Lawrence Livermore National Laboratory



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


2018

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

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