LLNL Biofuels Scientific Focus Area
Department of Energy – Office of Science – Genomic Science Program
2024
The NanoSIMS-HR: the next generation of high spatial resolution dynamic SIMS preprint
Spatially structured competition and cooperation alters algal carbon flow to bacteria preprint
Volatile organic compound specialists in the phycosphere preprint
Bacteria and protists assimilate and remineralize viral carbon and nitrogen in a coastal microbial community preprint
Multidimensional scaling informed by F-ratio: Visualizing microbiome for inference preprint
A nitrogen siphoning ectoparasite targeting a marine diatom represents a new cosmopolitan clade of uncultivated Rickettsiales (PDF) preprint
An algicidal bacterium shapes the microbiome during large-scale outdoor diatom cultivation collapse preprint
Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction preprint
A toxic environment selects for specialist microbiome in poison frogs preprint
Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library preprint
Transporter annotations are holding up progress in metabolic modeling
CyanoCyc cyanobacterial web portal
2023
Metal organic complexation in seawater: origins and future directions
Multi-scale models of whole cells: progress and challenges
Single cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum
Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites
Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities
The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis
Plant-soil feedback under drought: does history shape the future?
Leveraging microfluidic dielectrophoresis to distinguish compositional variations of lipopolysaccharide in E. coli
Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota
2022
Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre
Plant-associated fungi support bacterial resilience following water limitation
Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity
Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition
Bacterial community assembly, succession, and metabolic function during Microchloropsis salina outdoor cultivation
Characterizing engineered “microbial sentinels” with porous microplates for chemically interactive cell culture
2021
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae
Abiotic and Biotic Damage of Microalgae Generate Different Volatile Organic Compounds (VOCs) for Early Diagnosis of Algal Cultures for Biofuel Production
Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass
NanoSIP: NanoSIMS applications for microbial biology
Prokaryotic genome annotation
Curating constraint-based genome-scale models of metabolism
A beginner’s guide to the COBRA toolbox
The future of microbial ecological niche theory and modeling
Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport
A genomic catalog of Earth’s microbiomes
Managing Plant Microbiomes for Sustainable Biofuel Production
Microscale Carbon Cycling Between Bacteria and Algae Under the Sun
Multiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North America
A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae
The Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by Phaeodactylum tricornutum (Bacillariophyceae)
Widespread co‐occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrients
2020
Plant and Soil Drivers of Whole-Plant Microbiomes: Variation in Switchgrass Fungi from Coastal to Mountain Sites
Effects of Plant-Soil Feedback on Switchgrass Productivity Related to Microbial Origin
The switchgrass microbiome: A review of structure, function, and taxonomic distribution
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Low Molecular Weight Volatile Organic Compounds Indicate Grazing by the Marine Rotifer Brachionus plicatilis on the Microalgae Microchloropsis salina
Rhizosphere carbon turnover from cradle to grave: the role of microbe-plant interactions (V. Gupta and A.K. Sharma eds.)
Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism
NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts
Niche differentiation is spatially and temporally regulated in the rhizosphere
Symbiosis and stress: how plant microbiomes affect host evolution
2019
Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP
Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes
Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients
Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies
Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS
Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in Mn-deficient conditions
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria
System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris
Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis
Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere
Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle
2018
Combining multiple functional annotation tools increases coverage of metabolic annotation
Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat
Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions
Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community
Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease
High initial sputter rate found for Vaccinia virions using isotopic labeling and high lateral resolution secondary ion mass spectrometry
2017
Phylogenetically conserved resource partitioning in the coastal microbial loop
Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment
Measuring cyanobacterial metabolism in biofilms with NanoSIMS isotope imaging and scanning electron microscopy (SEM)
Using stable isotopes to explore root-microbe-mineral interactions in soil
Made for each other: ascomycete yeasts and insects
The fungal tree of life: from molecular systematics to genome-scale phylogenies
Combining multiple functional annotation tools increases completeness of metabolic annotation
Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat
Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate
2016
Genome evolution and nitrogen fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches
Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm
Establishment of stable synthetic mutualism without co-evolution between microalgae and bacteria demonstrated by mutual transfer of metabolites (NanoSIMS isotopic imaging) and persistent physical association (Fluorescent in situ hybridization)
Longitudinal analysis of microbiota in biofuel microalga Nannochloropsis salina cultures
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms
Tracking microbial interactions with NanoSIMS.
Changes in the structure of the microbial community associated with Nannochloropsis salina following treatment with antibiotics and bioactive compounds
Permanent draft genome of strain ESFC-1: Ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria
Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov
Comparative genomics of biotechnologically important yeasts
2015
Cyanobacterial reuse of extracellular organic carbon in microbial mats.
Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach
Subcellular structure and biochemical characters in fungal phylogeny
Do Genome-scale Models Need Exact Solvers or Clearer Standards?
2014
Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats
Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas
Phylogenetic patterns in the microbial response to resource availability: Amino acid incorporation in San Francisco Bay
Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community
Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus
3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography
2013
Trichosporon vanderwaltii sp. nov., an asexual basidiomycetous yeast isolated from soil and beetles
Correlated SEM, FIB-SEM, TEM, and NanoSIMS Imaging of Microbes from the Hindgut of a Lower Termite: Methods for in situ functional and ecological studies of uncultivable microbes
Draft genome sequence of the cyanobacterium ESFC-1
New combinations, Scheffersomyces amazonensis and S. ergatensis
Lignin depletion enhances the digestibility of cellulose in cultured xylem cells.
Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics
The gut of Guatemalan passalid beetles: a habitat colonized by cellobiose- and xylose-fermenting yeasts
Taxon-specific C/N relative use efficiency for amino acids in an estuarine community
An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition
2012
Diversity of yeasts associated with wood and the gut of wood-feeding insects
Enhanced cellulose degradation using cellulase-nanosphere complexes
Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene
Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum with Rhodopseudomonas palustris for hydrogen production
Integrating microbial ecology into ecosystem models: Challenges and priorities
Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis
“NanoSIP: NanoSIMS applications for microbial biology”, Microbial Systems Biology: Methods and Protocols [cover image]
Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough Estuary, Monterey Bay
The Hydrogenase Chip: A tiling oligonucleotide DNA microarray technique for characterizing hydrogen producing and consuming microbes in microbial communities
Patent US 20110195862: “Devices, Methods and Systems for Target Detection”
High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use
Development of constraint-based system-level models of microbial metabolism
Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach
2011
Response to Comments on “A Bacterium That Can Grow Using Arsenic Instead of Phosphorus”
A bacterium that can grow by using arsenic instead of phosphorus
Nitrogen mineralization and assimilation at millimeter scales
2010
Imaging cell wall architecture in single Zinnia elegans tracheary elements
