About

Adam Arkin is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering at the University of California, Berkeley and a Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. His laboratory develops experimental and computational technologies aimed at the discovery, prediction, control, and design of microbial and viral functions and behaviors within environmental contexts. He serves as the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), which is designed to understand, at a molecular level, the impact of microbial communities on their ecosystems, with a specific focus on terrestrial communities in contaminated watersheds. Additionally, he directs the Department of Energy Systems Biology Knowledgebase (KBase) program, an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants, and their communities, facilitating the sharing of results and methods among scientists. Arkin also directs the Center for Utilization of Biological Engineering in Space, which seeks microbial and plant-based biological solutions for in situ resource utilization to reduce launch mass and improve the reliability and quality of food, pharmaceuticals, fuels, and materials for astronauts on missions to Mars. Furthermore, he is the Co-Director of the Berkeley Synthetic Biology Institute, which unites scientists from U.C. Berkeley and Lawrence Berkeley National Laboratory with industry partners to advance technology and applications for sustainable biomanufacturing.

Research topics

• Computer Science
• Biology
• Genetics
• Computational biology
• Engineering
• Data science
• Ecology
• Evolutionary biology
• Artificial Intelligence
• Astrobiology
• Philosophy
• Management science
• Environmental ethics
• Mathematics
• Art
• Library science
• Biotechnology
• Astronomy
• Physics
• Art history
• Nanotechnology
• World Wide Web
• Systems engineering
• Programming language

Selected publications

• The WalRK two-component system in <i>Streptococcus pneumoniae</i> ensures robustness of secondary wall polymer attachment

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-26

  articleOpen access

  ABSTRACT Capsular polysaccharide (CPS) is essential for Streptococcus pneumoniae virulence. Yet, the mechanism linking CPS to peptidoglycan (PG) remains unclear. Here, we identified a strong negative genetic interaction between the genes encoding the putative capsule ligase CpsA and the WalK histidine kinase, a component of the WalRK two-component system regulating cell wall homeostasis. In the absence of cpsA , capsule polymers compete with wall teichoic acids for ligase activity to PG. This induces cell wall stress and is sensed by the WalRK system. Overexpression of the PG hydrolase pcsB or disruption of the PG-modifying enzymes pgdA and oatA restored growth of strains lacking cpsA and walK . Furthermore, CpsA overproduction compensates for the loss of other LytR-Cps2A-Psr (LCP) ligases, suggesting it can support capsule and wall teichoic acid syntheses. These findings support the model that LCP ligases are semi-redundant, although they may install secondary polymers on a different residue of PG. This work also suggests that WalRK signaling compensates for reduced capsule and WTA attachment by positively regulating PG hydrolases. SIGNIFICANT STATEMENT Streptococcus pneumoniae causes approximately half a million deaths annually. A powerful public health tool for controlling pneumococcal infections is vaccination against the protective capsule. Yet, the mechanisms by which the capsule layer attaches to the underlying cell wall remain poorly defined. This study shows that the conserved capsule gene CpsA is not strictly required for capsule attachment but instead works together with other LytRIZCpsAIZPsr (LCP) ligases. However, it requires the essential WalRK signaling system to maintain cell envelope integrity. Defects in LCP activity are alleviated by WalRKIZdriven upregulation of peptidoglycan hydrolases, overexpression of PcsB, or inactivating peptidoglycan modifications that limit hydrolysis. These findings reveal coordination among flux to capsule synthesis, secondary wall polymer attachment, and cell wall remodeling. TEASER The WalRK two-component system responds to cell envelope stress caused by reduced LCP ligase activity.

  PublisherOA PDFDOI

• Single_cell_carbon_storage_dynamics_drive_conditional_fitness_in_microbes

  Zenodo (CERN European Organization for Nuclear Research) · 2026-05-01

  datasetOpen accessSenior author

  Data and code deposit for the research paper "Single cell carbon storage dynamics drive conditional fitness in microbes".

  PublisherDOI

• Single_cell_carbon_storage_dynamics_drive_conditional_fitness_in_microbes

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-07

  datasetOpen accessSenior author

  Data and code deposit for the research paper "Single cell carbon storage dynamics drive conditional fitness in microbes".

  PublisherDOI

• Enabling the prediction of phage receptor specificity from genome data

  Figshare · 2026-04-02

  datasetOpen accessSenior author

  Supporting information for the manuscript entitled: "Enabling the prediction of phage receptor specificity from genome data". This records contains:Supplementary information (descriptive listing of all supplements)Supplementary Tables S1-S10Supplementary Datasets S1-S7Supplementary Figures S1-S13 (combined)All Supplementary Figures in high-resolution .png filesAll Figures in high-resolution .png files<br>

  PublisherDOI

• Single-cell carbon storage dynamics drive conditional fitness in microbes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-10

  articleOpen accessSenior authorCorresponding

  Summary Microbes frequently encounter fluctuating environments, requiring dynamic energy management strategies for survival. While carbon storage polymers like polyhydroxybutyrate (PHB) are ubiquitous across bacterial taxa, their precise ecological advantage remains poorly understood. 1 Here we show that carbon storage drives conditional fitness during environmental transitions. Using a high-throughput single-cell microfluidic platform, we tracked tens of thousands of Cupriavidus necator cells under precisely controlled carbon and nitrogen fluctuations. We found that PHB provides no advantage under nutrient abundance but becomes decisive at starvation boundaries: during carbon starvation, it enables ∼30% more progeny before arrest; during recovery from nitrogen starvation, it shortens lag and accelerates regrowth. Strikingly, at the single-cell level, PHB granules are inherited in an asymmetric, all-or-nothing fashion, concentrating resources into specific lineages to overcome the discrete energetic threshold required for cell division. Despite this single-cell variance, at the population level, PHB fractions robustly return to a common setpoint after nutrient shifts—a homeostatic behavior consistent with integral feedback control. These findings reveal that while PHB does not increase the basal exponential growth rate, it confers a distinct fitness advantage by prolonging the proliferative phase during nutrient depletion and facilitating successful recovery from starvation, explaining the evolutionary persistence of carbon storage in environments with pulsed resource availability.

  PublisherOA PDFDOI

• Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

  Microbiome · 2025-04-28 · 5 citations

  articleOpen access

  BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3). RESULTS: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.

  PublisherOA PDFDOI

• Niche exclusion of a lung pathogen in mice with designed probiotic communities

  eLife · 2025-12-16

  articleOpen accessSenior author

  For years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by Burkholderia thailandensis in mice. We demonstrate that understanding of antagonistic interactions between a pathogen and airway microbiota in vitro can guide identification of probiotics with protective capabilities in vivo. Specifically, we show that niche overlap between the probiotic and pathogen is indicative of probiotic performance in vivo. This work serves as a foundation for the rational design of probiotic communities for protection against and treatment of respiratory infections.

  PublisherDOI

• Tu1190: ALTERED METABOLITES DIFFERENTIATE CROHN’S DISEASE FROM CONTROLS: A SYSTEMATIC REVIEW

  Gastroenterology · 2025-05-01

  review
  PublisherDOI

• Finding sustainable, resilient, and scalable solutions for future indoor agriculture

  npj Science of Plants · 2025-09-01 · 3 citations

  articleOpen accessCorresponding

  Controlled environment agriculture (CEA) enhances food resilience. However, CEA faces major challenges—high energy intensity and carbon footprints. Technological advancements are essential to reduce operational costs and promote CEA sustainability. This perspective article explores key technological innovations poised to enhance CEA sustainability, emphasizing the necessity of transdisciplinary approaches. We examine integrated decision-making frameworks informed by comprehensive life cycle analysis, distributed indoor agriculture, electricity demand flexibility, Digital Twins, and engineered microbiomes and plants optimized for CEA systems. For each area, we assess the current state of research, identify knowledge gaps, and outline future directions. For example, comprehensive life cycle analysis incorporates environmental, economic and social dimensions can inform both CEA decision making and community-scale circular economy planning; grid-integrated control strategies can enable CEA facilities to provide ancillary grid services, improving both economic viability and grid resilience. A holistic transdisciplinary approach is essential to drive a sustainable future for the CEA sector.

  PublisherOA PDFDOI

• Lactuchelins: New lipopeptide siderophores from <i>Pseudomonas lactucae</i> inhibit <i>Xanthomonas campestris</i> pv. <i>campestris</i> 8004

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-28 · 2 citations

  preprintOpen access

  Abstract Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. Despite their critical importance, the molecular mechanisms driving intermicrobial competition within the seed microbiome remain poorly understood, limiting the potential to optimize seed inoculation strategies. In this study, we evaluated the inhibitory potential of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP13502 as a potent inhibitor of Xcc8004, mediated by exometabolites specifically induced in the presence of Lysobacterales (formerly Xanthomonadales). Transcriptomic analysis of CFBP13502 revealed upregulation of a gene cluster involved in the biosynthesis of a lipopeptide siderophore biosynthesis. Gene deletion confirmed that this cluster is essential for the growth inhibition of Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, providing strong evidence for the role of iron chelation. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, which we named lactuchelins, produced by CFBP13502. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM073010

  NIH · $1.5M · 2011

• Engineering Eukaryotic Protein Scaffolds to Reprogram Prokaryotic Signaling and Metabolic Pathways

  NSF · $540k · 2008–2012

• NIH Grant R01GM073058

  NIH · $2.3M · 2016

• NIH Grant R01GM063525

  NIH · $482k · 2004

• Collaborative Research - Biochemically-Constrained Genomic Signal Processing (BioGSP): A Multi-Scale Interdisciplinary Approach to Regulatory Network Inference

  NSF · $127k · 2009–2012

Frequent coauthors

• Adam M. Deutschbauer

  Lawrence Berkeley National Laboratory

  285 shared

• Terry C. Hazen

  University of Tennessee at Knoxville

  274 shared

• Jeffrey M. Skerker

  University of California, Berkeley

  244 shared

• Morgan N. Price

  Genomics (United Kingdom)

  210 shared

• Jizhong Zhou

  Tsinghua University

  206 shared

• Jay D. Keasling

  Joint BioEnergy Institute

  154 shared

• Vivek K. Mutalik

  126 shared

• Eric J. Alm

  Massachusetts Institute of Technology

  126 shared

Labs

• Arkin LaboratoryPI

Education

• Postdoctoral Fellow, Developmental Biology

  Stanford University

  1997

• Postdoctoral Fellow, Chemistry

  Stanford University

  1995

• Ph.D. Physical Chemistry, Chemistry

  Massachusetts Institute of Technology

  1992

• Bachelor of Art, Chemistry

  Carleton College

  1988