A robustly rooted tree of eukaryotes reveals their excavate ancestry

Nature, Год журнала: 2025, Номер unknown

Опубликована: Март 12, 2025

Язык: Английский

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Novel insights into the diversity of halophilic microorganisms and their functioning in hypersaline ecosystems

npj Biodiversity, Год журнала: 2024, Номер 3(1)

Опубликована: Авг. 2, 2024

Abstract Our understanding of the microbial diversity inhabiting hypersaline environments, here defined as containing >100–150 g/L salts, has greatly increased in past five years. Halophiles are found each three domains life. Many novel types have been cultivated, and metagenomics other cultivation-independent approaches revealed existence many previously unrecognized lineages. Syntrophic interactions between different phylogenetic lineages discovered, such symbiosis members archaeal class Halobacteria ‘ Candidatus Nanohalarchaeota’. Metagenomics techniques also shed light on biogeography halophiles, especially genera Salinibacter ( Bacteria ) Haloquadratum Halorubrum Archaea ). Exploration microbiome lakes led to discovery metabolism unknown occur at high salt concentrations. Studies environments with concentrations chaotropic ions magnesium, calcium, lithium refined our limits

Язык: Английский

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Seasonal Lake Ice Cover Drives the Restructuring of Bacteria-Archaea and Bacteria-Fungi Interdomain Ecological Networks Across Diverse Habitats

Environmental Research, Год журнала: 2025, Номер unknown, С. 120907 - 120907

Опубликована: Янв. 1, 2025

Язык: Английский

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Oxidative adaptations in prokaryotes imply the oxygenic photosynthesis before the crown group Cyanobacteria

PNAS Nexus, Год журнала: 2025, Номер 4(2)

Опубликована: Фев. 1, 2025

Abstract The metabolic transition from anaerobic to aerobic in prokaryotes reflects adaptations oxidative stress. Methanogen, one of the earliest life forms on Earth, has evolved into three major groups within Euryarchaeota, exhibiting different phylogenetic affiliations and characters. In comparison with other strictly methanogenic groups, Class II methanogens possess a better capability adapt limited oxygen pressure. Cyanobacteria is considered first only prokaryote evolving oxygenic photosynthesis responsible for Great Oxidation Event Earth. However, connection between evolutionary stress remains elusive. Here, through gene encoding structural maintenance chromosomes (SMC) protein, which was horizontally transferred ancient last common ancestor crown-group Cyanobacteria, we demonstrate that origin extant undoubtedly posterior occurrence oxygen-tolerant methanogens. addition, found certain prokaryotic lineages had tolerance mechanisms against before Cyanobacteria. contradiction predating implies existence more biological oxygenesis. We propose these potential organisms might represent extinct phototrophs emerge during Paleoarchean, contributing tree facilitating dispersal reaction centers across bacterial domain.

Язык: Английский

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Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb–Zn mining wastelands

Journal of Hazardous Materials, Год журнала: 2025, Номер 490, С. 137818 - 137818

Опубликована: Март 4, 2025

Язык: Английский

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Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along species tree explain differences between them via evolutionary events including duplications, transfers, losses. Here, we describe provides natural framework genome evolution highlight applications ancestral content inference, the rooting of trees, insights into metabolic ecological transitions they yield. Reconciliation analyses have elucidated diverse lineages, from Chlamydiae Asgard archaea, shedding light on adaptation, host-microbe interactions, symbiotic relationships. However, there are many opportunities broader application in microbiology. Continuing improvements make models more realistic scalable, integration metadata such habitat, pH, temperature, oxygen use offer enormous potential understanding rich tapestry life.

Язык: Английский

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Microbial Diversity and Open Questions about the Deep Tree of Life

Genome Biology and Evolution, Год журнала: 2024, Номер 16(4)

Опубликована: Апрель 1, 2024

Abstract In this perspective, we explore the transformative impact and inherent limitations of metagenomics single-cell genomics on our understanding microbial diversity their integration into Tree Life. We delve key challenges associated with incorporating new lineages Life through advanced phylogenomic approaches. Additionally, shed light enduring debates surrounding various aspects Life, focusing recent advances in some its deepest nodes, such as roots bacteria, archaea, eukaryotes. also bring forth current genome recovery methodology, well avenues research to uncover additional resolve shape

Язык: Английский

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Acidic proteomes are linked to microbial alkaline preference in African lakes

Water Research, Год журнала: 2024, Номер 266, С. 122393 - 122393

Опубликована: Сен. 3, 2024

Язык: Английский

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Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(10), С. 1856 - 1869

Опубликована: Авг. 12, 2024

Язык: Английский

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Deciphering the chemical landscape and potential ecological function of RiPPs from the untapped Archaea domain

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 8, 2024

Abstract Chemical communication is crucial in ecosystems with complex microbial communities. However, the difficulties inherent to cultivation of archaea have led a limited understanding their chemical language, especially regarding structure diversity and function secondary or specialized metabolites (SMs). Our comprehensive investigation into biosynthetic potential archaea, combined metabolic analyses first report heterologous expression has unveiled previously unexplored capabilities archaeal ribosomally synthesized post-translationally modified peptides (RiPPs). We identified twenty-four new lanthipeptides RiPPs exhibiting unique characteristics, including novel subfamily featuring an type diamino-dicarboxylic (DADC) termini, largely expanding landscape SMs. This sheds light on novelty emphasizes as untapped resource for natural product discovery. Additionally, demonstrate specific antagonistic activity against haloarchaea, mediating biotic interaction halophilic niche. Furthermore, they showcase ecological role enhancing host’s motility by inducing rod-shaped cell morphology upregulating archaellin gene expression, facilitating abiotic environments. These discoveries broaden our language provide promising prospects future exploration SM-mediated interaction. Figure

Язык: Английский

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