@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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

pubstate = {published},

tppubtype = {article}

}

@article{kempher_2020,

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

author = {Megan L Kempher and Xuanyu Tao and Rong Song and Bo Wu and David A Stahl and Judy D Wall and Adam P Arkin and Aifen Zhou and Jizhong Zhou},

url = {https://mbio.asm.org/content/11/4/e00569-20},

doi = {10.1128/mBio.00569-20},

issn = {2150-7511},

year  = {2020},

date = {2020-08-18},

urldate = {2021-05-25},

journal = {mBio},

volume = {11},

number = {4},

abstract = {Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes.IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints. Copyright copyright 2020 Kempher et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kothari2020ecogenomics,

title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance},

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

year  = {2020},

date = {2020-07-15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kothari_2020,

title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance},

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

url = {http://biorxiv.org/lookup/doi/10.1101/2020.07.14.203604},

doi = {10.1101/2020.07.14.203604},

year  = {2020},

date = {2020-07-15},

urldate = {2021-05-25},

journal = {BioRxiv},

abstract = {Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes, however little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes and identified 200 viral sequences, which clustered into 41 ~ genus-level viral clusters (equivalent to viral genera) including 9 known and 32 putative new genera. We use publicly available bacterial whole genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. The publicly available microbial genome sequences enabled mapping bacterial hosts to a breadth of viral sequences. The WGS of groundwater isolates increased depth of host prediction by allowing identification of hosts at the strain level. The latter included 4 viruses that were almost entirely (textgreater99% query coverage, textgreater99% identity) identified as integrated in the genomes of specific Pseudomonas, Acidovorax and Castellaniella strains, resulting in very high-confidence host assignments. Lastly, 21 of these viruses encoded putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they act as key players in microbial adaption to environmental stress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2020,

title = {Gapmind: automated annotation of amino acid biosynthesis.},

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

url = {http://dx.doi.org/10.1128/mSystems.00291-20},

doi = {10.1128/mSystems.00291-20},

year  = {2020},

date = {2020-06-23},

urldate = {2021-05-25},

journal = {mSystems},

volume = {5},

number = {3},

abstract = {GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids. Copyright copyright 2020 Price et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carlson_2020,

title = {Selective carbon sources influence the end products of microbial nitrate respiration.},

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

url = {http://www.nature.com/articles/s41396-020-0666-7},

doi = {10.1038/s41396-020-0666-7},

issn = {1751-7362},

year  = {2020},

date = {2020-05-05},

urldate = {2021-05-25},

journal = {The ISME Journal},

volume = {14},

number = {8},

pages = {2034-2045},

abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{uwu,

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

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

year  = {2020},

date = {2020-04-19},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tian_2020,

title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.},

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

url = {http://dx.doi.org/10.1186/s40168-020-00825-w},

doi = {10.1186/s40168-020-00825-w},

year  = {2020},

date = {2020-04-06},

urldate = {2021-05-25},

journal = {Microbiome},

volume = {8},

number = {1},

pages = {51},

abstract = {BACKGROUND: The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including textgreater 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RESULTS: Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of textgreater 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. CONCLUSIONS: We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lui2020method,

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

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

year  = {2020},

date = {2020-03-06},

journal = {BioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lui_2020,

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

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

url = {http://biorxiv.org/lookup/doi/10.1101/2020.03.05.979740},

doi = {10.1101/2020.03.05.979740},

year  = {2020},

date = {2020-03-06},

urldate = {2021-05-25},

journal = {BioRxiv},

abstract = {Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Only 63 circularized bacterial and archaeal genomes have been assembled 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 method to achieve circularized 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 copy of ribosomal RNA genes. We present 34 circular CPR genomes, one circular Margulisbacteria 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ning2020quantitativeb,

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

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

year  = {2020},

date = {2020-02-25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32817099,

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

author = {M L Kempher and X Tao and R Song and B Wu and D A Stahl and J D Wall and A P Arkin and A Zhou and J Zhou},

year  = {2020},

date = {2020-01-01},

journal = {mBio},

volume = {11},

number = {4},

abstract = {Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes.IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32252814,

title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity},

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

year  = {2020},

date = {2020-01-01},

journal = {Microbiome},

volume = {8},

number = {1},

pages = {51},

abstract = {The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32372050,

title = {Selective carbon sources influence the end products of microbial nitrate respiration},

author = {H K Carlson and L M Lui and M N Price and A E Kazakov and A V Carr and J V Kuehl and T K Owens and T Nielsen and A P Arkin and A M Deutschbauer},

year  = {2020},

date = {2020-00-01},

journal = {ISME J},

volume = {14},

number = {8},

pages = {2034--2045},

abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31387058,

title = {Ħigh spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer},

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

year  = {2019},

date = {2019-11-01},

journal = {Water Res.},

volume = {164},

pages = {114917},

abstract = {Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average > 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zelaya_2019,

title = {High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer.},

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

url = {http://dx.doi.org/10.1016/j.watres.2019.114917},

doi = {10.1016/j.watres.2019.114917},

year  = {2019},

date = {2019-11-01},

urldate = {2021-05-25},

journal = {Water Research},

volume = {164},

pages = {114917},

abstract = {Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average textgreater 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry. Copyright copyright 2019 Elsevier Ltd. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thorgersen_2019,

title = {Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation.},

author = {Michael P Thorgersen and Xiaoxuan Ge and Farris L Poole and Morgan N Price and Adam P Arkin and Michael W W Adams},

url = {http://dx.doi.org/10.1128/AEM.00896-19},

doi = {10.1128/AEM.00896-19},

year  = {2019},

date = {2019-09-01},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {85},

number = {17},

abstract = {Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities. Copyright copyright 2019 American Society for Microbiology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2019b,

title = {Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.},

author = {Morgan N Price and Grant M Zane and Jennifer V Kuehl and Ryan A Melnyk and Judy D Wall and Adam M Deutschbauer and Adam P Arkin},

url = {http://dx.doi.org/10.1371/journal.pgen.1008106},

doi = {10.1371/journal.pgen.1008106},

year  = {2019},

date = {2019-04-03},

urldate = {2021-05-25},

journal = {PLoS Genetics},

volume = {15},

number = {4},

pages = {e1008106},

abstract = {[This corrects the article DOI: 10.1371/journal.pgen.1007147.].},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2019a,

title = {Curated BLAST for genomes.},

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

url = {http://dx.doi.org/10.1128/mSystems.00072-19},

doi = {10.1128/mSystems.00072-19},

year  = {2019},

date = {2019-04-01},

urldate = {2021-05-25},

journal = {mSystems},

volume = {4},

number = {2},

abstract = {Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme's name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated. IMPORTANCE Given a microbe's genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2019,

title = {Oxidative pathways of deoxyribose and deoxyribonate catabolism.},

author = {Morgan N Price and Jayashree Ray and Anthony T Iavarone and Hans K Carlson and Elizabeth M Ryan and Rex R Malmstrom and Adam P Arkin and Adam M Deutschbauer},

url = {http://dx.doi.org/10.1128/mSystems.00297-18},

doi = {10.1128/mSystems.00297-18},

year  = {2019},

date = {2019-02-05},

urldate = {2021-05-25},

journal = {mSystems},

volume = {4},

number = {1},

abstract = {Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants' abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mutalik_2019,

title = {Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.},

author = {Vivek K Mutalik and Pavel S Novichkov and Morgan N Price and Trenton K Owens and Mark Callaghan and Sean Carim and Adam M Deutschbauer and Adam P Arkin},

url = {http://www.nature.com/articles/s41467-018-08177-8},

doi = {10.1038/s41467-018-08177-8},

issn = {2041-1723},

year  = {2019},

date = {2019-01-18},

urldate = {2021-05-25},

journal = {Nature Communications},

volume = {10},

number = {1},

pages = {308},

abstract = {A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29656383,

title = {Improved Method for Estimating Reaction Rates Đuring Push-Pull Ŧests},

author = {C J Paradis and E R Dixon and L M Lui and A P Arkin and J C Parker and J D Istok and E Perfect and L D McKay and T C Hazen},

year  = {2019},

date = {2019-01-01},

journal = {Ground Water},

volume = {57},

number = {2},

pages = {292--302},

abstract = {The breakthrough curve obtained from a single-well push-pull test can be adjusted to account for dilution of the injection fluid in the aquifer fluid. The dilution-adjusted breakthrough curve can be analyzed to estimate the reaction rate of a solute. The conventional dilution-adjusted method assumes that the ratios of the concentrations of the nonreactive and reactive solutes in the injection fluid vs. the aquifer fluid are equal. If this assumption is invalid, the conventional method will generate inaccurate breakthrough curves and may lead to erroneous conclusions regarding the reactivity of a solute. In this study, a new method that generates a dilution-adjusted breakthrough curve was theoretically developed to account for any possible combination of nonreactive and reactive solute concentrations in the injection and aquifer fluids. The newly developed method was applied to a field-based data set and was shown to generate more accurate dilution-adjusted breakthrough curves. The improved dilution-adjusted method presented here is simple, makes no assumptions regarding the concentrations of the nonreactive and reactive solutes in the injection and aquifer fluids, and easily allows for estimating reaction rates during push-pull tests.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30289197,

title = {Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle},

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

year  = {2019},

date = {2019-01-01},

journal = {Environ. Microbiol.},

volume = {21},

number = {1},

pages = {152--163},

abstract = {Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO42- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31253673,

title = {Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Ħeavily Contaminated Oak Ridge Reservation},

author = {M P Thorgersen and X Ge and F L Poole and M N Price and A P Arkin and M W W Adams},

year  = {2019},

date = {2019-01-01},

volume = {85},

number = {17},

abstract = {Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30523276,

title = {Ŧhe selective pressures on the microbial community in a metal-contaminated aquifer},

author = {H K Carlson and M N Price and M Callaghan and A Aaring and R Chakraborty and H Liu and J V Kuehl and A P Arkin and A M Deutschbauer},

year  = {2019},

date = {2019-01-01},

journal = {ISME J},

volume = {13},

number = {4},

pages = {937--949},

abstract = {In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carlson_2019,

title = {The selective pressures on the microbial community in a metal-contaminated aquifer.},

author = {Hans K Carlson and Morgan N Price and Mark Callaghan and Alex Aaring and Romy Chakraborty and Hualan Liu and Jennifer V Kuehl and Adam P Arkin and Adam M Deutschbauer},

url = {http://www.nature.com/articles/s41396-018-0328-1},

doi = {10.1038/s41396-018-0328-1},

issn = {1751-7362},

year  = {2019},

date = {2019-01-01},

urldate = {2021-05-25},

journal = {The ISME Journal},

volume = {13},

number = {4},

pages = {937-949},

abstract = {In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ge_2019,

title = {Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle.},

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

url = {http://dx.doi.org/10.1111/1462-2920.14435},

doi = {10.1111/1462-2920.14435},

year  = {2019},

date = {2019-01-01},

urldate = {2021-05-25},

journal = {Environmental Microbiology},

volume = {21},

number = {1},

pages = {152-163},

abstract = {Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO42- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment. copyright 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{paradis_2019,

title = {Improved Method for Estimating Reaction Rates During Push-Pull Tests.},

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

url = {http://dx.doi.org/10.1111/gwat.12770},

doi = {10.1111/gwat.12770},

year  = {2019},

date = {2019-01-01},

urldate = {2021-05-25},

journal = {Ground Water},

volume = {57},

number = {2},

pages = {292-302},

abstract = {The breakthrough curve obtained from a single-well push-pull test can be adjusted to account for dilution of the injection fluid in the aquifer fluid. The dilution-adjusted breakthrough curve can be analyzed to estimate the reaction rate of a solute. The conventional dilution-adjusted method assumes that the ratios of the concentrations of the nonreactive and reactive solutes in the injection fluid vs. the aquifer fluid are equal. If this assumption is invalid, the conventional method will generate inaccurate breakthrough curves and may lead to erroneous conclusions regarding the reactivity of a solute. In this study, a new method that generates a dilution-adjusted breakthrough curve was theoretically developed to account for any possible combination of nonreactive and reactive solute concentrations in the injection and aquifer fluids. The newly developed method was applied to a field-based data set and was shown to generate more accurate dilution-adjusted breakthrough curves. The improved dilution-adjusted method presented here is simple, makes no assumptions regarding the concentrations of the nonreactive and reactive solutes in the injection and aquifer fluids, and easily allows for estimating reaction rates during push-pull tests. copyright 2018 The Authors. Groundwater published by Wiley Periodicals, Inc. on behalf of National Ground Water Association.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{smith_2018,

title = {Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments.},

author = {H J Smith and A J Zelaya and K B De León and R Chakraborty and D A Elias and T C Hazen and A P Arkin and A B Cunningham and M W Fields},

url = {http://dx.doi.org/10.1093/femsec/fiy191},

doi = {10.1093/femsec/fiy191},

year  = {2018},

date = {2018-12-01},

urldate = {2021-05-25},

journal = {FEMS Microbiology Ecology},

volume = {94},

number = {12},

abstract = {Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2018a,

title = {Mutant phenotypes for thousands of bacterial genes of unknown function.},

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

url = {http://www.nature.com/articles/s41586-018-0124-0},

doi = {10.1038/s41586-018-0124-0},

issn = {0028-0836},

year  = {2018},

date = {2018-05-16},

urldate = {2021-05-25},

journal = {Nature},

volume = {557},

number = {7706},

pages = {503-509},

abstract = {One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{christensen_2018,

title = {Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition.},

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

url = {http://dx.doi.org/10.1371/journal.pone.0194663},

doi = {10.1371/journal.pone.0194663},

year  = {2018},

date = {2018-03-20},

urldate = {2021-05-25},

journal = {Plos One},

volume = {13},

number = {3},

pages = {e0194663},

abstract = {Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{he_2018,

title = {Microbial functional gene diversity predicts groundwater contamination and ecosystem functioning.},

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

url = {http://dx.doi.org/10.1128/mBio.02435-17},

doi = {10.1128/mBio.02435-17},

year  = {2018},

date = {2018-02-20},

urldate = {2021-05-25},

journal = {mBio},

volume = {9},

number = {1},

abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P textless 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology. Copyright copyright 2018 He et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{liu_2018,

title = {Magic pools: parallel assessment of transposon delivery vectors in bacteria.},

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

url = {http://dx.doi.org/10.1128/mSystems.00143-17},

doi = {10.1128/mSystems.00143-17},

year  = {2018},

date = {2018-02-01},

urldate = {2021-05-25},

journal = {mSystems},

volume = {3},

number = {1},

abstract = {Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term "magic pools." Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. To identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylum Bacteroidetes. IMPORTANCE Molecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a "magic pool." The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA "parts," we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}