@article{Goff2024,

title = {Genomic and environmental controls on\textit{Castellaniella}biogeography in an anthropogenically disturbed subsurface},

author = {Jennifer L. Goff and Elizabeth G. Szink and Konnor L. Durrence and Lauren M. Lui and Torben N. Nielsen and Jennifer V. Kuehl and Kristopher A. Hunt and John-Marc Chandonia and Jiawen Huang and Michael P. Thorgersen and Farris L. Poole and David A. Stahl and Romy Chakraborty and Adam M. Deutschbauer and Adam P. Arkin and Michael W. W. Adams},

url = {http://biorxiv.org/lookup/doi/10.1101/2024.02.03.578758},

doi = {10.1101/2024.02.03.578758},

year  = {2024},

date = {2024-02-04},

urldate = {2024-02-04},

publisher = {Cold Spring Harbor Laboratory},

abstract = {<jats:title>ABSTRACT</jats:title><jats:p><jats:italic>Castellaniella</jats:italic>species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the<jats:italic>Castellaniella</jats:italic>genus concurrent to increased denitrification rates. Thus, we asked how genomic and abiotic factors control the<jats:italic>Castellaniella</jats:italic>biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. ORR<jats:italic>Castellaniella</jats:italic>strains showed a higher degree of genetic diversification than those originating from non-ORR sites, which we attribute to the multitude of extreme stressors faced in the ORR subsurface. We report the isolation and characterization of several<jats:italic>Castellaniella</jats:italic>strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two<jats:italic>Castellaniella</jats:italic>amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least two decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (<jats:italic>nos</jats:italic>) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.</jats:p>},

howpublished = {bioRxiv},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Ning2024,

title = {Environmental stress mediates groundwater microbial community assembly},

author = {Daliang Ning and Yajiao Wang and Yupeng Fan and Jianjun Wang and Joy D. Van Nostrand and Liyou Wu and Ping Zhang and Daniel J. Curtis and Renmao Tian and Lauren Lui and Terry C. Hazen and Eric J. Alm and Matthew W. Fields and Farris Poole and Michael W. W. Adams and Romy Chakraborty and David A. Stahl and Paul D. Adams and Adam P. Arkin and Zhili He and Jizhong Zhou},

doi = {10.1038/s41564-023-01573-x},

issn = {2058-5276},

year  = {2024},

date = {2024-02-00},

urldate = {2024-02-00},

journal = {Nat Microbiol},

volume = {9},

number = {2},

pages = {490--501},

publisher = {Springer Science and Business Media LLC},

keywords = {Applied Microbiology and Biotechnology, Cell Biology, enigma, Genetics, Immunology, Microbiology, Microbiology (medical)},

pubstate = {published},

tppubtype = {article}

}

@article{paradis_2021,

title = {Sustained ability of a natural microbial community to remove nitrate from groundwater},

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

url = {http://biorxiv.org/lookup/doi/10.1101/2021.05.27.446013},

doi = {10.1101/2021.05.27.446013},

year  = {2021},

date = {2021-05-28},

urldate = {2021-06-04},

journal = {BioRxiv},

abstract = {Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation. ARTICLE IMPACT STATEMENT: Groundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{lui_2021,

title = {A method for achieving complete microbial genomes and improving bins from metagenomics data.},

author = {Lauren M Lui and Torben N Nielsen and Adam P Arkin},

url = {http://dx.doi.org/10.1371/journal.pcbi.1008972},

doi = {10.1371/journal.pcbi.1008972},

year  = {2021},

date = {2021-05-07},

urldate = {2021-05-26},

journal = {PLoS Computational Biology},

volume = {17},

number = {5},

pages = {e1008972},

abstract = {Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{nayfach_2021,

title = {A genomic catalog of Earth's microbiomes.},

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

url = {http://www.nature.com/articles/s41587-020-0718-6},

doi = {10.1038/s41587-020-0718-6},

issn = {1087-0156},

year  = {2021},

date = {2021-04-01},

urldate = {2021-06-04},

journal = {Nature Biotechnology},

volume = {39},

number = {4},

pages = {499-509},

abstract = {The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to textgreater10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{lui_2021a,

title = {Mechanism across scales: A holistic modeling framework integrating laboratory and field studies for microbial ecology.},

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

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.642422/full},

doi = {10.3389/fmicb.2021.642422},

issn = {1664-302X},

year  = {2021},

date = {2021-03-24},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {12},

pages = {642422},

abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments. Copyright copyright 2021 Lui, Majumder, Smith, Carlson, von Netzer, Fields, Stahl, Zhou, Hazen, Baliga, Adams and Arkin.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{wall_2021,

title = {Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough.},

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

url = {http://dx.doi.org/10.1128/MRA.00072-21},

doi = {10.1128/MRA.00072-21},

year  = {2021},

date = {2021-03-18},

urldate = {2021-05-25},

journal = {Microbiology Resource Announcements},

volume = {10},

number = {11},

abstract = {The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community. Copyright copyright 2021 Wall et al.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{song_2021,

title = {A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis},

author = {Fangchao Song and Jennifer V Kuehl and Arjun Chandran and Adam P Arkin},

url = {http://biorxiv.org/lookup/doi/10.1101/2021.03.01.433496},

doi = {10.1101/2021.03.01.433496},

year  = {2021},

date = {2021-03-02},

urldate = {2021-06-04},

journal = {BioRxiv},

abstract = {Bacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16s ribosomal RNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial amount of samples becomes necessary to analyses that parse the factors that determine microbial composition. A common bottleneck in performing these kinds of experiments is genomic DNA (gDNA) extraction, which can be biased on the types of species, time-consuming and expensive. Direct PCR methods are a potentially simpler and more accurate alternative to gDNA extraction methods that do not require the intervening purification step. In this study, we evaluated three variations of direct PCR methods using diverse heterogeneous bacterial cultures, ZymoBIOMICS Microbial Community Standards, and groundwater. By comparing direct PCR methods with DNeasy blood and tissue kits and DNeasy Powersoil kits, we found a specific variant of the direct PCR method exhibits a comparable overall accuracy to the conventional DNeasy Powersoil protocol. We also found the method showed higher efficiency for extracting gDNA from the gram negative strains compared to DNeasy blood and tissue protocol. This direct PCR method is 1600 times cheaper ($0.34 for 96 samples), 10 times simpler (15 min hands-on time for 96 samples) than DNeasy Powersoil protocol. The direct PCR method can also be fully automated, and is compatible with small volume samples, thereby permitting scaling of samples and replicates needed to support high-throughput large-scale bacterial community analysis.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{carim_2021,

title = {Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins.},

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

url = {http://www.nature.com/articles/s41396-021-00921-1},

doi = {10.1038/s41396-021-00921-1},

issn = {1751-7362},

year  = {2021},

date = {2021-03-01},

urldate = {2021-05-25},

journal = {The ISME Journal},

abstract = {Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{price_2021,

title = {Four families of folate-independent methionine synthases.},

author = {Morgan N Price and Adam M Deutschbauer and Adam P Arkin},

url = {http://dx.doi.org/10.1371/journal.pgen.1009342},

doi = {10.1371/journal.pgen.1009342},

year  = {2021},

date = {2021-02-03},

urldate = {2021-05-25},

journal = {PLoS Genetics},

volume = {17},

number = {2},

pages = {e1009342},

abstract = {Although most organisms synthesize methionine from homocysteine and methyl folates, some have "core" methionine synthases that lack folate-binding domains and use other methyl donors. In vitro, the characterized core synthases use methylcobalamin as a methyl donor, but in vivo, they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{trotter_2021,

title = {Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium},

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

url = {http://biorxiv.org/lookup/doi/10.1101/2021.01.13.426591},

doi = {10.1101/2021.01.13.426591},

year  = {2021},

date = {2021-01-13},

urldate = {2021-05-25},

journal = {BioRxiv},

abstract = {Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{ge_2020a,

title = {Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment.},

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

url = {http://dx.doi.org/10.1128/MRA.01149-20},

doi = {10.1128/MRA.01149-20},

year  = {2020},

date = {2020-10-29},

urldate = {2021-05-25},

journal = {Microbiology Resource Announcements},

volume = {9},

number = {44},

abstract = {Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation in Tennessee. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment. Copyright copyright 2020 Ge et al.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmicb.2020.587127,

title = {Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation},

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

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.587127/full},

doi = {https://doi.org/10.3389/fmicb.2020.587127},

year  = {2020},

date = {2020-10-19},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{ge_2020,

title = {Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation},

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

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.587127/full},

doi = {10.3389/fmicb.2020.587127},

issn = {1664-302X},

year  = {2020},

date = {2020-10-19},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {11},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{mutalik_2020,

title = {High-throughput mapping of the phage resistance landscape in E. coli.},

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

url = {https://dx.plos.org/10.1371/journal.pbio.3000877},

doi = {10.1371/journal.pbio.3000877},

issn = {1545-7885},

year  = {2020},

date = {2020-10-13},

urldate = {2021-05-25},

journal = {PLoS Biology},

volume = {18},

number = {10},

pages = {e3000877},

abstract = {Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{wilpiszeski_2020,

title = {In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.},

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

url = {http://dx.doi.org/10.1371/journal.pone.0232437},

doi = {10.1371/journal.pone.0232437},

year  = {2020},

date = {2020-09-28},

urldate = {2021-05-26},

journal = {Plos One},

volume = {15},

number = {9},

pages = {e0232437},

abstract = {Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{ning_2020,

title = {A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming.},

author = {Daliang Ning and Mengting Yuan and Linwei Wu and Ya Zhang and Xue Guo and Xishu Zhou and Yunfeng Yang and Adam P Arkin and Mary K Firestone and Jizhong Zhou},

url = {http://dx.doi.org/10.1038/s41467-020-18560-z},

doi = {10.1038/s41467-020-18560-z},

year  = {2020},

date = {2020-09-18},

urldate = {2021-05-25},

journal = {Nature Communications},

volume = {11},

number = {1},

pages = {4717},

abstract = {Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32417512,

title = {Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer},

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

year  = {2020},

date = {2020-09-01},

journal = {Chemosphere},

volume = {255},

pages = {126951},

abstract = {The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{moon_2020,

title = {Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer},

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

url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653520311449},

doi = {10.1016/j.chemosphere.2020.126951},

issn = {00456535},

year  = {2020},

date = {2020-09-01},

urldate = {2021-05-25},

journal = {Chemosphere},

volume = {255},

pages = {126951},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{kempher2020effects,

title = {Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature},

author = {Megan L. Kempher, Xuanyu Tao, Rong Song, Bo Wu, David A. Stahl, Judy D. Wall, Adam P. Arkin,

Aifen Zhou, Jizhong Zhou},

year  = {2020},

date = {2020-08-18},

journal = {Mbio},

volume = {11},

number = {4},

pages = {2020},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}