61 Result(s)
within
Francisco Rodriguez-Valera
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Article
Open AccessDistantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps
The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving ba...
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Article
Mechanisms of inward transmembrane proton translocation
Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elu...
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Article
Open AccessA novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics
Lake Baikal, the world’s deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recr...
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Reference Work Entry In depth
Bacteria
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Article
Open AccessElucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved...
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Protocol
Searching Metagenomes for New Rhodopsins
Most microbial groups have not been cultivated yet, and the only way to approach the enormous diversity of rhodopsins that they contain in a sensible timeframe is through the analysis of their genomes. High-th...
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Protocol
Microbial Rhodopsins
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as ...
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Article
Open AccessThe microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics
The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salin...
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Article
Open AccessViral rhodopsins 1 are an unique family of light-gated cation channels
Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organis...
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Article
Microorganisms of Lake Baikal—the deepest and most ancient lake on Earth
Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body...
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Article
Open AccessUncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil
Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in sha** microbial communities. Investigating the bacteriophage community from soil will shed light not only...
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Article
Open AccessUnique structure and function of viral rhodopsins
Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolut...
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Article
Open AccessMarine-freshwater prokaryotic transitions require extensive changes in the predicted proteome
The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the ...
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Article
Open AccessCorrection to: Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya
Following publication of the original article [1], the authors identified wrong citations in the maintext.
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Article
Open AccessGenomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya
Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, ...
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Article
Open AccessNumerous cultivated and uncultivated viruses encode ribosomal proteins
Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosom...
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Article
Open AccessCRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans
Smacoviridae is a family of small (~2.5 Kb) CRESS-DNA (Circular Rep Encoding Single-Stranded (ss) DNA) viruses. These viruses have been found in faeces, were thought to infect eukaryotes and are suspected to caus...
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Article
Open AccessMinimum Information about an Uncultivated Virus Genome (MIUViG)
This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.
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Article
Open AccessFine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location i...
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Article
Open AccessWild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution
Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in nat...
