A5026191557- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Photosynthetic Processes and Mechanisms
- Nitrogen and Sulfur Effects on Brassica
- Metalloenzymes and iron-sulfur proteins
- Dental Research and COVID-19
- SARS-CoV-2 and COVID-19 Research
- Enzyme Structure and Function
- Bacteriophages and microbial interactions
- Microbial Metabolic Engineering and Bioproduction
- Studies on Chitinases and Chitosanases
- Algal biology and biofuel production
- SARS-CoV-2 detection and testing
- Mine drainage and remediation techniques
- Protist diversity and phylogeny
- Metal Extraction and Bioleaching
- Geochemistry and Elemental Analysis
- Bacterial Genetics and Biotechnology
- Microbial Metabolites in Food Biotechnology
- Evolution and Genetic Dynamics
- Glycosylation and Glycoproteins Research
- ATP Synthase and ATPases Research
- Legume Nitrogen Fixing Symbiosis
- Biomedical and Engineering Education
Australian Regenerative Medicine Institute
2025
Monash University
2025
University of California, Berkeley
2020-2024
Innovative Genomics Institute
2021-2024
Berkeley College
2023-2024
Planetary Science Institute
2024
Woods Hole Oceanographic Institution
2020
Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of bioinformatic evidence suggests great diversity encapsulin nanocompartments remains unexplored. Here, we describe novel freshwater cyanobacterium
Abstract 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 DNA sequences primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where production occur. Four curated, complete genomes are linear, up to approximately Mb in length share genome organization, including...
Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted bacteria eukaryotes. Here, we show that anaerobic archaea encode diverse, active, ancient lineages through combining analysis existing new genomes with extensive biochemical experiments. are encoded by nine archaeal phyla expressed H2-producing Asgard archaeon...
Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles biogeochemical cycling. We studied chemoautotrophically based biofilms host diverse CPR bacteria and grow to investigate controls on Results Sulfide were investigated using bulk geochemical analysis, genome-resolved metagenomics, scanning transmission X-ray microscopy (STXM) at room temperature 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix Beggiatoa ,...
Abstract The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions soil ecosystems remain unknown. Of particular interest archaeal to methane cycling wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new lineage, genome Freyarchaeia, predicted metabolism situ. Metatranscriptomics reveals expression genes [NiFe]-hydrogenases, pyruvate oxidation carbon fixation via the...
Significance Photosynthetic phytoplankton are the foundation of marine ecosystems. Their growth in sunlit ocean depends on ample supply over a dozen essential elements. Of these elemental nutrients, metal cobalt is found at lowest concentrations seawater, but it unknown whether scarcity impacts growth. We have measured minimum requirements photosynthetic bacterium Prochlorococcus , which flourishes nutrient-poor regions where many other cannot survive. can grow with less than 50 atoms per...
Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria Candidate Phyla Radiation because minimal metabolic capabilities require associations microbial hosts.
Abstract 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 ∼40,000 aa eukaryotic Titin. Even larger proteins may occur rapidly expanding set metagenome-derived sequences, their existence be obscured by assembly fragmentation. Here, we leverage genome curation to complete sequences that encode predicted up 85,804 aa. Overall, findings illuminate huge knowledge gap related giant proteins. Although...
Bacteria of the phylum Acidobacteria are one most abundant groups across soil ecosystems, yet they represented by comparatively few sequenced genomes, leaving gaps in our understanding their metabolic diversity. Recently, genomes species with unusually large repertoires biosynthetic gene clusters (BGCs) were reconstructed from grassland metagenomes, but degree to which this trait widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled recovered permanently...
Abstract Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of bioinformatic evidence suggests great diversity encapsulin nanocompartments remains unexplored. Here, we describe novel freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation...
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to outbreak prevention on college and university campuses. Here we describe the voluntary saliva program instituted at University California, Berkeley during an early period pandemic in 2020. The was administered as a research study ahead clinical implementation, enabling us launch while continuing optimize assay. Results both protocol itself participants’ experience show how succeeded providing routine,...
Abstract The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions soil ecosystems unknown. Of particular interest archaeal to methane cycling wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new lineage, the first genome Freyarchaeia, defined metabolism situ . Metatranscriptomics highlights high expression [NiFe]-hydrogenases, pyruvate oxidation carbon fixation via...
Summary Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1 , yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where production occur, we discovered extraordinarily large, diverse DNA sequences primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length share genome organization, including replicore structure,...
Asgard archaea are of great interest as the progenitors Eukaryotes, but little is known about mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs replicate in Atabeyarchaeia, a wetland lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 for which genome structures were defined and precise chromosome integration sites could be identified confident host linkage. Additionally, 20.67 kbp...
ABSTRACT Borgs are huge extrachromosomal elements of anaerobic methane-oxidizing archaea. They exist in exceedingly complex microbiomes, lack cultivated hosts and have few protein functional annotations, precluding their classification as plasmids, viruses or other. Here, we used silico structure prediction methods to investigate potential roles for ∼10,000 Borg proteins. Prioritizing analysis multicopy genes that could signal importance lifestyles, uncovered highly represented...
Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts nuclear waste, CO2 H2 stored in subsurface. We carried out first multi-year study groundwater microbiomes sampled from defined intervals between 140 400 m below surface Horonobe Mizunami URLs, Japan. reconstructed draft genomes for > 90% all organisms detected over four year period. The are dissimilar, likely because URL is hosted granitic rock sedimentary...
ABSTRACT Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth’s ecosystems. Despite their prevalence, the distribution of CPR lineages habitats and genomic signatures transitions amongst these remain unclear. Here, we expand genome inventory for Absconditabacteria (SR1), Gracilibacteria, Saccharibacteria (TM7), known to occur in both animal-associated environmental microbiomes, investigate variation gene content with habitat origin. By...
Abstract Background Candidate Phyla Radiation (CPR) bacteria are commonly detected yet enigmatic members of diverse microbial communities. Their host associations, metabolic capabilities, and potential roles in biogeochemical cycles remain under-explored. We studied chemoautotrophically-based biofilms that CPR grow sulfide-rich springs using bulk geochemical analysis, genome-resolved metagenomics scanning transmission x-ray microscopy (STXM) at room temperature 87° K. Results CPR-affiliated...
Summary Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has played a vital role in outbreak prevention on college and university campuses. Here we describe the voluntary saliva program instituted at University California, Berkeley during an early period pandemic 2020. The was administered as research study ahead clinical implementation, enabling us to launch while continuing optimize assay. Results both protocol itself participants’ experience show how succeeded...
Lockdowns and “stay-at-home” orders, starting in March 2020, shuttered bench field dependent research across the world as a consequence of global COVID-19 pandemic. The pandemic continues to have an impact on progress career development, especially for graduate students early researchers, strict social distance limitations stifle ongoing impede in-person educational programs. goal Bioinformatics Virtual Coordination Network (BVCN) was reduce some these impacts by helping biologists learn new...
Abstract Asgard Archaea are of great interest as the progenitors Eukaryotes, but little is known about mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs replicate in Atabeyarchaeia, wetland archaea phylum represented by two complete genomes. We used soil depth-resolved population metagenomic datasets to track 18 for which genome structures were defined and precise chromosome integration sites could be identified confident host linkage....
Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts nuclear waste, CO2 H2 stored in subsurface. We carried out first multi-year study groundwater microbiomes sampled from defined intervals between 140 400 m below surface Horonobe Mizunami URLs, Japan. reconstructed draft genomes for >90% all organisms detected over four year period. The are dissimilar, likely because URL is hosted granitic rock sedimentary...
Hydrogenase-mediated hydrogen cycling underpins the diversity and functionality of diverse anoxic ecosystems. [FeFe]-hydrogenases were thought to be restricted bacteria eukaryotes. Here we show that archaea encode diverse, active, ancient lineages through combining analysis existing new genomes with extensive biochemical experiments. are encoded by nine archaeal phyla expressed H2-producing Asgard archaeon culture 'Candidatus Prometheoarchaeum syntrophicum'. We report a novel ultra-minimal...