R. Sachdeva

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

Genetic elements and defense systems drive diversification and evolution in Asgard archaea

This study identifies mobile genetic elements and defense systems in Asgard archaea, revealing their role in shaping genetic diversity and evolution.

Giant genes are rare but implicated in cell wall degradation by predatory bacteria

The paper identifies giant genes in predatory bacteria, showing they are associated with prey adhesion and cell wall degradation.

Asgard archaea modulate potential methanogenesis substrates in wetland soil

The paper reconstructs genomes of soil-associated Asgard archaea and uses metatranscriptomics to show their role in carbon compound metabolism relevant to methane production in wetlands.

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

The paper identifies and characterizes diverse extrachromosomal elements in Methanoperedens archaea, including mini-Borgs and viruses, and shows their genetic exchange and potential impact on archaeal activity.

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

The paper identifies conserved genetic repertoires in Borg extrachromosomal elements of methane-oxidizing archaea and shows their higher expression than host genes.

Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms

The paper predicts vitamin interdependencies in microbial communities using metagenomics-informed network analysis and validates these predictions in microcosms.

Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins

The paper analyzes Borg genomes to show tandem repeats evolve rapidly and create intrinsically disordered regions in proteins, contributing to functional diversity and host associations.

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

This study identifies microbial gene clusters involved in lanthanide metabolism in weathered granites, highlighting their role in phosphate mineral dissolution and soil formation.

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

This paper identifies large plasmids in Methanoperedens archaea that are essential for their physiology and may be used to study and manipulate methane oxidation.

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

The paper identifies Borgs, large extrachromosomal elements in Methanoperedens archaea, which enhance methane oxidation capacity and may influence greenhouse gas emissions.

Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes

The paper shows that thiocyanate and organic carbon inputs select for specific autotrophic Afipia and Thiobacillus strains in microbiomes, with molasses removal favoring a dominant Afipia variant.

Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria

This study examines gene content and co-occurrence patterns in CPR bacteria to understand their evolutionary transitions between environmental and animal-associated habitats.

Wide distribution of alternatively coded Lak megaphages in animal microbiomes

The paper identifies a wide distribution of alternatively coded Lak phages in animal microbiomes, including new genomes and associations with specific animal types.

Targeted Genome Editing of Bacteria Within Microbial Communities

This paper develops a method to edit specific bacteria within microbial communities using ET-Seq and DART systems, enabling genetic manipulation in complex environments.

Measurement error and resolution in quantitative stable isotope probing: implications for experimental design

This paper evaluates measurement error and resolution in qSIP, finding that variance decreases with taxon abundance and that nine density fractions balance cost and precision.

Rare microbes from diverse Earth biomes dominate community activity

The paper shows rare microbes dominate microbial activity across diverse biomes, contributing to ecosystem function and organismal health.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community

The paper analyzes metatranscriptomes of a coastal microbial community to identify B-vitamin synthesizers and consumers, finding mosaic patterns of synthesis and utilization.

290 Metagenome-assembled Genomes from the Mediterranean Sea: a resource for marine microbiology

The paper reports 290 high-quality metagenome-assembled genomes from the Mediterranean Sea, along with 2,786 lower-quality bins, and makes them publicly available for marine microbiology research.