Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Cell, Год журнала: 2023, Номер 186(22), С. 4803 - 4817.e13

Опубликована: Сен. 7, 2023

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation. Imaging fluorescent protein-labeled provides high spatiotemporal resolution phenomena accompanying epibiotic growth, transposon-insertion sequencing (Tn-seq) genome-wide screen reveals contribution enigmatic Saccharibacterial genes growth hosts. Finally, leverage metagenomic data provide cutting-edge protein structure-based bioinformatic resources support strain Southlakia epibionticum its corresponding host, Actinomyces israelii, model system unlocking molecular underpinnings lifestyle.

Язык: Английский

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Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Март 16, 2024

Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance of Patescibacteria due to low coverage commonly used PCR primers highly divergent bacterial phylum. Therefore, our current understanding global diversity, distribution, ecological role WWTPs very incomplete. This particularly relevant as considered be associated with microbial host cells can therefore influence temporal variability other groups that important WWTP functioning.

Язык: Английский

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

Water Research X, Год журнала: 2023, Номер 20, С. 100196 - 100196

Опубликована: Авг. 13, 2023

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in ecosystems are unexplored survival strategies that have long been known recently attracted attention because these interspecies may contribute the reduction of excess sludge. Here, community profiling 600 activated sludge samples taken from six industrial one municipal processes (WWTPs) was conducted. To identify shared lineages WWTPs, constituents were defined as family level taxa had ≥ 0.1% average relative abundance detected all The analysis assigned 106 families WWTPs. Correlation showed 98 significantly correlated with total carbon (TC) and/or nitrogen (TN) concentrations, suggesting they remediation. Most possible predatory or parasitic bacteria belonging phyla Bdellovibrionota, Myxococcota, Candidatus Patescibacteria found be negatively TC/TN; thus, frequently present WWTPs could involved removal carbon/nitrogen derived cell components. Shotgun metagenome-resolved metabolic reconstructions indicated gene homologs associated conserved Ca. genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, type IV pilus assembly proteins). This study provides insights into complex potentially linked biomass

Язык: Английский

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

mBio, Год журнала: 2024, Номер 15(3)

Опубликована: Фев. 7, 2024

To verify whether members of the phylum

Язык: Английский

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Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Янв. 26, 2024

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles biogeochemical cycling. We studied chemoautotrophically based biofilms host diverse CPR bacteria and grow to investigate controls on Results Sulfide were investigated using bulk geochemical analysis, genome-resolved metagenomics, scanning transmission X-ray microscopy (STXM) at room temperature 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix Beggiatoa , dominate the biofilms, which also contain Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, Parcubacteria. STXM imaging revealed ultra-small cells near surfaces of filamentous may be bacterial episymbionts. NEXAFS spectroscopy carbon K sulfur L 2,3 edges show protein-encapsulated spherical elemental granules, indicating they are oxidizers, likely . Berkelbacteria Moranbacteria same biofilm sample predicted have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively sulfhydrogenase, potentially linked metabolism via redox cofactors. This complex could contribute symbioses, for example, with such as is cryptic One Doudnabacteria genome encodes adjacent dioxygenase rhodanese genes convert thiosulfate sulfite. find similar conserved genomic architecture associated from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, structural bioinformatics analyses growing consortia Proteobacteria, new family within Beggiatoales. infer hydrogen

Язык: Английский

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Agricultural soil microbiomes differentiate in soil profiles with fertility source, tillage, and cover crops

Agriculture Ecosystems & Environment, Год журнала: 2024, Номер 368, С. 109002 - 109002

Опубликована: Апрель 6, 2024

Язык: Английский

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Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations

Frontiers in Microbiology, Год журнала: 2023, Номер 13

Опубликована: Янв. 9, 2023

form a highly diverse and widespread superphylum of uncultured microorganisms representing third the global microbial diversity. Most our knowledge on

Язык: Английский

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“ Candidatus Nealsonbacteria” Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture

Applied and Environmental Microbiology, Год журнала: 2023, Номер 89(5)

Опубликована: Апрель 26, 2023

The Candidate Phyla Radiation (CPR), also referred to as superphylum

Язык: Английский

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Habitat Transition in the Evolution of Bacteria and Archaea

Annual Review of Microbiology, Год журнала: 2023, Номер 77(1), С. 193 - 212

Опубликована: Апрель 26, 2023

Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics mechanisms these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review literature concerning transitions among a variety bacterial archaeal lineages, considering frequency migration events, potential environmental barriers, to new physicochemical conditions, including modification protein inventories other genomic characteristics. Cells dependent on microbial hosts, bacteria from Candidate Phyla Radiation, have undergone repeated sources into We compare their trajectories those both free-living cells-including Melainabacteria, Elusimicrobia, methanogenic archaea-and cellular endosymbionts bacteriophages, which made similar transitions. conclude by highlighting major related topics may be worthy future study.

Язык: Английский

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Investigating the synergic role of asynchronous dosed protease and lysozyme for facilitating excess sludge solubilization and acidogenic fermentation

The Science of The Total Environment, Год журнала: 2023, Номер 885, С. 163759 - 163759

Опубликована: Май 3, 2023

Язык: Английский

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