Centro de investigación y de estudios avanzados del instituto politécnico nacional

Abstract

The Cuatro Cienegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system with extremely low phosphorus levels (<0.3 μM). We sequenced the complete genome sequence of two bacillus isolates, the first is a new bacterial species isolated from a desiccation lagoon in CCB, named Bacillus coahuilensis, and the second bacillus called B. sp. m3-13 is not yet classified. At 3.35 Mega bases B. coahuilensis is the smallest genome sequenced to date of a Bacillus species and provides insights into the ways that an ancestral marine bacterium adapted into a new environment, thus giving support to the ancient marine origin hypothesis which is consistent with the geology of CCB. Some genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high light environments. The genome of B. sp. m3-13, was obtained in order to determine whether different adaptations to this environment could be uncovered, and to clear out phylogenetic relationships, while providing to the scientific community another environmental strain of Bacillus to unveil the dynamics of this genus with environmental, medical and industrial relevance. The pandemic distribution of the Bacilli reflects the vast repertoire of metabolic capabilities within the genus. Traditional phylogenetics had failed to solve the relationships amongst close relatives, so we decided to approach it using the core and accessory genes of the Bacillus. In order to define the core genome we took advantage of the 21 complete genomes available for the Bacillus, and defined a total of 815 orthologous genes universally conserved all across the Bacillus as the core genome. Using concatenated alignments of the core genome we solved, for the first time, the most robust phylogeny for the group. Using functional classifications of the genes we were able to determine group specific functions for the Bacillus. A fine analysis of the sporulation conservancy, diagnostic trait for the Bacilli, was done, finding that the sporulation mechanisms are much more diverse than expected according to the model system B. subtilis. Our results demonstrate that distinguishing between genomic components, especially core versus pangenome, provides insight into phylogeny and function that would otherwise be difficult or impossible to achieve.

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