F. Rodriguez-Valera

Large diversity in the O-chain biosynthetic cluster within populations ofPelagibacterales

The paper examines O-chain polysaccharide biosynthesis cluster diversity in Pelagibacterales using SAGs and long-read metagenomics, finding high diversity and limited recent horizontal gene transfer.

A host recognition module shared among distant Alteromonas bacteriophage families features tail fibers with transient chaperone caps

This study identifies a shared host recognition module in Alteromonas bacteriophages, showing structural adaptations in tail fibers and chaperones that affect functionality and suggest horizontal gene transfer.

Flotillin-Associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes

The paper identifies a new class of rhodopsins, FArhodopsins, found in marine and freshwater microbes, associated with membrane microdomains and potentially retinal-less function.

Phylogenomics of SAR116 clade reveals two subclades with different evolutionary trajectories and important role in the ocean sulfur cycle

This study uses genomic data to identify two subclades within SAR116 with distinct evolutionary trajectories and roles in the ocean sulfur cycle.

Metagenome-derived virus-microbe ratios across ecosystems

The paper estimates virus-to-microbe ratios using metagenomic data across ecosystems, finding viruses outnumber cells by ~13x in freshwater and ~2-4x in marine/saline plankton, but only ~2x in non-aquatic environments.

Long read metagenomics, the next step?

This study compares third-generation long-read sequencing technologies with short-read sequencing in metagenomics, finding that long reads improve gene and genome reconstruction, especially for microbes with high microdiversity.

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

The paper analyzes the Black Sea's microbiome using genome-centric metagenomics, revealing distinct microbial communities across different water layers and their metabolic capabilities.

New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal

The paper analyzes viral communities in Lake Baikal, identifying new viral roles in carbon and methylotrophy cycles through metagenomic data.

Viral channelrhodopsins: calcium-dependent Na+/K+ selective light-gated channels

The paper characterizes two viral channelrhodopsins, showing they are Ca2+-dependent Na+/K+ channels with unique optogenetic properties and structural differences from known channelrhodopsins.

High Resolution Structural Insights into Heliorhodopsin Family

The paper presents high-resolution structures of two HeR-48C12 states, revealing unique features and suggesting potential enzymatic activity and involvement in redox processes.

Uncovering a hidden diversity: optimized protocols for the extraction of bacteriophages from soil

This paper optimizes protocols for extracting bacteriophages from soil, improving phage recovery and reducing bacterial contamination, and discovers novel phage genomes.

Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

The paper analyzes marine viral communities across depth gradients using metagenomics to show that micro-diversity increases with depth and is linked to environmental factors.

Marine-freshwater prokaryotic transitions require extensive changes in the proteome

This study shows that marine and freshwater prokaryotes have distinct proteome isoelectric point distributions, with significant differences in surface residues and core genome adaptations.

Charting the diversity of Uncultured Viruses of Archaea and Bacteria

The paper classifies nearly 200,000 uncultured viral genomes into genomic lineages, revealing their ecological distribution and functional potential.

Numerous cultivated and uncultivated viruses encode ribosomal proteins

The paper identifies ribosomal proteins encoded by viruses across diverse genomes and metagenomes, challenging the assumption that viruses lack these core translation components.