Metabolic Potential of the Superphylum <i>Patescibacteria</i> Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant

Abstract

Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation analysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic analysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.

Novel Cross-domain Symbiosis between <i>Candidatus</i> Patescibacteria and Hydrogenotrophic Methanogenic Archaea <i>Methanospirillum</i> Discovered in a Methanogenic Ecosystem

“…Patescibacteria are known for their small cell (e.g., average diameter of ~0.2 μm) (He et al, 2021) and genome (e.g., 1.1±0.2 Mbp) sizes (Tian et al, 2020;Kagemasa et al, 2022), and genomic traits suggest that most Ca. Patescibacteria require external nutrient sources through symbiotic interactions (e.g., commensal, mutualistic, and parasitic relationships) due to a lack of biosynthesis genes (Castelle et al, 2018;Fujii et al, 2022). Although previous studies demonstrated Ca.…”

“…Patescibacteria require external nutrient sources through symbiotic interactions ( e.g. , commensal, mutualistic, and parasitic relationships) due to a lack of biosynthesis genes ( Castelle et al , 2018 ; Fujii et al , 2022 ).‍ ‍Although previous studies demonstrated Ca. Patescibacteria-Bacteria interactions through cultivation-based approaches ( He et al , 2015 ; Moreira et al , 2021 ; Yakimov et al , 2022 ), cross-domain symbiosis was only reported for Ca.…”

Gut microbial ecology and exposome of a healthy Pakistani cohort

“…Cyanobacteria, and, Elusimicrobiota, are also found in groundwater, as well as animal gut and soil, and the latter are associated with nitrogen metabolism (31,32). Patescibacteria were also detected as part of core microbiome in males with site speci c occupancy, which have small genome size are parasitic in nature and found in groundwater in rural regions (33), therefore their prevalence may indicate exposure to rural environments. Campilobacterota, Elusimicrobiota, and Patescibacteria have been previously reported as phyla prevalent in healthy individuals from west Bengal (34).…”

Unique episymbiotic relationship betweenGracilibacteriaandZoogloeain activated sludge flocs in a municipal wastewater treatment plant

“…Among these diverse bacteria, several members of the bacterial phylum Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum), a large and diverse bacterial group consisting of uncultivated bacteria, are universally present [1−4]. Patescibacteria are characterized by their limited metabolic potential, as inferred from metagenomic analyses [2,5,6]. Furthermore, microscopic observation using techniques such as fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) have revealed that most Patescibacteria have small cell sizes.…”

“…Recent studies have highlighted that Patescibacteria parasitize other bacterial or archaeal microorganisms, suggesting a lifestyle that may compensate for their metabolic deficiencies [7−12]. Within the Patescibacteria phylum, Saccharimonadia, Paceibacteria, and Gracilibacteria are commonly detected in the activated sludge flocs [1,2,5,13], and information on Gracilibacteria has only recently been obtained by metagenomic analyses. To better understand microbial interactions in activated sludge flocs, in situ visualization using FISH or TEM within the flocs is very important because FISH probes specific for Gracilibacteria did not exist until recently.…”