Abstract
The bacterial genus Rhodopseudomonas is comprised of photosynthetic
bacteria found widely distributed in aquatic sediments.
Members of the genus catalyze hydrogen gas production, carbon
dioxide sequestration, and biomass turnover. The genome sequence
of Rhodopseudomonas palustris CGA009 revealed a surprising
richness of metabolic versatility that would seem to explain
its ability to live in a heterogeneous environment like sediment.
However, there is considerable genotypic diversity among Rhodopseudomonas
isolates. Here we report the complete genome
sequences of four additional members of the genus isolated from
a restricted geographical area. The sequences confirm that the
isolates belong to a coherent taxonomic unit, but they also have
significant differences. Whole genome alignments show that the
circular chromosomes of the isolates consist of a collinear backbone
with a moderate number of genomic rearrangements that
impact local gene order and orientation. There are 3,319 genes,
70% of the genes in each genome, shared by four or more strains.
Between 10% and 18% of the genes in each genome are strain
specific. Some of these genes suggest specialized physiological
traits, which we verified experimentally, that include expanded
light harvesting, oxygen respiration, and nitrogen fixation capabilities,
as well as anaerobic fermentation. Strain-specific adaptations
include traits that may be useful in bioenergy applications.
This work suggests that against a backdrop of metabolic versatility
that is a defining characteristic of Rhodopseudomonas, different
ecotypes have evolved to take advantage of physical and chemical
conditions in sediment microenvironments that are too small for
human observation.
