LLNL Biofuels Scientific Focus Area
Department of Energy – Office of Science – Genomic Science Program


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


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


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


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


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


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


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


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


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


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?


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


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


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


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


Imaging cell wall architecture in single Zinnia elegans tracheary elements