Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability

<p>Abstract</p> <p>Background</p> <p>The <it>Burkholderia cepacia </it>complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF) or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional σ⁷⁰factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the σ⁷⁰family of these bacteria.</p> <p>Results</p> <p>Twenty σ⁷⁰paralogous genes were detected in the <it>Burkholderia cenocepacia </it>strain J2315 (<it>Bcen</it>-J2315) genome, of which 14 were of the ECF (extracytoplasmic function) group. Non-ECF paralogs were related to primary (<it>rpoD</it>), alternative primary, stationary phase (<it>rpoS</it>), flagellin biosynthesis (<it>fliA</it>), and heat shock (<it>rpoH</it>) factors. The number of σ⁷⁰genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of <it>Pseudomonas aeruginosa</it>, a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different σ⁷⁰family architectures, with only three ECF paralogs in common (<it>fecI</it>-like, <it>pvdS </it>and <it>algU</it>). <it>Bcen</it>-J2315 σ⁷⁰paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone (<it>ecfA2</it>), particular Bcc species (<it>sigI</it>), the <it>Burkholderia </it>genus (<it>ecfJ</it>, <it>ecfF</it>, and <it>sigJ</it>), certain proteobacterial groups (<it>ecfA1</it>, <it>ecfC</it>, <it>ecfD</it>, <it>ecfE</it>, <it>ecfG</it>, <it>ecfL</it>, <it>ecfM </it>and <it>rpoS</it>), or were broadly distributed in the eubacteria (<it>ecfI</it>, <it>ecfK</it>, <it>ecfH</it>, <it>ecfB</it>, and <it>rpoD</it>-, <it>rpoH</it>-, <it>fliA</it>-like genes). Genomic instability of this gene family was driven by chromosomal inversion (<it>ecfA2</it>), recent duplication events (<it>ecfA </it>and <it>RpoD</it>), localized (<it>ecfG</it>) and large scale deletions (<it>sigI</it>, <it>sigJ</it>, <it>ecfC</it>, <it>ecfH</it>, and <it>ecfK</it>), and a phage integration event (<it>ecfE</it>).</p> <p>Conclusion</p> <p>The Bcc σ⁷⁰gene family was found to be under strong selective pressures that could lead to acquisition/deletion, and duplication events modifying its architecture. Comparative analysis of Bcc and <it>Pseudomonas aeruginosa </it>σ⁷⁰gene families revealed distinct evolutionary strategies, with the Bcc having selected several alternative primary factors, something not recorded among <it>P. aeruginosa </it>and only previously reported to occur among the actinobacteria.</p

Caracterización de especies de Paraburkholderia como promotoras del crecimiento vegetal

Un desafío en la actualidad para la agricultura es proporcionar suficientes alimentos, debido a esto los agricultores han hecho uso excesivo de fertilizantes o plaguicidas, ocasionando problemas en el ecosistema y en la calidad del suelo. Con el fin de mantener la calidad y fertilidad del mismo, diversas investigaciones han hecho énfasis en la implementación del uso de microorganismos benéficos para el mantenimiento de la calidad del suelo. Este tipo de bacterias son nombrados rizobacterias promotoras del crecimiento de las plantas (PGPR). Los mecanismos por los cuales, pueden mejorar el estado nutricional de las plantas son: fijación de N2, producción de ácido indol acético (AIA), solubilización de fosfatos, producción de sideróforos y control de fitopatógenos, principalmente. Se han publicado investigaciones donde se muestra que el género Paraburkholderia, presenta características de PGPR, ubicando a este género como un potencial bioinsumo para aplicación agrícola. El objetivo general del trabajo es: Determinar el potencial de Paraburkholderia tropica, Paraburkholderia unamae, Paraburkholderia silvatlantica y Paraburkholderia caballeronis para promover el crecimiento en plantas de maíz y realizar su caracterización genómica. A partir de los 23 genomas en estudio, P. tropica (6), P. unamae (3), P. silvatlantica (6), P. caballeronis (8) se realizó la caracterización genómica, primero se hizo una comparación de las 4 con sus cepas tipo, utilizando identidad de nucleótidos promedio (ANI) y calculadora de distancia genoma a genoma (GGDC). Así mismo, se hizo una comparación de los genomas en estudio con los genomas más relacionados usando la plataforma TYGS, finalmente una construcción filogenómica y búsqueda de los genes in silico, usando las plataformas JGI y AntiSMASH, este último para la búsqueda de metabolitos secundarios. Para la caracterización in silico de las cepas como PGPR, se determinó la producción de AIA, utilizando el reactivo de Salkowski, donde se muestra que solo algunas cepas poseen valores significativos, seguido a esto se realizó la fijación de N2 mediante el método de la reducción del acetileno donde se observó esta característica en las 4 especies, posteriormente se realizaron las pruebas para producción de sideróforos (medio MM9) y solubilización de fosfatos (medio NBRIP modificado), las 23 cepas presentaron esta actividad, aunque en diferente medida a excepción de P. silvatlantica TPCrh-89 y SRCL-318, para la solubilización de fosfato. Finalmente, se realizaron las pruebas de inoculación en plantas de maíz y se determinó el peso en seco para cada una de ellas, obteniendo valores significativos en peso en seco de la parte aérea para P. tropica Sir-6529 y P. silvatlantica PSCR-88. Como conclusiones las cepas en estudio, concuerdan con la especie en las que se les había asignado previamente y esto se corrobora con el análisis filogenómico. Todas las cepas presentan la actividad de producción de AIA, aunque su comportamiento fue diferente entre las cepas a los diferentes tiempos, todas presentan la actividad de fijación de N2, producción de sideróforos, a excepción de 2 cepas todos solubilizaron fosfatos. Así mismo, las 4 especies cuentan en su genoma con diferentes genes relacionados a las actividades PGP. Se obtuvieron valores significativos en la parte de peso en seco respecto al control

Efecto de rizobacterias promotoras del crecimiento vegetal en plantas sometidas a estrés hídrico: un enfoque desde la fisiología vegetal

RESUMEN La sequía afecta significativamente el estado fisiológico de las plantas y, en consecuencia, la producción agrícola. El cambio climático supone un reto mayor para la agricultura, ya que las proyecciones indican la disminución del agua disponible para los cultivos en varias regiones del mundo. En este sentido, es necesario buscar estrategias que permitan la viabilidad de la producción sin provocar los daños que la agricultura intensiva convencional trae al equilibrio planetario. En este trabajo se abordan, desde un enfoque fisiológico, los impactos que tiene la sequía sobre las plantas y que afectan negativamente su productividad. Asimismo, se revisan los diferentes mecanismos de resistencia que han desarrollado las plantas para enfrentar la falta de agua para así comprender las características que presentan las rizobacterias promotoras del crecimiento vegetal y que, de diversas maneras, refuerzan o inducen resistencia ante el estrés hídrico en las plantas con las que se asocian, convirtiéndolas en una opción de interés para la adaptación de los cultivos ante condiciones de baja disponibilidad de agua. Asimismo, se plantea la importancia de transitar hacia la concepción de los ecosistemas rizosféricos como un sistema complejo y favorecer prácticas agrícolas basadas en el profundo entendimiento de los procesos ecológicos que se llevan a cabo entre el microbioma y la planta para coadyuvar a generar agroecosistemas productivos y resilientes ante los embates del cambio climático, reduciendo las afectaciones al ambiente y la salud humana. ABSTRACT Drought is a stressor that significantly affects the physiological state of plants and, consequently, agricultural production. Climate change possess a major challenge to agriculture as projections indicate a decrease in water availability for crops in various world regions. Therefore, it is necessary to seek strategies that enable viable production without causing the damage associated with conventional intensified agriculture which disrupts the planetary balance. This review focuses on the physiological impacts of drought on plants which negatively affect productivity. It also examines the different resistance mechanisms that plants have developed to cope with water scarcity, aiming to understand the characteristics of plant growth promoting rhizobacteria. These bacteria, in various ways, reinforce or induce resistance to water stress in the plants they associated with, making them an interesting option for adapting crops to conditions of low water availability. Additionally, we highlight the importance of viewing rhizospheric ecosystems as complex systems that favor agricultural practices based on a deep understanding of the ecological processes occurring between the microbiome and the plant. The creation of productive and resilient agroecosystems in the face of climate change will likely reduce negative effects on the environment and human health

PHÂN TÍCH DI TRUYỀN KHẢ NĂNG DI CHUYỂN THEO PHENANTHRENE CỦA VI KHUẨN PSEUDOMONAS STUTZERI E1

ABSTRACTPseudomonas stutzeri strain E1 shows a two-time accelerated swarming behavior in minimal medium with sprayed phenanthrene in swimming assays and a five-time higher chemotaxis towards dissolved phenanthrene in capillary assays.  A mutant bank of strain E1 was constructed using the pTnMod-OGm plasposon mutagenesis system.  82 out of 2639 electroporants screened showed an altered phenotype of phenanthrene-driven motility and/or phenanthrene degradation. 16 representative mutants were selected for sequencing the genes flanking the plasposon insertion. Mutations in flhA resulted in abolished swimming and swarming phenotype, and in flgK resulted in abolished swimming and diminished swarming phenotype.  A mutation in cheY performed abolished swimming and reduced swarming activity while a gidA mutation resulted in decreased phenanthrene degradation and both decreased swimming and swarming behavior. A mutation in gene encoding a Zn dependent protease and in a gene encoding capsular polysaccharide biosynthesis protein resulted in abolished swarming suggesting that these proteins also play a potential role in the swarming activity of P. stutzeri E1.Keywords: Pseudomonas stutzeri, polycyclic aromatic hydrocarbon, phenanthrene, chemotaxis, plasposon pTnMod-OGm, swimming, swarmingTitle: Genetic analysis of phenanthrene-driven motility by the phenanthrene-degrading soil isolate Pseudomonas stutzeri E1TóM TắTPseudomonas stutzeri dòng E1 có khả năng di chuyển bề mặt tăng gấp đôi khi nuôi trong môi trường tối thiểu được phủ phenanthrene.  Thí nghiệm mao dẫn cũng cho thấy E1 di chuyển nhanh gấp năm lần về hướng có phenanthrene.  Plasposon pTnMod-OGm được dùng để tạo thư viện đột biến dòng E1.  Trong số 2639 đột biến đã khảo sát, 82 đột biến biểu hiện những thay đổi về khả năng di chuyển theo phenanthrene và/hoặc phân hủy phenanthrene.  16 đột biến được chọn để giải trình tự của các gen đột biến tương ứng. Đột biến gen flhA làm E1 mất khả năng bơi và di chuyển bề mặt, đột biến gen flgK làm mất khả năng bơi và giảm khả năng di chuyển bề mặt của E1.  Đột biến gen cheY làm mất khả năng bơi và giảm khả năng di chuyển bề mặt trong khi đột biến gen gidA làm giảm khả năng phân hủy phenanthrene và giảm cả khả năng bơi và di chuyển bề mặt của E1.  Đột biến gen tổng hợp protein Zn-dependent protease và gen tổng hợp vỏ polysaccharide làm cho E1 mất khả năng di chuyển bề mặt chứng tỏ các protein này cũng giữ vai trò tiềm năng trong hoạt động di chuyển bề mặt của P. stutzeri E1.Từ khoá: Pseudomonas stutzeri, hydrocarbon đa vòng thơm, phenanthrene, hóa hướng động, plasposon pTnMod-OGm, bơi, di chuyển bề mặt</p

Enkele proeven over de invloed van de stikstofvorm op het optreden van stip bij paprika

<p><b>Copyright information:</b></p><p>Taken from "Architecture of complex σgene family: evidence of alternative primary and clade-specific factors, and genomic instability"</p><p>http://www.biomedcentral.com/1471-2164/8/308</p><p>BMC Genomics 2007;8():308-308.</p><p>Published online 4 Sep 2007</p><p>PMCID:PMC2194791.</p><p></p>mes using ACT [36]. -J2315 ORF annotations were assigned using other annotated genomes. ORF numbers assigned by the Sanger Institute are indicated. Dashes indicate missing regions. Phage DNA in (c) indicates a potential phage insertion. Arrows indicating ORF of sigma factors are filled with dots, and of anti-sigma factors are filled with vertical bars

Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations

Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N 2 fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N 2 fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N 2 -fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen-fixing property was undertaken. A 40-kb-long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen-free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N 2 -fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N 2 -fixing deficiencies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75167/1/j.1462-2920.2007.01240.x.pd

Determinación de la capacidad de P. protegens EMM-1 para inhibir a R. oryzae EMM en interacción con plántulas de maíz rojo criollo

El maíz es una especie que se originó en México y uno de los principales problemas para su producción es la contaminación por microorganismos patógenos, dentro de los que destacan los hongos fitopatógenos, ya que afectan el crecimiento y desarrollo de la plántula e incluso el almacenamiento de semilla. En el presente estudio se identificó, mediante su descripción fenotípica y molecular a R. oryzae EMM; una cepa aislada de germinados de maíz rojo criollo infectado. Posteriormente, se evaluó la acción antagónica de Pseudomonas protegens EMM- 1 utilizando como control positivo a Bacillus licheniformis LG sobre R. oryzae EMM por medio de los métodos de inhibición de placa dual y doble capa, aunado a esto se realizó una cinética de crecimiento de P. protegens EMM-1 en interacción con R. oryzae EMM en medio líquido y se determinó la acción de P. protegens EMM-1 en interacción tripartida con plántulas de maíz rojo criollo en un medio hidropónico con solución MSJ para lo que se determinó peso húmedo y seco de la plántula al igual que adhesión y colonización de P. protegens EMM-1. En placa dual se observó un porcentaje de inhibición de 83.11±3.66 causado por P. protegens EMM-1 y un 94.20±4.71 causado por B. licheniformis LG a las 96 h. En el método de doble capa, solo P. protegens EMM-1 presentó un halo de inhibición de 0.9±0.04 mm. En la cinética de crecimiento se observó que P. protegens EMM-1 ejerce un efecto inhibidor sobre el micelio de R. oryzae EMM. En la interacción de P. protegens EMM- 1 con R. oryzae EMM en presencia de plántulas de maíz en un sistema hidropónico se observó una disminución la capacidad de R. oyzae EMM para infectar a las plántulas de maíz. Además, la adhesión y colonización de P. protegens EMM-1 en la raíz del maíz fue mayor que la de R. oryzae EMM. En conclusión, P. protegens EMM-1 muestra un muy buen potencial para inhibir el crecimiento de R. oryzae EMM en interacción con plántulas de maíz rojo criollo

Author correction : roadmap for naming uncultivated archaea and bacteria

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity