Archaea
View article: Rapid ecosystem collapse and biofilter formation following seabed methane leakage
Rapid ecosystem collapse and biofilter formation following seabed methane leakage Open
Globally, vast amounts of methane are trapped within subseafloor gas hydrates1. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release2-5, yet the response of deep-se…
View article: Rumen bacterial and archaeal diversity.
Rumen bacterial and archaeal diversity. Open
(A) Total bacterial DNA copies. (B) Total methanogen DNA copies. (C) Bacterial Venn diagram. (D) Archaeal Venn diagram. (E) Bacterial alpha-diversity indices. (F) Archaeal alpha-diversity indices. (G) Bacterial beta-diversity indices. (H) …
View article: Data Sheet 1_Gut microbial communities of Rocky Mountain Sculpin (Cottus bondi) and suckerfish (Catostomus spp.) in the East Gallatin River.pdf
Data Sheet 1_Gut microbial communities of Rocky Mountain Sculpin (Cottus bondi) and suckerfish (Catostomus spp.) in the East Gallatin River.pdf Open
The gastrointestinal (GI) microbiome plays a critical role in animal health and fitness, yet it remains understudied in many species—particularly those inhabiting freshwater environments affected by anthropogenic activity. This study inves…
View article: Suggested interactions between DOM production and decay in the ocean water column, with concurrent cycling of inorganic N.
Suggested interactions between DOM production and decay in the ocean water column, with concurrent cycling of inorganic N. Open
This schematic is informed from experimental and simulation results. Panels A), B) and C) show the DOC, NH4+ and NO3- results from incubations in experiments 1 (Fig 1, ‘Community’) and 2 (…
View article: gapseq reference sequence databases for Bacteria and Archaea
gapseq reference sequence databases for Bacteria and Archaea Open
The repository contains the protein sequences used by gapseq to predict the presence of metabolic reactions and to construct metabolic models.
View article: Formate and hydrogen metabolism in the hyperthermophile Thermococcus and their application in waste-to-hydrogen conversion
Formate and hydrogen metabolism in the hyperthermophile Thermococcus and their application in waste-to-hydrogen conversion Open
Fossil fuel-driven climate change is worsening at an alarming rate with energy demands expected to keep rising in the coming decades. Hence, novel sustainable energy technologies are needed to curb climate change and meet growing energy ne…
View article: gapseq reference sequence databases for Bacteria and Archaea
gapseq reference sequence databases for Bacteria and Archaea Open
The repository contains the protein sequences used by gapseq to predict the presence of metabolic reactions and to construct metabolic models.
View article: Taxonomic and Genomic Characterization of Brevibacillus sp. JNUCC 42 from Baengnokdam Crater Lake, Mt. Halla, and Its Cosmeceutical Potential
Taxonomic and Genomic Characterization of Brevibacillus sp. JNUCC 42 from Baengnokdam Crater Lake, Mt. Halla, and Its Cosmeceutical Potential Open
Jeju Island, a volcanic island located off the southern coast of the Korean Peninsula, harbors highly specialized microbial communities shaped by its unique geological and climatic diversity. In particular, Baengnokdam Crater Lake at the s…
View article: Presentation 1_Different structuring factors and distribution patterns of marine prokaryotic and eukaryotic communities in the subtropical Kuroshio region.pdf
Presentation 1_Different structuring factors and distribution patterns of marine prokaryotic and eukaryotic communities in the subtropical Kuroshio region.pdf Open
To clarify the differences in the effect of environments on community structures and in distribution patterns between marine prokaryotes and microbial eukaryotes, microbial communities were investigated spatially and seasonally in the surf…
View article: Convergent Strategies for Life at the Edge: Hypometabolism and Extremophile Adaptation
Convergent Strategies for Life at the Edge: Hypometabolism and Extremophile Adaptation Open
Life has colonized nearly every conceivable niche on Earth, including environments once thought incompatible with biological activity. These extreme environments, ranging from boiling hot springs to freezing polar ice, highly saline lakes,…
View article: Convergent Strategies for Life at the Edge: Hypometabolism and Extremophile Adaptation
Convergent Strategies for Life at the Edge: Hypometabolism and Extremophile Adaptation Open
Life has colonized nearly every conceivable niche on Earth, including environments once thought incompatible with biological activity. These extreme environments, ranging from boiling hot springs to freezing polar ice, highly saline lakes,…
View article: Image 1_Temperature changes are signaled in cyanobacteria through the PipX interaction network.tif
Image 1_Temperature changes are signaled in cyanobacteria through the PipX interaction network.tif Open
Cyanobacteria perform oxygenic photosynthesis and have evolved sophisticated mechanisms to adapt their metabolism to challenging environmental changes. Despite their ecological and biotechnological importance, many regulatory proteins are …
View article: Temperature changes are signaled in cyanobacteria through the PipX interaction network
Temperature changes are signaled in cyanobacteria through the PipX interaction network Open
Cyanobacteria perform oxygenic photosynthesis and have evolved sophisticated mechanisms to adapt their metabolism to challenging environmental changes. Despite their ecological and biotechnological importance, many regulatory proteins are …
View article: Cultivation and characterization of halophilic archaea from Moroccan Atlantic salterns: insights into diversity and bioactive potential
Cultivation and characterization of halophilic archaea from Moroccan Atlantic salterns: insights into diversity and bioactive potential Open
This study provides the first culture-based survey of archaeal diversity in Moroccan Atlantic solar salterns (Oualidia and Khenifiss), using sediment samples collected across a gradient of moderate to extreme salinities (16.7–29.2% w/v) an…
View article: Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes
Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes Open
Background Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, h…
View article: Table 1_Temperature changes are signaled in cyanobacteria through the PipX interaction network.docx
Table 1_Temperature changes are signaled in cyanobacteria through the PipX interaction network.docx Open
Cyanobacteria perform oxygenic photosynthesis and have evolved sophisticated mechanisms to adapt their metabolism to challenging environmental changes. Despite their ecological and biotechnological importance, many regulatory proteins are …
View article: Emerging CRISPR/Cas-Based Strategies for ExtracellularVesicle Detection: A Comprehensive Review
Emerging CRISPR/Cas-Based Strategies for ExtracellularVesicle Detection: A Comprehensive Review Open
Extracellular vesicles (EVs), which carry a variety of molecules such as proteins and nucleic acids, have great potential for broad application in liquid biopsy. However, achieving highly sensitive detection of biomarkers within EVs remain…
View article: Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments
Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments Open
Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time,…
View article: Opsins are phospholipid scramblases in all domains of life
Opsins are phospholipid scramblases in all domains of life Open
Opsins are highly abundant retinal proteins in the membranes of photoheterotrophic bacteria. However, some microbial genomes encode an opsin but lack the gene for the final enzyme in retinal synthesis. To account for this paradox, we hypot…
View article: Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems
Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems Open
An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in…
View article: Image 2_Temperature changes are signaled in cyanobacteria through the PipX interaction network.tif
Image 2_Temperature changes are signaled in cyanobacteria through the PipX interaction network.tif Open
Cyanobacteria perform oxygenic photosynthesis and have evolved sophisticated mechanisms to adapt their metabolism to challenging environmental changes. Despite their ecological and biotechnological importance, many regulatory proteins are …
View article: Nitrogen-fixing microbes gain genes in diverse types of living environments
Nitrogen-fixing microbes gain genes in diverse types of living environments Open
Biological nitrogen fixation (BNF), which is catalyzed by a large nitrogenase enzyme complex, has evolved in both bacteria and archaea. Indeed, nitrogen-fixing species are found in diverse living environments, and BNF has evolved even in a…
View article: Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors
Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors Open
Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Sca…
View article: Evolution, structure and function of L-cysteine desulfidase, an enzyme involved in sulfur metabolism in the methanogenic archeon Methanococcus maripaludis
Evolution, structure and function of L-cysteine desulfidase, an enzyme involved in sulfur metabolism in the methanogenic archeon Methanococcus maripaludis Open
The biosynthesis of sulfur-containing molecules, which play essential roles in cell metabolism, often relies on enzymes that mobilize sulfur from cysteine. The function of such enzyme, L-cysteine desulfidase CyuA, which catalyzes L-cystein…
View article: Supplementary file 1_Divergent gut microbial metabolism supports niche partitioning in giant and red pandas.docx
Supplementary file 1_Divergent gut microbial metabolism supports niche partitioning in giant and red pandas.docx Open
Introduction The gut microbiota plays a pivotal role in regulating the host's physiological functions and behavior. The coevolutionary relationship between the host and its gut microbiota facilitates adaptation to specific ecological niche…
View article: Rumen Microbiota-Based Machine Learning Approach for Predicting Heat Stress and Identifying Associated Microbes
Rumen Microbiota-Based Machine Learning Approach for Predicting Heat Stress and Identifying Associated Microbes Open
Heat stress poses a significant global challenge to sustainable livestock production, leading to detrimental impacts on animal production and welfare. Reduced appetite and increased body temperature further disrupt the gastrointestinal mic…
View article: An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes
An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes Open
Background Biological chitin degradation is a major process in the ocean, governed primarily by the action of microorganisms. It is known that the structure and taxonomic profile of chitin-degrading microbial communities change across mari…
View article: Transition Fingerprints: A Needle‑Eye Principle for Detecting Minimal Life and Trojan Entities Across Scales
Transition Fingerprints: A Needle‑Eye Principle for Detecting Minimal Life and Trojan Entities Across Scales Open
Minimal biological entities—from single proteins to ultra‑reduced archaea and viral RNA elements—occupy a "twilight zone" between living and non‑living systems. Traditional characterization focuses on static composition (genome size, morph…
View article: Transition Fingerprints: A Needle‑Eye Principle for Detecting Minimal Life and Trojan Entities Across Scales
Transition Fingerprints: A Needle‑Eye Principle for Detecting Minimal Life and Trojan Entities Across Scales Open
Minimal biological entities—from single proteins to ultra‑reduced archaea and viral RNA elements—occupy a "twilight zone" between living and non‑living systems. Traditional characterization focuses on static composition (genome size, morph…
View article: Divergent gut microbial metabolism supports niche partitioning in giant and red pandas
Divergent gut microbial metabolism supports niche partitioning in giant and red pandas Open
Introduction The gut microbiota plays a pivotal role in regulating the host's physiological functions and behavior. The coevolutionary relationship between the host and its gut microbiota facilitates adaptation to specific ecological niche…