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 Van D; 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

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

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

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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

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

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

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Wall, Judy D; Zane, Grant M; Juba, Thomas R; Kuehl, Jennifer V; Ray, Jayashree; Chhabra, Swapnil R; Trotter, Valentine V; Shatsky, Maxim; León, Kara De B; 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

Microbiology Resource Announcements, 10 (11), 2021.

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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

BioRxiv, 2021.

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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

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

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

Four families of folate-independent methionine synthases. Journal Article

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

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Trotter, Valentine V; Shatsky, Maxim; Price, Morgan N; Juba, Thomas R; Zane, Grant M; Leon, Kara De P; 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

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

Microbiology Resource Announcements, 9 (44), 2020.

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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.

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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

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

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

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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 Van D; Zhou, Jizhong; Arkin, Adam P; Elias, Dwayne A

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

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

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, 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

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 Poole L; Lui, Lauren M; Adams, Benjamin G; León, Kara De B; 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

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

Links | 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

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

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

Abstract | Links | 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

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

BioRxiv, 2020.

Abstract | Links | BibTeX

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

Gapmind: automated annotation of amino acid biosynthesis. Journal Article

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

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

Abstract | Links | 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.

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

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

Abstract | Links | BibTeX

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

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

BioRxiv, 2020.

Abstract | Links | 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.

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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

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

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

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

Abstract | Links | BibTeX

Price, Morgan N; Arkin, Adam P

Curated BLAST for genomes. Journal Article

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

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

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

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.

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

ISME J, 13 (4), pp. 937–949, 2019.

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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

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 De B; 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

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

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

Abstract | Links | BibTeX

Smith, H J; Zelaya, A J; León, 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 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

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

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Christensen, Geoff A; 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

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 Van D; 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

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

mSystems, 3 (1), 2018.

Abstract | Links | BibTeX

128 entries « 1 of 3 »