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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Paradis, Charles J; Miller, John I; Moon, Ji-Won; Spencer, Sarah J; Lui, Lauren M; Nostrand, Joy D Van; Ning, Daliang; Steen, Andrew D; McKay, Larry D; Arkin, Adam P; Zhou, Jizhong; Alm, Eric J; Hazen, Terry C

Sustained ability of a natural microbial community to remove nitrate from groundwater Journal Article

In: BioRxiv, 2021.

Abstract | Links | BibTeX

Lui, Lauren M; Nielsen, Torben N; Arkin, Adam P

A method for achieving complete microbial genomes and improving bins from metagenomics data. Journal Article

In: PLoS Computational Biology, 17 (5), pp. e1008972, 2021.

Abstract | Links | BibTeX

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T B K; Nielsen, Torben; Kirton, Edward; Faria, José P; Edirisinghe, Janaka N; Henry, Christopher S; Jungbluth, Sean P; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M; Arkin, Adam P; Tringe, Susannah G; Visel, Axel; IMG,; Woyke, Tanja; Mouncey, Nigel J; Ivanova, Natalia N; Kyrpides, Nikos C; Eloe-Fadrosh, Emiley A

A genomic catalog of Earth's microbiomes. Journal Article

In: Nature Biotechnology, 39 (4), pp. 499-509, 2021, ISSN: 1087-0156.

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Lui, Lauren M; Majumder, Erica L-W; Smith, Heidi J; Carlson, Hans K; von Netzer, Frederick; Fields, Matthew W; Stahl, David A; Zhou, Jizhong; Hazen, Terry C; Baliga, Nitin S; Adams, Paul D; Arkin, Adam P

Mechanism across scales: A holistic modeling framework integrating laboratory and field studies for microbial ecology. Journal Article

In: Frontiers in microbiology, 12 , pp. 642422, 2021, ISSN: 1664-302X.

Abstract | Links | BibTeX

Wall, Judy D; Zane, Grant M; Juba, Thomas R; Kuehl, Jennifer V; Ray, Jayashree; Chhabra, Swapnil R; Trotter, Valentine V; Shatsky, Maxim; León, Kara B De; Keller, Kimberly L; Bender, Kelly S; Butland, Gareth; Arkin, Adam P; Deutschbauer, Adam M

Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Journal Article

In: Microbiology Resource Announcements, 10 (11), 2021.

Abstract | Links | BibTeX

Song, Fangchao; Kuehl, Jennifer V; Chandran, Arjun; Arkin, Adam P

A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis Journal Article

In: BioRxiv, 2021.

Abstract | Links | BibTeX

Carim, Sean; Azadeh, Ashley L; Kazakov, Alexey E; Price, Morgan N; Walian, Peter J; Lui, Lauren M; Nielsen, Torben N; Chakraborty, Romy; Deutschbauer, Adam M; Mutalik, Vivek K; Arkin, Adam P

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. Journal Article

In: The ISME Journal, 2021, ISSN: 1751-7362.

Abstract | Links | BibTeX

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

Four families of folate-independent methionine synthases. Journal Article

In: PLoS Genetics, 17 (2), pp. e1009342, 2021.

Abstract | Links | BibTeX

Trotter, Valentine V; Shatsky, Maxim; Price, Morgan N; Juba, Thomas R; Zane, Grant M; Leon, Kara P De; Majumder, Erica L; Gui, Qin; Ali, Rida; Wetmore, Kelly M; Kuehl, Jennifer V; Arkin, Adam P; Wall, Judy D; Deutschbauer, Adam M; Chandonia, John-Marc; Butland, Gareth P

Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium Journal Article

In: BioRxiv, 2021.

Abstract | Links | BibTeX

Ge, Xiaoxuan; Thorgersen, Michael P; Poole, Farris L; Deutschbauer, Adam M; Chandonia, John-Marc; Novichkov, Pavel S; Adams, Paul D; Arkin, Adam P; Hazen, Terry C; Adams, Michael W W

Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Journal Article

In: Microbiology Resource Announcements, 9 (44), 2020.

Abstract | Links | BibTeX

Michael P. Thorgersen Xiaoxuan Ge, Farris L. Poole II; Adams, Michael W. W.

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation Journal Article

In: 2020.

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Ge, Xiaoxuan; Thorgersen, Michael P; Poole, Farris L; Deutschbauer, Adam M; Chandonia, John-Marc; Novichkov, Pavel S; Gushgari-Doyle, Sara; Lui, Lauren M; Nielsen, Torben; Chakraborty, Romy; Adams, Paul D; Arkin, Adam P; Hazen, Terry C; Adams, Michael W W

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation Journal Article

In: Frontiers in microbiology, 11 , 2020, ISSN: 1664-302X.

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Mutalik, Vivek K; Adler, Benjamin A; Rishi, Harneet S; Piya, Denish; Zhong, Crystal; Koskella, Britt; Kutter, Elizabeth M; Calendar, Richard; Novichkov, Pavel S; Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P

High-throughput mapping of the phage resistance landscape in E. coli. Journal Article

In: PLoS Biology, 18 (10), pp. e3000877, 2020, ISSN: 1545-7885.

Abstract | Links | BibTeX

Wilpiszeski, Regina L; Gionfriddo, Caitlin M; Wymore, Ann M; Moon, Ji-Won; Lowe, Kenneth A; Podar, Mircea; Rafie, Sa'ad; Fields, Matthew W; Hazen, Terry C; Ge, Xiaoxuan; Poole, Farris; Adams, Michael W W; Chakraborty, Romy; Fan, Yupeng; Nostrand, Joy D Van; Zhou, Jizhong; Arkin, Adam P; Elias, Dwayne A

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations. Journal Article

In: Plos One, 15 (9), pp. e0232437, 2020.

Abstract | Links | BibTeX

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

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

In: Nature Communications, 11 (1), pp. 4717, 2020.

Abstract | Links | BibTeX

Moon, J W; Paradis, C J; Joyner, D C; von Netzer, F; Majumder, E L; Dixon, E R; Podar, M; Ge, X; Walian, P J; Smith, H J; Wu, X; Zane, G M; Walker, K F; Thorgersen, M P; Ii, F L Poole; Lui, L M; Adams, B G; Leon, K B De; Brewer, S S; Williams, D E; Lowe, K A; Rodriguez, M; Mehlhorn, T L; Pfiffner, S M; Chakraborty, R; Arkin, A P; Wall, J D; Fields, M W; Adams, M W W; Stahl, D A; Elias, D A; Hazen, T C

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer Journal Article

In: Chemosphere, 255 , pp. 126951, 2020.

Abstract | BibTeX

Moon, Ji-Won; Paradis, Charles J; Joyner, Dominique C; von Netzer, Frederick; Majumder, Erica L; Dixon, Emma R; Podar, Mircea; Ge, Xiaoxuan; Walian, Peter J; Smith, Heidi J; Wu, Xiaoqin; Zane, Grant M; Walker, Kathleen F; Thorgersen, Michael P; II, Farris L Poole; Lui, Lauren M; Adams, Benjamin G; León, Kara B De; Brewer, Sheridan S; Williams, Daniel E; Lowe, Kenneth A; Rodriguez, Miguel; Mehlhorn, Tonia L; Pfiffner, Susan M; Chakraborty, Romy; Arkin, Adam P; Wall, Judy D; Fields, Matthew W; Adams, Michael W W; Stahl, David A; Elias, Dwayne A; Hazen, Terry C

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer Journal Article

In: Chemosphere, 255 , pp. 126951, 2020, ISSN: 00456535.

Links | BibTeX

Xuanyu Tao Megan L. Kempher, Rong Song

Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature Journal Article

In: Mbio, 11 (4), pp. 2020, 2020.

BibTeX

Kempher, Megan L; Tao, Xuanyu; Song, Rong; Wu, Bo; Stahl, David A; Wall, Judy D; Arkin, Adam P; Zhou, Aifen; Zhou, Jizhong

Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature. Journal Article

In: mBio, 11 (4), 2020, ISSN: 2150-7511.

Abstract | Links | BibTeX

Simon Rouxb Ankita Kotharia, Hanqiao Zhanga

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article

In: 2020.

BibTeX

Kothari, Ankita; Roux, Simon; Zhang, Hanqiao; Prieto, Anatori; Soneja, Drishti; Chandonia, John-Marc; Spencer, Sarah J; Wu, Xiaoqin; Altenburg, Sarah; Fields, Matthew W; Deutschbauer, Adam M; Arkin, Adam P; Alm, Eric J; Chakraborty, Romy; Mukhopadhyay, Aindrila

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article

In: BioRxiv, 2020.

Abstract | Links | BibTeX

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

Gapmind: automated annotation of amino acid biosynthesis. Journal Article

In: mSystems, 5 (3), 2020.

Abstract | Links | BibTeX

Carlson, Hans K; Lui, Lauren M; Price, Morgan N; Kazakov, Alexey E; Carr, Alex V; Kuehl, Jennifer V; Owens, Trenton K; Nielsen, Torben; Arkin, Adam P; Deutschbauer, Adam M

Selective carbon sources influence the end products of microbial nitrate respiration. Journal Article

In: The ISME Journal, 14 (8), pp. 2034-2045, 2020, ISSN: 1751-7362.

Abstract | Links | BibTeX

Caitlin M. Gionfriddo Regina L. Wilpiszeski, Ann M. Wymore

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations Journal Article

In: bioRxiv, 2020.

BibTeX

Tian, Renmao; Ning, Daliang; He, Zhili; Zhang, Ping; Spencer, Sarah J; Gao, Shuhong; Shi, Weiling; Wu, Linwei; Zhang, Ya; Yang, Yunfeng; Adams, Benjamin G; Rocha, Andrea M; Detienne, Brittny L; Lowe, Kenneth A; Joyner, Dominique C; Klingeman, Dawn M; Arkin, Adam P; Fields, Matthew W; Hazen, Terry C; Stahl, David A; Alm, Eric J; Zhou, Jizhong

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Journal Article

In: Microbiome, 8 (1), pp. 51, 2020.

Abstract | Links | BibTeX

Torben N. Nielsen Lauren M. Lui, Adam P. Arkin

A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article

In: BioRxiv, 2020.

BibTeX

Lui, Lauren M; Nielsen, Torben N; Arkin, Adam P

A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article

In: BioRxiv, 2020.

Abstract | Links | BibTeX

Mengting Yuan Daliang Ning, Linwei Wu

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

In: 2020.

BibTeX

Kempher, M L; Tao, X; Song, R; Wu, B; Stahl, D A; Wall, J D; Arkin, A P; Zhou, A; Zhou, J

Effects of Genetic and Physiological Đivergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Ŧemperature Journal Article

In: mBio, 11 (4), 2020.

Abstract | BibTeX

Tian, R; Ning, D; He, Z; Zhang, P; Spencer, S J; Gao, S; Shi, W; Wu, L; Zhang, Y; Yang, Y; Adams, B G; Rocha, A M; Detienne, B L; Lowe, K A; Joyner, D C; Klingeman, D M; Arkin, A P; Fields, M W; Hazen, T C; Stahl, D A; Alm, E J; Zhou, J

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Journal Article

In: Microbiome, 8 (1), pp. 51, 2020.

Abstract | BibTeX

Carlson, H K; Lui, L M; Price, M N; Kazakov, A E; Carr, A V; Kuehl, J V; Owens, T K; Nielsen, T; Arkin, A P; Deutschbauer, A M

Selective carbon sources influence the end products of microbial nitrate respiration Journal Article

In: ISME J, 14 (8), pp. 2034–2045, 2020.

Abstract | BibTeX

Zelaya, A J; Parker, A E; Bailey, K L; Zhang, P; Nostrand, J Van; Ning, D; Elias, D A; Zhou, J; Hazen, T C; Arkin, A P; Fields, M W

Ħigh spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer Journal Article

In: Water Res., 164 , pp. 114917, 2019.

Abstract | BibTeX

Zelaya, Anna J; Parker, Albert E; Bailey, Kathryn L; Zhang, Ping; Nostrand, Joy Van; Ning, Daliang; Elias, Dwayne A; Zhou, Jizhong; Hazen, Terry C; Arkin, Adam P; Fields, Matthew W

High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Journal Article

In: Water Research, 164 , pp. 114917, 2019.

Abstract | Links | BibTeX

Thorgersen, Michael P; Ge, Xiaoxuan; Poole, Farris L; Price, Morgan N; Arkin, Adam P; Adams, Michael W W

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Journal Article

In: Applied and Environmental Microbiology, 85 (17), 2019.

Abstract | Links | BibTeX

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

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

In: PLoS Genetics, 15 (4), pp. e1008106, 2019.

Abstract | Links | BibTeX

Price, Morgan N; Arkin, Adam P

Curated BLAST for genomes. Journal Article

In: mSystems, 4 (2), 2019.

Abstract | Links | BibTeX

Price, Morgan N; Ray, Jayashree; Iavarone, Anthony T; Carlson, Hans K; Ryan, Elizabeth M; Malmstrom, Rex R; Arkin, Adam P; Deutschbauer, Adam M

Oxidative pathways of deoxyribose and deoxyribonate catabolism. Journal Article

In: mSystems, 4 (1), 2019.

Abstract | Links | BibTeX

Mutalik, Vivek K; Novichkov, Pavel S; Price, Morgan N; Owens, Trenton K; Callaghan, Mark; Carim, Sean; Deutschbauer, Adam M; Arkin, Adam P

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Journal Article

In: Nature Communications, 10 (1), pp. 308, 2019, ISSN: 2041-1723.

Abstract | Links | BibTeX

Paradis, C J; Dixon, E R; Lui, L M; Arkin, A P; Parker, J C; Istok, J D; Perfect, E; McKay, L D; Hazen, T C

Improved Method for Estimating Reaction Rates Đuring Push-Pull Ŧests Journal Article

In: Ground Water, 57 (2), pp. 292–302, 2019.

Abstract | BibTeX

Ge, X; Vaccaro, B J; Thorgersen, M P; Poole, F L; Majumder, E L; Zane, G M; Le?n, K B De; Lancaster, W A; Moon, J W; Paradis, C J; von Netzer, F; Stahl, D A; Adams, P D; Arkin, A P; Wall, J D; Hazen, T C; Adams, M W W

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle Journal Article

In: Environ. Microbiol., 21 (1), pp. 152–163, 2019.

Abstract | BibTeX

Thorgersen, M P; Ge, X; Poole, F L; Price, M N; Arkin, A P; Adams, M W W

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Ħeavily Contaminated Oak Ridge Reservation Journal Article

In: 85 (17), 2019.

Abstract | BibTeX

Carlson, H K; Price, M N; Callaghan, M; Aaring, A; Chakraborty, R; Liu, H; Kuehl, J V; Arkin, A P; Deutschbauer, A M

Ŧhe selective pressures on the microbial community in a metal-contaminated aquifer Journal Article

In: ISME J, 13 (4), pp. 937–949, 2019.

Abstract | BibTeX

Carlson, Hans K; Price, Morgan N; Callaghan, Mark; Aaring, Alex; Chakraborty, Romy; Liu, Hualan; Kuehl, Jennifer V; Arkin, Adam P; Deutschbauer, Adam M

The selective pressures on the microbial community in a metal-contaminated aquifer. Journal Article

In: The ISME Journal, 13 (4), pp. 937-949, 2019, ISSN: 1751-7362.

Abstract | Links | BibTeX

Ge, Xiaoxuan; Vaccaro, Brian J; Thorgersen, Michael P; Poole, Farris L; Majumder, Erica L; Zane, Grant M; León, Kara B De; Lancaster, Andrew W; Moon, Ji Won; Paradis, Charles J; von Netzer, Frederick; Stahl, David A; Adams, Paul D; Arkin, Adam P; Wall, Judy D; Hazen, Terry C; Adams, Michael W W

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Journal Article

In: Environmental Microbiology, 21 (1), pp. 152-163, 2019.

Abstract | Links | BibTeX

Paradis, Charles J; Dixon, Emma R; Lui, Lauren M; Arkin, Adam P; Parker, Jack C; Istok, Jonathan D; Perfect, Edmund; McKay, Larry D; Hazen, Terry C

Improved Method for Estimating Reaction Rates During Push-Pull Tests. Journal Article

In: Ground Water, 57 (2), pp. 292-302, 2019.

Abstract | Links | BibTeX

Smith, H J; Zelaya, A J; León, K B De; 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

In: FEMS Microbiology Ecology, 94 (12), 2018.

Abstract | Links | BibTeX

Price, Morgan N; Wetmore, Kelly M; Waters, Jordan R; Callaghan, Mark; Ray, Jayashree; Liu, Hualan; Kuehl, Jennifer V; Melnyk, Ryan A; Lamson, Jacob S; Suh, Yumi; Carlson, Hans K; Esquivel, Zuelma; Sadeeshkumar, Harini; Chakraborty, Romy; Zane, Grant M; Rubin, Benjamin E; Wall, Judy D; Visel, Axel; Bristow, James; Blow, Matthew J; Arkin, Adam P; Deutschbauer, Adam M

Mutant phenotypes for thousands of bacterial genes of unknown function. Journal Article

In: Nature, 557 (7706), pp. 503-509, 2018, ISSN: 0028-0836.

Abstract | Links | BibTeX

Christensen, Geoff A; Moon, JiWon; Veach, Allison M; Mosher, Jennifer J; Wymore, Ann M; van Nostrand, Joy D; Zhou, Jizhong; Hazen, Terry C; Arkin, Adam P; Elias, Dwayne A

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. Journal Article

In: Plos One, 13 (3), pp. e0194663, 2018.

Abstract | Links | BibTeX

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Nostrand, Joy D Van; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

Microbial functional gene diversity predicts groundwater contamination and ecosystem functioning. Journal Article

In: mBio, 9 (1), 2018.

Abstract | Links | BibTeX

Liu, Hualan; Price, Morgan N; Waters, Robert Jordan; Ray, Jayashree; Carlson, Hans K; Lamson, Jacob S; Chakraborty, Romy; Arkin, Adam P; Deutschbauer, Adam M

Magic pools: parallel assessment of transposon delivery vectors in bacteria. Journal Article

In: mSystems, 3 (1), 2018.

Abstract | Links | BibTeX

128 entries « 1 of 3 »