated when V. fischeri cells present in the surrounding seawater enter pores on the surface of the nascent organ and colonize deep epithelia-lined crypts. We discovered that when newly hatched squid were experimentally exposed to natural seawater, the animals responded by secreting a viscous material from the pores of the organ. Animals maintained in filtered seawater produced no secretions unless Gram-negative bacteria, either living or dead, were reintroduced. The viscous material bound only lectins that are specific for either N-acetylneuraminic acid or N-acetylgalactosamine, suggesting that it was composed of a mucus-containing matrix. Complex ciliated fields on the surface of the organ produced water currents that focused the matrix into a mass that was tethered to, and suspended above, the light organ pores. When V. fischeri cells were introduced into the seawater surrounding the squid, the bacteria were drawn into its fluid-filled body cavity during ventilation and were captured in the matrix. After residing as an aggregate for several hours, the symbionts migrated into the pores and colonized the crypt epithelia. This mode of infection may be an example of a widespread strategy by which aquatic hosts increase the likelihood of successful colonization by rarely encountered symbionts.

The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium “Thiodendron latens.” By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This “earliest branching protist” that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

A novel application of gene arrays: Escherichia coli array provides insight into the biology of the obligate endosymbiont of tsetse flies

Symbiotic associations with microorganisms are pivotal in many insects. Yet, the functional roles of obligate symbionts have been difficult to study because it has not been possible to cultivate these organisms in vitro. The medically important tsetse fly (Diptera: Glossinidae) relies on its obligate endosymbiont, Wigglesworthia glossinidia, a member of the Enterobacteriaceae, closely related to Escherichia coli, for fertility and possibly nutrition. We show here that the intracellular Wigglesworthia has a reduced genome size smaller than 770 kb. In an attempt to understand the composition of its genome, we used the gene arrays developed for E. coli. We were able to identify 650 orthologous genes in Wigglesworthia corresponding to ≈85% of its genome. The arrays were also applied for expression analysis using Wigglesworthia cDNA and 61 gene products were detected, presumably coding for some of its most abundant products. Overall, genes involved in cell processes, DNA replication, transcription, and translation were found largely retained in the small genome of Wigglesworthia. In addition, genes coding for transport proteins, chaperones, biosynthesis of cofactors, and some amino acids were found to comprise a significant portion, suggesting an important role for these proteins in its symbiotic life. Based on its expression profile, we predict that Wigglesworthia may be a facultative anaerobic organism that utilizes ammonia as its major source of nitrogen. We present an application of E. coli gene arrays to obtain broad genome information for a closely related organism in the absence of complete genome sequence data.

Regulation of Oleoresinosis in Grand Fir (Abies grandis)1 : Differential Transcriptional Control of Monoterpene, Sesquiterpene, and Diterpene Synthase Genes in Response to Wounding

Grand fir (Abies grandis Lindl.) has been developed as a model system for the study of wound-induced oleoresinosis in conifers as a response to insect attack. Oleoresin is a roughly equal mixture of turpentine (85% monoterpenes [C10] and 15% sesquiterpenes [C15]) and rosin (diterpene [C20] resin acids) that acts to seal wounds and is toxic to both invading insects and their pathogenic fungal symbionts. The dynamic regulation of wound-induced oleoresin formation was studied over 29 d at the enzyme level by in vitro assay of the three classes of synthases directly responsible for the formation of monoterpenes, sesquiterpenes, and diterpenes from the corresponding C10, C15, and C20 prenyl diphosphate precursors, and at the gene level by RNA-blot hybridization using terpene synthase class-directed DNA probes. In overall appearance, the shapes of the time-course curves for all classes of synthase activities are similar, suggesting coordinate formation of all of the terpenoid types. However, closer inspection indicates that the monoterpene synthases arise earlier, as shown by an abbreviated time course over 6 to 48 h. RNA-blot analyses indicated that the genes for all three classes of enzymes are transcriptionally activated in response to wounding, with the monoterpene synthases up-regulated first (transcripts detectable 2 h after wounding), in agreement with the results of cell-free assays of monoterpene synthase activity, followed by the coordinately regulated sesquiterpene synthases and diterpene synthases (transcription beginning on d 3–4). The differential timing in the production of oleoresin components of this defense response is consistent with the immediate formation of monoterpenes to act as insect toxins and their later generation at solvent levels for the mobilization of resin acids responsible for wound sealing.

Respiratory Elicitors from Rhizobium meliloti Affect Intact Alfalfa Roots1

Molecules produced by Rhizobium meliloti increase respiration of alfalfa (Medicago sativa L.) roots. Maximum respiratory increases, measured either as CO2 evolution or as O2 uptake, were elicited in roots of 3-d-old seedlings by 16 h of exposure to living or dead R. meliloti cells at densities of 107 bacteria/mL. Excising roots after exposure to bacteria and separating them into root-tip- and root-hair-containing segments showed that respiratory increases occurred only in the root-hair region. In such assays, CO2 production by segments with root hairs increased by as much as 100% in the presence of bacteria. Two partially purified compounds from R. meliloti 1021 increased root respiration at very low, possibly picomolar, concentrations. One factor, peak B, resembled known pathogenic elicitors because it produced a rapid (15-min), transitory increase in respiration. A second factor, peak D, was quite different because root respiration increased slowly for 8 h and was maintained at the higher level. These molecules differ from lipo-chitin oligosaccharides active in root nodulation for the following reasons: (a) they do not curl alfalfa root hairs, (b) they are synthesized by bacteria in the absence of known plant inducer molecules, and (c) they are produced by a mutant R. meliloti that does not synthesize known lipo-chitin oligosaccharides. The peak-D compound(s) may benefit both symbionts by increasing CO2, which is required for growth of R. meliloti, and possibly by increasing the energy that is available in the plant to form root nodules.

Intracellular coexistence of methano- and thioautotrophic bacteria in a hydrothermal vent mussel.

The coexistence of two phylogenetically distinct symbiont species within a single cell, a condition not previously known in any metazoan, is demonstrated in the gills of a Mid-Atlantic Ridge hydrothermal vent mussel (family Mytilidae). Large and small symbiont morphotypes within the gill bacteriocytes are shown to be separate bacterial species by molecular phylogenetic analysis and fluorescent in situ hybridization. The two symbiont species are affiliated with thioautotrophic and methanotrophic symbionts previously found in monospecific associations with closely related mytilids from deep-sea hydrothermal vents and hydrocarbon seeps.