##  [Publications](/publications) 

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

## 2025

[Nitrogen fixation in *Pampinifervens,* a new species-rich genus of *Aquificaceae* that inhabits a wide pH range in terrestrial hot springs](https://doi.org/10.1016/j.syapm.2025.126644)

[Bacterial volatile organic compound specialists in the phycosphere](https://doi.org/10.1093/ismejo/wraf229)

[Diatom volatile organic compound production is driven by diel metabolism and the cell cycle](https://doi.org/10.3389/fmicb.2025.1620542)

[Impact of nutritional history, prey quality, and quantity on grazing and photophysiological responses in the mixoplanktonic dinoflagellate *Karenia brevis*](https://doi.org/10.1002/lno.70158)

[Spatially structured bacterial interactions alter algal carbon flow to bacteria](https://doi.org/10.1093/ismejo/wraf096)

[A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse](https://doi.org/10.1128/msystems.00375-25)

[MCount: An automated colony counting tool for high-throughput microbiology](https://doi.org/10.1371/journal.pone.0311242)

[Persistence of bacterial-mediated anti-rotifer protection in preliminary outdoor cultivation trial for *Microchloropsis salina*](https://doi.org/10.1016/j.algal.2025.103942)

## 2024

[Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs](https://doi.org/10.1016/j.cub.2024.10.069)

[The NanoSIMS-HR: the next generation of high spatial resolution dynamic SIMS](https://doi.org/10.1021/acs.analchem.4c03091)

[Coastal bacteria and protists assimilate viral carbon and nitrogen](https://doi.org/10.1093/ismejo/wrae231)

[Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library](https://doi.org/10.1016/j.orggeochem.2024.104880)

[Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction](https://doi.org/10.1093/ismejo/wrae140)

[Transporter annotations are holding up progress in metabolic modeling](https://doi.org/10.3389/fsysb.2024.1394084)

[CyanoCyc cyanobacterial web portal](https://doi.org/10.3389/fmicb.2024.1340413)

[Spatially structured competition and cooperation alters algal carbon flow to bacteria](https://doi.org/10.1101/2024.06.14.598523) preprint

[Volatile organic compound specialists in the phycosphere](https://doi.org/10.1101/2024.06.14.599129) preprint

[Multidimensional scaling informed by *F*-ratio: Visualizing microbiome for inference](https://doi.org/10.48550/arXiv.2308.00354) preprint

[An algicidal bacterium shapes the microbiome during large-scale outdoor diatom cultivation collapse](https://doi.org/10.1101/2024.06.11.598583) preprint

## 2023

[Metal organic complexation in seawater: origins and future directions](https://doi.org/10.1146/annurev-marine-033023-083652)

[Multi-scale models of whole cells: progress and challenges](https://doi.org/10.3389%2Ffcell.2023.1260507)

[Single cell isotope tracing reveals functional guilds of bacteria associated with the diatom *Phaeodactylum tricornutum*](https://doi.org/10.1038/s41467-023-41179-9)

[Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites](https://doi.org/10.3390/microorganisms11092149)

[Dynamic *Phaeodactylum tricornutum* exometabolites shape surrounding bacterial communities](https://doi.org/10.1111/nph.19051)

[The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis](https://doi.org/10.1016/j.cub.2023.05.020)

[Plant-soil feedback under drought: does history shape the future?](https://doi.org/10.1016/j.tree.2023.03.001)

[Leveraging microfluidic dielectrophoresis to distinguish compositional variations of lipopolysaccharide in *E. coli*](https://doi.org/10.3389/fbioe.2023.991784)

[Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota](https://doi.org/10.1111/1462-2920.16299)

## 2022

[Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre](https://doi.org/10.1038/s41467-022-34585-y)

[Plant-associated fungi support bacterial resilience following water limitation](https://doi.org/10.1038/s41396-022-01308-6)

[Bacterial exometabolites influence *Chlamydomonas* cell cycle and double algal productivity](https://doi.org/10.1093/femsec/fiac091)

[Simple steps to enable reproducibility: culture conditions affecting *Chlamydomonas* growth and elemental composition](https://doi.org/10.1111/tpj.15867)

[Bacterial community assembly, succession, and metabolic function during *Microchloropsis salina* outdoor cultivation](https://doi.org/10.1128/msphere.00231-22)

[Characterizing engineered “microbial sentinels” with porous microplates for chemically interactive cell culture](https://doi.org/10.15252/msb.202110785)

## 2021

[Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate](https://doi.org/10.1038/s41396-021-01147-x)

[Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae](https://doi.org/10.1128/mSystems.00835-21)

[Abiotic and Biotic Damage of Microalgae Generate Different Volatile Organic Compounds (VOCs) for Early Diagnosis of Algal Cultures for Biofuel Production](https://doi.org/10.3390/metabo11100707)

[Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass](https://doi.org/10.1007/s00248-021-01836-2)

[NanoSIP: NanoSIMS applications for microbial biology](https://doi.org/10.1007/978-1-61779-827-6_13)

[Prokaryotic genome annotation](https://doi.org/10.1007/978-1-0716-1585-0_10)

[Curating constraint-based genome-scale models of metabolism](https://doi.org/10.1007/978-1-0716-1585-0_14)

[A beginner’s guide to the COBRA toolbox](https://doi.org/10.1007/978-1-0716-1585-0_15)

[The future of microbial ecological niche theory and modeling](https://doi.org/10.1111/nph.17373)

[Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport](https://doi.org/10.1111/nph.17527)

[A genomic catalog of Earth’s microbiomes](https://doi.org/10.1038/s41587-020-0718-6)

[Managing Plant Microbiomes for Sustainable Biofuel Production](https://doi.org/10.1094/PBIOMES-12-20-0090-E)

[Microscale Carbon Cycling Between Bacteria and Algae Under the Sun](https://doi.org/10.1007/978-3-030-63512-1_13)

[Multiple lineages of *Streptomyces* produce antimicrobials within passalid beetle galleries across eastern North America](https://doi.org/10.7554/eLife.65091)

[A novel d-xylose isomerase from the gut of the wood feeding beetle *Odontotaenius disjunctus* efficiently expressed in *Saccharomyces cerevisiae*](https://doi.org/10.1038/s41598-021-83937-z)

[The Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by *Phaeodactylum tricornutum* (Bacillariophyceae)](https://doi.org/10.1111/jpy.13132)

[Widespread co‐occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrients](https://doi.org/10.1002/ppp3.10181)

## 2020

[Plant and Soil Drivers of Whole-Plant Microbiomes: Variation in Switchgrass Fungi from Coastal to Mountain Sites](https://doi.org/10.1094/PBIOMES-07-20-0056-FI)

[Effects of Plant-Soil Feedback on Switchgrass Productivity Related to Microbial Origin](https://doi.org/10.3390/agronomy10121860)

[The switchgrass microbiome: A review of structure, function, and taxonomic distribution](https://doi.org/10.1094/PBIOMES-04-20-0029-FI)

[The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes](https://doi.org/10.1093/nar/gkaa746)

[Low Molecular Weight Volatile Organic Compounds Indicate Grazing by the Marine Rotifer *Brachionus plicatilis* on the Microalgae *Microchloropsis salina*](https://doi.org/10.3390/metabo10090361)

[Rhizosphere carbon turnover from cradle to grave: the role of microbe-plant interactions](https://www.springer.com/gp/book/9789811561245) (V. Gupta and A.K. Sharma eds.)

[Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism](https://doi.org/10.1038/s41396-020-00738-4)

[NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts](https://www.annualreviews.org/doi/abs/10.1146/annurev-marine-010419-010714)

[Niche differentiation is spatially and temporally regulated in the rhizosphere](https://www.nature.com/articles/s41396-019-0582-x)

[Symbiosis and stress: how plant microbiomes affect host evolution](https://doi.org/10.1098/rstb.2019.0590)

## 2019

[Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP](https://www.frontiersin.org/articles/10.3389/fmicb.2019.02682/full)

[Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes](https://www.nature.com/articles/s41598-019-50125-z)

[Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients](https://www.sciencedirect.com/science/article/pii/S0304380019301723)

[Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies](https://www.nature.com/articles/s41597-019-0287-z)

[Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS](https://link.springer.com/protocol/10.1007/978-1-4939-9721-3_6)

[Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in Mn-deficient conditions](http://www.jbc.org/content/early/2019/09/16/jbc.RA119.009130.short)

[EcoFABs: advancing microbiome science through standardized fabricated ecosystems](https://www.nature.com/articles/s41592-019-0465-0)

[Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria](https://www.frontiersin.org/articles/10.3389/fmicb.2019.01204/full)

[System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in *Rhodopseudomonas palustris*](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2844-z)

[Bacterial communities protect the alga *Microchloropsis salina* from grazing by the rotifer *Brachionus plicatilis*](https://www.sciencedirect.com/science/article/pii/S2211926418310051)

[Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere](https://www.sciencedirect.com/science/article/pii/S2211926418307379)

[Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle](https://doi.org/10.1038/s41564-019-0384-y)

## 2018

[Combining multiple functional annotation tools increases coverage of metabolic annotation](https://doi.org/10.1186/s12864-018-5221-9)

[Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat](https://doi.org/10.1371/journal.pone.0202792)

[Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions](https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.14357)

[Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community](https://academic.oup.com/femsec/article/94/5/fiy047/4944225)

[Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease](http://pubs.rsc.org/en/content/articlehtml/2018/mt/c7mt00349h)

[High initial sputter rate found for Vaccinia virions using isotopic labeling and high lateral resolution secondary ion mass spectrometry](https://dx.doi.org/10.1021/acs.analchem.7b02786)

## 2017

[Phylogenetically conserved resource partitioning in the coastal microbial loop](https://doi.org/10.1038/ismej.2017.128)

[Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment](https://dx.doi.org/10.1038/ismej.2016.156)

[Measuring cyanobacterial metabolism in biofilms with NanoSIMS isotope imaging and scanning electron microscopy (SEM)](https://doi.org/10.21769/BioProtoc.2263)

[Using stable isotopes to explore root-microbe-mineral interactions in soil](https://dx.doi.org/10.1016/j.rhisph.2017.04.016)

[Made for each other: ascomycete yeasts and insects](https://dx.doi.org/10.1128/microbiolspec.FUNK-0081-2016)

[The fungal tree of life: from molecular systematics to genome-scale phylogenies](https://dx.doi.org/10.1128/microbiolspec.FUNK-0053-2016)

[Combining multiple functional annotation tools increases completeness of metabolic annotation](https://doi.org/10.1101/160887)

[Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat](https://doi.org/10.1101/151704)

[Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate](https://doi.org/10.1186/s40793-017-0279-6)

## 2016

[Genome evolution and nitrogen fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches](http://aem.asm.org/content/early/2016/05/23/AEM.00611-16)

[Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm](http://mbio.asm.org/content/7/3/e00650-16.abstract)

[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)](http://www.sciencedirect.com/science/article/pii/S2211926416300583)

[Longitudinal analysis of microbiota in biofuel microalga *Nannochloropsis salina* cultures](http://link.springer.com/article/10.1007/s00248-016-0746-4)

[Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations](http://dx.doi.org/10.1186/s12859-016-0887-y)

[Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms](http://dx.doi.org/10.1111/1758-2229.12352)

[Tracking microbial interactions with NanoSIMS.](http://www.sciencedirect.com/science/article/pii/S0958166916301574)

[Changes in the structure of the microbial community associated with *Nannochloropsis salina* following treatment with antibiotics and bioactive compounds](http://journal.frontiersin.org/article/10.3389/fmicb.2016.01155/full)

[Permanent draft genome of strain ESFC-1: Ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria](https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0174-6)

[Description of *Teunomyces* gen. nov. for the *Candida kruisii* clade, *Suhomyces* gen. nov. for the *Candida tanzawaensis* clade and *Suhomyces kilbournensis* sp. nov](http://femsyr.oxfordjournals.org/content/16/5/fow041.long)

[Comparative genomics of biotechnologically important yeasts](http://www.pnas.org/content/113/35/9882.long)

## 2015

[Cyanobacterial reuse of extracellular organic carbon in microbial mats.](http://dx.doi.org/10.1038/ismej.2015.180)

[Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach](http://dx.doi.org/10.1038/ismej.2014.144)

[Subcellular structure and biochemical characters in fungal phylogeny](http://dx.doi.org/10.1007/978-3-662-46011-5_9)

[Do Genome-scale Models Need Exact Solvers or Clearer Standards?](http://onlinelibrary.wiley.com/doi/10.15252/msb.20156157/abstract)

## 2014

[Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats](http://dx.doi.org/10.3389/fmicb.2014.00061)

[Subcellular metal imaging identifies dynamic sites of Cu accumulation in *Chlamydomonas*](http://dx.doi.org/10.1038/nchembio.1662)

[Phylogenetic patterns in the microbial response to resource availability: Amino acid incorporation in San Francisco Bay](http://dx.doi.org/10.1371/journal.pone.0095842)

[Identification of *Desulfobacterales* as primary hydrogenotrophs in a complex microbial mat community](http://dx.doi.org/10.1111/gbi.12080)

[Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of *Odontotaenius disjunctus*](http://dx.doi.org/10.1038/ismej.2013.134)

[3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography](http://www.nature.com/nmeth/journal/v10/n9/full/nmeth.2596.html)

## 2013

[*Trichosporon vanderwaltii* sp. nov., an asexual basidiomycetous yeast isolated from soil and beetles](http://dx.doi.org/10.1007/s10482-012-9811-2)

[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](http://dx.doi.org/10.1017/S1431927613013482)

[Draft genome sequence of the cyanobacterium ESFC-1](http://dx.doi.org/10.1128/genomeA.00527-13)

[New combinations, *Scheffersomyces amazonensis* and *S. ergatensis*](http://dx.doi.org/10.5248/123.233)

[Lignin depletion enhances the digestibility of cellulose in cultured xylem cells.](http://dx.doi.org/10.1371/journal.pone.0068266)

[*Scheffersomyces cryptocercus*: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the *Sugiyamaella* yeast clade](http://dx.doi.org/10.3852/12-094)

[Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics](http://dx.doi.org/10.1038/ismej.2012.150)

[The gut of Guatemalan passalid beetles: a habitat colonized by cellobiose- and xylose-fermenting yeasts](http://dx.doi.org/10.1016/j.funeco.2013.06.005)

[Taxon-specific C/N relative use efficiency for amino acids in an estuarine community](http://dx.doi.org/10.1111/j.1574-6941.12000.x)

[An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition](http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12081/abstract)

## 2012

Diversity of yeasts associated with wood and the gut of wood-feeding insects

[Enhanced cellulose degradation using cellulase-nanosphere complexes](http://dx.doi.org/10.1371/journal.pone.0042116)

[Multilocus phylogenetic study of the *Scheffersomyces* yeast clade and characterization of the N-terminal region of xylose reductase gene](http://dx.doi.org/10.1371/journal.pone.0039128)

[Syntrophic metabolism of a co-culture containing *Clostridium cellulolyticum* with *Rhodopseudomonas palustris* for hydrogen production](http://dx.doi.org/10.1016/j.ijhydene.2012.05.100)

[Integrating microbial ecology into ecosystem models: Challenges and priorities](http://dx.doi.org/10.1007/s10533-011-9636-5)

[Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis](http://dx.doi.org/10.1038/ismej.2011.200)

[“NanoSIP: NanoSIMS applications for microbial biology”, Microbial Systems Biology: Methods and Protocols](http://dx.doi.org/10.1007/978-1-61779-827-6_13) \[cover image\]

[Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough Estuary, Monterey Bay](http://dx.doi.org/10.1038/ismej.2011.142)

[The Hydrogenase Chip: A tiling oligonucleotide DNA microarray technique for characterizing hydrogen producing and consuming microbes in microbial communities](http://dx.doi.org/10.1038/ismej.2011.136)

Patent US 20110195862: “Devices, Methods and Systems for Target Detection”

[High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use](http://dx.doi.org/10.1038/ismej.2011.175)

[Development of constraint-based system-level models of microbial metabolism](http://link.springer.com/protocol/10.1007%2F978-1-61779-827-6_18)

[Genome-level transcription data of *Yersinia pestis* analyzed with a new metabolic constraint-based approach](http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-150)

## 2011

[Nitrogen mineralization and assimilation at millimeter scales](http://dx.doi.org/10.1016/B978-0-12-386489-5.00004-X)

## 2010

[Imaging cell wall architecture in single *Zinnia elegans* tracheary elements](http://dx.doi.org/10.1104/pp.110.155242)