Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Abstract

Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.

Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems

“…Omnitrophota in a recent metagenomic study, in which most Ca . Omnitrophota bacteria are predators and parasites ( Perez-Molphe-Montoya et al., 2022 ; Seymour et al., 2023 ).…”

Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea

“…V. archaevorus LiM and Ca. Omnitrophica bacterium OLB16, encoding SpeDC enzymes investigated in the current study, biosynthetic pathways for PLP are missing or incomplete across the phylum ( 42 ).…”

Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems

“…Microsyncoccus PMX.50 (Tables S2 and S4), which are encoded by type IV pilus assembly proteins (Table S2). In a previous study, ATPase and type IV pili were predicted to function in attachment and motility on larger host surfaces ( 18 ). Furthermore, some active peptidase-like proteins with signal peptides (PMX_810_sub_00385, PMX_810_sub_00508, PMX.108_00125, PMX.108_00310, PMX.108_00457, PMX.108_00476, and PMX.50_00413) (Table S2) and substrate-binding proteins of amino acid/metal transport systems were found in the three Ca .…”

“…Previous studies have suggested that the competence protein ComEC, secretion systems, pilus, and several transporters are important for the parasitism or predatory lifestyles of ultrasmall microbes, including Ca . Patescibacteria ( 15 – 18 ). Accordingly, these genes were highly expressed in the genome of Ca .…”