ENIGMA

A program for predictive and causal microbial ecology

The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Scientific Focus Area that we help lead is dedicated to developing a generalizable approach to predictive causal microbial ecology. We seek to molecularly dissect the dispersal, drift, and selective forces that shape the assembly and activity of microbial communities in complex spatially and temporally variable niches. Our driving biological problem focused on the Y12 site at the Oak Ridge National Lab, a watershed that is highly contaminated by high nitrate and heavy metal contamination that resulted from nuclear programs over the last century. We seek to quantify the anthropogenic impact on the structure and function of the microbial communities that are present in this complex environment and to develop a predictive, increasingly mechanistic, understanding of the multiscale, interlinked environmental and biological processes that mediate denitrification and metal reduction activities of the microbial communities of sufficient resolution to allow effective optimization of these processes.

In this large collaborative project, for which we have a lead role in visioning, our central work is to help identify from sophisticated field measurements the critical active and interacting microbial subcommunities emblematic of the most active interactive subcommunities in different field conditions and to capture and characterize this diversity at gene-level resolution in the laboratory. We are most interested in understanding the novel phyla and pathways that carry out and mediate these critical activities and the role of predation and carbon constraints on overall community efficiency and selection.

For more information visit https://enigma.lbl.gov

Selected Publications

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Price, Morgan N; Zane, Grant M; Kuehl, Jennifer V; Melnyk, Ryan A; Wall, Judy D; Deutschbauer, Adam M; Arkin, Adam P

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. Journal Article

PLoS Genetics, 14 (1), pp. e1007147, 2018.

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Smith, H J; Zelaya, A J; Le?n, De K B; Chakraborty, R; Elias, D A; Hazen, T C; Arkin, A P; Cunningham, A B; Fields, M W

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments Journal Article

FEMS Microbiol. Ecol., 94 (12), 2018.

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Rand, Jacqueline M; Pisithkul, Tippapha; Clark, Ryan L; Thiede, Joshua M; Mehrer, Christopher R; Agnew, Daniel E; Campbell, Candace E; Markley, Andrew L; Price, Morgan N; Ray, Jayashree; Wetmore, Kelly M; Suh, Yumi; Arkin, Adam P; Deutschbauer, Adam M; Amador-Noguez, Daniel; Pfleger, Brian F

A metabolic pathway for catabolizing levulinic acid in bacteria. Journal Article

Nature Microbiology, 2 (12), pp. 1624-1634, 2017.

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Zhou, Aifen; Lau, Rebecca; Baran, Richard; Ma, Jincai; von Netzer, Frederick; Shi, Weiling; Gorman-Lewis, Drew; Kempher, Megan L; He, Zhili; Qin, Yujia; Shi, Zhou; Zane, Grant M; Wu, Liyou; Bowen, Benjamin P; Northen, Trent R; Hillesland, Kristina L; Stahl, David A; Wall, Judy D; Arkin, Adam P; Zhou, Jizhong

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. Journal Article

mBio, 8 (6), 2017.

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León, Kara De B; Zane, Grant M; Trotter, Valentine V; Krantz, Gregory P; Arkin, Adam P; Butland, Gareth P; Walian, Peter J; Fields, Matthew W; Wall, Judy D

Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. Journal Article

mBio, 8 (5), 2017.

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Justice, N B; Sczesnak, A; Hazen, T C; Arkin, A P

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing. Journal Article

Applied and Environmental Microbiology, 83 (20), 2017.

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Price, Morgan N; Arkin, Adam P

PaperBLAST: Text Mining Papers for Information about Homologs. Journal Article

mSystems, 2 (4), 2017.

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Thorgersen, Michael P; Lancaster, Andrew W; Ge, Xiaoxuan; Zane, Grant M; Wetmore, Kelly M; Vaccaro, Brian J; Poole, Farris L; Younkin, Adam D; Deutschbauer, Adam M; Arkin, Adam P; Wall, Judy D; Adams, Michael W W

Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions. Journal Article

Frontiers in microbiology, 8 , pp. 1529, 2017.

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Wu, Xiaoqin; Deutschbauer, Adam M; Kazakov, Alexey E; Wetmore, Kelly M; Cwick, Bryson A; Walker, Robert M; Novichkov, Pavel S; Arkin, Adam P; Chakraborty, Romy

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Journal Article

Genome announcements, 5 (26), 2017.

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Sagawa, Shiori; Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P

Validating regulatory predictions from diverse bacteria with mutant fitness data. Journal Article

Plos One, 12 (5), pp. e0178258, 2017.

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Zhang, Ping; He, Zhili; Nostrand, Joy Van D; Qin, Yujia; Deng, Ye; Wu, Liyou; Tu, Qichao; Wang, Jianjun; Schadt, Christopher W; Fields, Matthew W; Hazen, Terry C; Arkin, Adam P; Stahl, David A; Zhou, Jizhong

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. Journal Article

Environmental Science & Technology, 51 (7), pp. 3609-3620, 2017.

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King, Andrew J; Preheim, Sarah P; Bailey, Kathryn L; Robeson, Michael S; Chowdhury, Taniya Roy; Crable, Bryan R; Hurt, Richard A; Mehlhorn, Tonia; Lowe, Kenneth A; Phelps, Tommy J; Palumbo, Anthony V; Brandt, Craig C; Brown, Steven D; Podar, Mircea; Zhang, Ping; Lancaster, Andrew W; Poole, Farris; Watson, David B; Fields, Matthew W; Chandonia, John-Marc; Alm, Eric J; Zhou, Jizhong; Adams, Michael W W; Hazen, Terry C; Arkin, Adam P; Elias, Dwayne A

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Journal Article

Environmental Science & Technology, 51 (5), pp. 2879-2889, 2017.

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Thorgersen, Michael P; Lancaster, Andrew W; Rajeev, Lara; Ge, Xiaoxuan; Vaccaro, Brian J; Poole, Farris L; Arkin, Adam P; Mukhopadhyay, Aindrila; Adams, Michael W W

A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium. Journal Article

Applied and Environmental Microbiology, 83 (4), 2017.

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Chakraborty, Romy; Woo, Hannah; Dehal, Paramvir; Walker, Robert; Zemla, Marcin; Auer, Manfred; Goodwin, Lynne A; Kazakov, Alexey; Novichkov, Pavel; Arkin, Adam P; Hazen, Terry C

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Journal Article

Standards in genomic sciences, 12 , pp. 23, 2017.

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Bosak, Tanja; Schubotz, Florence; de Santiago-Torio, Ana; Kuehl, Jennifer V; Carlson, Hans K; Watson, Nicki; Daye, Mirna; Summons, Roger E; Arkin, Adam P; Deutschbauer, Adam M

System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. Journal Article

Plos One, 11 (12), pp. e0168719, 2016.

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Price, Morgan N; Wetmore, Kelly M; Deutschbauer, Adam M; Arkin, Adam P

A comparison of the costs and benefits of bacterial gene expression. Journal Article

Plos One, 11 (10), pp. e0164314, 2016.

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Vaccaro, Brian J; Lancaster, Andrew W; Thorgersen, Michael P; Zane, Grant M; Younkin, Adam D; Kazakov, Alexey E; Wetmore, Kelly M; Deutschbauer, Adam; Arkin, Adam P; Novichkov, Pavel S; Wall, Judy D; Adams, Michael W W

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Journal Article

Applied and Environmental Microbiology, 82 (19), pp. 6046-6056, 2016.

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Price, Morgan N; Wetmore, Kelly M; Waters, Robert Jordan; Callaghan, Mark; Ray, Jayashree; Kuehl, Jennifer V; Melnyk, Ryan A; Lamson, Jacob S; Suh, Yumi; Esquivel, Zuelma; Sadeeshkumar, Harini; Chakraborty, Romy; Rubin, Benjamin E; Bristow, James; Blow, Matthew J; Arkin, Adam P; Deutschbauer, Adam M

Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes Journal Article

BioRxiv, 2016.

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Kosina, Suzanne M; Danielewicz, Megan A; Mohammed, Mujahid; Ray, Jayashree; Suh, Yumi; Yilmaz, Suzan; Singh, Anup K; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

Exometabolomics assisted design and validation of synthetic obligate mutualism. Journal Article

ACS synthetic biology [electronic resource], 5 (7), pp. 569-576, 2016.

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Price, Morgan N; Arkin, Adam P

A theoretical lower bound for selection on the expression levels of proteins. Journal Article

Genome Biology and Evolution, 8 (6), pp. 1917-1928, 2016.

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Hemme, Christopher L; Green, Stefan J; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M; Nostrand, Joy Van D; Wu, Liyou; He, Zhili; Jordan, King I; Hazen, Terry C; Arkin, Adam P; Kostka, Joel E; Zhou, Jizhong

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. Journal Article

mBio, 7 (2), pp. e02234-15, 2016.

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Vaccaro, Brian J; Thorgersen, Michael P; Lancaster, Andrew W; Price, Morgan N; Wetmore, Kelly M; Poole, Farris L; Deutschbauer, Adam; Arkin, Adam P; Adams, Michael W W

Determining roles of accessory genes in denitrification by mutant fitness analyses. Journal Article

Applied and Environmental Microbiology, 82 (1), pp. 51-61, 2016.

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Price, Morgan N; Arkin, Adam P

Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes. Journal Article

mBio, 6 (6), pp. e01302-15, 2015.

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Zhang, Ping; Nostrand, Joy Van D; He, Zhili; Chakraborty, Romy; Deng, Ye; Curtis, Daniel; Fields, Matthew W; Hazen, Terry C; Arkin, Adam P; Zhou, Jizhong

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction. Journal Article

Environmental Science & Technology, 49 (21), pp. 12922-12931, 2015.

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Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. Journal Article

The ISME Journal, 9 (11), pp. 2360-2372, 2015.

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Hemme, Christopher L; Tu, Qichao; Shi, Zhou; Qin, Yujia; Gao, Weimin; Deng, Ye; Nostrand, Joy Van D; Wu, Liyou; He, Zhili; Chain, Patrick S G; Tringe, Susannah G; Fields, Matthew W; Rubin, Edward M; Tiedje, James M; Hazen, Terry C; Arkin, Adam P; Zhou, Jizhong

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Journal Article

Frontiers in microbiology, 6 , pp. 1205, 2015.

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León, Kara De B; Utturkar, Sagar M; Camilleri, Laura B; Elias, Dwayne A; Arkin, Adam P; Fields, Matthew W; Brown, Steven D; Wall, Judy D

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. Journal Article

Genome announcements, 3 (5), 2015.

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Thorgersen, Michael P; Lancaster, Andrew W; Vaccaro, Brian J; Poole, Farris L; Rocha, Andrea M; Mehlhorn, Tonia; Pettenato, Angelica; Ray, Jayashree; Waters, Jordan R; Melnyk, Ryan A; Chakraborty, Romy; Hazen, Terry C; Deutschbauer, Adam M; Arkin, Adam P; Adams, Michael W W

Molybdenum availability is key to nitrate removal in contaminated groundwater environments. Journal Article

Applied and Environmental Microbiology, 81 (15), pp. 4976-4983, 2015.

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Zhang, Ping; Wu, Wei-Min; Nostrand, Joy Van D; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W; Watson, David; Jardine, Phil; Criddle, Craig S; Brooks, Scott; Marsh, Terence L; Tiedje, James M; Arkin, Adam P; Zhou, Jizhong

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Journal Article

Applied and Environmental Microbiology, 81 (12), pp. 4164-4172, 2015.

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Carlson, Hans K; Kuehl, Jennifer V; Hazra, Amrita B; Justice, Nicholas B; Stoeva, Magdalena K; Sczesnak, Andrew; Mullan, Mark R; Iavarone, Anthony T; Engelbrektson, Anna; Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P; Coates, John D

Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. Journal Article

The ISME Journal, 9 (6), pp. 1295-1305, 2015.

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Ray, Jayashree; Waters, Jordan R; Skerker, Jeffrey M; Kuehl, Jennifer V; Price, Morgan N; Huang, Jiawen; Chakraborty, Romy; Arkin, Adam P; Deutschbauer, Adam

Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Journal Article

Genome announcements, 3 (3), 2015.

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Wetmore, Kelly M; Price, Morgan N; Waters, Robert J; Lamson, Jacob S; He, Jennifer; Hoover, Cindi A; Blow, Matthew J; Bristow, James; Butland, Gareth; Arkin, Adam P; Deutschbauer, Adam

Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. Journal Article

mBio, 6 (3), pp. e00306-15, 2015.

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Smith, Mark B; Rocha, Andrea M; Smillie, Chris S; Olesen, Scott W; Paradis, Charles; Wu, Liyou; Campbell, James H; Fortney, Julian L; Mehlhorn, Tonia L; Lowe, Kenneth A; Earles, Jennifer E; Phillips, Jana; Techtmann, Steve M; Joyner, Dominique C; Elias, Dwayne A; Bailey, Kathryn L; Hurt, Richard A; Preheim, Sarah P; Sanders, Matthew C; Yang, Joy; Mueller, Marcella A; Brooks, Scott; Watson, David B; Zhang, Ping; He, Zhili; Dubinsky, Eric A; Adams, Paul D; Arkin, Adam P; Fields, Matthew W; Zhou, Jizhong; Alm, Eric J; Hazen, Terry C

Natural bacterial communities serve as quantitative geochemical biosensors. Journal Article

mBio, 6 (3), pp. e00326-15, 2015.

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Melnyk, Ryan A; Youngblut, Matthew D; Clark, Iain C; Carlson, Hans K; Wetmore, Kelly M; Price, Morgan N; Iavarone, Anthony T; Deutschbauer, Adam M; Arkin, Adam P; Coates, John D

Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase. Journal Article

mBio, 6 (3), pp. e00233-15, 2015.

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Ramsay, Bradley D; Hwang, Chiachi; Woo, Hannah L; Carroll, Sue L; Lucas, Susan; Han, James; Lapidus, Alla L; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren J; Kyrpides, Nikos C; Ivanova, Natalia N; Mikhailova, Natalia; Pagani, Ioanna; Woyke, Tanja; Arkin, Adam P; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C; Fields, Matthew W

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Journal Article

Genome announcements, 3 (2), 2015.

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Korte, Hannah L; Saini, Avneesh; Trotter, Valentine V; Butland, Gareth P; Arkin, Adam P; Wall, Judy D

Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Journal Article

Environmental Science & Technology, 49 (2), pp. 924-931, 2015.

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Christensen, G A; Zane, G M; Kazakov, A E; Li, X; Rodionov, D A; Novichkov, P S; Dubchak, I; Arkin, A P; Wall, J D

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. Journal Article

Journal of Bacteriology, 197 (1), pp. 29-39, 2015.

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Meyer, Birte; Kuehl, Jennifer V; Price, Morgan N; Ray, Jayashree; Deutschbauer, Adam M; Arkin, Adam P; Stahl, David A

The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Journal Article

Environmental Microbiology, 16 (11), pp. 3463-3486, 2014.

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Price, Morgan N; Ray, Jayashree; Wetmore, Kelly M; Kuehl, Jennifer V; Bauer, Stefan; Deutschbauer, Adam M; Arkin, Adam P

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Journal Article

Frontiers in microbiology, 5 , pp. 577, 2014.

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Deutschbauer, Adam; Price, Morgan N; Wetmore, Kelly M; Tarjan, Daniel R; Xu, Zhuchen; Shao, Wenjun; Leon, Dacia; Arkin, Adam P; Skerker, Jeffrey M

Towards an informative mutant phenotype for every bacterial gene. Journal Article

Journal of Bacteriology, 196 (20), pp. 3643-3655, 2014.

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Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H; Kurczy, Michael E; Benton, Paul H; Rinehart, Duane; Nguyen, Thomas; Ray, Jayashree; Kuehl, Jennifer; Arevalo, Bernardo; Westenskow, Peter D; Wang, Junhua; Arkin, Adam P; Deutschbauer, Adam M; Patti, Gary J; Siuzdak, Gary

Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Journal Article

Analytical Chemistry, 86 (14), pp. 6931-6939, 2014.

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Shao, Wenjun; Price, Morgan N; Deutschbauer, Adam M; Romine, Margaret F; Arkin, Adam P

Conservation of transcription start sites within genes across a bacterial genus. Journal Article

mBio, 5 (4), pp. e01398-14, 2014.

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Rinehart, Duane; Johnson, Caroline H; Nguyen, Thomas; Ivanisevic, Julijana; Benton, Paul H; Lloyd, Jessica; Arkin, Adam P; Deutschbauer, Adam M; Patti, Gary J; Siuzdak, Gary

Metabolomic data streaming for biology-dependent data acquisition. Journal Article

Nature Biotechnology, 32 (6), pp. 524-527, 2014, ISSN: 1087-0156.

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Kuehl, Jennifer V; Price, Morgan N; Ray, Jayashree; Wetmore, Kelly M; Esquivel, Zuelma; Kazakov, Alexey E; Nguyen, Michelle; Kuehn, Raquel; Davis, Ronald W; Hazen, Terry C; Arkin, Adam P; Deutschbauer, Adam

Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Journal Article

mBio, 5 (3), pp. e01041-14, 2014.

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Korte, Hannah L; Fels, Samuel R; Christensen, Geoff A; Price, Morgan N; Kuehl, Jennifer V; Zane, Grant M; Deutschbauer, Adam M; Arkin, Adam P; Wall, Judy D

Genetic basis for nitrate resistance in Desulfovibrio strains. Journal Article

Frontiers in microbiology, 5 , pp. 153, 2014.

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Butland, Gareth; Saini, Avneesh; Trotter, Valentine; Price, Morgan; He, Jennifer; Kuehl, Jennifer; Wetmore, Kelly; Liu, Nancy; Zane, Grant; Fels, Samuel; Juba, Thomas; Shatsky, Maxim; Arkin, Adam; Chandonia, John-Marc; Wall, Judy; Deutschbauer, Adam

Novel aspects of iron sulfur cluster biosynthesis in sulfate reducing bacteria (768.17) Journal Article

The FASEB Journal, 2014.

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Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Nostrand, Joy Van D; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A; Hazen, Terry C; Tiedje, James M; Arkin, Adam P

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 111 (9), pp. E836-45, 2014.

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Novichkov, Pavel S; Li, Xiaoqing; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Price, Morgan N; Rodionov, Dmitry A

Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Journal Article

Environmental Microbiology, 16 (1), pp. 1-8, 2014.

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Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Podar, Mircea; Phelps, Tommy J; Brown, Steven D; Yang, Zamin K; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Nostrand, Joy Van D; Zhou, Jizhong; Elias, Dwayne A

Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. Journal Article

Plos One, 8 (12), pp. e83909, 2013.

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Louie, Katherine B; Bowen, Benjamin P; Cheng, Xiaoliang; Berleman, James E; Chakraborty, Romy; Deutschbauer, Adam; Arkin, Adam; Northen, Trent R

"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Journal Article

Analytical Chemistry, 85 (22), pp. 10856-10862, 2013.

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128 entries « 2 of 3 »