Adam P Arkin

University of California, Berkeley | UCB · Department of Bioengineering

Most TonB-dependent transporters in Bacteroides belong to the SusC family and work with an outer-membrane lipoprotein from the SusD family that functions like a lid. But the best-studied strain, B. thetaiotaomicron VPI-5482, also contains 18 TonB-dependent transporters that are not from the SusC family. We identified six families of putative lids f...

Single-strand RNA (ssRNA) Fiersviridae phages cause host lysis with a product of single gene (sgl for single-gene lysis; product Sgl) that induces autolysis. Many different Sgls have been discovered, but the molecular targets of only a few have been identified. In this study, we used a high-throughput genetic screen to uncover genome-wide host supp...

The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzin...

The E. coli genome-scale metabolic model (GEM) is a gold standard for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint model uncertainty and ensure continued development of accurate models. Here we assessed the accuracy of the E. coli GEM using published mutant fitness data for the growth...

Background: Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achie...

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the ch...

Computational models are increasingly used to investigate and predict the complex dynamics of biological and biochemical systems. Nevertheless, governing equations of a biochemical system may not be (fully) known, which would necessitate learning the system dynamics directly from, often limited and noisy, observed data. On the other hand, when expe...

A protein’s function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered when annotating a protein’s function. To help biologists investigate the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree....

Microbial communities have consequential effects on health and the environment yet remain uncontrollable due to their complex dynamics. Ecological modeling offers a platform to overcome their nonlinear and interconnected nature but traditionally does not account for context-dependence. Here, we extend the generalized Lotka-Volterra (gLV) model to a...

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lin...

Background: Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science and h...

A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate gene discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut bacter...

Species of bacteria from the genus Cupriavidus are known, in part, for their ability to produce high amounts of poly-hydroxybutyrate (PHB) making them attractive candidate bioplastic producers. The native production of PHB occurs during periods of metabolic stress, and the process regulating the initiation of PHB accumulation in these organisms is...

Biclustering can reveal functional patterns in common biological data such as gene expression. Biclusters are ordered submatrices of a larger matrix that represent coherent data patterns. A critical requirement for biclusters is high coherence across a subset of columns, where coherence is defined as a fit to a mathematical model of similarity or c...

Bacillus cereus strain CPT56D‐587‐MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% ide...

As renewed interest in human space-exploration intensifies, a coherent and modernized strategy for mission-design and planning has become increasingly crucial. Biotechnology has emerged as a promising approach to increase mission resilience, flexibility, and efficiency by virtue of its ability to efficiently utilize in situ resources and reclaim re...

Spirulina is the common name for the edible, non-heterocystous, filamentous cyanobacterium Arthrospira platensis that is grown industrially as a food supplement, animal feedstock, and pigment source. Although there are many applications for engineering this organism, until recently no genetic tools or reproducible transformation methods have been p...

A protein's function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered when annotating a protein's function. To help biologists investigate the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree....

Rhodanobacter denitrificans is capable of denitrification and is also resistant to toxic heavy metals and low pH. Accordingly, the presence of Rhodanobacter species at a particular environmental site is considered an indicator of nitrate and uranium contamination.

Space bioprocess engineering (SBE) is an emerging multi-disciplinary field to design, realize, and manage biologically-driven technologies specifically with the goal of supporting life on long term space missions. SBE considers synthetic biology and bioprocess engineering under the extreme constraints of the conditions of space. A coherent strategy...

Electromicrobial production (EMP) processes based on CO 2 -fixing microbes that directly accept electrons from a cathode have received significant attention in the past decade. However, fundamental questions about the performance limits and viability of this strategy remain unanswered. Here, we sought to determine what would be necessary for such a...

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is m...

Bacillus cereus strain CPT56D-587-MTF was isolated from nitrate- and toxic metal-contaminated subsurface sediment at the Oak Ridge Reservation (ORR) (Oak Ridge, TN, USA). Here, we report the complete genome sequence of this strain to provide genomic insight into its strategies for survival at this mixed-waste site.

To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29...

Annotating ecological functions of environmental metagenomes is challenging due to a lack of specialized reference database and computational barriers. Here we present Ecological Function oriented Metagenomic Analysis Pipeline (EcoFun-MAP) for efficient analysis of shotgun metagenomes in the context of ecological functions. We manually curated refe...

A central question surrounding possible human exploration of Mars is whether crewed missions can be supported by available technologies using in situ resources. Here, we show that photovoltaics-based power systems would be adequate and practical to sustain a crewed outpost for an extended period over a large fraction of the planet’s surface. Climat...

Computational models are increasingly used to investigate and predict the complex dynamics of biological and biochemical systems. Nevertheless, governing equations of a biochemical system may not be (fully) known, which would necessitate learning the system dynamics directly from, often limited and noisy, observed data. On the other hand, when expe...

At its current rate, the rise of antimicrobial resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)- viruses targeting bacteria- offer...

Computational models are increasingly used to investigate and predict the complex dynamics of biological and biochemical systems. Nevertheless, governing equations of a biochemical system may not be (fully) known, which would necessitate learning the system dynamics directly from, often limited and noisy, observed data. On the other hand, when expe...

The fitness effects of all possible mutations available to an organism largely shapes the dynamics of evolutionary adaptation. Tremendous progress has been made in quantifying the strength and abundance of selected mutations available to single microbial species in simple environments, lacking strong ecological interactions. However, the adaptive p...

Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with vary...

Magnetotactic bacteria (MTB) are a group of bacteria that can form nano-sized crystals of magnetic minerals. MTB are likely an important part of their ecosystems, because they can account for up to a third of the microbial biomass in an aquatic habitat and consume large amounts of iron, potentially impacting the iron cycle.

In contrast to canonical dsDNA phages, lysis in ssRNA Fiersviridae and ssDNA Microviridae phages is encoded by a minimal single gene (sgl), to meet the size constraints of some of the smallest genomes on earth. To achieve lysis, Sgl proteins exploit evolutionary "weak spots" in the bacterial cell wall by inhibiting specific steps in cell wall synth...

Electromicrobial production (EMP) systems can store renewable energy and CO2 in many-carbon molecules inaccessible to abiotic electrochemistry. Here, we develop a multiphysics model to investigate the fundamental and practical limits of EMP enabled by direct electron uptake. We also identify potential electroautotrophic organisms and metabolic engi...

Reinvigorated public interest in human space exploration has led to the need to address the science and engineering challenges described by NASA's Space Technology Grand Challenges (STGCs) for expanding the human presence in space. Here we define Space Bioprocess Engineering (SBE) as a multi-disciplinary approach to design, realize, and manage a bi...

Reinvigorated public interest in human space exploration has led to the need to address the science and engineering challenges described by NASA's Space Technology Grand Challenges (STGCs) for expanding the human presence in space. Here we define Space Bioprocess Engineering (SBE) as a multi-disciplinary approach to design, realize, and manage a bi...

Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven div...

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wast...

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse colla...

GapMind for carbon sources is an automated tool for annotating catabolic pathways in bacterial and archaeal genomes. GapMind includes 62 compounds and identifies potential transporters and enzymes by their similarity to experimentally-characterized proteins. To improve GapMind's coverage, we used high-throughput genetic data from 29 bacteria and sy...

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth...

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface...

A central question surrounding possible human exploration of Mars is whether crewed missions can be supported by available technologies using in situ resources. Here, we show that photovoltaics-based power systems would be adequate and practical to sustain a crewed outpost for an extended period over a large fraction of the planet's surface. Climat...

There are medical treatment vulnerabilities in longer-duration space missions present in the current International Space Station crew health care system with risks, arising from spaceflight-accelerated pharmaceutical degradation and resupply lag times. Bioregenerative life support systems may be a way to close this risk gap by leveraging in situ re...

Bacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16S rRNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial numbe...

Microbial‐mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon‐bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the com...

To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea strain sp. MT58 (MT58), we used a multi-omic strategy combining two global techniques, random bar code transposon-site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was...

Magnetotactic bacteria (MTB) are a phylogenetically diverse group of bacteria remarkable for their ability to biomineralize magnetite (Fe 3 O 4 ) or greigite (Fe 3 S 4 ) in organelles called magnetosomes. The majority of genes required for magnetosome formation are encoded by a magnetosome gene island (MAI). Here, we conducted random barcoded trans...

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wast...

Providing life-support materials to crewed space exploration missions is pivotal for mission success. However, as missions become more distant and extensive, obtaining these materials from in situ resource utilization is paramount. The combination of microorganisms with electrochemical technologies offers a platform for the production of critical c...

A crewed mission to and from Mars may include an exciting array of enabling biotechnologies that leverage inherent mass, power, and volume advantages over traditional abiotic approaches. In this perspective, we articulate the scientific and engineering goals and constraints, along with example systems, that guide the design of a surface biomanufact...

To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral...

Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally...

There are medical treatment vulnerabilities in longer-duration space missions present in the current International Space Station crew health care system with risks, arising from spaceflight-accelerated pharmaceutical degradation and resupply lag times. Bioregenerative life support systems may be a way to close this risk gap by leveraging in situ re...

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the com...

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes an...

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and a...

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.