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Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

https://doi.org/10.1371/journal.pgen.1004784

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Metabolism of halophilic archaea

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Halophilic adaptation of enzymes

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Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales

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Compatible solutes of organisms that live in hot saline environments

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FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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H aloarcula

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H alococcus

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N atronobacterium

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Survival Strategies and Stress Adaptations in Halophilic Archaebacteria

inferred← citeshttps://doi.org/10.1038/ismej.2016.203openalex-snapshot

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats

inferred← citeshttps://doi.org/10.1038/nrg3962openalex-snapshot

Horizontal gene transfer: building the web of life

inferred← citeshttps://doi.org/10.1038/s41396-018-0060-xopenalex-snapshot

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

inferred← citeshttps://doi.org/10.1038/s41396-021-01079-6openalex-snapshot

Salt tolerance-based niche differentiation of soil ammonia oxidizers

inferred← citeshttps://doi.org/10.1038/s41467-020-19200-2openalex-snapshot

Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition

inferred← citeshttps://doi.org/10.1038/s41522-024-00615-4openalex-snapshot

Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater

inferred← citeshttps://doi.org/10.1038/s41564-024-01647-4openalex-snapshot

Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments

inferred← citeshttps://doi.org/10.1038/s41579-018-0136-7openalex-snapshot

An evolving view of methane metabolism in the Archaea

inferred← citeshttps://doi.org/10.1038/s41598-020-59681-1openalex-snapshot

Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon

inferred← citeshttps://doi.org/10.1038/s41598-020-62446-5openalex-snapshot

A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes

inferred← citeshttps://doi.org/10.1038/s41598-020-77723-6openalex-snapshot

Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order

inferred← citeshttps://doi.org/10.1038/s41598-022-23437-wopenalex-snapshot

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

inferred← citeshttps://doi.org/10.1038/srep32467openalex-snapshot

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

inferred← citeshttps://doi.org/10.1039/c9np00017hopenalex-snapshot

Catalytic mechanism and properties of pyridoxal 5′-phosphate independent racemases: how enzymes alter mismatched acidity and basicity

inferred← citeshttps://doi.org/10.1073/pnas.1618463114openalex-snapshot

Integrative modeling of gene and genome evolution roots the archaeal tree of life

inferred← citeshttps://doi.org/10.1073/pnas.2205037119openalex-snapshot

Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus

inferred← citeshttps://doi.org/10.1093/femsle/fnae001openalex-snapshot

Assessing the metabolism, phylogenomic, and taxonomic classification of the halophilic genus Halarchaeum

inferred← citeshttps://doi.org/10.1093/femsle/fnae106openalex-snapshot

Metataxonomic analysis of halophilic archaea community in two geothermal oases in the southern Tunisian Sahara

inferred← citeshttps://doi.org/10.1093/femsre/fuy009openalex-snapshot

Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations

inferred← citeshttps://doi.org/10.1093/gbe/evw114openalex-snapshot

Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association

inferred← citeshttps://doi.org/10.1093/jpe/rtx066openalex-snapshot

Solutes in native plants in the Arabian Gulf region and the role of microorganisms: future research

inferred← citeshttps://doi.org/10.1093/molbev/msab146openalex-snapshot

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties

inferred← citeshttps://doi.org/10.1093/molbev/msv015openalex-snapshot

Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life

inferred← citeshttps://doi.org/10.1093/molbev/msv249openalex-snapshot

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

inferred← citeshttps://doi.org/10.1093/nar/gkaa1196openalex-snapshot

Mechanical and structural properties of archaeal hypernucleosomes

inferred← citeshttps://doi.org/10.1093/nar/gkx1302openalex-snapshot

Structural and functional adaptation of Haloferax volcanii TFEα/β

inferred← citeshttps://doi.org/10.1093/nargab/lqz021openalex-snapshot

Expanding the type IIB DNA topoisomerase family: identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements

inferred← citeshttps://doi.org/10.1093/pnasnexus/pgad023openalex-snapshot

The origin and evolution of methanogenesis and Archaea are intertwined

inferred← citeshttps://doi.org/10.1098/rsif.2024.0630openalex-snapshot

Determination of in cellulo proteome molecular dynamics in different halophilic Archaea

inferred← citeshttps://doi.org/10.1099/ijsem.0.002810openalex-snapshot

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.

inferred← citeshttps://doi.org/10.1099/ijsem.0.005960openalex-snapshot

Natrinema salsiterrestre sp. nov., an extremely halophilic archaeon isolated from a hypersaline soil

inferred← citeshttps://doi.org/10.1099/ijsem.0.006157openalex-snapshot

Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach

inferred← citeshttps://doi.org/10.1101/2020.06.16.153114openalex-snapshot

The ribbon-helix-helix domain proteins CdrS and CdrL regulate cell division in archaea

inferred← citeshttps://doi.org/10.1101/2022.02.17.480683openalex-snapshot

Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

inferred← citeshttps://doi.org/10.1101/2022.03.22.485428openalex-snapshot

Comparative analysis of genome-wide protein-DNA interactions across domains of life reveals unique binding patterns for hypersaline archaeal histones

inferred← citeshttps://doi.org/10.1101/2022.08.16.504008openalex-snapshot

Analysis of the complete genome sequence for Halococcus dombrowskii ATCC BAA-364 T

inferred← citeshttps://doi.org/10.1101/2023.07.03.547478openalex-snapshot

Several independent adaptations of archaea to hypersaline environments

inferred← citeshttps://doi.org/10.1101/2023.10.24.563781openalex-snapshot

Metataxonomic analysis of halophilic archaea community in two geothermal springs sources in southern Tunisian Sahara

inferred← citeshttps://doi.org/10.1111/1462-2920.13156openalex-snapshot

Strangers in the archaeal world: osmostress‐responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus

inferred← citeshttps://doi.org/10.1111/1462-2920.13259openalex-snapshot

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

inferred← citeshttps://doi.org/10.1111/1462-2920.13397openalex-snapshot

Organization and mode of action of two component system signaling circuits from the various kingdoms of life

inferred← citeshttps://doi.org/10.1111/1462-2920.15524openalex-snapshot

Microbiology of a NaCl stalactite ‘salticle’ in Triassic halite

inferred← citeshttps://doi.org/10.1111/1462-2920.16451openalex-snapshot

Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars

inferred← citeshttps://doi.org/10.1111/1758-2229.12596openalex-snapshot

Analysis of multiple haloarchaeal genomes suggests that the quinone‐dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments

inferred← citeshttps://doi.org/10.1126/science.aaf3883openalex-snapshot

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

inferred← citeshttps://doi.org/10.1128/aem.01097-15openalex-snapshot

Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems

inferred← citeshttps://doi.org/10.1128/jb.00244-18openalex-snapshot

GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii

inferred← citeshttps://doi.org/10.1128/jb.00576-18openalex-snapshot

Species Widely Distributed in Halophilic Archaea Exhibit Opsin-Mediated Inhibition of Bacterioruberin Biosynthesis

inferred← citeshttps://doi.org/10.1128/mbio.00649-15openalex-snapshot

Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein

inferred← citeshttps://doi.org/10.1128/mbio.01007-20openalex-snapshot

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea

inferred← citeshttps://doi.org/10.1128/mbio.02371-20openalex-snapshot

Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments

inferred← citeshttps://doi.org/10.1128/mbio.03449-22openalex-snapshot

The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria

inferred← citeshttps://doi.org/10.1128/mmbr.00040-18openalex-snapshot

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

inferred← citeshttps://doi.org/10.1146/annurev-micro-040820-124627openalex-snapshot

Horizontal Gene Transfer in Archaea—From Mechanisms to Genome Evolution

inferred← citeshttps://doi.org/10.11594/jtls.11.03.11openalex-snapshot

A Review on Enzymatic Response to Salt Stress and Genomic/Metagenomic Analysis of Adaptation Protein in Hypersaline Environment

inferred← citeshttps://doi.org/10.1177/00368504251364316openalex-snapshot

Genomic insights into Halorubrum ezzemoulense strain TC23: Genetic basis for halophilic traits and biotechnological potential

inferred← citeshttps://doi.org/10.1186/s12864-016-2920-yopenalex-snapshot

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

inferred← citeshttps://doi.org/10.1186/s12866-023-03133-zopenalex-snapshot

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

inferred← citeshttps://doi.org/10.1186/s13059-018-1454-9openalex-snapshot

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

inferred← citeshttps://doi.org/10.1186/s40709-017-0072-0openalex-snapshot

HaloDom: a new database of halophiles across all life domains

inferred← citeshttps://doi.org/10.1186/s40793-022-00455-9openalex-snapshot

Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

inferred← citeshttps://doi.org/10.1186/s40793-025-00739-wopenalex-snapshot

Salinization alters microbial methane cycling in freshwater sediments

inferred← citeshttps://doi.org/10.1371/journal.pbio.2005163openalex-snapshot

With a pinch of extra salt—Did predatory protists steal genes from their food?

inferred← citeshttps://doi.org/10.1371/journal.pgen.1007582openalex-snapshot

Structure and function of archaeal histones

inferred← citeshttps://doi.org/10.1371/journal.pone.0150404openalex-snapshot

Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix

inferred← citeshttps://doi.org/10.1371/journal.pone.0156543openalex-snapshot

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

inferred← citeshttps://doi.org/10.1371/journal.pone.0215986openalex-snapshot

Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq

inferred← citeshttps://doi.org/10.2139/ssrn.4882405openalex-snapshot

Salinity Acclimation of Nitrifying Microorganisms: Nitrification Performance, Microbial Community, Osmotic Adaptation Strategies

inferred← citeshttps://doi.org/10.2174/0122115501425807251017044247openalex-snapshot

Isolation and Characterization of Several Halophilic Bacteria from Marine Environments

inferred← citeshttps://doi.org/10.3389/fenrg.2023.1125619openalex-snapshot

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage

inferred← citeshttps://doi.org/10.3389/fmars.2024.1421769openalex-snapshot

Unveiling the genomic landscape and adaptive mechanisms of the haloarchaeal genus Halogeometricum: spotlight on thiamine biosynthesis

inferred← citeshttps://doi.org/10.3389/fmicb.2015.00661openalex-snapshot

Domain organization of DNase from Thioalkalivibrio sp. provides insights into retention of activity in high salt environments

inferred← citeshttps://doi.org/10.3389/fmicb.2017.01589openalex-snapshot

Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii

inferred← citeshttps://doi.org/10.3389/fmicb.2018.01800openalex-snapshot

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

inferred← citeshttps://doi.org/10.3389/fmicb.2019.01928openalex-snapshot

New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea

inferred← citeshttps://doi.org/10.3389/fmicb.2020.02082openalex-snapshot

Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate

inferred← citeshttps://doi.org/10.3389/fmicb.2020.581903openalex-snapshot

Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience

inferred← citeshttps://doi.org/10.3389/fmicb.2020.605859openalex-snapshot

Exploring the Molecular Machinery of Denitrification in Haloferax mediterranei Through Proteomics

inferred← citeshttps://doi.org/10.3389/fmicb.2021.625599openalex-snapshot

Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

inferred← citeshttps://doi.org/10.3389/fmicb.2022.848908openalex-snapshot

Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1625916openalex-snapshot

Life in the brine of Lunenburg, Germany: unveiling microorganisms associated with Zechstein salt deposits

inferred← citeshttps://doi.org/10.3389/frmbi.2023.1329925openalex-snapshot

Extreme fluctuations in ambient salinity select for bacteria with a hybrid “salt-in”/”salt-out” osmoregulation strategy

inferred← citeshttps://doi.org/10.3390/biology14050538openalex-snapshot

Traces of a Primitive RNA Ring in Current Genomes

inferred← citeshttps://doi.org/10.3390/biology9050088openalex-snapshot

Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

inferred← citeshttps://doi.org/10.3390/biom10101390openalex-snapshot

The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

inferred← citeshttps://doi.org/10.3390/genes10030220openalex-snapshot

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome

inferred← citeshttps://doi.org/10.3390/genes10110891openalex-snapshot

Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses

inferred← citeshttps://doi.org/10.3390/genes12010058openalex-snapshot

Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation

inferred← citeshttps://doi.org/10.3390/genes12020149openalex-snapshot

The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea

inferred← citeshttps://doi.org/10.3390/genes12101609openalex-snapshot

Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern

inferred← citeshttps://doi.org/10.3390/genes13010148openalex-snapshot

Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns

inferred← citeshttps://doi.org/10.3390/genes13060939openalex-snapshot

The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7

inferred← citeshttps://doi.org/10.3390/genes9030152openalex-snapshot

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)

inferred← citeshttps://doi.org/10.3390/genes9040177openalex-snapshot

Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis

inferred← citeshttps://doi.org/10.3390/life5021427openalex-snapshot

A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes

inferred← citeshttps://doi.org/10.3390/life7040046openalex-snapshot

Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi

inferred← citeshttps://doi.org/10.3390/microorganisms12020334openalex-snapshot

Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species

inferred← citeshttps://doi.org/10.3390/microorganisms12081738openalex-snapshot

Haloarchaea as Promising Chassis to Green Chemistry

inferred← citeshttps://doi.org/10.3390/microorganisms13040761openalex-snapshot

Strategies of Environmental Adaptation in the Haloarchaeal Genera Haloarcula and Natrinema

inferred← citeshttps://doi.org/10.3390/microorganisms13071653openalex-snapshot

Irrigation of Suaeda salsa with Saline Wastewater and Microalgae: Improving Saline–Alkali Soil and Revealing the Composition and Function of Rhizosphere Bacteria

inferred← citeshttps://doi.org/10.3390/microorganisms8121900openalex-snapshot

The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances

inferred← citeshttps://doi.org/10.59717/j.xinn-life.2026.100235openalex-snapshot

Radiating pattern revealed by a deep learning model traces the evolutionary dynamics of the Archaea domain

inferred← citeshttps://doi.org/10.6084/m9.figshare.26556461openalex-snapshot

Additional file 1 of Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

inferred← citeshttps://doi.org/10.70675/16d801b1z23dfz475az8b07zaf20d0424d35openalex-snapshot

Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean

inferred← citeshttps://doi.org/10.70675/d2a702bfzb170z4a5fz9317z2d27179942d0openalex-snapshot

Deep archaeal phylogeny and evolutionary dynamics of DPANNs

inferred← citeshttps://doi.org/10.70675/f9fbb237z6ebfz42f5zb132zaed46e39783aopenalex-snapshot

Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis

inferred← citeshttps://doi.org/10.7939/r3cv4c741openalex-snapshot

Mechanistic studies of PLP-independent racemases

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