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

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

2020.

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, Poole F L; Lui, L M; Adams, B G; Leon, De K B; 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

Chemosphere, 255 , pp. 126951, 2020.

Abstract | BibTeX

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

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

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

BibTeX

Ankita Kotharia Simon Rouxb, Hanqiao Zhanga Anatori Prietoa Drishti Sonejaa John-MarcChandoniaa Sarah Spencer Xiaoqin Wud Sara Altenburgl Matthew Fields Adam M.Deutschbauer Adam Arkinc Eric Almh Romy Chakrabortyd Aindrila Mukhopadhyay W P J

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

2020.

BibTeX

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

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

bioRxiv, 2020.

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

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

BioRxiv, 2020.

BibTeX

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

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

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

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

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

ISME J, 14 (8), pp. 2034–2045, 2020.

Abstract | BibTeX

Zelaya, A J; Parker, A E; Bailey, K L; Zhang, P; Nostrand, Van J; 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

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

Abstract | 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

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, De K B; 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

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

85 (17), 2019.

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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

ISME J, 13 (4), pp. 937–949, 2019.

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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.

Abstract | BibTeX

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

0000.

BibTeX