Chimeric inheritance and crown-group acquisitions of Carbon fixation genes within Chlorobiales

The geological record of microbial metabolisms and ecologies primarily
consists of stable isotope fractionations and the diagenetic products of
biogenic lipids. Carotenoid lipid biomarkers are particularly useful
proxies for reconstructing this record, providing information on microbial
phototroph primary productivity, redox couples, and oxygenation. The
biomarkers okenane, chlorobactane, and isorenieratene are generally
considered to be evidence of anoxygenic phototrophs, and provide a record
that extends to ~1.64 Ga. The utility of the carotenoid biomarker
record may be enhanced by examining the carbon isotopic ratios in these
products, which are diagnostic for specific pathways of biological carbon
fixation found today within different microbial groups. However, this
joint inference assumes that microbes have conserved these pathways across
the duration of the preserved biomarker record. Testing this hypothesis,
we performed phylogenetic analyses of the enzymes constituting the
reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of
anoxygenic phototrophic bacteria usually implicated in the deposition of
chlorobactane and isorenieretane. We find phylogenetically
incongruent patterns of inheritance across all enzymes, indicative of
horizontal gene transfers to both stem and crown Chlorobiales from
multiple potential donor lineages. This indicates that a complete rTCA
cycle was independently acquired at least twice within Chlorobiales and
was not present in the last common ancestor. When combined with recent
molecular clock analyses, these results predict that the Mesoproterzoic
lipid biomarker record diagnostic for Chlorobiales should not preserve
isotopic fractionations indicative of a full rTCA cycle. Furthermore, we
conclude that coupling isotopic and biomarker records is insufficient for
reliably reconstructing microbial paleoecologies in the absence of a
complementary and consistent phylogenomic narrative.