Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique
physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the
genus Ferroplasma with a validly published name, we assessed its central metabolism and genome
stability during a long-term cultivation experiment. Consistently with physiology, the genome
analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside
with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake,
although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose
1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate
dehydrogenases are substituted by ‘ancient’ CoA-dependent pyruvate and alpha-ketoglutarate
ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the
mutation rate of ≥1.3 × 10−8 single nucleotide substitutions per site per generation, which is among
the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T,
their distribution between coding and non-coding regions and synonymous-to-non-synonymous
mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture.
Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic
conservation in F. acidiphilum YT variants from geographically distant populations.