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2. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

Author

Cailleau, Guillaume, primary, Hanson, Buck T., additional, Cravero, Melissa, additional, Zhioua, Sami, additional, Hilpish, Patrick, additional, Ruiz, Celia, additional, Robinson, Aaron J., additional, Kelliher, Julia M., additional, Morales, Demosthenes, additional, Gallegos-Graves, La Verne, additional, Bonito, Gregory, additional, Chain, Patrick S.G., additional, Bindschedler, Saskia, additional, and Junier, Pilar, additional

Published
2023
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3. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Author

Prescott, Rebecca D., primary, Chan, Yvonne L., additional, Tong, Eric J., additional, Bunn, Fiona, additional, Onouye, Chiyoko T., additional, Handel, Christy, additional, Lo, Chien-Chi, additional, Davenport, Karen, additional, Johnson, Shannon, additional, Flynn, Mark, additional, Saito, Jennifer A., additional, Lee, Herb, additional, Wong, Kaleomanuiwa, additional, Lawson, Brittany N., additional, Hiura, Kayla, additional, Sager, Kailey, additional, Sadones, Mia, additional, Hill, Ethan C., additional, Esibill, Derek, additional, Cockell, Charles S., additional, Santomartino, Rosa, additional, Chain, Patrick S.G., additional, Decho, Alan W., additional, and Donachie, Stuart P., additional

Published
2023
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5. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

Author

Scott, Kathleen M., Sievert, Stefan M., Abril, Fereniki N., Ball, Lois A., Barrett, Chantell J., Blake, Rodrigo A., Boller, Amanda J., Chain, Patrick S.G., Clark, Justine A., Davis, Carisa R., Detter, Chris, Do, Kimberly F., Dobrinski, Kimberly P., Faza, Brandon I., Fitzpatrick, Kelly A., Freyermuth, Sharyn K., Harmer, Tara L., Hauser, Loren J., Hugler, Michael, Kerfeld, Cheryl A., Klotz, Martin G., Kong, William W., Land, Miriam, Lapidus, Alla, Larimer, Frank W., Longo, Dana L., Lucas, Susan, Malfatti, Stephanie A., Massey, Steven E., Martin, Darlene D., McCuddin, Zoe, Meyer, Folker, Moore, Jessica L., Ocampo, Luis H., Paul, John H., Paulsen, Ian T., Reep, Douglas K., Ren, Qinghu, Ross, Rachel L., Sato, Priscila Y., Thomas, Phaedra, Tinkham, Lance E., and Zeruth, Gary T.

Subjects
Basic biological sciences, complete genome sequence
Abstract

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 bp), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of CDSs encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. T. crunogena XCL-2 is unusual among obligate sulfur oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. A 38 kb prophage is present, and a high level of prophage induction was observed, which may play a role in keeping competing populations of close relatives in check. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

Published
2006

6. Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

Author

Chain, Patrick S.G., Hu, Ping, Malfatti, Stephanie A., Radnedge, Lyndsay, Larimer, Frank, Vergez, Lisa M., Worsham, Patricia, Chu, May C., and Andersen, Gary L.

Subjects
Environmental sciences, Applied life sciences, Yersinia pestis genome
Abstract

Yersinia pestis, the causative agent of bubonic and pneumonic plague, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" Antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Y. pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein coding regions, which were used to assess evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure and many of the inactivations are probably related to the organism s interaction with its host environment. The results presented here clearly demonstrate the differences between the two Antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. Comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

Published
2006

8. Bacterial spores, from ecology to biotechnology

Author

Paul, Christophe, primary, Filippidou, Sevasti, additional, Jamil, Isha, additional, Kooli, Wafa, additional, House, Geoffrey L., additional, Estoppey, Aislinn, additional, Hayoz, Mathilda, additional, Junier, Thomas, additional, Palmieri, Fabio, additional, Wunderlin, Tina, additional, Lehmann, Anael, additional, Bindschedler, Saskia, additional, Vennemann, Torsten, additional, Chain, Patrick S.G., additional, and Junier, Pilar, additional

Published
2019
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9. Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource

Author

Kelliher, Julia M., Xu, Yan, Flynn, Mark C., Babinski, Michal, Canon, Shane, Cavanna, Eric, Clum, Alicia, Corilo, Yuri E., Fujimoto, Grant, Giberson, Cameron, Johnson, Leah Y.D., Li, Kaitlyn J., Li, Po-E, Li, Valerie, Lo, Chien-Chi, Lynch, Wendi, Piehowski, Paul, Prime, Kaelan, Purvine, Samuel, Rodriguez, Francisca, Roux, Simon, Shakya, Migun, Smith, Montana, Sarrafan, Setareh, Cholia, Shreyas, McCue, Lee Ann, Mungall, Chris, Hu, Bin, Eloe-Fadrosh, Emiley A., and Chain, Patrick S.G.

Published
2024
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11. Whole-genome-based phylogeny and divergence of the genus Brucella

Author

Foster, Jeffrey T., Beckstrom-Sternberg, Stephen M., Pearson, Talima, Beckstrom-Sternberg, James S., Chain, Patrick S.G., Roberto, Francisco F., Hnath, Jonathan, Brettin, Tom, and Keim, Paul

Subjects
Phylogeny -- Research, Biological sciences
Abstract

Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species--Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis--using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen, Ochrobactrum anthropi. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the Brucella genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with Ochrobactrum anthropi reveals that the B. ovis lineage is basal to the rest of the Brucella lineage. We found that B. suis is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore, B. suis was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the B. canis genome was included. Using a molecular clock with these data suggests that most Brucella species diverged from their common B. ovis ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the Brucella phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.

Published
2009

14. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments

Author

Oda, Yasuhiro, Larimer, Frank W., Chain, Patrick S.G., Malfatti, Stephanie, Shin, Maria V., Vergez, Lisa M., Hauser, Loren, Land, Miriam L., Braatsch, Stephan, Beatty, J. Thomas, Pelletier, Dale A., Schaefer, Amy L., and Harwood, Caroline S.

Subjects
Bacteria, Photosynthetic -- Genetic aspects, Bacteria, Photosynthetic -- Physiological aspects, Bacteria, Photosynthetic -- Natural history, Genomes -- Properties, Adaptation (Physiology) -- Genetic aspects, Sediments (Geology) -- Influence, Science and technology
Abstract

The bacterial genus Rhodopseudomonas is comprised of photosynthetic bacteria found widely distributed in aquatic sediments. Members of the genus catalyze hydrogen gas production, carbon dioxide sequestration, and biomass turnover. The genome sequence of Rhodopseudomonas palustris CGA009 revealed a surprising richness of metabolic versatility that would seem to explain its ability to live in a heterogeneous environment like sediment. However, there is considerable genotypic diversity among Rhodopseudomonas isolates. Here we report the complete genome sequences of four additional members of the genus isolated from a restricted geographical area. The sequences confirm that the isolates belong to a coherent taxonomic unit, but they also have significant differences. Whole genome alignments show that the circular chromosomes of the isolates consist of a collinear backbone with a moderate number of genomic rearrangements that impact local gene order and orientation. There are 3,319 genes, 70% of the genes in each genome, shared by four or more strains. Between 10% and 18% of the genes in each genome are strain specific. Some of these genes suggest specialized physiological traits, which we verified experimentally, that include expanded light harvesting, oxygen respiration, and nitrogen fixation capabilities, as well as anaerobic fermentation. Strain-specific adaptations include traits that may be useful in bioenergy applications. This work suggests that against a backdrop of metabolic versatility that is a defining characteristic of Rhodopseudomonas, different ecotypes have evolved to take advantage of physical and chemical conditions in sediment microenvironments that are too small for human observation. alphaproteobacteria | ecotype | genomes | photosynthesis | rhodopseudomonas

Published
2008

15. Divergence among genes encoding the elongation factor Tu of Yersinia species

Author

Isabel, Sandra, Leblanc, Eric, Boissinot, Maurice, Boudreau, Dominique K., Grondin, Myrian, Picard, Francois J., Martel, Eric A., Parham, Nicholas J., Chain, Patrick S.G., Bader, Douglas E., Mulvey, Michael R., Bryden, Louis, Roy, Paul H., Ouellette, Marc, and Bergeron, Michel G.

Subjects
Genes -- Physiological aspects, Genes -- Research, Yersinia -- Genetic aspects, Yersinia -- Research, Bacterial proteins -- Physiological aspects, Bacterial proteins -- Research, Biological sciences
Abstract

Elongation factor Tu (EF-Tu), encoded by tufgenes, carries aminoacyl-tRNA to the ribosome during protein synthesis. Duplicated tufgenes (tufA and tufB), which are commonly found in enterobacterial species, usually coevolve via gene conversion and are very similar to one another. However, sequence analysis of tuf genes in our laboratory has revealed highly divergent copies in 72 strains spanning the genus Yersinia (representing 12 Yersinia species). The levels of intragenomic divergence between tufA and tufB sequences ranged from 8.3 to 16.2% for the genus Yersinia, which is significantly greater than the 0.0 to 3.6% divergence observed for other enterobacterial genera. We further explored tuf gene evolution in Yersinia and other Enterobacteriaceae by performing directed sequencing and phylogenetic analyses. Phylogenetic trees constructed using concatenated tufA and tufB sequences revealed a monophyletic genus Yersinia in the family Enterobacteriaceae. Moreover, Yersinia strains form clades within the genus that mostly correlate with their phenotypic and genetic classifications. These genetic analyses revealed an unusual divergence between Yersinia tufA and tufB sequences, a feature unique among sequenced Enterobacteriaceae and indicative of a genus-wide loss of gene conversion. Furthermore, they provided valuable phylogenetic information for possible reclassification and identification of Yersinia species.

Published
2008

16. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author

Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos, Lane, Christopher, Papke, R. Thane, Parks, Donovan, Rossello-Mora, Ramon, Stott, Matthew, Sutcliffe, Iain, Thrash, J. Cameron, Venter, Stephanus, Whitman, William, Acinas, Silvia, Amann, Rudolf, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett, Barco, Roman, Bode, Helge, Boyd, Eric, Brady, Carrie, Carini, Paul, Chain, Patrick, Colman, Daniel, DeAngelis, Kristen, de los Rios, Maria Asuncion, Estrada-De Los Santos, Paulina, Dunlap, Christopher, Eisen, Jonathan, Emerson, David, Ettema, Thijs, Girguis, Peter, Hentschel, Ute, Hollibaugh, James, Hug, Laura, Inskeep, William, Ivanova, Elena, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen, Löffler, Frank, Makhalanyane, Thulani, Moser, Duane, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander, Smits, Theo, Steen, Andrew, Steenkamp, Emma, Spang, Anja, Stewart, Frank, Tiedje, James, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Hedlund, Brian, Reysenbach, Anna-Louise, Murray, Alison, Avalon, Nicole, Bishop, Lucas, Davenport, Karen, Delage, Erwan, Dichosa, Armand E.K., Eveillard, Damien, Higham, Mary, Kokkaliari, Sofia, Lo, Chien-Chi, Riesenfeld, Christian, Young, Ryan, Chain, Patrick S.G., Baker, Bill, Metacohorts Consortium, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], University of Queensland [Brisbane], Justus-Liebig-Universität Gießen (JLU), Louisiana State University (LSU), Botanical and Environmental Consultant, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin [Austin], Buchmann Institute for Molecular Life Sciences [Frankfurt am Main] (BMLS), Goethe-Universität Frankfurt am Main, ISAO [Bologna, Italy], Universidad Nacional Autónoma de México (UNAM), Bigelow Laboratory for Ocean Sciences, Uppsala University, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Montana State University (MSU), Laboratoire de l'intégration, du matériau au système (IMS), Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China, Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley], University of California-University of California, Royal Netherlands Institute for Sea Research (NIOZ), The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Universiteit Gent [Ghent], Hochschule Aalen, Institut für Angewandte Forschung, Hochschule Aalen, Martin-Luther-University Halle-Wittenberg, Université de Nantes - Faculté des Sciences et des Techniques, and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques

Subjects
Range (biology), ascidian, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Antarctic Regions, microbiome, Pharmaceutical Science, Biology, Genome, Article, Polyketide, 03 medical and health sciences, RNA, Ribosomal, 16S, co-occurrence, Drug Discovery, Animals, Marine ecosystem, Urochordata, 14. Life underwater, Microbiome, palmerolide A, Gene, lcsh:QH301-705.5, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Islands, Whole genome sequencing, 0303 health sciences, geography, geography.geographical_feature_category, Phylum, 030306 microbiology, Microbiota, Bacterioplankton, 15. Life on land, 16S ribosomal RNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Holobiont, Taxon, lcsh:Biology (General), Evolutionary biology, microbial diversity, Archipelago, Antarctica, Macrolides, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64&deg, 46'S, 64&deg, 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3&ndash, V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)&mdash, 20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

Published
2020
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17. Correction: Roadmap for naming uncultivated Archaea and Bacteria

Author

Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R.T., Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J.C., Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen Jun, Lloyd, Karen G., Löffler, Frank E., Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma T., Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng Ping, Yarza, Pablo, Hedlund, Brian P., Reysenbach, Anna Louise, Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R.T., Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J.C., Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen Jun, Lloyd, Karen G., Löffler, Frank E., Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma T., Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng Ping, Yarza, Pablo, Hedlund, Brian P., and Reysenbach, Anna Louise

Published
2021

18. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1

Author

Kane, Staci R., Chakicherla, Anu Y., Chain, Patrick S.G., Schmidt, Radomir, Shin, Maria W., Legler, Tina C., Scow, Kate M., Larimer, Frank W., Lucas, Susan M., Richardson, Paul M., and Hristova, Krassimira R.

Subjects
Genomes -- Analysis, Plasmids -- Research, Insertion elements, DNA -- Research, Biological sciences
Abstract

Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain ([C.sub.5] to [C.sub.12]) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an ~4-Mb circular chromosome and an ~600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PMI's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (~99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

Published
2007

19. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria

Author

Arp, Daniel J., Chain, Patrick S.G., and Klotz, Martin G.

Subjects
Nucleotide sequence -- Analysis, Bacterial genetics -- Analysis, Biological sciences
Abstract

The article describes genome-scale analysis for understanding the ammonia-oxidizing bacteria (AOB). The genome sequences helps in knowing the ecology, evolution and environmental roles of these bacteria.

Published
2007

20. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

Author

Chain, Patrick S.G., Denef, Vincent J., Konstantinidis, Konstantinos T., Vergez, Lisa M., Agullo, Loreine, Reyes, Valeria Latorre, Hauser, Loren, Cordova, Macarena, Gomez, Luis, Gonzalez, Myriam, Landi, Miriam, Lao, Victoria, Larimer, Frank, LiPuma, John J., Mahenthiralingam, Eshwar, Malfatti, Stephanie A., Marx, Christopher J., Parnell, J. Jacob, Ramette, Alban, Richardson, Paul, Seeger, Michael, Smith, Daryl, Spilker, Theodore, Sul, Woo Jun, Tsoi, Tamara V., Ulrich, Luke E., Zhulin, Igor B., and Tiedje, James M.

Subjects
Polychlorinated biphenyls -- Structure, Bacterial genetics -- Research, Biodegradation -- Research, Science and technology
Abstract

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven 'central aromatic' and twenty 'peripheral aromatic' pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes. Genomics | niche adaptation | evolution | biodegradation | redundancy

Published
2006

21. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

Author

Starkenburg, Shawn R., Chain, Patrick S.G., Sayavedra-Soto, Luis A., Hauser, Loren, Land, Miriam L., Larimer, Frank W., Malfatti, Stephanie A., Klotz, Martin G., Bottomley, Peter J., Arp, Daniel J., and Hickey, William J.

Subjects
Bacteria, Nitrifying -- Genetic aspects, Autotrophs -- Genetic aspects, Nitrites -- Chemical properties, Biological sciences
Abstract

The genome sequencing and analysis of the alphaproteobacterium Nitrobacter winogradskyi revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. Approximately 10 percent of the Nitrobacter winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules.

Published
2006

22. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans

Author

Beller, Harry R., Chain, Patrick S.G., Letain, Tracy E., Chakicherla, Anu, Larimer, Frank W., Richardson, Paul M., Coleman, Matthew A., Wood, Ann P., and Kelly, Donovan P.

Subjects
Sulfur bacteria -- Genetic aspects, Nucleotide sequence -- Research, Bacterial genetics -- Research, Biological sciences
Abstract

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, [beta]-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by [beta]-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.

Published
2006

23. Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

Author

Murray, Alison E., primary, Lo, Chien-Chi, additional, Daligault, Hajnalka E., additional, Avalon, Nicole E., additional, Read, Robert W., additional, Davenport, Karen W., additional, Higham, Mary L., additional, Kunde, Yuliya, additional, Dichosa, Armand E.K., additional, Baker, Bill J., additional, and Chain, Patrick S.G., additional

Published
2021
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26. Genomics for Key Players in the N Cycle

Author

Chain, Patrick S.G., primary, Xie, Gary, additional, Starkenburg, Shawn R., additional, Scholz, Matthew B., additional, Beckloff, Nicholas, additional, Lo, Chien-Chi, additional, Davenport, Karen W., additional, Reitenga, Krista G., additional, Daligault, Hajnalka E., additional, Detter, J. Chris, additional, Freitas, Tracey A.K., additional, Gleasner, Cheryl D., additional, Green, Lance D., additional, Han, Cliff S., additional, McMurry, Kim K., additional, Meincke, Linda J., additional, Shen, Xiaohong, additional, and Zeytun, Ahmet, additional

Published
2011
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27. The genome sequence of Yersinia pestis bacteriophage [phi]A1122 reveals an intimate history with the coliphage T3 and T7 genomes

Author

Garcia, Emilio, Elliott, Jeffrey M., Ramanculov, Erlan, Chain, Patrick S.G., Chu, May C., and Molineux, Ian J.

Subjects
Plague -- Causes of, Yersinia pestis -- Genetic aspects, Genomes -- Genetic aspects, Bacteriophages -- Genetic aspects, Bacteriology -- Research, Biological sciences
Abstract

The genome sequence of bacteriophage [phi]A1122 has been determined. [phi]A1122 grows on almost all isolates of Yersinia pestis and is used by the Centers for Disease Control and Prevention as a diagnostic agent for the causative agent of plague. [phi]A1122 is very closely related to coliphage T7; the two genomes are colinear, and the genome-wide level of nucleotide identity is about 89%. However, a quarter of the [phi]A1122 genome, one that includes about half of the morphogenetic and maturation functions, is significantly more closely related to coliphage T3 than to T7. It is proposed that the yersiniophage [phi]A1122 recombined with a close relative of the Y. enterocolitica phage [phi]YeO3-12 to yield progeny phages, one of which became the classic T3 coliphage of Demerec and Fano (M. Demerec and U. Fano, Genetics 30:119-136, 1945).

Published
2003

28. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author

Murray, Alison E., primary, Avalon, Nicole E., additional, Bishop, Lucas, additional, Davenport, Karen W., additional, Delage, Erwan, additional, Dichosa, Armand E.K., additional, Eveillard, Damien, additional, Higham, Mary L., additional, Kokkaliari, Sofia, additional, Lo, Chien-Chi, additional, Riesenfeld, Christian S., additional, Young, Ryan M., additional, Chain, Patrick S.G., additional, and Baker, Bill J., additional

Published
2020
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29. PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection

Author

Li, Po-E, primary, Russell, Joseph A., additional, Yarmosh, David, additional, Shteyman, Alan G., additional, Parker, Kyle, additional, Wood, Hillary, additional, Aspinwall, J.R., additional, Winegar, Richard, additional, Davenport, Karen, additional, Lo, Chien-chi, additional, Bagnoli, John, additional, Davis, Phillip, additional, Jacobs, Jonathan L., additional, and Chain, Patrick S.G., additional

Published
2020
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30. Dissecting the microbiome of a polyketide-producing ascidian across the Anvers Island archipelago, Antarctica

Author

Murray, Alison E., Avalon, Nicole E., Bishop, Lucas, Chain, Patrick S.G., Davenport, Karen W., Delage, Erwan, Dichosa, Armand E.K., Eveillard, Damien, Higham, Mary L., Kokkaliari, Sofia, Lo, Chien-Chi, Riesenfeld, Christian S., Young, Ryan M., and Baker, Bill J.

Abstract

The ascidian, S. adareanum , from the Antarctic Peninsula near Anvers Island, is known to produce a bioactive compound, palmerolide A (PalA) that has specific activity to melanoma, a particularly invasive and metastatic form of skin cancer. The combined non-ribosomal peptide polyketide structure of PalA has similarities to microbially-produced macrolides which motivated this study utilizing culture-dependent and -independent investigations coupled with PalA detection to improve our understanding of the host-associated microbiome and relationship to PalA. Cultivation efforts yielded seven different bacteria, none of which produced PalA under the conditions tested. The genome sequence was mined for one of the most abundant members of the microbiome, Pseudovibrio sp. str. TunPSC04-5.I4, revealing eight biosynthetic gene clusters, none supporting the potential for PalA biosynthesis. PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island archipelago. These 63 samples were used to assess microbiome composition (V3-V4 16S rRNA gene sequence variants) which revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several subsystems that may interact functionally and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Sequence variant relative abundance and biosynthetic potential of related organisms pointed to a subset of the core membership as potential PalA producers which provides a gateway to identifying the producer of palmerolides in future work. IMPORTANCE Palmerolide A (PalA), has potential as a chemotherapeutic agent to target melanoma. Uniform, high levels of PalA were present across a regional survey of the PalA-producing Antarctic ascidian, Synoicum adareanum , based on multi-lobed colonies sampled in the Anvers Island archipelago. Likewise, we identified a core suite of microorganisms that occur concurrently with the PalA-containing ascidians which spanned four phyla with lineages representing both heterotrophic and chemoautotrophic (nitrifying) metabolisms and are distinct from the bacterioplankton. These represent leads for the PalA producer. Cultivation efforts yielded several isolates; however, none were found to produce PalA under laboratory growth conditions. One of these isolates was a member of the core microbiome of the PalA-producing S. adareanum , although the appropriate biosynthetic genes were not found in its genome. Recognition of the ascidian core microbiome informs downstream studies with a target population of potential PalA-producing microorganisms.

Published
2020
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33. Roadmap for naming uncultivated Archaea and Bacteria

Author

National Science Foundation (US), Agencia Estatal de Investigación (España), Murray, Alison, Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rosselló-Mora, Ramón, Stott, Matthew B., Sutcliffe, Iain, Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., Ríos, Asunción de los, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen-Jun, Lloyd, Karen G., Löffler, Frank, Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro-García, Víctor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma, Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Yarza, Pablo, Hedlund, Brian P., Reysenbach, A. L., National Science Foundation (US), Agencia Estatal de Investigación (España), Murray, Alison, Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rosselló-Mora, Ramón, Stott, Matthew B., Sutcliffe, Iain, Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., Ríos, Asunción de los, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen-Jun, Lloyd, Karen G., Löffler, Frank, Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro-García, Víctor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma, Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Yarza, Pablo, Hedlund, Brian P., and Reysenbach, A. L.

Abstract

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity

Published
2020

34. Roadmap for naming uncultivated Archaea and Bacteria

Author

Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R.T., Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J.C., Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen Jun, Lloyd, Karen G., Löffler, Frank E., Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma T., Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng Ping, Hedlund, Brian P., Reysenbach, Anna Louise, Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R.T., Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J.C., Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S.G., Colman, Daniel R., DeAngelis, Kristen M., de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A., Eisen, Jonathan A., Emerson, David, Ettema, Thijs J.G., Eveillard, Damien, Girguis, Peter R., Hentschel, Ute, Hollibaugh, James T., Hug, Laura A., Inskeep, William P., Ivanova, Elena P., Klenk, Hans Peter, Li, Wen Jun, Lloyd, Karen G., Löffler, Frank E., Makhalanyane, Thulani P., Moser, Duane P., Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J., Smits, Theo H.M., Steen, Andrew D., Steenkamp, Emma T., Spang, Anja, Stewart, Frank J., Tiedje, James M., Vandamme, Peter, Wagner, Michael, Wang, Feng Ping, Hedlund, Brian P., and Reysenbach, Anna Louise

Abstract

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

Published
2020

35. Uncovering the core microbiome and distributions of palmerolide inSynoicum adareanumacross the Anvers Island archipelago, Antarctica

Author

Murray, Alison, primary, Avalon, Nicole, additional, Bishop, Lucas, additional, Davenport, Karen W., additional, Delage, Erwan, additional, Dichosa, Armand E.K., additional, Eveillard, Damien, additional, Higham, Mary L., additional, Kokkaliari, Sofia, additional, Lo, Chien-Chi, additional, Riesenfeld, Christian S., additional, Young, Ryan M., additional, Chain, Patrick S.G., additional, and Baker, Bill J., additional

Published
2020
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36. Consent insufficient for data release−Response

Author

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., Xenarios, Ioannis, Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis

Published
2019

37. Data access: Toward unrestricted use of public genomic data

Author

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, De Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., Xenarios, Ioannis, Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, De Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis

Published
2019

38. Adaptive strategies in a poly-extreme environment: differentiation of vegetative cells in Serratia ureilytica and resistance to extreme conditions

Author

Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Kooli, Wafa M., Palmieri, Ilona, Al-Dourobi, Andrej, Molina, Veronica, Lienhard, Reto, Spangenberg, Jorge E., Johnson, Shannon L., Chain, Patrick S.G., Dorador, Cristina, Junier, Pilar, Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Kooli, Wafa M., Palmieri, Ilona, Al-Dourobi, Andrej, Molina, Veronica, Lienhard, Reto, Spangenberg, Jorge E., Johnson, Shannon L., Chain, Patrick S.G., Dorador, Cristina, and Junier, Pilar

Abstract

Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime example of such a survival strategy is the modification of vegetative cells into resistant resting structures. These differentiated cells are often observed in response to harsh environmental conditions. The environmental strain (strain Lr5/4) belonging to Serratia ureilytica was isolated from a geothermal spring in Lirima, Atacama Desert, Chile. The Atacama Desert is the driest habitat on Earth and furthermore, due to its high altitude, it is exposed to an increased amount of UV radiation. The geothermal spring from which the strain was isolated is oligotrophic and the temperature of 54∘C exceeds mesophilic conditions (15 to 45∘C). Although the vegetative cells were tolerant to various environmental insults (desiccation, extreme pH, glycerol), a modified cell type was formed in response to nutrient deprivation, UV radiation and thermal shock. Scanning (SEM) and Transmission Electron Microscopy (TEM) analyses of vegetative cells and the modified cell structures were performed. In SEM, a change toward a circular shape with reduced size was observed. These circular cells possessed what appears as extra coating layers under TEM. The resistance of the modified cells was also investigated, they were resistant to wet heat, UV radiation and desiccation, while vegetative cells did not withstand any of those conditions. A phylogenomic analysis was undertaken to investigate the presence of known genes involved in dormancy in other bacterial clades. Genes related to spore-formation in Myxococcus and Firmicutes were found in S. ureilytica Lr5/4 genome; however, these genes were not enough for a full sporulation pathway that resembles ei

Published
2019

39. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from soil environment

Author

Norton, Jeanette M., Klotz, Martin G., Stein, Lisa Y., Arp, Daniel J., Bottomley, Peter J., Chain, Patrick S.G., Hauser, Loren J., Land, Miriam L., Larimer, Frank W., Shin, Maria W., and Starkenburg, Shawn R.

Subjects
Genomics -- Analysis, Glycogen -- Chemical properties, Nitrification -- Analysis, Bacteria, Nitrifying -- Genetic aspects, Bacteria, Nitrifying -- Environmental aspects, Biological sciences
Abstract

A study was conducted to identify gene clusters of glycogen, polyphosphate, and cyanophycin storage and utilization which are responsible for mechanisms to meet energy requirements under substrate-limited conditions. The results obtained revealed that the genome of Nitrosomonas multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

Published
2008

40. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter

Author

Starkenburg, Shawn R., Larimer, Frank W., Stein, Lisa Y., Klotz, Martin G., Chain, Patrick S.G., Sayavedra-Soto, Luis A., Poret-Peterson, Amisha T., Gentry, Mira E., Arp, Daniel J., Ward, Bess, and Bottomley, Peter J.

Subjects
DNA replication -- Analysis, Nitrites -- Chemical properties, Bacteria, Nitrifying -- Genetic aspects, Bacteria, Nitrifying -- Environmental aspects, Oxidation-reduction reaction -- Analysis, Biological sciences
Abstract

Sequencing and analysis of the Nitrobacter hamburgensis X14 genome has shown four replicons comprised of one chromosome and three plasmids. Many of the subcore genes have diverged from the alphaproteobacterial lineage and have shown some of the unique genetic requirements for nitrite oxidation in Nitrobacter.

Published
2008

41. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans

Author

Sievert, Stefan M., Scott, Kathleen M., Klotz, Martin G., Chain, Patrick S.G., Hauser, Loren J., Hemp, James, Hugler, Michael, Land, Miriam, Lapidus, Alla, Larimer, Frank W., Lucas, Susan, Malfatti, Stephanie A., Meyer, Folker, Paulsen, Ian T., Qinghu Ren, and Simon, Jorg

Subjects
Bacterial genetics -- Research, Oxidation-reduction reaction -- Analysis, Sulfur bacteria -- Genetic aspects, Sulfur bacteria -- Environmental aspects, Biological sciences
Abstract

The genome of Sulfurimonas denitrificans DSM1251 is sequenced in order to understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, particularly those of the widespread genus Sulfurimonas. Many resistance-nodulation-development family transporter genes are described and several are predicted to encode heavy metal efflux transporters.

Published
2008

42. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707

Author

Ward, Bess B., Klotz, Martin G., Arp, Daniel J., Chain, Patrick S.G., El-Sheikh, Amal F., Hauser, Loren J., Hommes, Norman G., Larimer, Frank W., Malfatti, Stephanie A., Norton, Jeanette M., Poret-Peterson, Amisha T., and Vergez, Lisa M.

Subjects
Nucleotide sequence -- Research, Bacterial genetics -- Research, Phosphates -- Research, Biological sciences
Abstract

Nitrosococcus oceani (ATCC 19707) is one of only two known ammonia-oxidizing bacteria classified as Gammaproteobacteria, while the large majority of isolated ammonia-oxidizing bacteria are classified as Betaproteobacteria. The N. oceani genome contains genes for 13 complete two-component systems, all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Emblem-Mcycrhof-Parnass and pentose phosphate pathways.

Published
2006

44. Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258Klebsiella pneumoniaeStrains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones

Author

Ramirez, María Soledad, primary, Xie, Gang, additional, Traglia, German M., additional, Johnson, Shannon L., additional, Davenport, Karen W., additional, van Duin, David, additional, Ramazani, Azam, additional, Perez, Federico, additional, Jacobs, Michael R., additional, Sherratt, David J., additional, Bonomo, Robert A., additional, Chain, Patrick S.G., additional, and Tolmasky, Marcelo E., additional

Published
2016
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47. Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Swan, Brandon K., Chaffin, Mark D., Martinez-Garcia, Manuel, Morrison, Hilary G., Field, Erin K., Poulton, Nicole J., Masland, E. Dashiell P., Harris, Christopher C., Sczyrba, Alexander, Chain, Patrick S.G., Koren, Sergey, Woyke, Tanja, Stepanauskas, Ramunas, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Swan, Brandon K., Chaffin, Mark D., Martinez-Garcia, Manuel, Morrison, Hilary G., Field, Erin K., Poulton, Nicole J., Masland, E. Dashiell P., Harris, Christopher C., Sczyrba, Alexander, Chain, Patrick S.G., Koren, Sergey, Woyke, Tanja, and Stepanauskas, Ramunas

Abstract

Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.

Published
2014

48. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Martinez-Garcia, Manuel, Brazel, David M., Swan, Brandon K., Arnosti, Carol, Chain, Patrick S.G., Reitenga, Krista G., Xie, Gary, Poulton, Nicole J., Lluesma Gómez, Mónica, Masland, Dashiell E.D., Thompson, Brian, Bellows, Wendy K., Ziervogel, Kai, Lo, Chien-Chi, Ahmed, Sanaa, Gleasner, Cheryl D., Detter, Chris J., Stepanauskas, Ramunas, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Martinez-Garcia, Manuel, Brazel, David M., Swan, Brandon K., Arnosti, Carol, Chain, Patrick S.G., Reitenga, Krista G., Xie, Gary, Poulton, Nicole J., Lluesma Gómez, Mónica, Masland, Dashiell E.D., Thompson, Brian, Bellows, Wendy K., Ziervogel, Kai, Lo, Chien-Chi, Ahmed, Sanaa, Gleasner, Cheryl D., Detter, Chris J., and Stepanauskas, Ramunas

Abstract

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.

Published
2012

49. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Author

Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien Bonazzi, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi, Chain, Patrick S.G., Charlson, Emily, Costello, Elizabeth K., Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A., Gallery, Rachel E., Gevers, Dirk, Gibbs, Richard A., Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I., Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L., Kelley, Scott T., Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L., Legg, Teresa, Ley, Ruth E., Lozupone, Catherine A., Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A., Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E., Nemergut, Diana, Neufeld, Josh D., Newbold, Lindsay K., Oliver, Anna E., Pace, Norman R., Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A., Assunta-Sansone, Susanna, Schloss, Patrick D., Schriml, Lynn, Sinha, Rohini, Smith, Michelle I., Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M., Ward, Doyle V., Weinstock, George M., Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R., Yatsunenko, Tanya, Glöckner, Frank Oliver, Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien Bonazzi, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi, Chain, Patrick S.G., Charlson, Emily, Costello, Elizabeth K., Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A., Gallery, Rachel E., Gevers, Dirk, Gibbs, Richard A., Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I., Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L., Kelley, Scott T., Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L., Legg, Teresa, Ley, Ruth E., Lozupone, Catherine A., Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A., Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E., Nemergut, Diana, Neufeld, Josh D., Newbold, Lindsay K., Oliver, Anna E., Pace, Norman R., Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A., Assunta-Sansone, Susanna, Schloss, Patrick D., Schriml, Lynn, Sinha, Rohini, Smith, Michelle I., Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M., Ward, Doyle V., Weinstock, George M., Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R., Yatsunenko, Tanya, and Glöckner, Frank Oliver

Abstract

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2011

50. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names ‘Nitrosococcus halophilus’ and ‘Nitrosomonas mobilis’

Author

Campbell, Mark A., primary, Chain, Patrick S.G., additional, Dang, Hongyue, additional, El Sheikh, Amal F., additional, Norton, Jeanette M., additional, Ward, Naomi L., additional, Ward, Bess B., additional, and Klotz, Martin G., additional

Published
2011
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