Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum

Abstract

Phylum Cloacimonadota (previously Cloacimonetes, WWE1) is an understudied bacterial lineage frequently associated with engineered and wastewater systems. Cloacimonadota members were abundant and diverse in metagenomic datasets from a municipal landfill, prompting an examination of phylogenetic relationships, metabolic diversity, and pangenomic dynamics across the phylum, based on the 30 publicly available genomes and 24 new metagenome-assembled genomes (MAGs) from landfill samples. We found that Cloacimonadota have distinct evolutionary histories associated with engineered versus natural environments and identified genomic features and metabolic strategies that correlate to habitat of origin. Metabolic reconstructions for MAGs predict an anaerobic, acetogenic, and mixed fermentative and flavin-bifurcation-based anaerobic respiratory lifestyle for the majority of Cloacimonadota surveyed. Genomes from engineered ecosystems encode a suite of genes not typically found in genomes from natural environments including acetate kinase, genes for cysteine degradation to pyruvate, increased diversity of carbon utilization enzymes, and different mechanisms for generating membrane potential and ATP synthesis. This phylumlevel examination also clarifies the distribution of functions previously observed for members of the phylum, where propionate oxidation and reverse TCA cycles are not common components of Cloacimonadota metabolism.

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria

“…To date, members of Cloacimonadota have not been enriched in any marine environment, and previous reports of their presence are based on incubations and metagenomic analyses [ 20 , 28 , 29 ]. Here, we report an increase in the cell density of Cloa-SY6, a member of Cloacimonadota , in a medium containing propionate (0.2 g L −1 ), indicating its ability to use this substrate.…”

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

“…In general, the results obtained for Euryarchaeota suggest that methanogenic archaea are under a strong selective pressure and harbor a large amount of genetic variability. The metabolic roles of species belonging to Candidatus Cloacimonetes and Synergistetes are still not completely clear, however, it was previously reported that some of them are characterized by acetogenesis [ 98 ], or can compete for acetate utilization with Methanosaeta [ 99 ].…”

Organic matter degradation in the deep, sulfidic waters of the Black Sea: Insights into the ecophysiology of novel anaerobic bacteria

“…To date, members of Cloacimonadota have not been enriched in any marine environment, and previous reports of their presence are based on incubations and metagenomic analyses 20,28,29 . Here, we report an increase in the cell density of Cloa-SY6, a member of Cloacimonadota , in a medium containing propionate (0.2 gL −1 ), indicating its ability to use this substrate.…”