How Divergent Is the Cuatro Ciénegas Oasis? Genomic Studies of Microbial Populations and Niche Differentiation
In this chapter, we describe some genomic studies that have been conducted in the CCB to describe the microdiversity of different microbial taxa. Firstly, we describe the genomic variation in the endemic species B. coahuilensis, for which we analyzed three strains, and the evolutionary mechanism that have shaped their genomes, in particular for their adaptations to a low phosphorus environment. Secondly, we describe population genomics of Proteobacteria such as Pseudomonas, Vibrio, Photobacterium, and Aeromonas, finding many genes related to bacterial interactions, such as type III and VI secretion systems, which led us to propose that these systems play an important role in interactions among bacterial communities. Many of these interaction genes have been classified previously as virulence factors. However, at CCB these genes were not found in a cassette configuration—such as an integron or a pathogenicity island—in any strain suggesting that they are very ancestral adaptive responses to keep both the cohesion within the community and the cheaters out of the community. Interestingly, even if B. coahuilensis presents many mobile elements, these elements are rare in the surveyed Proteobacteria, whose genomes present many CRISPS elements. The presence of CRISPR regions may also explain why there are few ISs or plasmids since it has been reported that CRISPR spacers can act as barriers against HGT.
The research was funded in part by Papiit-UNAM project IG200215 for Vibrio comparative genomics to VS and LEE, and CONACYT CB-2013-01 No. 220536 to GO-A. This chapter was written during a sabbatical leave of VS in the Department of Ecology, Evolution, and Behavior, University of Minnesota in Dr. Michael Travisano´s laboratory, and of LEE, in the Department of Plant and Microbial Biology, University of Minnesota in Dr. Peter Tiffin’s laboratory, both supported by the program PASPA-DGAPA, UNAM.
- Meyer JL, Huber JA (2014) Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. Int Soc Microb Ecol J 8(4):867–880Google Scholar
- Peña A et al (2010) Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. Int Soc Microb Ecol J 4(7):882–895Google Scholar
- Ponce-Soto GY, Aguirre-von-Wobeser E, Eguiarte LE, Elser JJ, Lee ZMP, Souza V (2015) Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment. Front in Microbiology 6(246). https://doi.org/10.3389/fmicb.2015.00246
- Vázquez-Rosas-Landa M, Yaxal Ponce-Soto G, Eguiarte LE, Souza V (2017) Comparative genomics of free-living Gammaproteobacteria: pathogenesis-related genes or interaction-related genes?. FEMS Pathogens and Disease 75(5):1–12Google Scholar
- Vélez P, Gasca-Pineda J, Rosique-Gil E, Eguiarte LE, Espinosa-Asuar L, Souza V (2016) Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico. PeerJ, 4, e2064. https://doi.org/10.7717/peerj.2064 CrossRefGoogle Scholar