A5051974642- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Protist diversity and phylogeny
- Wastewater Treatment and Nitrogen Removal
- Hydrocarbon exploration and reservoir analysis
- Bacteriophages and microbial interactions
- Microbial Fuel Cells and Bioremediation
- Anaerobic Digestion and Biogas Production
- Gut microbiota and health
- Photosynthetic Processes and Mechanisms
- Soil and Water Nutrient Dynamics
- Metalloenzymes and iron-sulfur proteins
- Groundwater and Isotope Geochemistry
- Enzyme Structure and Function
- Metal Extraction and Bioleaching
- Atmospheric and Environmental Gas Dynamics
- Geochemistry and Geologic Mapping
- Plant-Microbe Interactions and Immunity
- Polar Research and Ecology
- Genetics, Bioinformatics, and Biomedical Research
- Ammonia Synthesis and Nitrogen Reduction
- Microbial metabolism and enzyme function
- Marine and coastal ecosystems
- Plant Virus Research Studies
California State University, San Bernardino
2016-2025
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
California State University System
2017
University of Nevada, Las Vegas
2009-2015
University of Nevada, Reno
2013
University of Washington
2003-2010
Czech Academy of Sciences, Institute of Microbiology
2010
U.S. National Science Foundation
2010
Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled...
The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report comprehensive, cultivation-independent census microbial communities 37 samples collected from these encompassing sites ranging temperature 55.1 to 93.6°C, pH 2.5 9.4, mineralogy silicates carbonates Ruidian. Richness was low all samples, with 21–123 species-level OTUs detected. bacterial phylum Aquificae or archaeal...
The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome 1,661,137 bp. Of (open reading frames [ORFs]), 44% were assigned function, 48% conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) unique to M. maripaludis. ORFs, 27 confirmed encode proteins by mass spectrometric identification peptides. Genes for most known functions pathways identified. For...
In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide coenzyme M B (CoM-S-S-CoB). Reduction this by reductase to regenerate HS-CoM HS-CoB is an exergonic process. Thauer et al. [Thauer, 2008 Nat Rev Microbiol 6:579–591] recently suggested that in hydrogenotrophic methanogens energy reduction powers most endergonic reaction pathway, catalyzed formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence these two...
Summary Many thermophiles catalyse free energy‐yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured source water sediments two ∼80°C springs the US Great Basin. Ammonia oxidation occurred mainly sediments. rates using 15 N‐NO 3 ‐ pool dilution ranged from 5.5 ± 0.8 8.6 0.9 nmol N g −1 h unaffected...
The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number essential pieces. Whereas it currently accepted that the process eukaryogenesis involved interplay between host cell and alphaproteobacterial endosymbiont, we lack detailed information regarding identity nature these players. A studies have provided increasing support for emergence eukaryotic from within archaeal domain life, displaying specific affiliation with TACK superphylum. Recent shown genomic...
Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) W. gerlachensis encodes putative tungsten membrane transport systems, as well pathways anaerobic oxidation sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that...
Abstract Background The Atribacterota are widely distributed in the subsurface biosphere. Recently, first isolate was described and number of genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, evolution remain poorly understood. Results We report isolation second member , Thermatribacter velox gen. nov., sp. within a new family Thermatribacteraceae fam. short-term laboratory cultivation JS1 lineage,...
Microorganisms that colonize plant roots are recruited from, and in turn contribute substantially to, the vast virtually uncharacterized phylogenetic diversity of soil microbiota. The diverse, but poorly understood, microorganisms mediate mineral transformations nutrient cycles central to biosphere functioning. Here, we report results epifluorescence microscopy culture-independent recovery small subunit (SSU) ribosomal RNA (rRNA) gene sequences showing members a previously reported clade...
A culture-independent community census was combined with chemical and thermodynamic analyses of three springs located within the Long Valley Caldera, Little Hot Creek (LHC) 1, 3, 4. All were approximately 80 degrees C, circumneutral, apparently anaerobic had similar water chemistries. 16S rRNA gene libraries constructed from DNA isolated spring sediment revealed moderately diverse but highly novel microbial communities. Over half phylotypes could not be grouped into known taxonomic classes....
A thermophilic, filamentous, heterotrophic bacterium, designated strain JAD2 T , a member of an as-yet uncultivated lineage that is present and sometimes abundant in some hot springs worldwide, was isolated from sediment Great Boiling Spring Nevada, USA. Cells had mean diameter 0.3 µm length 4.0 µm, formed filaments typically ranged 20 to 200 µm. Filaments were negative for the Gram stain reaction, spores not motility observed. The optimum temperature growth 72.5–75 °C, with range 67.5–75 pH...
Summary Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within upper euphotic zone of temperate waters. However, factors controlling distribution MGII poorly delineated physiology ecological functions these still‐uncultured organisms remain elusive. In this study, we investigated planktonic associated with particles free‐living forms Pearl River Estuary (PRE) over a 10‐month period. We detected high abundance particle‐associated PRE...
Posttranslational regulation of nitrogenase, or switch-off, in the methanogenic archaeon Methanococcus maripaludis requires both nifI(1) and nifI(2), which encode members PII family nitrogen-regulatory proteins. Previous work demonstrated that nitrogenase activity cell extracts was inhibited presence NifI(1) NifI(2), 2-oxoglutarate (2OG), a potential signal nitrogen limitation, relieved this inhibition. To further explore role NifI proteins we found interact with NifI(2) determined whether...
Ambient nitrous oxide (N2O) emissions from Great Boiling Spring (GBS) in the US Basin depended on temperature, with highest flux, 67.8 ± 2.6 μmol N2O-N m−2 day−1, occurring large source pool at 82 °C. This rate of N2O production contrasted negligible nearby soils and was similar to rates sediments impacted agricultural fertilizers. To investigate N2O, a variety approaches were used enrich isolate heterotrophic micro-organisms, isolates screened for nitrate reduction ability....
Several closely related, thermophilic and cellulolytic bacterial strains, designated JKG1 T , JKG2, JKG3, JKG4 JKG5, were isolated from a enrichment (corn stover) incubated in the water column of Great Boiling Spring, NV. Strain had cells diameter 0.7–0.9 µm length ~2.0 that formed non-branched, multicellular filaments reaching >300 µm. Spores not dense liquid cultures red. The temperature range for growth was 45–65 °C, with an optimum 55 °C. pH 5.6–9.0, 7.5. grew as aerobic heterotroph,...