ABSTRACTChthonomonas calidiroseaT49Tis a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that theC. calidiroseagenome 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 fourC. calidiroseaisolates 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 inC. calidirosearelative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of theC. calidiroseaisolates 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 ofC. calidiroseadistribution. This dispersal and extinction mechanism is likely not limited toC. calidiroseabut may shape the populations and genomes of many other low-abundance free-living taxa.IMPORTANCEThis study compares the genomic sequence variations and metabolisms of four strains ofChthonomonas calidirosea, a rare thermophilic bacterium from the phylumArmatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the fourC. calidiroseastrains were isolated.C. calidiroseawas 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, theC. calidiroseagenome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting thatC. calidiroseagenotypes are not primarily determined by adaptive evolution. Instead, the presence ofC. calidiroseamay be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.
On zero-dimensional Milutin maps and Michael selection theorems