Publications

4467

El Huanglongbing (HLB) es una enfermedad considerada como la más destructiva para los cítricos en el mundo, es causada por Candidatus Liberibacter asiaticus (CLas) y diseminada por el vector Diaphorina citri. El HLB ha generado cuantiosas pérdidas económicas en la citricultura mundial. Todas las variedades comerciales de cítricos son susceptibles a esta enfermedad. La naturaleza de CLas como parásito intra celular estricto limitado al floema dificulta el estudio fitopatológico de la enfermedad. Las herramientas “ómicas”, que permiten aplicar análisis comparativos con enfoque masivos, han resultado útiles para describir la interacción entre el agente patogénico y diferentes especies de cítricos, generando conocimiento sobre las bases moleculares de la patogenicidad de CLas y de las respuestas de los hospederos ante la infección. Sin embargo, muchos procesos inmersos en la compleja interacción CLas-cítricos aún no son del todo comprendidos. En la presente revisión se resumen algunos de los principales hallazgos en la última década relacionados con los posibles mecanismos de patogenicidad de CLas a nivel molecular, así como de las respuestas transcripcionales y metabólicas inducidas en cítricos tolerantes o susceptibles, ante la infección. Este conocimiento es necesario para el diseño e implementación de nuevas estrategias para el manejo sustentable de la enfermedad.

Candidatus Liberibacter asiaticus (CLas) se ha dispersado rápidamente a las regiones productoras de cítricos en México, ocasionando impactos económicos y sociales diferenciados. En México, los principales avances en investigación se han centrado en el manejo del vector, Diaphorina citri y en estudios de la interacción de CLas con limón mexicano. Sin embargo, la variabilidad genética de la bacteria en regiones productoras de México se ha estudiado poco. Por lo que, en el presente estudio se analizó la variación de la población mexicana de CLas con procedimientos basados en PCR, secuenciación y electroforesis capilar a través de la detección del número de repeticiones en tándem (TRN) con dos marcadores STR, AGACACA y TACAGAA, el primero localizado en locus genómicos CLIBASIA_01645 y adenosina deaminasas. La distribución de los TRNs en la población mexicana de CLas en ambos loci mostraron variaciones con las poblaciones previamente reportadas en Florida, China y Brasil. Además, en la población mexicana se encontraron tres haplotipos, HA, HB y HC, siendo el primer reporte del haplotipo HC en las regiones citrícolas en México. Interesantemente, las subpoblaciones de CLas del Occidente y Noroeste son diferentes a la del Sureste.

IntroductionNatural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism.MethodsIn this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America.ResultsNine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters.DiscussionContinued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.

The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).

Abstract Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, ‘Candidatus Taurinisymbion ianthellae’, residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. ‘Candidatus Taurinisymbion ianthellae’ incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, ‘Candidatus Nitrosospongia ianthellae’. Metaproteogenomic analyses also suggest that ‘Candidatus Taurinisymbion ianthellae’ imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

AbstractChlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen “Candidatus Clavichlamydia salmonicola”, representing a separate genus within the human and animal pathogenic Chlamydiaceae. The “Ca. Clavichlamydia salmonicola” genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of “Ca. Clavichlamydia salmonicola” allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.