M. Mehrshad

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity

This study uses phylogenomic analysis of metagenome-assembled genomes to show that bacterial species rarely exist in multiple biomes and that cross-biome transitions involve proteome reorganization and gene content changes.

Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community

The paper analyzes antibiotic resistance genes in Caspian Sea metagenomes using HMM, homology alignment, and deep learning to classify ARGs by resistance category and link them to ecological strategies.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity

The paper investigates how dissolved organic matter (DOM) chemodiversity sustains taxonomic and functional diversity of aquatic heterotrophs across different model communities.

Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents

The paper analyzes microbial communities in the Persian Gulf along a pollution continuum, showing chronic oil exposure shifts microbial profiles and promotes oil-degrading microbes.

A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

The paper analyzes genome size distribution across Earth's microbiomes and finds that environmental microorganisms have smaller genomes than lab-cultivated ones, with ecological and phylogenetic factors influencing genome size.

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.

Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

The paper analyzes global metagenomes to study metabolic specialization of freshwater Chlorobia, revealing widespread distribution and niche-specific adaptations.

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

The paper identifies a core microbiome in deep oligotrophic groundwater, showing cooperative microbial communities adapted to low-energy environments through ecological traits and partnerships.

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

This study uses ultra-deep metagenomics to reveal phage-centric ecological interactions in freshwater ecosystems, identifying phage genes that enhance microbial survival against grazing and showing spatiotemporal dynamics of phage and host abundances.

The sunlit microoxic niche of the archaeal eukaryotic ancestor comes to light

The paper uses phylogenetic analyses and metabolic reconstructions to infer the lifestyle and metabolic environment of the closest archaeal relatives of eukaryotes, revealing microoxic lifestyles and novel metabolic pathways.

A Swiftian Voyage from Brobdingnag to Lilliput: Freshwater Planctomycetes drifting towards the poles of the genome size spectrum

This study uses ecogenomics to explore the evolutionary history and genome architecture of freshwater Planctomycetes, revealing niche-driven genome reduction and specialized lifestyles.

Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi

The paper examines the diversity and distribution of freshwater Chloroflexi in various pelagic habitats, revealing their genomic diversity and ecological roles.