Rohan Sachdeva
YOU?
Author Swipe
View article: Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i>
Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i> Open
Summary Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in lengt…
View article: Phage-based microbiome manipulation elucidates interactions within community context
Phage-based microbiome manipulation elucidates interactions within community context Open
Testing microbial interaction hypotheses remains a major challenge in microbiome research. Bacteriophages have the potential to probe organism-organism interactions within complex microbiomes, yet are rarely used for this purpose. Here, we…
View article: Circular 23S rRNA within archaeal ribosomes
Circular 23S rRNA within archaeal ribosomes Open
The ribosomal RNAs (rRNAs) that form the core of ribosomes are believed to occur as linear molecules. Here, we investigated rRNAs from diverse and mostly uncultivated archaea and found evidence that, in at least eight phylum-level archaeal…
View article: Overturning circulation structures the microbial functional landscape of the South Pacific
Overturning circulation structures the microbial functional landscape of the South Pacific Open
Global overturning circulation partitions the deep ocean into regions with unique physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems remains unknown. Here, we integrate extensive genom…
View article: The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts
The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts Open
Mediterranean grasslands, vital natural and agricultural ecosystems, experience seasonal variation in water content that likely affect microbial activity. We used metagenomics-informed stable isotope probing to investigate how the activiti…
View article: Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories
Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories Open
Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow ground…
View article: Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling
Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling Open
Rice paddies contribute substantially to atmospheric methane (CH 4 ) and these emissions are expected to increase as the need to feed the human population grows. Here, we show that two independent rice genotypes overexpressing genes for PL…
View article: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements Open
Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland …
View article: Asgard archaea modulate potential methanogenesis substrates in wetland soil
Asgard archaea modulate potential methanogenesis substrates in wetland soil Open
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetl…
View article: Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires Open
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new g…
View article: Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation
Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation Open
Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of gro…
View article: Genetic elements and defense systems drive diversification and evolution in Asgard archaea
Genetic elements and defense systems drive diversification and evolution in Asgard archaea Open
Asgard Archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, wetland As…
View article: Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes
Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes Open
Background Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Current…
View article: Asgard archaea modulate potential methanogenesis substrates in wetland soil
Asgard archaea modulate potential methanogenesis substrates in wetland soil Open
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems are unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland…
View article: Giant genes are rare but implicated in cell wall degradation by predatory bacteria
Giant genes are rare but implicated in cell wall degradation by predatory bacteria Open
Across the tree of life, gene lengths vary, but most are no more than a few thousand base pairs in length. The largest protein often reported is the ∼40,000 aa eukaryotic Titin. Even larger proteins may occur in the rapidly expanding set o…
View article: Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms
Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms Open
View article: Methanotrophic<i>Methanoperedens</i>archaea host diverse and interacting extrachromosomal elements
Methanotrophic<i>Methanoperedens</i>archaea host diverse and interacting extrachromosomal elements Open
Methane emissions that contribute to climate change can be mitigated by anaerobic methane-oxidizing archaea such as Methanoperedens . Some Methanoperedens have huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate th…
View article: Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires Open
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new g…
View article: Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms
Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms Open
Microbial communities are fundamental components of most ecosystems but little is known about the interactions that structure them. Metagenomic data have revolutionized our understanding of complex consortia, yet predicted interactions are…
View article: Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins
Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins Open
Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate …
View article: A widespread group of large plasmids in methanotrophic Methanoperedens archaea
A widespread group of large plasmids in methanotrophic Methanoperedens archaea Open
View article: Borgs are giant genetic elements with potential to expand metabolic capacity
Borgs are giant genetic elements with potential to expand metabolic capacity Open
Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1 , yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse …
View article: Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes Open
View article: Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins
Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins Open
Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate …
View article: Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?
Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites? Open
Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for the release of phosphate to the biosphere, yet the micr…
View article: Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Life and death in the soil microbiome: how ecological processes influence biogeochemistry Open
View article: A widespread group of large plasmids in methanotrophic <i>Methanoperedens</i> archaea
A widespread group of large plasmids in methanotrophic <i>Methanoperedens</i> archaea Open
Anaerobic methanotrophic (ANME) archaea conserve energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME archaea are little understood. Here …
View article: Species- and site-specific genome editing in complex bacterial communities
Species- and site-specific genome editing in complex bacterial communities Open
View article: Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes Open
The genetic code is a highly conserved feature of life. However, some “alternative” genetic codes use reassigned stop codons to code for amino acids. Here, we survey stop codon recoding across bacteriophages (phages) in human and animal gu…
View article: Closely related Lak megaphages replicate in the microbiomes of diverse animals
Closely related Lak megaphages replicate in the microbiomes of diverse animals Open