@article{price_2018,

title = {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.1007147},

doi = {10.1371/journal.pgen.1007147},

year  = {2018},

date = {2018-01-11},

urldate = {2021-05-26},

journal = {PLoS Genetics},

volume = {14},

number = {1},

pages = {e1007147},

abstract = {For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30265315,

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 Le?n and R Chakraborty and D A Elias and T C Hazen and A P Arkin and A B Cunningham and M W Fields},

year  = {2018},

date = {2018-01-01},

journal = {FEMS Microbiol. Ecol.},

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{rand_2017,

title = {A metabolic pathway for catabolizing levulinic acid in bacteria.},

author = {Jacqueline M Rand and Tippapha Pisithkul and Ryan L Clark and Joshua M Thiede and Christopher R Mehrer and Daniel E Agnew and Candace E Campbell and Andrew L Markley and Morgan N Price and Jayashree Ray and Kelly M Wetmore and Yumi Suh and Adam P Arkin and Adam M Deutschbauer and Daniel Amador-Noguez and Brian F Pfleger},

url = {http://dx.doi.org/10.1038/s41564-017-0028-z},

doi = {10.1038/s41564-017-0028-z},

year  = {2017},

date = {2017-12-01},

urldate = {2021-05-25},

journal = {Nature Microbiology},

volume = {2},

number = {12},

pages = {1624-1634},

abstract = {Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. This discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhou_2017,

title = {Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.},

author = {Aifen Zhou and Rebecca Lau and Richard Baran and Jincai Ma and Frederick von Netzer and Weiling Shi and Drew Gorman-Lewis and Megan L Kempher and Zhili He and Yujia Qin and Zhou Shi and Grant M Zane and Liyou Wu and Benjamin P Bowen and Trent R Northen and Kristina L Hillesland and David A Stahl and Judy D Wall and Adam P Arkin and Jizhong Zhou},

url = {http://dx.doi.org/10.1128/mBio.01780-17},

doi = {10.1128/mBio.01780-17},

year  = {2017},

date = {2017-11-14},

urldate = {2021-05-25},

journal = {mBio},

volume = {8},

number = {6},

abstract = {Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ømega9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ømega9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection.IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ømega9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution. Copyright copyright 2017 Zhou et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{delen_2017,

title = {Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough.},

author = {Kara B De León and Grant M Zane and Valentine V Trotter and Gregory P Krantz and Adam P Arkin and Gareth P Butland and Peter J Walian and Matthew W Fields and Judy D Wall},

url = {http://dx.doi.org/10.1128/mBio.01696-17},

doi = {10.1128/mBio.01696-17},

year  = {2017},

date = {2017-10-17},

urldate = {2021-05-25},

journal = {mBio},

volume = {8},

number = {5},

abstract = {Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered.IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm. Copyright copyright 2017 De León et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{justice_2017,

title = {Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing.},

author = {N B Justice and A Sczesnak and T C Hazen and A P Arkin},

url = {http://dx.doi.org/10.1128/AEM.01253-17},

doi = {10.1128/AEM.01253-17},

year  = {2017},

date = {2017-10-15},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {83},

number = {20},

abstract = {A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly.IMPORTANCE Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2017,

title = {PaperBLAST: Text Mining Papers for Information about Homologs.},

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

url = {http://dx.doi.org/10.1128/mSystems.00039-17},

doi = {10.1128/mSystems.00039-17},

year  = {2017},

date = {2017-08-15},

urldate = {2021-05-27},

journal = {mSystems},

volume = {2},

number = {4},

abstract = {Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST's database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins' functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thorgersen_2017a,

title = {Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions.},

author = {Michael P Thorgersen and Andrew W Lancaster and Xiaoxuan Ge and Grant M Zane and Kelly M Wetmore and Brian J Vaccaro and Farris L Poole and Adam D Younkin and Adam M Deutschbauer and Adam P Arkin and Judy D Wall and Michael W W Adams},

url = {http://dx.doi.org/10.3389/fmicb.2017.01529},

doi = {10.3389/fmicb.2017.01529},

year  = {2017},

date = {2017-08-10},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {8},

pages = {1529},

abstract = {Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI][Formula: see text]) or uranyl oxycation (U[VI][Formula: see text]). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wu_2017,

title = {Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.},

author = {Xiaoqin Wu and Adam M Deutschbauer and Alexey E Kazakov and Kelly M Wetmore and Bryson A Cwick and Robert M Walker and Pavel S Novichkov and Adam P Arkin and Romy Chakraborty},

url = {http://dx.doi.org/10.1128/genomeA.00582-17},

doi = {10.1128/genomeA.00582-17},

year  = {2017},

date = {2017-06-29},

urldate = {2021-05-25},

journal = {Genome announcements},

volume = {5},

number = {26},

abstract = {We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P and GW458P, isolated from groundwater samples collected from a background site at the Oak Ridge Field Research Center. Production of a purple pigment by these two strains was observed when grown on diluted (1/10) LB agar plates. Copyright copyright 2017 Wu et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sagawa_2017,

title = {Validating regulatory predictions from diverse bacteria with mutant fitness data.},

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

url = {http://dx.doi.org/10.1371/journal.pone.0178258},

doi = {10.1371/journal.pone.0178258},

year  = {2017},

date = {2017-05-24},

urldate = {2021-05-25},

journal = {Plos One},

volume = {12},

number = {5},

pages = {e0178258},

abstract = {Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium's growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomics predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhang_2017,

title = {Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.},

author = {Ping Zhang and Zhili He and Joy D Van Nostrand and Yujia Qin and Ye Deng and Liyou Wu and Qichao Tu and Jianjun Wang and Christopher W Schadt and Matthew W Fields and Terry C Hazen and Adam P Arkin and David A Stahl and Jizhong Zhou},

url = {http://dx.doi.org/10.1021/acs.est.6b02980},

doi = {10.1021/acs.est.6b02980},

year  = {2017},

date = {2017-04-04},

urldate = {2021-05-25},

journal = {Environmental Science & Technology},

volume = {51},

number = {7},

pages = {3609-3620},

abstract = {To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4-2, U(VI), NO3-, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P textless 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{king_2017,

title = {Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.},

author = {Andrew J King and Sarah P Preheim and Kathryn L Bailey and Michael S Robeson and Taniya Roy Chowdhury and Bryan R Crable and Richard A Hurt and Tonia Mehlhorn and Kenneth A Lowe and Tommy J Phelps and Anthony V Palumbo and Craig C Brandt and Steven D Brown and Mircea Podar and Ping Zhang and Andrew W Lancaster and Farris Poole and David B Watson and Matthew W Fields and John-Marc Chandonia and Eric J Alm and Jizhong Zhou and Michael W W Adams and Terry C Hazen and Adam P Arkin and Dwayne A Elias},

url = {http://dx.doi.org/10.1021/acs.est.6b04751},

doi = {10.1021/acs.est.6b04751},

year  = {2017},

date = {2017-03-07},

urldate = {2021-05-25},

journal = {Environmental Science & Technology},

volume = {51},

number = {5},

pages = {2879-2889},

abstract = {Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thorgersen_2017,

title = {A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium.},

author = {Michael P Thorgersen and Andrew W Lancaster and Lara Rajeev and Xiaoxuan Ge and Brian J Vaccaro and Farris L Poole and Adam P Arkin and Aindrila Mukhopadhyay and Michael W W Adams},

url = {http://dx.doi.org/10.1128/AEM.03044-16},

doi = {10.1128/AEM.03044-16},

year  = {2017},

date = {2017-02-15},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {83},

number = {4},

abstract = {Cell suspensions of Pelosinus sp. strain UFO1 were previously shown, using spectroscopic analysis, to sequester uranium as U(IV) complexed with carboxyl and phosphoryl group ligands on proteins. The goal of our present study was to characterize the proteins involved in uranium binding. Virtually all of the uranium in UFO1 cells was associated with a heterodimeric protein, which was termed the uranium-binding complex (UBC). The UBC was composed of two S-layer domain proteins encoded by UFO1_4202 and UFO1_4203. Samples of UBC purified from the membrane fraction contained 3.3 U atoms/heterodimer, but significant amounts of phosphate were not detected. The UBC had an estimated molecular mass by gel filtration chromatography of 15 MDa, and it was proposed to contain 150 heterodimers (UFO1_4203 and UFO1_4202) and about 500 uranium atoms. The UBC was also the dominant extracellular protein, but when purified from the growth medium, it contained only 0.3 U atoms/heterodimer. The two genes encoding the UBC were among the most highly expressed genes within the UFO1 genome, and their expressions were unchanged by the presence or absence of uranium. Therefore, the UBC appears to be constitutively expressed and is the first line of defense against uranium, including by secretion into the extracellular medium. Although S-layer proteins were previously shown to bind U(VI), here we showed that U(IV) binds to S-layer proteins, we identified the proteins involved, and we quantitated the amount of uranium bound. IMPORTANCE: Widespread uranium contamination from industrial sources poses hazards to human health and to the environment. Herein, we identified a highly abundant uranium-binding complex (UBC) from Pelosinus sp. strain UFO1. The complex makes up the primary protein component of the S-layer of strain UFO1 and binds 3.3 atoms of U(IV) per heterodimer. While other bacteria have been shown to bind U(VI) on their S-layer, we demonstrate here an example of U(IV) bound by an S-layer complex. The UBC provides a potential tool for the microbiological sequestration of uranium for the cleaning of contaminated environments. Copyright copyright 2017 American Society for Microbiology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chakraborty_2017,

title = {Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.},

author = {Romy Chakraborty and Hannah Woo and Paramvir Dehal and Robert Walker and Marcin Zemla and Manfred Auer and Lynne A Goodwin and Alexey Kazakov and Pavel Novichkov and Adam P Arkin and Terry C Hazen},

url = {http://dx.doi.org/10.1186/s40793-017-0233-7},

doi = {10.1186/s40793-017-0233-7},

year  = {2017},

date = {2017-02-08},

urldate = {2021-05-25},

journal = {Standards in genomic sciences},

volume = {12},

pages = {23},

abstract = {Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bosak_2016,

title = {System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions.},

author = {Tanja Bosak and Florence Schubotz and Ana de Santiago-Torio and Jennifer V Kuehl and Hans K Carlson and Nicki Watson and Mirna Daye and Roger E Summons and Adam P Arkin and Adam M Deutschbauer},

url = {http://dx.doi.org/10.1371/journal.pone.0168719},

doi = {10.1371/journal.pone.0168719},

year  = {2016},

date = {2016-12-28},

urldate = {2021-06-04},

journal = {Plos One},

volume = {11},

number = {12},

pages = {e0168719},

abstract = {The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2016a,

title = {A comparison of the costs and benefits of bacterial gene expression.},

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

url = {http://dx.doi.org/10.1371/journal.pone.0164314},

doi = {10.1371/journal.pone.0164314},

year  = {2016},

date = {2016-10-06},

urldate = {2021-05-25},

journal = {Plos One},

volume = {11},

number = {10},

pages = {e0164314},

abstract = {To study how a bacterium allocates its resources, we compared the costs and benefits of most (86%) of the proteins in Escherichia coli K-12 during growth in minimal glucose medium. The cost or investment in each protein was estimated from ribosomal profiling data, and the benefit of each protein was measured by assaying a library of transposon mutants. We found that proteins that are important for fitness are usually highly expressed, and 95% of these proteins are expressed at above 13 parts per million (ppm). Conversely, proteins that do not measurably benefit the host (with a benefit of less than 5% per generation) tend to be weakly expressed, with a median expression of 13 ppm. In aggregate, genes with no detectable benefit account for 31% of protein production, or about 22% if we correct for genetic redundancy. Although some of the apparently unnecessary expression could have subtle benefits in minimal glucose medium, the majority of the burden is due to genes that are important in other conditions. We propose that at least 13% of the cell's protein is "on standby" in case conditions change.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vaccaro_2016a,

title = {Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri.},

author = {Brian J Vaccaro and Andrew W Lancaster and Michael P Thorgersen and Grant M Zane and Adam D Younkin and Alexey E Kazakov and Kelly M Wetmore and Adam Deutschbauer and Adam P Arkin and Pavel S Novichkov and Judy D Wall and Michael W W Adams},

url = {http://dx.doi.org/10.1128/AEM.01845-16},

doi = {10.1128/AEM.01845-16},

year  = {2016},

date = {2016-10-01},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {82},

number = {19},

pages = {6046-6056},

abstract = {UNLABELLED: Metal ion transport systems have been studied extensively, but the specificity of a given transporter is often unclear from amino acid sequence data alone. In this study, predicted Cu(2+) and Zn(2+) resistance systems in Pseudomonas stutzeri strain RCH2 are compared with those experimentally implicated in Cu(2+) and Zn(2+) resistance, as determined by using a DNA-barcoded transposon mutant library. Mutant fitness data obtained under denitrifying conditions are combined with regulon predictions to yield a much more comprehensive picture of Cu(2+) and Zn(2+) resistance in strain RCH2. The results not only considerably expand what is known about well-established metal ion exporters (CzcCBA, CzcD, and CusCBA) and their accessory proteins (CzcI and CusF), they also reveal that isolates with mutations in some predicted Cu(2+) resistance systems do not show decreased fitness relative to the wild type when exposed to Cu(2+) In addition, new genes are identified that have no known connection to Zn(2+) (corB, corC, Psest_3226, Psest_3322, and Psest_0618) or Cu(2+) resistance (Mrp antiporter subunit gene, Psest_2850, and Psest_0584) but are crucial for resistance to these metal cations. Growth of individual deletion mutants lacking corB, corC, Psest_3226, or Psest_3322 confirmed the observed Zn-dependent phenotypes. Notably, to our knowledge, this is the first time a bacterial homolog of TMEM165, a human gene responsible for a congenital glycosylation disorder, has been deleted and the resulting strain characterized. Finally, the fitness values indicate Cu(2+)- and Zn(2+)-based inhibition of nitrite reductase and interference with molybdenum cofactor biosynthesis for nitrate reductase. These results extend the current understanding of Cu(2+) and Zn(2+) efflux and resistance and their effects on denitrifying metabolism. IMPORTANCE: In this study, genome-wide mutant fitness data in P. stutzeri RCH2 combined with regulon predictions identify several proteins of unknown function that are involved in resisting zinc and copper toxicity. For zinc, these include a member of the UPF0016 protein family that was previously implicated in Ca(2+)/H(+) antiport and a human congenital glycosylation disorder, CorB and CorC, which were previously linked to Mg(2+) transport, and Psest_3322 and Psest_0618, two proteins with no characterized homologs. Experiments using mutants lacking Psest_3226, Psest_3322, corB, corC, or czcI verified their proposed functions, which will enable future studies of these little-characterized zinc resistance determinants. Likewise, Psest_2850, annotated as an ion antiporter subunit, and the conserved hypothetical protein Psest_0584 are implicated in copper resistance. Physiological connections between previous studies and phenotypes presented here are discussed. Functional and mechanistic understanding of transport proteins improves the understanding of systems in which members of the same protein family, including those in humans, can have different functions. Copyright copyright 2016, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2016,

title = {Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes},

author = {Morgan N Price and Kelly M Wetmore and Robert Jordan Waters and Mark Callaghan and Jayashree Ray and Jennifer V Kuehl and Ryan A Melnyk and Jacob S Lamson and Yumi Suh and Zuelma Esquivel and Harini Sadeeshkumar and Romy Chakraborty and Benjamin E Rubin and James Bristow and Matthew J Blow and Adam P Arkin and Adam M Deutschbauer},

url = {http://biorxiv.org/lookup/doi/10.1101/072470},

doi = {10.1101/072470},

year  = {2016},

date = {2016-08-31},

urldate = {2021-06-04},

journal = {BioRxiv},

abstract = {The function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kosina_2016,

title = {Exometabolomics assisted design and validation of synthetic obligate mutualism.},

author = {Suzanne M Kosina and Megan A Danielewicz and Mujahid Mohammed and Jayashree Ray and Yumi Suh and Suzan Yilmaz and Anup K Singh and Adam P Arkin and Adam M Deutschbauer and Trent R Northen},

url = {http://dx.doi.org/10.1021/acssynbio.5b00236},

doi = {10.1021/acssynbio.5b00236},

year  = {2016},

date = {2016-07-15},

urldate = {2021-05-25},

journal = {ACS synthetic biology [electronic resource]},

volume = {5},

number = {7},

pages = {569-576},

abstract = {Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2016b,

title = {A theoretical lower bound for selection on the expression levels of proteins.},

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

url = {http://dx.doi.org/10.1093/gbe/evw126},

doi = {10.1093/gbe/evw126},

year  = {2016},

date = {2016-07-02},

urldate = {2021-05-25},

journal = {Genome Biology and Evolution},

volume = {8},

number = {6},

pages = {1917-1928},

abstract = {We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient. Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral. copyright The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hemme_2016,

title = {Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.},

author = {Christopher L Hemme and Stefan J Green and Lavanya Rishishwar and Om Prakash and Angelica Pettenato and Romy Chakraborty and Adam M Deutschbauer and Joy D Van Nostrand and Liyou Wu and Zhili He and King I Jordan and Terry C Hazen and Adam P Arkin and Joel E Kostka and Jizhong Zhou},

url = {http://dx.doi.org/10.1128/mBio.02234-15},

doi = {10.1128/mBio.02234-15},

year  = {2016},

date = {2016-04-05},

urldate = {2021-05-25},

journal = {mBio},

volume = {7},

number = {2},

pages = {e02234-15},

abstract = {UNLABELLED: Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. IMPORTANCE: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses. Copyright copyright 2016 Hemme et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vaccaro_2016,

title = {Determining roles of accessory genes in denitrification by mutant fitness analyses.},

author = {Brian J Vaccaro and Michael P Thorgersen and Andrew W Lancaster and Morgan N Price and Kelly M Wetmore and Farris L Poole and Adam Deutschbauer and Adam P Arkin and Michael W W Adams},

url = {http://dx.doi.org/10.1128/AEM.02602-15},

doi = {10.1128/AEM.02602-15},

year  = {2016},

date = {2016-01-01},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {82},

number = {1},

pages = {51-61},

abstract = {Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation. Copyright copyright 2015, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2015,

title = {Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes.},

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

url = {http://dx.doi.org/10.1128/mBio.01302-15},

doi = {10.1128/mBio.01302-15},

year  = {2015},

date = {2015-12-15},

urldate = {2021-05-25},

journal = {mBio},

volume = {6},

number = {6},

pages = {e01302-15},

abstract = {UNLABELLED: Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, "background selection" against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 10(12) individuals and a typical level of homologous recombination (r/m = 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is textless 10(7). An argument for high Ne values for bacteria has been the high genetic diversity within many bacterial "species," but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate of Ne, standard population genetics models imply that selection should be sufficient to drive evolution if Ne × s is textgreater1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10(-7) or so. IMPORTANCE: Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10(-9) per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. We used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10(-7) are effectively neutral. Copyright copyright 2015 Price and Arkin.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhang_2015,

title = {A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction.},

author = {Ping Zhang and Joy D Van Nostrand and Zhili He and Romy Chakraborty and Ye Deng and Daniel Curtis and Matthew W Fields and Terry C Hazen and Adam P Arkin and Jizhong Zhou},

url = {http://dx.doi.org/10.1021/acs.est.5b00024},

doi = {10.1021/acs.est.5b00024},

year  = {2015},

date = {2015-11-03},

urldate = {2021-05-25},

journal = {Environmental Science & Technology},

volume = {49},

number = {21},

pages = {12922-12931},

abstract = {Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for textgreater3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. In this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase long-term in response to this slowly degrading, complex substrate. To test these hypotheses, groundwater microbial communities were monitored after HRC amendment for textgreater1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO3-, Cr(VI), Fe(II) and SO4(2-). Our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer toward long-term Cr(VI) reduction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhou_2015,

title = {Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.},

author = {Aifen Zhou and Kristina L Hillesland and Zhili He and Wendy Schackwitz and Qichao Tu and Grant M Zane and Qiao Ma and Yuanyuan Qu and David A Stahl and Judy D Wall and Terry C Hazen and Matthew W Fields and Adam P Arkin and Jizhong Zhou},

url = {http://dx.doi.org/10.1038/ismej.2015.45},

doi = {10.1038/ismej.2015.45},

year  = {2015},

date = {2015-11-01},

urldate = {2021-05-25},

journal = {The ISME Journal},

volume = {9},

number = {11},

pages = {2360-2372},

abstract = {To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hemme_2015,

title = {Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.},

author = {Christopher L Hemme and Qichao Tu and Zhou Shi and Yujia Qin and Weimin Gao and Ye Deng and Joy Van D Nostrand and Liyou Wu and Zhili He and Patrick S G Chain and Susannah G Tringe and Matthew W Fields and Edward M Rubin and James M Tiedje and Terry C Hazen and Adam P Arkin and Jizhong Zhou},

url = {http://dx.doi.org/10.3389/fmicb.2015.01205},

doi = {10.3389/fmicb.2015.01205},

year  = {2015},

date = {2015-10-31},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {6},

pages = {1205},

abstract = {To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( textgreater55%) of the community is composed of poorly characterized low abundance (individually textless 1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{delen_2015,

title = {Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.},

author = {Kara B De León and Sagar M Utturkar and Laura B Camilleri and Dwayne A Elias and Adam P Arkin and Matthew W Fields and Steven D Brown and Judy D Wall},

url = {http://dx.doi.org/10.1128/genomeA.01090-15},

doi = {10.1128/genomeA.01090-15},

year  = {2015},

date = {2015-09-24},

urldate = {2021-05-25},

journal = {Genome announcements},

volume = {3},

number = {5},

abstract = {The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45. Copyright copyright 2015 De León et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thorgersen_2015,

title = {Molybdenum availability is key to nitrate removal in contaminated groundwater environments.},

author = {Michael P Thorgersen and Andrew W Lancaster and Brian J Vaccaro and Farris L Poole and Andrea M Rocha and Tonia Mehlhorn and Angelica Pettenato and Jayashree Ray and Jordan R Waters and Ryan A Melnyk and Romy Chakraborty and Terry C Hazen and Adam M Deutschbauer and Adam P Arkin and Michael W W Adams},

url = {http://dx.doi.org/10.1128/AEM.00917-15},

doi = {10.1128/AEM.00917-15},

year  = {2015},

date = {2015-08-01},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {81},

number = {15},

pages = {4976-4983},

abstract = {The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 μM to 230 mM and textless 0.2 nM to 580 μM, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (≥126 nM). They included cadmium, manganese, and cobalt, which were 1,300- to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed. Copyright copyright 2015, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhang_2015a,

title = {Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.},

author = {Ping Zhang and Wei-Min Wu and Joy D Van Nostrand and Ye Deng and Zhili He and Thomas Gihring and Gengxin Zhang and Chris W Schadt and David Watson and Phil Jardine and Craig S Criddle and Scott Brooks and Terence L Marsh and James M Tiedje and Adam P Arkin and Jizhong Zhou},

url = {http://dx.doi.org/10.1128/AEM.00043-15},

doi = {10.1128/AEM.00043-15},

year  = {2015},

date = {2015-06-15},

urldate = {2021-05-25},

journal = {Applied and Environmental Microbiology},

volume = {81},

number = {12},

pages = {4164-4172},

abstract = {A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Copyright copyright 2015, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carlson_2015,

title = {Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate.},

author = {Hans K Carlson and Jennifer V Kuehl and Amrita B Hazra and Nicholas B Justice and Magdalena K Stoeva and Andrew Sczesnak and Mark R Mullan and Anthony T Iavarone and Anna Engelbrektson and Morgan N Price and Adam M Deutschbauer and Adam P Arkin and John D Coates},

url = {http://dx.doi.org/10.1038/ismej.2014.216},

doi = {10.1038/ismej.2014.216},

year  = {2015},

date = {2015-06-01},

urldate = {2021-05-25},

journal = {The ISME Journal},

volume = {9},

number = {6},

pages = {1295-1305},

abstract = {We investigated perchlorate (ClO(4)(-)) and chlorate (ClO(3)(-)) (collectively (per)chlorate) in comparison with nitrate as potential inhibitors of sulfide (H(2)S) production by mesophilic sulfate-reducing microorganisms (SRMs). We demonstrate the specificity and potency of (per)chlorate as direct SRM inhibitors in both pure cultures and undefined sulfidogenic communities. We demonstrate that (per)chlorate and nitrate are antagonistic inhibitors and resistance is cross-inducible implying that these compounds share at least one common mechanism of resistance. Using tagged-transposon pools we identified genes responsible for sensitivity and resistance in Desulfovibrio alaskensis G20. We found that mutants in Dde_2702 (Rex), a repressor of the central sulfate-reduction pathway were resistant to both (per)chlorate and nitrate. In general, Rex derepresses its regulon in response to increasing intracellular NADH:NAD(+) ratios. In cells in which respiratory sulfate reduction is inhibited, NADH:NAD(+) ratios should increase leading to derepression of the sulfate-reduction pathway. In support of this, in (per)chlorate or nitrate-stressed wild-type G20 we observed higher NADH:NAD(+) ratios, increased transcripts and increased peptide counts for genes in the core Rex regulon. We conclude that one mode of (per)chlorate and nitrate toxicity is as direct inhibitors of the central sulfate-reduction pathway. Our results demonstrate that (per)chlorate are more potent inhibitors than nitrate in both pure cultures and communities, implying that they represent an attractive alternative for controlling sulfidogenesis in industrial ecosystems. Of these, perchlorate offers better application logistics because of its inhibitory potency, solubility, relative chemical stability, low affinity for mineral cations and high mobility in environmental systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ray_2015,

title = {Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.},

author = {Jayashree Ray and Jordan R Waters and Jeffrey M Skerker and Jennifer V Kuehl and Morgan N Price and Jiawen Huang and Romy Chakraborty and Adam P Arkin and Adam Deutschbauer},

url = {http://dx.doi.org/10.1128/genomeA.00322-15},

doi = {10.1128/genomeA.00322-15},

year  = {2015},

date = {2015-05-14},

urldate = {2021-05-25},

journal = {Genome announcements},

volume = {3},

number = {3},

abstract = {Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%. Copyright copyright 2015 Ray et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wetmore_2015,

title = {Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons.},

author = {Kelly M Wetmore and Morgan N Price and Robert J Waters and Jacob S Lamson and Jennifer He and Cindi A Hoover and Matthew J Blow and James Bristow and Gareth Butland and Adam P Arkin and Adam Deutschbauer},

url = {http://dx.doi.org/10.1128/mBio.00306-15},

doi = {10.1128/mBio.00306-15},

year  = {2015},

date = {2015-05-12},

urldate = {2021-05-25},

journal = {mBio},

volume = {6},

number = {3},

pages = {e00306-15},

abstract = {UNLABELLED: Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative d-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. IMPORTANCE: A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data. Copyright copyright 2015 Wetmore et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{smith_2015,

title = {Natural bacterial communities serve as quantitative geochemical biosensors.},

author = {Mark B Smith and Andrea M Rocha and Chris S Smillie and Scott W Olesen and Charles Paradis and Liyou Wu and James H Campbell and Julian L Fortney and Tonia L Mehlhorn and Kenneth A Lowe and Jennifer E Earles and Jana Phillips and Steve M Techtmann and Dominique C Joyner and Dwayne A Elias and Kathryn L Bailey and Richard A Hurt and Sarah P Preheim and Matthew C Sanders and Joy Yang and Marcella A Mueller and Scott Brooks and David B Watson and Ping Zhang and Zhili He and Eric A Dubinsky and Paul D Adams and Adam P Arkin and Matthew W Fields and Jizhong Zhou and Eric J Alm and Terry C Hazen},

url = {http://dx.doi.org/10.1128/mBio.00326-15},

doi = {10.1128/mBio.00326-15},

year  = {2015},

date = {2015-05-12},

urldate = {2021-05-25},

journal = {mBio},

volume = {6},

number = {3},

pages = {e00326-15},

abstract = {UNLABELLED: Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. IMPORTANCE: Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts. Copyright copyright 2015 Smith et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{melnyk_2015,

title = {Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase.},

author = {Ryan A Melnyk and Matthew D Youngblut and Iain C Clark and Hans K Carlson and Kelly M Wetmore and Morgan N Price and Anthony T Iavarone and Adam M Deutschbauer and Adam P Arkin and John D Coates},

url = {http://dx.doi.org/10.1128/mBio.00233-15},

doi = {10.1128/mBio.00233-15},

year  = {2015},

date = {2015-05-12},

urldate = {2021-05-25},

journal = {mBio},

volume = {6},

number = {3},

pages = {e00233-15},

abstract = {UNLABELLED: Reactive chlorine species (RCS) defense mechanisms are important for bacterial fitness in diverse environments. In addition to the anthropogenic use of RCS in the form of bleach, these compounds are also produced naturally through photochemical reactions of natural organic matter and in vivo by the mammalian immune system in response to invading microorganisms. To gain insight into bacterial RCS defense mechanisms, we investigated Azospira suillum strain PS, which produces periplasmic RCS as an intermediate of perchlorate respiration. Our studies identified an RCS response involving an RCS stress-sensing sigma/anti-sigma factor system (SigF/NrsF), a soluble hypochlorite-scavenging methionine-rich periplasmic protein (MrpX), and a putative periplasmic methionine sulfoxide reductase (YedY1). We investigated the underlying mechanism by phenotypic characterization of appropriate gene deletions, chemogenomic profiling of barcoded transposon pools, transcriptome sequencing, and biochemical assessment of methionine oxidation. Our results demonstrated that SigF was specifically activated by RCS and initiated the transcription of a small regulon centering around yedY1 and mrpX. A yedY1 paralog (yedY2) was found to have a similar fitness to yedY1 despite not being regulated by SigF. Markerless deletions of yedY2 confirmed its synergy with the SigF regulon. MrpX was strongly induced and rapidly oxidized by RCS, especially hypochlorite. Our results suggest a mechanism involving hypochlorite scavenging by sacrificial oxidation of the MrpX in the periplasm. Reduced MrpX is regenerated by the YedY methionine sulfoxide reductase activity. The phylogenomic distribution of this system revealed conservation in several Proteobacteria of clinical importance, including uropathogenic Escherichia coli and Brucella spp., implying a putative role in immune response evasion in vivo. IMPORTANCE: Bacteria are often stressed in the environment by reactive chlorine species (RCS) of either anthropogenic or natural origin, but little is known of the defense mechanisms they have evolved. Using a microorganism that generates RCS internally as part of its respiratory process allowed us to uncover a novel defense mechanism based on RCS scavenging by reductive reaction with a sacrificial methionine-rich peptide and redox recycling through a methionine sulfoxide reductase. This system is conserved in a broad diversity of organisms, including some of clinical importance, invoking a possible important role in innate immune system evasion. Copyright copyright 2015 Melnyk et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ramsay_2015,

title = {High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.},

author = {Bradley D Ramsay and Chiachi Hwang and Hannah L Woo and Sue L Carroll and Susan Lucas and James Han and Alla L Lapidus and Jan-Fang Cheng and Lynne A Goodwin and Samuel Pitluck and Lin Peters and Olga Chertkov and Brittany Held and John C Detter and Cliff S Han and Roxanne Tapia and Miriam L Land and Loren J Hauser and Nikos C Kyrpides and Natalia N Ivanova and Natalia Mikhailova and Ioanna Pagani and Tanja Woyke and Adam P Arkin and Paramvir Dehal and Dylan Chivian and Craig S Criddle and Weimin Wu and Romy Chakraborty and Terry C Hazen and Matthew W Fields},

url = {http://dx.doi.org/10.1128/genomeA.00092-15},

doi = {10.1128/genomeA.00092-15},

year  = {2015},

date = {2015-03-12},

urldate = {2021-05-25},

journal = {Genome announcements},

volume = {3},

number = {2},

abstract = {Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing delta-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction. Copyright copyright 2015 Ramsay et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{korte_2015,

title = {Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth.},

author = {Hannah L Korte and Avneesh Saini and Valentine V Trotter and Gareth P Butland and Adam P Arkin and Judy D Wall},

url = {http://dx.doi.org/10.1021/es504484m},

doi = {10.1021/es504484m},

year  = {2015},

date = {2015-01-20},

urldate = {2021-05-25},

journal = {Environmental Science & Technology},

volume = {49},

number = {2},

pages = {924-931},

abstract = {Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause textquotedblleftsouringtextquotedblright of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{christensen_2015,

title = {Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.},

author = {G A Christensen and G M Zane and A E Kazakov and X Li and D A Rodionov and P S Novichkov and I Dubchak and A P Arkin and J D Wall},

url = {http://dx.doi.org/10.1128/JB.02083-14},

doi = {10.1128/JB.02083-14},

year  = {2015},

date = {2015-01-01},

urldate = {2021-05-25},

journal = {Journal of Bacteriology},

volume = {197},

number = {1},

pages = {29-39},

abstract = {Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbe Desulfovibrio vulgaris Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction in D. vulgaris Hildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putative rex gene was made in D. vulgaris Hildenborough, and transcript expression studies of sat, encoding sulfate adenylyl transferase, showed increased levels in the D. vulgaris Hildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream of sat was identified, confirming RexDvH to be a repressor of sat. We established in vitro that the presence of elevated NADH disrupted the interaction between RexDvH and DNA. Examination of the 5' transcriptional start site for the sat mRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvH as a transcription repressor for sat that senses the redox status of the cell. Copyright copyright 2015, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{meyer_2014,

title = {The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf.},

author = {Birte Meyer and Jennifer V Kuehl and Morgan N Price and Jayashree Ray and Adam M Deutschbauer and Adam P Arkin and David A Stahl},

url = {http://dx.doi.org/10.1111/1462-2920.12405},

doi = {10.1111/1462-2920.12405},

year  = {2014},

date = {2014-11-01},

urldate = {2021-05-25},

journal = {Environmental Microbiology},

volume = {16},

number = {11},

pages = {3463-3486},

abstract = {The adaptation capability of Desulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying Desulfovibrio alaskensis strain G20 under varying respiratory, fermentative and methanogenic coculture conditions in chemostats. Transition from lactate to pyruvate in coculture resulted in a dramatic shift in the population structure and closer interspecies cell-to-cell interactions. Lower methane production rates in coculture than predicted from pyruvate input was attributed to redirection of electron flow to fumarate reduction. Without a methanogenic partner, accumulation of H₂and formate resulted in greater succinate production. Comparative transcript and gene fitness analysis in concert with physiological data of G20 wildtype and mutants demonstrated that pyruvate fermentation involves respiration of cytoplasmically formed fumarate using cytoplasmic and membrane-bound energy-conserving complexes, Rnf, Hdr-Flox-1 and Hmc. At the low H₂/formate levels maintained in coculture, Rnf likely functions as proton-pumping ferredoxin (Fd): type-I cytochrome c oxidoreductase, which transitions to a proton-pumping Fd(red):  nicotinamide adenine dinucleotide (NAD⁺) oxidoreductase at high H₂/formate levels during fermentation in monoculture. Hdr-Flox-1 is postulated to recycle Fd(red) via a flavin-based electron bifurcation involving NADH, Fdox and the thiol/disulphide-containing DsrC. In a menaquinone (MQ)-based electron confurcation reaction, the high-molecular-weight cytochrome-c₃complex, Hmc, is proposed to then couple DsrC(red) and periplasmic H₂/formate oxidation using the MQ pool to fuel a membrane-bound fumarate reductase. copyright 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{price_2014,

title = {The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20.},

author = {Morgan N Price and Jayashree Ray and Kelly M Wetmore and Jennifer V Kuehl and Stefan Bauer and Adam M Deutschbauer and Adam P Arkin},

url = {http://dx.doi.org/10.3389/fmicb.2014.00577},

doi = {10.3389/fmicb.2014.00577},

year  = {2014},

date = {2014-10-31},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {5},

pages = {577},

abstract = {Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deutschbauer_2014,

title = {Towards an informative mutant phenotype for every bacterial gene.},

author = {Adam Deutschbauer and Morgan N Price and Kelly M Wetmore and Daniel R Tarjan and Zhuchen Xu and Wenjun Shao and Dacia Leon and Adam P Arkin and Jeffrey M Skerker},

url = {http://dx.doi.org/10.1128/JB.01836-14},

doi = {10.1128/JB.01836-14},

year  = {2014},

date = {2014-10-01},

urldate = {2016-11-02},

journal = {Journal of Bacteriology},

volume = {196},

number = {20},

pages = {3643-3655},

abstract = {Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness. Copyright copyright 2014, American Society for Microbiology. All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gowda_2014,

title = {Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.},

author = {Harsha Gowda and Julijana Ivanisevic and Caroline H Johnson and Michael E Kurczy and Paul H Benton and Duane Rinehart and Thomas Nguyen and Jayashree Ray and Jennifer Kuehl and Bernardo Arevalo and Peter D Westenskow and Junhua Wang and Adam P Arkin and Adam M Deutschbauer and Gary J Patti and Gary Siuzdak},

url = {http://dx.doi.org/10.1021/ac500734c},

doi = {10.1021/ac500734c},

year  = {2014},

date = {2014-07-15},

urldate = {2021-05-25},

journal = {Analytical Chemistry},

volume = {86},

number = {14},

pages = {6931-6939},

abstract = {XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shao_2014,

title = {Conservation of transcription start sites within genes across a bacterial genus.},

author = {Wenjun Shao and Morgan N Price and Adam M Deutschbauer and Margaret F Romine and Adam P Arkin},

url = {http://dx.doi.org/10.1128/mBio.01398-14},

doi = {10.1128/mBio.01398-14},

year  = {2014},

date = {2014-07-01},

urldate = {2021-05-25},

journal = {mBio},

volume = {5},

number = {4},

pages = {e01398-14},

abstract = {Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function. Importance: The first step of gene expression is the initiation of transcription from promoters, which have been traditionally thought to be located upstream of genes. Recently, studies showed that in diverse bacteria, promoters are often located inside genes. It has not been clear if these unexpected promoters are important to the organism or if they result from transcriptional noise. Here, we identify and examine promoters in eight related bacterial species. Promoters that lie within genes on the sense strand are often conserved as locations and in their sequences. Furthermore, these promoters often affect the bacterium's growth. Thus, many of these unexpected promoters are likely functional. Fewer promoters that lie within genes on the antisense strand are conserved, but the conserved ones seem to drive the expression of nearby genes. Copyright copyright 2014 Shao et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rinehart_2014,

title = {Metabolomic data streaming for biology-dependent data acquisition.},

author = {Duane Rinehart and Caroline H Johnson and Thomas Nguyen and Julijana Ivanisevic and Paul H Benton and Jessica Lloyd and Adam P Arkin and Adam M Deutschbauer and Gary J Patti and Gary Siuzdak},

url = {http://www.nature.com/doifinder/10.1038/nbt.2927},

doi = {10.1038/nbt.2927},

issn = {1087-0156},

year  = {2014},

date = {2014-06-01},

urldate = {2021-05-25},

journal = {Nature Biotechnology},

volume = {32},

number = {6},

pages = {524-527},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kuehl_2014,

title = {Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.},

author = {Jennifer V Kuehl and Morgan N Price and Jayashree Ray and Kelly M Wetmore and Zuelma Esquivel and Alexey E Kazakov and Michelle Nguyen and Raquel Kuehn and Ronald W Davis and Terry C Hazen and Adam P Arkin and Adam Deutschbauer},

url = {http://dx.doi.org/10.1128/mBio.01041-14},

doi = {10.1128/mBio.01041-14},

year  = {2014},

date = {2014-05-27},

urldate = {2021-05-25},

journal = {mBio},

volume = {5},

number = {3},

pages = {e01041-14},

abstract = {UNLABELLED: The genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance. IMPORTANCE: Sulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria. Copyright copyright 2014 Kuehl et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{korte_2014,

title = {Genetic basis for nitrate resistance in Desulfovibrio strains.},

author = {Hannah L Korte and Samuel R Fels and Geoff A Christensen and Morgan N Price and Jennifer V Kuehl and Grant M Zane and Adam M Deutschbauer and Adam P Arkin and Judy D Wall},

url = {http://dx.doi.org/10.3389/fmicb.2014.00153},

doi = {10.3389/fmicb.2014.00153},

year  = {2014},

date = {2014-04-21},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {5},

pages = {153},

abstract = {Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{butland_2014,

title = {Novel aspects of iron sulfur cluster biosynthesis in sulfate reducing bacteria (768.17)},

author = {Gareth Butland and Avneesh Saini and Valentine Trotter and Morgan Price and Jennifer He and Jennifer Kuehl and Kelly Wetmore and Nancy Liu and Grant Zane and Samuel Fels and Thomas Juba and Maxim Shatsky and Adam Arkin and John-Marc Chandonia and Judy Wall and Adam Deutschbauer},

url = {https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.28.1_supplement.768.17},

year  = {2014},

date = {2014-04-01},

urldate = {2021-06-04},

journal = {The FASEB Journal},

publisher = {John Wiley & Sons, Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhou_2014,

title = {Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.},

author = {Jizhong Zhou and Ye Deng and Ping Zhang and Kai Xue and Yuting Liang and Joy D Van Nostrand and Yunfeng Yang and Zhili He and Liyou Wu and David A Stahl and Terry C Hazen and James M Tiedje and Adam P Arkin},

url = {http://dx.doi.org/10.1073/pnas.1324044111},

doi = {10.1073/pnas.1324044111},

year  = {2014},

date = {2014-03-04},

urldate = {2021-05-25},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {111},

number = {9},

pages = {E836-45},

abstract = {Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{novichkov_2014,

title = {Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.},

author = {Pavel S Novichkov and Xiaoqing Li and Jennifer V Kuehl and Adam M Deutschbauer and Adam P Arkin and Morgan N Price and Dmitry A Rodionov},

url = {http://dx.doi.org/10.1111/1462-2920.12273},

doi = {10.1111/1462-2920.12273},

year  = {2014},

date = {2014-01-01},

urldate = {2021-05-25},

journal = {Environmental Microbiology},

volume = {16},

number = {1},

pages = {1-8},

abstract = {Sulphur is an essential element in the metabolism. The sulphur-containing amino acid methionine is a metabolic precursor for S-adenosylmethionine (SAM), which serves as a coenzyme for ubiquitous methyltrtansferases. Recycling of organic sulphur compounds, e.g. via the SAM cycle, is an important metabolic process that needs to be tightly regulated. Knowledge about transcriptional regulation of these processes is still limited for many free-living bacteria. We identified a novel transcription factor SahR from the ArsR family that controls the SAM cycle genes in diverse microorganisms from soil and aquatic ecosystems. By using comparative genomics, we predicted SahR-binding DNA motifs and reconstructed SahR regulons in the genomes of 62 Proteobacteria. The conserved core of SahR regulons includes all enzymes required for the SAM cycle: the SAH hydrolase AhcY, the methionine biosynthesis enzymes MetE/MetH and MetF, and the SAM synthetase MetK. By using a combination of experimental techniques, we validated the SahR regulon in the sulphate-reducing Deltaproteobacterium Desulfovibrio alaskensis. SahR functions as a negative regulator that responds to the S-adenosylhomocysteine (SAH). The elevated SAH level in the cell dissociates SahR from its DNA operators and induces the expression of SAM cycle genes. The effector-sensing domain in SahR is related to SAM-dependent methylases that are able to tightly bind SAH. SahR represents a novel type of transcriptional regulators for the control of sulphur amino acid metabolism. copyright 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{somenahally_2013,

title = {Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.},

author = {Anil C Somenahally and Jennifer J Mosher and Tong Yuan and Mircea Podar and Tommy J Phelps and Steven D Brown and Zamin K Yang and Terry C Hazen and Adam P Arkin and Anthony V Palumbo and Joy D Van Nostrand and Jizhong Zhou and Dwayne A Elias},

url = {http://dx.doi.org/10.1371/journal.pone.0083909},

doi = {10.1371/journal.pone.0083909},

year  = {2013},

date = {2013-12-23},

urldate = {2021-05-25},

journal = {Plos One},

volume = {8},

number = {12},

pages = {e83909},

abstract = {Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{louie_2013,

title = {"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria.},

author = {Katherine B Louie and Benjamin P Bowen and Xiaoliang Cheng and James E Berleman and Romy Chakraborty and Adam Deutschbauer and Adam Arkin and Trent R Northen},

url = {http://dx.doi.org/10.1021/ac402240q},

doi = {10.1021/ac402240q},

year  = {2013},

date = {2013-11-19},

urldate = {2021-05-25},

journal = {Analytical Chemistry},

volume = {85},

number = {22},

pages = {10856-10862},

abstract = {Traditionally, microbes are studied under controlled laboratory conditions as isolates in planktonic culture. However, this is a vast extrapolation from their natural state; development of new techniques is required to decipher the largely unknown world of microbial chemical interactions in more realistic environments. The field of mass spectrometry imaging has made significant progress in localizing metabolites in and around bacterial colonies, primarily by using MALDI and ESI-based techniques that interrogate the top surface of the sample. Unfortunately, surface-based laser-desorption techniques, such as nanostructure-initiator mass spectrometry (NIMS), which has advantages in detection of small metabolite compounds and low background, has not been suitable for direct microbe imaging because desorption/ionization occurs on the bottom of the sample. Here, we describe a "replica-extraction-transfer" (REX) technique that overcomes this barrier by transferring biomolecules from agar cultures of spatially arrayed bacterial colonies onto NIMS surfaces; further, we demonstrate that acoustic printing of bacteria can be used to create complex colony geometries to probe microbial interactions with NIMS imaging. REX uses a solvent-laden semisolid (e.g., gel) to first extract metabolites from a microbial sample, such as a biofilm or agar culture; the metabolites are then replica "stamped" onto the NIMS surface. Using analytical standards we show that REX-NIMS effectively transfers and detects a range of small molecule compounds including amino acids and polyamines. This approach is then used to analyze the metabolite composition of streaked Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2 colonies and further resolve complex patterns produced by acoustic printing of liquid microbial cultures. Applying multivariate statistical analysis of the NIMS imaging data identified ions that were localized to different regions between and within colonies, as well as to the agar gel. Subsequent high-resolution tandem mass spectrometry was used to characterize two species-specific lipids that correlated with the spatial location of each microbial species and were found to be highly abundant in cell extracts. Overall, the use of acoustic printing of bacteria with REX-NIMS imaging will extend the range of analytical capabilities available for characterization of microbial interactions with mass spectrometry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}