A rooted phylogeny resolves early bacterial evolution

Science, Journal Year: 2021, Volume and Issue: 372(6542)

Published: May 6, 2021

A rooted bacterial tree is necessary to understand early evolution, but the position of root contested. Here, we model evolution 11,272 gene families identify root, extent horizontal transfer (HGT), and nature last common ancestor (LBCA). Our analyses between major clades Terrabacteria Gracilicutes suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary recent proposals, our reject basal placement Candidate Phyla Radiation, which instead branches sister Chloroflexota within Terrabacteria. While most (92%) have evidence HGT, overall, two-thirds transmissions been vertical, suggesting provides meaningful frame reference for interpreting evolution.

Language: Английский

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Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(3), P. 354 - 365

Published: Jan. 25, 2021

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity host association CPR has not been studied. Here, we performed genome-resolved metagenomic analysis one agricultural seven pristine microbial communities recovered 746 genomes total. sites, which serve as local sources drinking water, contained up to 31% 4% archaea. We observed little species-level overlap metagenome-assembled (MAGs) across indicating may be differentiated according physicochemical conditions populations. Cryogenic transmission electron microscopy imaging genomic analyses enabled us identify lineages reproducibly attach cells showed growth seems stimulated by attachment host-cell surfaces. Our reveals site-specific coexist with diverse hosts aquifers. Given organisms have identified human microbiomes their presence is correlated diseases such periodontitis, our findings relevant considerations water quality health.

Language: Английский

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Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(45)

Published: Nov. 3, 2021

Significance Diverse microbial life has been detected in the cold desert soils of Antarctica once thought to be barren. Here, we provide metagenomic, biogeochemical, and culture-based evidence that Antarctic soil microorganisms are phylogenetically functionally distinct from those other adopt various metabolic ecological strategies. The most abundant community members metabolically versatile aerobes use ubiquitous atmospheric trace gases potentially meet energy, carbon, and, through water production, hydration needs. Lineages capable harvesting solar oxidizing edaphic inorganic substrates, or adopting symbiotic lifestyles were also identified. Altogether, these findings insights into adaptation extreme energy limitation will inform ongoing efforts conserve unique biodiversity on this continent.

Language: Английский

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

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: March 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.

Language: Английский

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Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor

Water, Journal Year: 2021, Volume and Issue: 13(2), P. 208 - 208

Published: Jan. 16, 2021

Although the anaerobic ammonium oxidation (anammox) process has attracted attention regarding its application in ammonia wastewater treatment based on efficiency, physiological characteristics of anammox bacteria remain unclear because lack pure-culture representatives. The coexistence heterotrophic often been observed reactors, even those fed with synthetic inorganic nutrient medium. In this study, we recovered 37 draft genome bins from a long-term-operated column reactor and predicted metabolic pathway coexisting bacteria, especially Patescibacteria (also known as Candidate phyla radiation). Genes related to nitrogen cycle were not detected Patescibacterial bins, whereas nitrite, nitrate, nitrous oxide-related genes identified most other bacteria. for suggests marker ability utilize poly-N-acetylglucosamine produced by dominant Coexisting may play an ecological role providing lactate formate supporting growth reactor. Patescibacteria-centric which produce substrates scavenge organic compounds within reactor, might be essential ecosystem.

Language: Английский

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An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Feb. 22, 2022

Core gene phylogenies provide a window into early evolution, but different sets and analytical methods have yielded substantially views of the tree life. Trees inferred from small set universal core genes typically supported long branch separating archaeal bacterial domains. By contrast, recent analyses broader non-ribosomal suggested that Archaea may be less divergent Bacteria, estimates inter-domain distance are inflated due to accelerated evolution ribosomal proteins along branch. Resolving this debate is key determining diversity domains, shape life, our understanding course cellular evolution. Here, we investigate evolutionary history marker debate. We show reduced Archaea-Bacteria (AB) length result transfers hidden paralogy in expanded set. analysis broad range manually curated datasets an evenly sampled 700 Bacteria reveals current likely underestimate AB substitutional saturation poor model fit; best-performing phylogenetic markers tend support longer lengths; lengths statistically indistinguishable. Furthermore, phylogeny 27 highest-ranked recovers clade DPANN at base places Candidate Phyla Radiation (CPR) within as sister group Chloroflexota.

Language: Английский

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The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Dec. 1, 2021

The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response environmental drivers or host organisms. Their mechanisms employed cope with oxidative stress largely unknown. Here, we utilized genome-resolved metagenomics investigate the adaptive genome repertoire oxic anoxic groundwaters, infer putative ranges.Within six groundwater wells, was most dominant (up 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 0.1 µm filters after sequential filtration. Of reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Patescibacteria. Paceibacteria Microgenomates enriched exclusively fractions, whereas candidate division ABY1 Gracilibacteria fractions. On average, smaller filter fractions had 22% genomes, 13.4% lower replication measures, higher proportion rod-shape determining proteins, genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored rates than downstream characterized by longer water residence time. Except prevalence superoxide dismutase genes groundwaters (83%), no major phylogenetic differences observed. abundant MAG encoded a nitrate transporter, nitrite reductase, F-type ATPase, an alternative energy conservation mechanism. consistently co-occurred one another members phyla Nanoarchaeota, Bacteroidota, Nitrospirota, Omnitrophota. Among fractions,, only 8% showed significant one-to-one correlation, mostly Motility transport related certain similar other (Omnitrophota, Proteobacteria Nanoarchaeota).Other stress, found little evidence for niche adaptation groundwaters. Given that could detect specific preference few MAGs, speculate majority is able attach multiple hosts just long enough loot exchange supplies.

Language: Английский

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Evolutionary stasis of a deep subsurface microbial lineage

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(10), P. 2830 - 2842

Published: April 6, 2021

Abstract Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found geographically widespread subsurface locations. In order to constrain models for microbial evolution, we compared CDA genomes from Africa, North America Eurasia using single cell genomics. Unexpectedly, 126 partial amplified the three continents, a complete genome of an isolate Eurasia, metagenome-assembled Africa shared >99.2% average nucleotide identity, low frequency SNP’s, near-perfectly conserved prophages CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, unusually strong purifying selection as likely explanations these unexpected results. We therefore conclude that analyzed populations underwent only minimal evolution their physical separation, potentially far back breakup Pangea between 165 55 Ma ago. High-fidelity DNA replication repair mechanisms are most plausible explanation highly CDA. presents stark contrast current model organisms evolutionary studies, which often develop adaptive traits over shorter periods time.

Language: Английский

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The microbial dimension of submarine groundwater discharge: current challenges and future directions

FEMS Microbiology Reviews, Journal Year: 2021, Volume and Issue: 45(5)

Published: Jan. 28, 2021

ABSTRACT Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, microbial dimension SGD remains poorly understood. can influence marine communities through supplying chemical compounds and microorganisms, in turn, microbes at land–ocean transition zone determine chemistry reaching ocean. However, compared with inland groundwater, little is known about coastal aquifers. Here, we review state art SGD, emphasis on prokaryotes, identify current challenges future directions. Main include improving diversity description microbiota, characterized by ultrasmall, inactive novel taxa, high ratios sediment-attached versus free-living cells. Studies should explore dynamics their role cycles aquifers, bidirectional dispersal seawater bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization linking taxonomy activity but also considering entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, ecology) are needed frame study terrestrial aquatic microorganisms beyond limits presumed habitats, foster our understanding processes biogeochemical cycles.

Language: Английский

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Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Dec. 27, 2022

When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form deposits. These actively venting deposits support a rich diversity thermophilic microorganisms which are involved in range carbon, sulfur, nitrogen, hydrogen metabolisms. Global patterns microbial ecosystems have illustrated the strong connectivity between geological processes colonization, but little is known about genomic physiological potential these novel taxa. Here we explore this 42 metagenomes from four vent fields volcano collected 2004 to 2018 document their implications biogeochemical cycles.

Language: Английский

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