Autotrophic CO₂ fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage

Abstract

Autotrophic carbon fixation was characterized in representative members of the three lineages of the bacterial phylum Aquificae. Enzyme activity measurements and the detection of key genes demonstrated that Aquificae use the reductive tricarboxylic acid (TCA) cycle for autotrophic CO(2) fixation. This is the first time that strains of the Hydrogenothermaceae and 'Desulfurobacteriaceae' have been investigated for enzymes of autotrophic carbon fixation. Unexpectedly, two different mechanisms of citrate cleavage could be identified within the Aquificae. Aquificaceae use citryl-CoA synthetase and citryl-CoA lyase, whereas Hydrogenothermaceae and 'Desulfurobacteriaceae' use ATP citrate lyase. The first mechanism is likely to represent the ancestral version of the reductive TCA cycle. Sequence analyses further suggest that ATP citrate lyase formed by a gene fusion of citryl-CoA synthetase and citryl-CoA lyase and subsequently became involved in a modified version of this pathway. However, rather than having evolved within the Aquificae, our phylogenetic analyses indicate that Aquificae obtained their ATP citrate lyase through lateral gene transfer. Aquificae play an important role in biogeochemical processes in a variety of high-temperature habitats. Thus, these findings substantiate the hypothesis that autotrophic carbon fixation through the reductive TCA cycle is widespread and contributes significantly to biomass production particularly in hydrothermal habitats.

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

“…Sphingobacteria have been recovered from geothermal springs that are more alkaline (pH range of 7.7-9.5) than that found at Site 3 (pH 3.9) (Tekere et al, 2011;Tobler and Benning, 2011). OTUs affiliated with Aquificae, a hyperthermophilic chemoautotroph found in both terrestrial hot springs as well as hydrothermal vents (Hügler et al, 2007), were recovered from all sites and were abundant in Site 4 (∼94% relative abundance) ( Figure 3A). A single Aquificae OTU in Site 4 accounted for ∼75% of the total sequences recovered from the gray filaments.…”

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

“…In particular, our survey of the beta subunit of the ATP 528 citrate lyase from Broken Spur revealed a novel group of AclB sequences (BSaclB9, 15, 529 21 and 31) related to uncultured Aquificales previously detected at vents located on the 530 EPR ( Fig. 2) (Campbell et al 2004, Hügler et al 2007). Furthermore, we detected an 531 analogous group of AclA clones (represented by BSaclA17) that did not include any 532 sequence from cultured organisms, and that formed a lineage distinct from the 533 Persephonella marina enzyme (Fig.…”

“…Epsilonproteobacteria and Aquificae, which include representatives of hydrothermal vent 109 bacteria, fix carbon dioxide via the rTCA cycle (Ferrera et al 2007, Hügler et al 2007, 110…”

“…Reactions involving pyridine 155 nucleotides were followed spectrophotometrically at 365 nm (ε 365 nm NAD(P)H = 3.4 • 156 ). 158 ATP citrate lyase activity was determined according to (Hügler et al 2007). …”

Carboxylases in Natural and Synthetic Microbial Pathways

“…The oxygen sensitivity of these enzymes limits ferredoxin-dependent carboxylationsand therefore also the rTCA cycle-to certain anoxic environments. Accordingly, the rTCA cycle is mainly found to occur in anaerobic and microaerobic bacteria, such as green sulfur bacteria, and in many delta-and epsilonproteobacteria, as well as in members of the Aquificae clade (14,65,108). Interestingly, the thermophile Hydrogenobacter thermophilus (order Aquificales) is known to use the rTCA cycle under aerobic conditions as well.…”