Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti

Abstract

Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

“…In addition to the “simple” hydrogenases, which are present in all species of Preaxostyla, [FeFe] hydrogenases with N-terminal homology to the NuoG subunit of NADH-quinone oxidoreductase and a C-terminal homology to NADPH-dependent sulfite reductase (CysJ), were identified in the MRO-containing T. marina and P. pyriformis (Fig 3, S4D File). Similar “fused” hydrogenases have been previously reported in other eukaryotic anaerobes, including T. vaginalis [49], the breviate Pygsuia biforma [50], the jakobid Stygiella incarcerata [51], and the amoebozoan Pelomyxa schiedti [52]. Although they do not belong to the group of A3 trimeric hydrogenases [53] known to be capable of NADH oxidation via electron confurcation [54], they were hypothesized to catalyze NAD(P)H-dependent formation of H 2 [49].…”

“…The final fate of the electrons carried by ferredoxin often lies in the reduction of protons to molecular hydrogen through the activity of [FeFe] hydrogenases (HydA; [48]). In addition to the "simple" hydrogenases, which are present in all species of Preaxostyla, hydrogenases have been previously reported in other eukaryotic anaerobes, including T. vaginalis [49], the breviate Pygsuia biforma [50], the jakobid Stygiella incarcerata [51], and the amoebozoan Pelomyxa schiedti [52]. Although they do not belong to the group of A3 trimeric hydrogenases [53] known to be capable of NADH oxidation via electron confurcation [54], they were hypothesized to catalyze NAD(P)H-dependent formation of H2 [49].…”

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

“…In addition to the "simple" hydrogenases, which are present in all species of Preaxostyla, [FeFe] hydrogenases with N-terminal homology to the NuoG subunit of NADH-quinone oxidoreductase and a C-terminal homology to NADPH-dependent sulfite reductase (CysJ), were identified in the MRO-containing T. marina and P. pyriformis (Figs 3 and D in S4 File). Similar "fused" hydrogenases have been previously reported in other eukaryotic anaerobes, including T. vaginalis [49], the breviate Pygsuia biforma [50], the jakobid Stygiella incarcerata [51], and the amoebozoan Pelomyxa schiedti [52]. Although they do not belong to the group of A3 trimeric hydrogenases [53] known to be capable of NADH oxidation via electron confurcation [54], they were hypothesized to catalyze NAD(P)H-dependent formation of H 2 [49].…”

Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods

“…Moreover, most anaerobic protists in the hindgut of arthropods possess hydrogenosomes and provide a stable substrate source for their hydrogenotrophic symbionts. Associations between methanogens and protists are also common in sediments and are regarded as mutualistic because of the cross-feeding of H 2 ( Fenchel and Finlay, 2018 ; Treitli et al, 2023 ).…”