Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Nature Reviews Microbiology, Год журнала: 2019, Номер 18(2), С. 67 - 83

Опубликована: Дек. 19, 2019

Язык: Английский

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Clades of huge phages from across Earth’s ecosystems

Nature, Год журнала: 2020, Номер 578(7795), С. 425 - 431

Опубликована: Фев. 12, 2020

Bacteriophages typically have small genomes

Язык: Английский

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CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Nature Methods, Год журнала: 2023, Номер 20(8), С. 1203 - 1212

Опубликована: Июль 27, 2023

Язык: Английский

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Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Апрель 6, 2020

Abstract Background The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, other aquifer environments. Recently increasing attention paid this diverse including > 20 candidate phyla (a large part of the phylum radiation, CPR) because it refreshed our view tree life. However, adaptive traits contributing its prevalence are still not well known. Results Here, we investigated genomic features metabolic pathways groundwater through genome-resolved metagenomics analysis 600 Gbp sequence data. We observed that, while members have reduced genomes (~ 1 Mbp) exclusively, functions essential growth reproduction genetic information processing were retained. Surprisingly, they sharply redundant nonessential functions, specific activities stress response systems. ultra-small cells simplified membrane structures, flagellar assembly, transporters, two-component Despite lack CRISPR viral defense, bacteria may evade predation deletion common phage receptors alternative strategies, which explain low representation prophage proteins their CRISPR. By establishing linkages between bacterial environmental conditions, results provide important insights into evolution CPR group. Conclusions that streamlined many acquiring advantages avoiding invasion, adapt environment. unique small genome size, cell lacking lineage bringing new understandings on life Bacteria. Our mechanisms for adaptation environments, demonstrate a case where less is more, mighty.

Язык: Английский

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Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Nature Biotechnology, Год журнала: 2019, Номер 37(11), С. 1314 - 1321

Опубликована: Сен. 30, 2019

Язык: Английский

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A rooted phylogeny resolves early bacterial evolution

Science, Год журнала: 2021, Номер 372(6542)

Опубликована: Май 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.

Язык: Английский

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The role of microbial motility and chemotaxis in symbiosis

Nature Reviews Microbiology, Год журнала: 2019, Номер 17(5), С. 284 - 294

Опубликована: Март 28, 2019

Язык: Английский

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Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Июнь 20, 2019

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms formation a groundwater microbiome subsequent differentiation Patescibacteria. In Hainich Critical Zone Exploratory, Germany, trace microorganisms from forested soils preferential recharge areas through fractured aquifers along 5.4 km hillslope well transect. were preferentially mobilized constituted 66% species-level OTUs shared between seepage shallow groundwater. These OTUs, mostly related to Kaiserbacteraceae, Nomurabacteraceae, unclassified UBA9983 at family level, represented relative abundance 71.4% community shallowest well, still 44.4% end Several subclass-level groups exhibited preferences for different conditions two aquifer assemblages investigated: Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Nomurabacteraceae negatively correlated. Co-occurrence network analysis revealed central role microbial communities pointed potential associations specific organisms, including abundant autotrophic taxa involved nitrogen, sulfur iron cycling. Strong among themselves further suggested that many within this phylum, distribution was mainly driven by commonly supporting fermentative life style without direct dependence on hosts. We propose import soil, hydrochemical conditions, availability organic resources hosts, determine success environments.

Язык: Английский

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Genomic diversity, lifestyles and evolutionary origins of DPANN archaea

FEMS Microbiology Letters, Год журнала: 2019, Номер 366(2)

Опубликована: Янв. 1, 2019

Archaea—a primary domain of life besides Bacteria—have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery large diversity archaea non-extreme environments enabled by use cultivation-independent methods. These approaches have allowed reconstruction genomes uncultivated microorganisms and revealed are diverse broadly distributed biosphere seemingly include putative symbiotic organisms, most which belong to tentative archaeal superphylum referred DPANN. This group encompasses at least 10 different lineages includes extremely small cell genome sizes limited metabolic capabilities. Therefore, many members DPANN may be obligately dependent on interactions other even novel parasites. In contribution, we review current knowledge gene repertoires lifestyles discuss their placement tree life, is basis our understanding deep microbial roots role symbiosis evolution Earth.

Язык: Английский

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

Nature Microbiology, Год журнала: 2021, Номер 6(3), С. 354 - 365

Опубликована: Янв. 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.

Язык: Английский

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