title: Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features.
abstract: The genomic features of Azoarcus sp. CIB reflect its most distinguishing phenotypes as a diazotroph, facultative anaerobe, capable of degrading either aerobically and/or anaerobically a wide range of aromatic compounds, including some toxic hydrocarbons such as toluene and m-xylene, as well as its endophytic lifestyle. The analyses of its genome have expanded the catabolic potential of strain CIB toward common natural compounds, such as certain diterpenes, that were not anticipated as carbon sources. The high number of predicted solvent efflux pumps and heavy metal resistance gene clusters has provided the first evidence for two environmentally relevant features of this bacterium that remained unknown. Genome mining has revealed several gene clusters likely involved in the endophytic lifestyle of strain CIB, opening the door to the molecular characterization of some plant growth promoting traits. Horizontal gene transfer and mobile genetic elements appear to have played a major role as a mechanism of adaptation of this bacterium to different lifestyles. This work paves the way for a systems biology-based understanding of the abilities of Azoarcus sp. CIB to integrate aerobic and anaerobic metabolism of aromatic compounds, tolerate stress conditions, and interact with plants as an endophyte of great potential for phytostimulation and phytoremediation strategies. Comparative genomics provides an Azoarcus pan genome that confirms the global metabolic flexibility of this genus, and suggests that its phylogeny should be revisited.
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Zaira
authors.initials: Z
authors.lastname: Martín-Moldes
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: María Teresa
authors.initials: MT
authors.lastname: Zamarro
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Del Cerro
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Valencia
authors.affiliation: Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain.
authors.forename: Manuel José
authors.initials: MJ
authors.lastname: Gómez
authors.affiliation: Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain.
authors.forename: Aida
authors.initials: A
authors.lastname: Arcas
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Zulema
authors.initials: Z
authors.lastname: Udaondo
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: José Luis
authors.initials: JL
authors.lastname: García
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Juan
authors.initials: J
authors.lastname: Nogales
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Carmona
authors.affiliation: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain. Electronic address: ediaz@cib.csic.es.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Díaz
mesh_terms: D000220:Adaptation, Biological; D000332:Aerobiosis; D000693:Anaerobiosis; D020627:Azoarcus / Q000235:genetics* / Q000502:physiology*; D019295:Computational Biology; D024881:Drug Resistance, Bacterial; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D020071:Interspersed Repetitive Sequences; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D019216:Metals, Heavy / Q000378:metabolism / Q000633:toxicity; D008969:Molecular Sequence Data; D005810:Multigene Family; D009586:Nitrogen Fixation; D017422:Sequence Analysis, DNA
chemical_list: D019216:Metals, Heavy
keywords: Aromatic compounds; Azoarcus; Comparative genomics; Endophyte; Metals resistance; Mobile genetic elements