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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Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. Journal Article

BMC Genomics, 14 , pp. 745, 2013.

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Meyer, Birte; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Stahl, David A

Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal Article

Journal of Bacteriology, 195 (21), pp. 4900-4914, 2013.

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Kazakov, Alexey E; Rajeev, Lara; Luning, Eric G; Zane, Grant M; Siddartha, Kavya; Rodionov, Dmitry A; Dubchak, Inna; Arkin, Adam P; Wall, Judy D; Mukhopadhyay, Aindrila; Novichkov, Pavel S

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal Article

Journal of Bacteriology, 195 (19), pp. 4466-4475, 2013.

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Zhou, Aifen; He, Zhili; Qin, Yujia; Lu, Zhenmei; Deng, Ye; Tu, Qichao; Hemme, Christopher L; Nostrand, Joy Van D; Wu, Liyou; Hazen, Terry C; Arkin, Adam P; Zhou, Jizhong

StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Journal Article

Environmental Science & Technology, 47 (17), pp. 9841-9849, 2013.

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Zhou, Aifen; Baidoo, Edward; He, Zhili; Mukhopadhyay, Aindrila; Baumohl, Jason K; Benke, Peter; Joachimiak, Marcin P; Xie, Ming; Song, Rong; Arkin, Adam P; Hazen, Terry C; Keasling, Jay D; Wall, Judy D; Stahl, David A; Zhou, Jizhong

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. Journal Article

The ISME Journal, 7 (9), pp. 1790-1802, 2013.

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Price, Morgan N; Deutschbauer, Adam M; Skerker, Jeffrey M; Wetmore, Kelly M; Ruths, Troy; Mar, Jordan S; Kuehl, Jennifer V; Shao, Wenjun; Arkin, Adam P

Indirect and suboptimal control of gene expression is widespread in bacteria. Journal Article

Molecular Systems Biology, 9 , pp. 660, 2013.

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Brown, Steven D; Utturkar, Sagar M; Arkin, Adam P; Deutschbauer, Adam M; Elias, Dwayne A; Hazen, Terry C; Chakraborty, Romy

Draft Genome Sequence for Desulfovibrio africanus Strain PCS. Journal Article

Genome announcements, 1 (2), pp. e0014413, 2013.

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Cipriano, Michael J; Novichkov, Pavel N; Kazakov, Alexey E; Rodionov, Dmitry A; Arkin, Adam P; Gelfand, Mikhail S; Dubchak, Inna

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. Journal Article

BMC Genomics, 14 , pp. 213, 2013.

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

Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. Journal Article

Journal of Bacteriology, 195 (5), pp. 990-1004, 2013.

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Wang, Liming; Wang, Xiaodong; Arkin, Adam P; Samoilov, Michael S

Inference of gene regulatory networks from genome-wide knockout fitness data. Journal Article

Bioinformatics, 29 (3), pp. 338-346, 2013.

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Baran, Richard; Bowen, Benjamin P; Price, Morgan N; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. Journal Article

ACS Chemical Biology, 8 (1), pp. 189-199, 2013.

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Pang, Lee W; Kaur, Amardeep; Ratushny, Alexander V; Cvetkovic, Aleksandar; Kumar, Sunil; Pan, Min; Arkin, Adam P; Aitchison, John D; Adams, Michael W W; Baliga, Nitin S

Metallochaperones regulate intracellular copper levels. Journal Article

PLoS Computational Biology, 9 (1), pp. e1002880, 2013.

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Chivian, Dylan; Dehal, Paramvir S; Keller, Keith; Arkin, Adam P

MetaMicrobesOnline: phylogenomic analysis of microbial communities. Journal Article

Nucleic Acids Research, 41 (Database issue), pp. D648-54, 2013.

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Kazakov, Alexey E; Rodionov, Dmitry A; Price, Morgan N; Arkin, Adam P; Dubchak, Inna; Novichkov, Pavel S

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. Journal Article

Journal of Bacteriology, 195 (1), pp. 29-38, 2013.

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Walker, Christopher B; Redding-Johanson, Alyssa M; Baidoo, Edward E; Rajeev, Lara; He, Zhili; Hendrickson, Erik L; Joachimiak, Marcin P; Stolyar, Sergey; Arkin, Adam P; Leigh, John A; Zhou, Jizhong; Keasling, Jay D; Mukhopadhyay, Aindrila; Stahl, David A

Functional responses of methanogenic archaea to syntrophic growth. Journal Article

The ISME Journal, 6 (11), pp. 2045-2055, 2012.

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Rajeev, Lara; Hillesland, Kristina L; Zane, Grant M; Zhou, Aifen; Joachimiak, Marcin P; He, Zhili; Zhou, Jizhong; Arkin, Adam P; Wall, Judy D; Stahl, David A

Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal Article

Journal of Bacteriology, 194 (21), pp. 5783-5793, 2012.

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León, Kara Bowen De; Young, Mary Lynn; Camilleri, Laura B; Brown, Steven D; Skerker, Jeffrey M; Deutschbauer, Adam M; Arkin, Adam P; Fields, Matthew W

Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. Journal Article

Journal of Bacteriology, 194 (19), pp. 5456-5457, 2012.

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Brown, Steven D; Podar, Mircea; Klingeman, Dawn M; Johnson, Courtney M; Yang, Zamin K; Utturkar, Sagar M; Land, Miriam L; Mosher, Jennifer J; Hurt, Richard A; Phelps, Tommy J; Palumbo, Anthony V; Arkin, Adam P; Hazen, Terry C; Elias, Dwayne A

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. Journal Article

Journal of Bacteriology, 194 (18), pp. 5147-5148, 2012.

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Novichkov, Pavel S; Brettin, Thomas S; Novichkova, Elena S; Dehal, Paramvir S; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Journal Article

Nucleic Acids Research, 40 (Web Server issue), pp. W604-8, 2012.

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Clark, Melinda E; He, Zhili; Redding, Alyssa M; Joachimiak, Marcin P; Keasling, Jay D; Zhou, Jizhong Z; Arkin, Adam P; Mukhopadhyay, Aindrila; Fields, Matthew W

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. Journal Article

BMC Genomics, 13 , pp. 138, 2012.

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Mosher, Jennifer J; Phelps, Tommy J; Podar, Mircea; Hurt, Richard A; Campbell, James H; Drake, Meghan M; Moberly, James G; Schadt, Christopher W; Brown, Steven D; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Faybishenko, Boris A; Elias, Dwayne A

Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Journal Article

Applied and Environmental Microbiology, 78 (7), pp. 2082-2091, 2012.

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Zhou, Aifen; Chen, Yunyu I; Zane, Grant M; He, Zhili; Hemme, Christopher L; Joachimiak, Marcin P; Baumohl, Jason K; He, Qiang; Fields, Matthew W; Arkin, Adam P; Wall, Judy D; Hazen, Terry C; Zhou, Jizhong

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Journal Article

Applied and Environmental Microbiology, 78 (4), pp. 1168-1177, 2012.

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Deutschbauer, Adam; Price, Morgan N; Wetmore, Kelly M; Shao, Wenjun; Baumohl, Jason K; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W; Arkin, Adam P

Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. Journal Article

PLoS Genetics, 7 (11), pp. e1002385, 2011.

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Jajamovich, Guido H; Wang, Xiaodong; Arkin, Adam P; Samoilov, Michael S

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites. Journal Article

Nucleic Acids Research, 39 (21), pp. e146, 2011.

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Price, Morgan N; Deutschbauer, Adam M; Kuehl, Jennifer V; Liu, Haichuan; Witkowska, Ewa H; Arkin, Adam P

Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Journal Article

Journal of Bacteriology, 193 (20), pp. 5716-5727, 2011.

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Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K

Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Journal Article

Lab on A Chip, 11 (16), pp. 2673-2679, 2011.

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Price, Morgan N; Dehal, Paramvir S; Arkin, Adam P

FastTree 2 — approximately maximum-likelihood trees for large alignments. Journal Article

Plos One, 5 (3), pp. e9490, 2010.

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Daliang Ning Mengting Yuan, Linwei Wu Ya Zhang Xue Guo Xishu Zhou Yunfeng Yang Adam Arkin Mary Firestone P K; Zhou, Jizhong

A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming Journal Article

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128 entries « 3 of 3 »