@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 = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30297967,

title = {Genetic dissection of interspecific differences in yeast thermotolerance},

author = {C V Weiss and J I Roop and R K Hackley and J N Chuong and I V Grigoriev and A P Arkin and J M Skerker and R B Brem},

year  = {2018},

date = {2018-01-01},

journal = {Nat. Genet.},

volume = {50},

number = {11},

pages = {1501--1504},

abstract = {Some of the most unique and compelling survival strategies in the natural world are fixed in isolated species1. To date, molecular insight into these ancient adaptations has been limited, as classic experimental genetics has focused on interfertile individuals in populations2. Here we use a new mapping approach, which screens mutants in a sterile interspecific hybrid, to identify eight housekeeping genes that underlie the growth advantage of Saccharomyces cerevisiae over its distant relative Saccharomyces paradoxus at high temperature. Pro-thermotolerance alleles at these mapped loci were required for the adaptive trait in S. cerevisiae and sufficient for its partial reconstruction in S. paradoxus. The emerging picture is one in which S. cerevisiae improved the heat resistance of multiple components of the fundamental growth machinery in response to selective pressure. Our study lays the groundwork for the mapping of genotype to phenotype in clades of sister species across Eukarya.},

keywords = {arkin lab},

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 = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30254120,

title = {Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Ħost},

author = {P Cernak and R Estrela and S Poddar and J M Skerker and Y F Cheng and A K Carlson and B Chen and V M Glynn and M Furlan and O W Ryan and M K Donnelly and A P Arkin and J W Taylor and J H D Cate},

year  = {2018},

date = {2018-01-01},

journal = {mBio},

volume = {9},

number = {5},

abstract = {Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits-thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.IMPORTANCE The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications. Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30247489,

title = {Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli},

author = {G Cambray and J C Guimaraes and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {Nat. Biotechnol.},

volume = {36},

number = {10},

pages = {1005--1015},

abstract = {Comparative analyses of natural and mutated sequences have been used to probe mechanisms of gene expression, but small sample sizes may produce biased outcomes. We applied an unbiased design-of-experiments approach to disentangle factors suspected to affect translation efficiency in E. coli. We precisely designed 244,000 DNA sequences implementing 56 replicates of a full factorial design to evaluate nucleotide, secondary structure, codon and amino acid properties in combination. For each sequence, we measured reporter transcript abundance and decay, polysome profiles, protein production and growth rates. Associations between designed sequences properties and these consequent phenotypes were dominated by secondary structures and their interactions within transcripts. We confirmed that transcript structure generally limits translation initiation and demonstrated its physiological cost using an epigenetic assay. Codon composition has a sizable impact on translatability, but only in comparatively rare elongation-limited transcripts. We propose a set of design principles to improve translation efficiency that would benefit from more accurate prediction of secondary structures in vivo.},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29979655,

title = {KBase: Ŧhe United States Đepartment of Energy Systems Biology Knowledgebase},

year  = {2018},

date = {2018-01-01},

journal = {Nat. Biotechnol.},

volume = {36},

number = {7},

pages = {566--569},

keywords = {kbase},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29930200,

title = {Đeciphering microbial interactions in synthetic human gut microbiome communities},

author = {O S Venturelli and A C Carr and G Fisher and R H Hsu and R Lau and B P Bowen and S Hromada and T Northen and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {Mol. Syst. Biol.},

volume = {14},

number = {6},

pages = {e8157},

abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29769716,

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

author = {M N Price and K M Wetmore and R J Waters and M Callaghan and J Ray and H Liu and J V Kuehl and R A Melnyk and J S Lamson and Y Suh and H K Carlson and Z Esquivel and H Sadeeshkumar and R Chakraborty and G M Zane and B E Rubin and J D Wall and A Visel and J Bristow and M J Blow and A P Arkin and A M Deutschbauer},

year  = {2018},

date = {2018-01-01},

journal = {Nature},

volume = {557},

number = {7706},

pages = {503--509},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29558522,

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

author = {G A Christensen and J Moon and A M Veach and J J Mosher and A M Wymore and J D van Nostrand and J Zhou and T C Hazen and A P Arkin and D A Elias},

year  = {2018},

date = {2018-01-01},

journal = {PLoS ONE},

volume = {13},

number = {3},

pages = {e0194663},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29521624,

title = {Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides},

author = {S T Coradetti and D Pinel and G M Geiselman and M Ito and S J Mondo and M C Reilly and Y F Cheng and S Bauer and I V Grigoriev and J M Gladden and B A Simmons and R B Brem and A P Arkin and J M Skerker},

year  = {2018},

date = {2018-01-01},

journal = {Elife},

volume = {7},

abstract = {The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29463661,

title = {Microbial Functional Gene Điversity Predicts Groundwater Contamination and Ecosystem Functioning},

author = {Z He and P Zhang and L Wu and A M Rocha and Q Tu and Z Shi and B Wu and Y Qin and J Wang and Q Yan and D Curtis and D Ning and J D Van Nostrand and L Wu and Y Yang and D A Elias and D B Watson and M W W Adams and M W Fields and E J Alm and T C Hazen and P D Adams and A P Arkin and J Zhou},

year  = {2018},

date = {2018-01-01},

journal = {mBio},

volume = {9},

number = {1},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29359196,

title = {Magic Pools: Parallel Assessment of Ŧransposon Đelivery Vectors in Bacteria},

author = {H Liu and M N Price and R J Waters and J Ray and H K Carlson and J S Lamson and R Chakraborty and A P Arkin and A M Deutschbauer},

year  = {2018},

date = {2018-01-01},

journal = {mSystems},

volume = {3},

number = {1},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29324779,

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

author = {M N Price and G M Zane and J V Kuehl and R A Melnyk and J D Wall and A M Deutschbauer and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {PLoS Genet.},

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 = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28947739,

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

author = {J M Rand and T Pisithkul and R L Clark and J M Thiede and C R Mehrer and D E Agnew and C E Campbell and A L Markley and M N Price and J Ray and K M Wetmore and Y Suh and A P Arkin and A M Deutschbauer and D Amador-Noguez and B F Pfleger},

year  = {2017},

date = {2017-12-01},

journal = {Nat Microbiol},

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{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 = {enigma},

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 = {enigma},

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 = {enigma},

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 = {enigma},

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 = {enigma},

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 = {enigma},

pubstate = {published},

tppubtype = {article}

}