Published version, 2.202Mb
Lee, K. C., Stott, M. B., Dunfield, P. F., Huttenhower, C., McDonald, I. R., & Morgan, X. C. (2016). The Chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in New Zealand’s Taupo Volcanic Zone. Applied and Environmental Microbiology, 82(12), 3572–3581. http://doi.org/10.1128/AEM.00139-16
Permanent Research Commons link: https://hdl.handle.net/10289/10625
Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa.
American Society for Microbiology
Copyright © 2016 Lee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.