The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone
Authors: Lee Kevin C. , Stott Matthew B. , Dunfield Peter F. , Huttenhower Curtis , McDonald Ian R. , Morgan Xochitl C. 
Published: April 2016

ABSTRACT

Chthonomonas calidirosea
T49
T
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.

IMPORTANCE
This study compares the genomic sequence variations and metabolisms of four strains of
Chthonomonas calidirosea
, a rare thermophilic bacterium from the phylum
Armatimonadetes
. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four
C. calidirosea
strains were isolated.
C. calidirosea
was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the
C. calidirosea
genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that
C. calidirosea
genotypes are not primarily determined by adaptive evolution. Instead, the presence of
C. calidirosea
may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.