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231 results on '"Murray Alison E"'

1. Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery

Author

Avalon, Nicole E, Murray, Alison E, and Baker, Bill J

Subjects
Analytical Chemistry, Chemical Sciences, Genetics, Complementary and Integrative Health, Biotechnology, Human Genome, Generic health relevance, Biological Products, Drug Discovery, Genomics, Metabolomics, Workflow, Other Chemical Sciences, Medical biochemistry and metabolomics, Analytical chemistry, Chemical engineering
Abstract

The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.

Published
2022

2. Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

Author

Murray, Alison E, Lo, Chien-Chi, Daligault, Hajnalka E, Avalon, Nicole E, Read, Robert W, Davenport, Karen W, Higham, Mary L, Kunde, Yuliya, Dichosa, Armand EK, Baker, Bill J, and Chain, Patrick SG

Subjects
Microbiology, Biological Sciences, Biotechnology, Genetics, Human Genome, Animals, Antarctic Regions, Macrolides, Microbiota, Multigene Family, Phylogeny, RNA, Ribosomal, 16S, Urochordata, Verrucomicrobia, Antarctic, Synoicihabitans palmerolidicus, Synoicum adareanum, anticancer, ascidian natural product, biosynthetic gene cluster, microbiome metagenome, palmerolide, secondary metabolite
Abstract

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as "Candidatus Synoicihabitans palmerolidicus." The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium. IMPORTANCE Palmerolide A has potential as a chemotherapeutic agent to target melanoma. We interrogated the microbiome of the Antarctic ascidian, Synoicum adareanum, using a cultivation-independent high-throughput sequencing and bioinformatic strategy. The metagenome-encoded biosynthetic machinery predicted to produce palmerolide A was found to be associated with the genome of a member of the S. adareanum core microbiome. Phylogenomic analysis suggests the organism represents a new deeply branching genus, "Candidatus Synoicihabitans palmerolidicus," in the Opitutaceae family of the Verrucomicrobia phylum. The Ca. Synoicihabitans palmerolidicus 4.29-Mb genome encodes a repertoire of carbohydrate-utilizing and transport pathways, a chemotaxis system, flagellar biosynthetic capacity, and other regulatory elements enabling its ascidian-associated lifestyle. The palmerolide producer's genome also contains five distinct copies of the large palmerolide biosynthetic gene cluster that may provide structural complexity of palmerolide variants.

Published
2021

3. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1

Author

Gralnick Jeffrey A, Rodrigues Jorge LM, Murray Alison E, Cruz-García Claribel, McCue Lee, Romine Margaret F, Löffler Frank E, and Tiedje James M

Subjects
Microbiology, QR1-502
Abstract

Abstract Background EtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Results The expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down-regulated at least 2-fold in the mutant, which, showed lower or no reduction of these electron acceptors when compared to the wild type, suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down-regulation of genes implicated in aerobic metabolism. Conclusion In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and, in conjunction with other regulators, fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1. Transcriptomic and sequence analyses of the genes differentially expressed showed that those mostly affected by the mutation belonged to the "Energy metabolism" category, while stress-related genes were indirectly regulated in the mutant possibly as a result of a secondary perturbation (e.g. oxidative stress, starvation). We also conclude based on sequence, physiological and expression analyses that this regulator is more appropriately termed Fnr and recommend this descriptor be used in future publications.

Published
2011
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5. 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 Thane, Parks, Donovan H, Rossello-Mora, Ramon, Stott, Matthew B, Sutcliffe, Iain C, Thrash, J Cameron, 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 SG, 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 JG, 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 HM, 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

Subjects
Microbiology, Biological Sciences, Ecology, Archaea, Bacteria, DNA, Bacterial, Metagenome, Phylogeny, Prokaryotic Cells, Sequence Analysis, DNA, Terminology as Topic, Medical Microbiology
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

7. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Author

Sevim, Volkan, Lee, Juna, Egan, Robert, Clum, Alicia, Hundley, Hope, Lee, Janey, Everroad, R Craig, Detweiler, Angela M, Bebout, Brad M, Pett-Ridge, Jennifer, Göker, Markus, Murray, Alison E, Lindemann, Stephen R, Klenk, Hans-Peter, O'Malley, Ronan, Zane, Matthew, Cheng, Jan-Fang, Copeland, Alex, Daum, Christopher, Singer, Esther, and Woyke, Tanja

Subjects
Biotechnology
Abstract

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.

Published
2019

8. A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle

Author

Barret, Maialen, Gandois, Laure, Thalasso, Frederic, Martinez Cruz, Karla, Sepulveda Jauregui, Armando, Lavergne, Céline, Teisserenc, Roman, Aguilar, Polette, Gerardo Nieto, Oscar, Etchebehere, Claudia, Martins Dellagnezze, Bruna, Bovio Winkler, Patricia, Fochesatto, Gilberto J., Tananaev, Nikita, Svenning, Mette M., Seppey, Christophe, Tveit, Alexander, Chamy, Rolando, Astorga España, María Soledad, Mansilla, Andrés, Van de Putte, Anton, Sweetlove, Maxime, Murray, Alison E., and Cabrol, Léa

Published
2022
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12. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensisMR-1

Author

Cruz-García, Claribel, Murray, Alison E, Rodrigues, Jorge LM, Gralnick, Jeffrey A, McCue, Lee Ann, Romine, Margaret F, Löffler, Frank E, and Tiedje, James M

Subjects
Microbiology, Biological Sciences, Genetics, Anaerobiosis, Bacterial Proteins, Energy Metabolism, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Metabolic Networks and Pathways, Nitrates, Sequence Analysis, DNA, Shewanella, Transcription Factors, Agricultural and Veterinary Sciences, Medical and Health Sciences, Medical microbiology
Abstract

BackgroundEtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood.ResultsThe expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down-regulated at least 2-fold in the mutant, which, showed lower or no reduction of these electron acceptors when compared to the wild type, suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down-regulation of genes implicated in aerobic metabolism.ConclusionIn contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and, in conjunction with other regulators, fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1. Transcriptomic and sequence analyses of the genes differentially expressed showed that those mostly affected by the mutation belonged to the "Energy metabolism" category, while stress-related genes were indirectly regulated in the mutant possibly as a result of a secondary perturbation (e.g. oxidative stress, starvation). We also conclude based on sequence, physiological and expression analyses that this regulator is more appropriately termed Fnr and recommend this descriptor be used in future publications.

Published
2011

13. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

Author

Cruz-García, Claribel, Murray, Alison E, Rodrigues, Jorge LM, Gralnick, Jeffrey A, McCue, Lee Ann, Romine, Margaret F, Löffler, Frank E, and Tiedje, James M

Subjects
Shewanella, Nitrates, Bacterial Proteins, Transcription Factors, Gene Expression Profiling, Sequence Analysis, DNA, Gene Expression Regulation, Bacterial, Gene Deletion, Anaerobiosis, Energy Metabolism, Metabolic Networks and Pathways, Sequence Analysis, DNA, Gene Expression Regulation, Bacterial, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract

BackgroundEtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood.ResultsThe expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down-regulated at least 2-fold in the mutant, which, showed lower or no reduction of these electron acceptors when compared to the wild type, suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down-regulation of genes implicated in aerobic metabolism.ConclusionIn contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and, in conjunction with other regulators, fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1. Transcriptomic and sequence analyses of the genes differentially expressed showed that those mostly affected by the mutation belonged to the "Energy metabolism" category, while stress-related genes were indirectly regulated in the mutant possibly as a result of a secondary perturbation (e.g. oxidative stress, starvation). We also conclude based on sequence, physiological and expression analyses that this regulator is more appropriately termed Fnr and recommend this descriptor be used in future publications.

Published
2011

14. Iron cycling in the anoxic cryo-ecosystem of Antarctic Lake Vida

Author

Proemse, Bernadette C., Murray, Alison E., Schallenberg, Christina, McKiernan, Breege, Glazer, Brian T., Young, Seth A., Ostrom, Nathaniel E., Bowie, Andrew R., Wieser, Michael E., Kenig, Fabien, Doran, Peter T., and Edwards, Ross

Published
2017

18. Planetary oceanography: leveraging expertise among earth and planetary science

Author

German, Christopher R., Arrigo, Kevin R., Murray, Alison E., Rhoden, Alyssa, German, Christopher R., Arrigo, Kevin R., Murray, Alison E., and Rhoden, Alyssa

Abstract

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in German, C., Institution, W., Arrigo, K., Murray, A., & Rhoden, A. Planetary oceanography: leveraging expertise among earth and planetary science. Oceanography. 35(1), (2022): 10-15, https://doi.org/10.5670/oceanog.2021.410., The study of planetary oceanography is a new and exciting field of research. While humanity’s formal scientific studies of Earth’s ocean began nearly 150 years ago with the launch of the Challenger Expedition (Thomson et al., 1873), the study of oceans beyond Earth commenced only in this millennium. The first confirmation of an extensive saltwater ocean anywhere beyond Earth came relatively late within the lifetime of NASA’s Galileo mission (1989–2003; Kivelson et al., 2000), but continuing exploration has now revealed compelling evidence for large-volume watery oceans on five ice-covered moons of our outer solar system (Figure 1), with as many as 10–20 candidate moons and dwarf planets also under consideration (Hendrix et al., 2019). Of the five confirmed ocean worlds (Jupiter’s moons Europa, Callisto, and Ganymede; Saturn’s moons Enceladus and Titan), three have oceans so deep that a high-pressure form of ice develops deep within the ocean, beneath the liquid water but overlying any rocky interior (Nimmo and Papallardo, 2016). As a consequence, the watery ocean is trapped within an “ice sandwich.” By contrast, the other two confirmed ocean worlds (Europa and Enceladus) have oceans that are in direct contact with a rocky interior., This work was funded through support of NASA Awards 80NSSC19K1427 to CG, 80NSSC20K1258 to KRA, 80NSSC19K0920 to AEM, and 80NSSC19K0919 to ARR.

Published
2023

19. Author 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. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, 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
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20. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Author

Whitman, William B., primary, Chuvochina, Maria, additional, Hedlund, Brian P., additional, Hugenholtz, Philip, additional, Konstantinidis, Konstantinos T., additional, Murray, Alison E., additional, Palmer, Marike, additional, Parks, Donovan H., additional, Probst, Alexander J., additional, Reysenbach, Anna-Louise, additional, Rodriguez-R, Luis M., additional, Rossello-Mora, Ramon, additional, Sutcliffe, Iain, additional, and Venter, Stephanus N., additional

Published
2022
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21. Microbial life at — 13 °C in the brine of an ice-sealed Antarctic lake

Author

Murray, Alison E., Kenig, Fabien, Fritsen, Christian H., McKay, Christopher P., Cawley, Kaelin M., Edwards, Ross, Kuhn, Emanuele, McKnight, Diane M., Ostrom, Nathaniel E., Peng, Vivian, Ponce, Adrian, Priscu, John C., Samarkin, Vladimir, Townsend, Ashley T., Wagh, Protima, Young, Seth A., Yung, Pung To, and Doran, Peter T.

Published
2012

25. Science goals and mission architecture of the Europa Lander mission concept

Author

Hand, Kevin P., Phillips, Cynthia B., Murray, Alison E., Garvin, James B., Maize, Earl H., Gibbs, Roger G., Reeves, Glenn, San Martin, A. Miguel, Tan-Wang, Grace H., Krajewski, Joel, Hurst, Kenneth, Crum, Ray, Kennedy, Brett A., McElrath, Timothy P., Gallon, John C., Sabahi, Dara, Thurman, Sam W., Goldstein, Barry, Estabrook, Polly, Lee, Steven W., Dooley, Jennifer A., Brinckerhoff, William B., Edgett, Kenneth S., German, Christopher R., Hoehler, Tori M., Hörst, Sarah M., Lunine, Jonathan I., Paranicas, Christopher, Nealson, Kenneth H., Smith, David E., Templeton, Alexis S., Russell, Michael J., Schmidt, Britney E., Christner, Brent C., Ehlmann, Bethany L., Hayes, Alexander, Rhoden, Alyssa, Willis, Peter, Yingst, R. Aileen, Craft, Kate, Cameron, Marissa E., Nordheim, Tom A., Pitesky, Jo, Scully, Jennifer, Hofgartner, Jason D., Sell, Steve W., Barltrop, Kevin J., Izraelevitz, Jacob, Brandon, Erik J., Seong, J., Jones, John-Paul, Pasalic, Jasmina, Billings, Keith J., Ruiz, John Paul, Bugga, Ratnakumar V., Graham, Dan, Arenas, L. A., Takeyama, Deidre, Drummond, Mai, Aghazarian, Hrand, Andersen, Allen J., Andersen, Kayla B., Anderson, E. W., Babuscia, Alessandra, Backes, Paul G., Bailey, Elizabeth S., Balentine, Daniel, Ballard, Christopher G., Berisford, Daniel F., Bhandari, Pradeep, Blackwood, Krys, Bolotin, Gary S., Bovre, Emilee A., Bowkett, Joseph, Boykins, Kobie T., Bramble, Michael S., Brice, Timothy M., Briggs, Paul, Brinkman, Alexander P., Brooks, Shawn M., Buffington, Brent B., Burns, Brandon, Cable, Morgan L., Campagnola,Stefano, Cangahuala, Laureano A., Carr, Gregory A., Casani, John R., Chahat, Nacer E., Chamberlain-Simon, Brendan K., Cheng, Yun-Ting, Chien, Steve A., Cook, B. T., Cooper, Moogega, Dinicola, Michael, Clement, Brian G., Dean, Zachary S., Cullimore, Emily A., Curtis, Aaron G., de la Croix, Jean-Pierre, Di Pasquale, Peter, Dodd, Emma M., Dubord, Luke A., Edlund, Jeffrey A., Ellyin, Raymond, Emanuel, Blair, Foster, Jeffrey T., Ganino, Anthony J., Garner, Gregory J., Gibson, Matt T., Gildner, Matt, Glazebrook, Kenneth J., Greco, Martin E., Green, W. M., Hatch, Sara J., Hetzel, Mark M., Hoey, William A., Hofmann, Amy E., Ionasescu, Rodica, Jain, Abhinandan, Jasper, Jay D., Johannesen, Jennie R., Johnson, Glenn K., Jun, Insoo, Katake, Anup B., Kim-Castet, So Young, Kim, David Inkyu, Kim, Wousik, Klonicki, Emily F., Kobeissi, Brad, Kobie, Bryan D., Kochocki, Joseph, Kokorowski, Michael, Kosberg, Jacob A., Kriechbaum, Kristopher, Kulkarni, Tejas P., Lam, Rebekah L., Landau, Damon F., Lattimore, Myra A., Laubach, Sharon L., Lawler, Christopher R., Lim, Grace, Li, Jui-Lin, Litwin, Todd E., Lo, Martin W., Logan, Cambria A., Maghasoudi, Elham, Mandrake, Lukas, Marchetti, Yuliya, Marteau, Eloise, Maxwell, Kimberly A., McNamee, John B., McIntyre, Ocean, Meacham, Michael, Melko, Joseph P., Mueller, Juergen, Muliere, David, Mysore, Aprameya, Nash, Jeremy, Ono, Masahiro, Parker, Jay M., Perkins, Rebecca C., Petropoulos, Anastassios E., Gaut, Aaron, Piette Gomez, Marie Y., Casillas, Raul Polit, Preudhomme, Michael, Pyrzak, Guy, Rapinchuk, Jacqueline, Ratliff, John Martin, Ray, T. L., Roberts, Eric T., Roffo, Kenneth, Roth, Duane C., Russino, Joseph A., Schmidt, Tyler M., Schoppers, Marcel J., Senent, Juan S., Serricchio, Fred, Sheldon, Douglas J., Shiraishi, Lori R., Shirvanian, James, Siegel, Katherine J., Singh, Gurjeet, Sirota, Allen R., Skulsky, Eli D., Stehly, Joseph S., Strange, Nathan J., Stevens, Sarah U., Sunada, Eric T., Tepsuporn, Scott P., Tosi, Luis Phillipe C., Trawny, Nikolas, Uchenik, Igor, Verma, Vandi, Volpe, Richard A., Wagner, Caleb T., Wang, D., Willson, Reg G., Wolff, John Luke, Wong, A. T., Zimmer, Aline K., Sukhatme, Kalyani G., Bago, Kevin A., Chen, Yang, Deardorff, Alyssa M., Kuch, Roger S., Lim, Christopher, Syvertson, Marguerite L., Arakaki, Genji A., Avila, Art, DeBruin, Kevin J., Frick, Andreas, Harris, Joby R., Heverly, Matthew C., Kawata, Jessie M., Kim‬, Sung-Kyun, Kipp, Devin M., Murphy, Juliana, Smith, Matthew W., Spaulding, Matthew D., Thakker, Rohan, Warner, Noah Z., Yahnker, Chris R., Young, M. E., Magner, Tom, Adams, Danica, Bedini, Peter, Mehr, Lauren, Sheldon, Colin, Vernon, Steven, Bailey, Vince, Briere, Marc, Butler, Michael, Davis, Amanda, Ensor, Susan, Gannon, Michele, Haapala-Chalk, Amanda, Hartka, Ted, Holdridge, Mark, Hong, Albert, Hunt, J., Iskow, Joe, Kahler, Faith, Murray, Kimberly, Napolillo, David, Norkus, Michael, Pfisterer, Rick, Porter, Jamie, Roth, David, Schwartz, Paul, Wolfarth, Lawrence, Cardiff, Eric, Davis, Anita, Grob, Eric W., Adam, Jason R., Betts, Erin, Norwood, Jason, Heller, M. M., Voskuilen, Tyler, Sakievich, Philip, Gray, L., Hansen, D. J., Irick, Kevin W., Hewson, John C., Lamb, Joshua, Stacy, S. C., Brotherton, Chris M., Tappan, Alexander S., Benally, Darryl, Thigpen, Hannah, Ortiz, Erick, Sandoval, Dan, Ison, Aaron M., Warren, M., Stromberg, Peter G., Thelen, Paul Mark, Blasy, B., Nandy, Prabal, Haddad, Alexandria W., Trujillo, Lynna B., Wiseley, T. H., Bell, S. A., Teske, Nicholas P., Post, C., Torres-Castro, Loraine, Grosso, Chris, Wasiolek, Maryla, Hand, Kevin P., Phillips, Cynthia B., Murray, Alison E., Garvin, James B., Maize, Earl H., Gibbs, Roger G., Reeves, Glenn, San Martin, A. Miguel, Tan-Wang, Grace H., Krajewski, Joel, Hurst, Kenneth, Crum, Ray, Kennedy, Brett A., McElrath, Timothy P., Gallon, John C., Sabahi, Dara, Thurman, Sam W., Goldstein, Barry, Estabrook, Polly, Lee, Steven W., Dooley, Jennifer A., Brinckerhoff, William B., Edgett, Kenneth S., German, Christopher R., Hoehler, Tori M., Hörst, Sarah M., Lunine, Jonathan I., Paranicas, Christopher, Nealson, Kenneth H., Smith, David E., Templeton, Alexis S., Russell, Michael J., Schmidt, Britney E., Christner, Brent C., Ehlmann, Bethany L., Hayes, Alexander, Rhoden, Alyssa, Willis, Peter, Yingst, R. Aileen, Craft, Kate, Cameron, Marissa E., Nordheim, Tom A., Pitesky, Jo, Scully, Jennifer, Hofgartner, Jason D., Sell, Steve W., Barltrop, Kevin J., Izraelevitz, Jacob, Brandon, Erik J., Seong, J., Jones, John-Paul, Pasalic, Jasmina, Billings, Keith J., Ruiz, John Paul, Bugga, Ratnakumar V., Graham, Dan, Arenas, L. A., Takeyama, Deidre, Drummond, Mai, Aghazarian, Hrand, Andersen, Allen J., Andersen, Kayla B., Anderson, E. W., Babuscia, Alessandra, Backes, Paul G., Bailey, Elizabeth S., Balentine, Daniel, Ballard, Christopher G., Berisford, Daniel F., Bhandari, Pradeep, Blackwood, Krys, Bolotin, Gary S., Bovre, Emilee A., Bowkett, Joseph, Boykins, Kobie T., Bramble, Michael S., Brice, Timothy M., Briggs, Paul, Brinkman, Alexander P., Brooks, Shawn M., Buffington, Brent B., Burns, Brandon, Cable, Morgan L., Campagnola,Stefano, Cangahuala, Laureano A., Carr, Gregory A., Casani, John R., Chahat, Nacer E., Chamberlain-Simon, Brendan K., Cheng, Yun-Ting, Chien, Steve A., Cook, B. T., Cooper, Moogega, Dinicola, Michael, Clement, Brian G., Dean, Zachary S., Cullimore, Emily A., Curtis, Aaron G., de la Croix, Jean-Pierre, Di Pasquale, Peter, Dodd, Emma M., Dubord, Luke A., Edlund, Jeffrey A., Ellyin, Raymond, Emanuel, Blair, Foster, Jeffrey T., Ganino, Anthony J., Garner, Gregory J., Gibson, Matt T., Gildner, Matt, Glazebrook, Kenneth J., Greco, Martin E., Green, W. M., Hatch, Sara J., Hetzel, Mark M., Hoey, William A., Hofmann, Amy E., Ionasescu, Rodica, Jain, Abhinandan, Jasper, Jay D., Johannesen, Jennie R., Johnson, Glenn K., Jun, Insoo, Katake, Anup B., Kim-Castet, So Young, Kim, David Inkyu, Kim, Wousik, Klonicki, Emily F., Kobeissi, Brad, Kobie, Bryan D., Kochocki, Joseph, Kokorowski, Michael, Kosberg, Jacob A., Kriechbaum, Kristopher, Kulkarni, Tejas P., Lam, Rebekah L., Landau, Damon F., Lattimore, Myra A., Laubach, Sharon L., Lawler, Christopher R., Lim, Grace, Li, Jui-Lin, Litwin, Todd E., Lo, Martin W., Logan, Cambria A., Maghasoudi, Elham, Mandrake, Lukas, Marchetti, Yuliya, Marteau, Eloise, Maxwell, Kimberly A., McNamee, John B., McIntyre, Ocean, Meacham, Michael, Melko, Joseph P., Mueller, Juergen, Muliere, David, Mysore, Aprameya, Nash, Jeremy, Ono, Masahiro, Parker, Jay M., Perkins, Rebecca C., Petropoulos, Anastassios E., Gaut, Aaron, Piette Gomez, Marie Y., Casillas, Raul Polit, Preudhomme, Michael, Pyrzak, Guy, Rapinchuk, Jacqueline, Ratliff, John Martin, Ray, T. L., Roberts, Eric T., Roffo, Kenneth, Roth, Duane C., Russino, Joseph A., Schmidt, Tyler M., Schoppers, Marcel J., Senent, Juan S., Serricchio, Fred, Sheldon, Douglas J., Shiraishi, Lori R., Shirvanian, James, Siegel, Katherine J., Singh, Gurjeet, Sirota, Allen R., Skulsky, Eli D., Stehly, Joseph S., Strange, Nathan J., Stevens, Sarah U., Sunada, Eric T., Tepsuporn, Scott P., Tosi, Luis Phillipe C., Trawny, Nikolas, Uchenik, Igor, Verma, Vandi, Volpe, Richard A., Wagner, Caleb T., Wang, D., Willson, Reg G., Wolff, John Luke, Wong, A. T., Zimmer, Aline K., Sukhatme, Kalyani G., Bago, Kevin A., Chen, Yang, Deardorff, Alyssa M., Kuch, Roger S., Lim, Christopher, Syvertson, Marguerite L., Arakaki, Genji A., Avila, Art, DeBruin, Kevin J., Frick, Andreas, Harris, Joby R., Heverly, Matthew C., Kawata, Jessie M., Kim‬, Sung-Kyun, Kipp, Devin M., Murphy, Juliana, Smith, Matthew W., Spaulding, Matthew D., Thakker, Rohan, Warner, Noah Z., Yahnker, Chris R., Young, M. E., Magner, Tom, Adams, Danica, Bedini, Peter, Mehr, Lauren, Sheldon, Colin, Vernon, Steven, Bailey, Vince, Briere, Marc, Butler, Michael, Davis, Amanda, Ensor, Susan, Gannon, Michele, Haapala-Chalk, Amanda, Hartka, Ted, Holdridge, Mark, Hong, Albert, Hunt, J., Iskow, Joe, Kahler, Faith, Murray, Kimberly, Napolillo, David, Norkus, Michael, Pfisterer, Rick, Porter, Jamie, Roth, David, Schwartz, Paul, Wolfarth, Lawrence, Cardiff, Eric, Davis, Anita, Grob, Eric W., Adam, Jason R., Betts, Erin, Norwood, Jason, Heller, M. M., Voskuilen, Tyler, Sakievich, Philip, Gray, L., Hansen, D. J., Irick, Kevin W., Hewson, John C., Lamb, Joshua, Stacy, S. C., Brotherton, Chris M., Tappan, Alexander S., Benally, Darryl, Thigpen, Hannah, Ortiz, Erick, Sandoval, Dan, Ison, Aaron M., Warren, M., Stromberg, Peter G., Thelen, Paul Mark, Blasy, B., Nandy, Prabal, Haddad, Alexandria W., Trujillo, Lynna B., Wiseley, T. H., Bell, S. A., Teske, Nicholas P., Post, C., Torres-Castro, Loraine, Grosso, Chris, and Wasiolek, Maryla

Abstract

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hand, K., Phillips, C., Murray, A., Garvin, J., Maize, E., Gibbs, R., Reeves, G., San Martin, A., Tan-Wang, G., Krajewski, J., Hurst, K., Crum, R., Kennedy, B., McElrath, T., Gallon, J., Sabahi, D., Thurman, S., Goldstein, B., Estabrook, P., Lee, S. W., Dooley, J. A., Brinckerhoff, W. B., Edgett, K. S., German, C. R., Hoehler, T. M., Hörst, S. M., Lunine, J. I., Paranicas, C., Nealson, K., Smith, D. E., Templeton, A. S., Russell, M. J., Schmidt, B., Christner, B., Ehlmann, B., Hayes, A., Rhoden, A., Willis, P., Yingst, R. A., Craft, K., Cameron, M. E., Nordheim, T., Pitesky, J., Scully, J., Hofgartner, J., Sell, S. W., Barltrop, K. J., Izraelevitz, J., Brandon, E. J., Seong, J., Jones, J.-P., Pasalic, J., Billings, K. J., Ruiz, J. P., Bugga, R. V., Graham, D., Arenas, L. A., Takeyama, D., Drummond, M., Aghazarian, H., Andersen, A. J., Andersen, K. B., Anderson, E. W., Babuscia, A., Backes, P. G., Bailey, E. S., Balentine, D., Ballard, C. G., Berisford, D. F., Bhandari, P., Blackwood, K., Bolotin, G. S., Bovre, E. A., Bowkett, J., Boykins, K. T., Bramble, M. S., Brice, T. M., Briggs, P., Brinkman, A. P., Brooks, S. M., Buffington, B. B., Burns, B., Cable, M. L., Campagnola, S., Cangahuala, L. A., Carr, G. A., Casani, J. R., Chahat, N. E., Chamberlain-Simon, B. K., Cheng, Y., Chien, S. A., Cook, B. T., Cooper, M., DiNicola, M., Clement, B., Dean, Z., Cullimore, E. A., Curtis, A. G., Croix, J-P. de la, Pasquale, P. Di, Dodd, E. M., Dubord, L. A., Edlund, J. A., Ellyin, R., Emanuel, B., Foster, J. T., Ganino, A. J., Garner, G. J., Gibson, M. T., Gildner, M., Glazebrook, K. J., Greco, M. E., Green, W. M., Hatch, S. J., Hetzel, M. M., Hoey, W. A., Hofmann, A. E., Ionasescu, R., Jain, A., Jasper, J. D., Johannesen, J. R., Johnson, G. K., Jun, I., Katake, A. B., Kim-Castet, S. Y., Kim, D. I., Kim, W., Klonicki, E. F., Kobeis, Europa is a premier target for advancing both planetary science and astrobiology, as well as for opening a new window into the burgeoning field of comparative oceanography. The potentially habitable subsurface ocean of Europa may harbor life, and the globally young and comparatively thin ice shell of Europa may contain biosignatures that are readily accessible to a surface lander. Europa's icy shell also offers the opportunity to study tectonics and geologic cycles across a range of mechanisms and compositions. Here we detail the goals and mission architecture of the Europa Lander mission concept, as developed from 2015 through 2020. The science was developed by the 2016 Europa Lander Science Definition Team (SDT), and the mission architecture was developed by the preproject engineering team, in close collaboration with the SDT. In 2017 and 2018, the mission concept passed its mission concept review and delta-mission concept review, respectively. Since that time, the preproject has been advancing the technologies, and developing the hardware and software, needed to retire risks associated with technology, science, cost, and schedule., K.P.H., C.B.P., E.M., and all authors affiliated with the Jet Propulsion Laboratory carried out this research at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (grant No. 80NM0018D0004). J.I.L. was the David Baltimore Distinguished Visiting Scientist during the preparation of the SDT report. JPL/Caltech2021.

Published
2022

30. Development of the SeqCode : A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Author

Whitman, William B., Chuvochina, Maria, Hedlund, Brian P., Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain, and Venter, Stephanus N.

Subjects
Biologie
Abstract

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.

Published
2022

33. Perchlorate and Volatiles of the Brine of Lake Vida (Antarctica): Implication for the in Situ Analysis of Mars Sediments

Author

Kenig, Fabien, Chou, Luoth, McKay, Christopher P, Jackson, W. Andrew, Doran, Peter T, Murray, Alison E, and Fritsen, Christian H

Subjects
Lunar And Planetary Science And Exploration
Abstract

The cold (-13.4 C), cryoencapsulated, anoxic, interstitial brine of the 27 m-thick ice of Lake Vida (Victoria Valley, Antarctica) contains 49 microgram L-1 of perchlorate and 11 microgram L-1 of chlorate. Lake Vida brine (LVBr) may provide an analog for potential oxychlorine-rich subsurface brine on Mars. LVBr volatiles were analyzed by solid-phase microextraction (SPME) gas chromatography-mass spectrometry (GC-MS) with two different SPME fibers. With the exception of volatile organic sulfur compounds, most other volatiles observed were artifacts produced in the GC injector when the thermal decomposition products of oxychlorines reacted with reduced carbon derived from LVBr and the SPME fiber phases. Analysis of MilliQ water with perchlorate (40 microgram L-1) showed low level of organic artifacts, reflecting carbon limitation. In order to observe sample-derived organic compounds, both in analog samples and on Mars, the molar abundance of reduced carbon in a sample must exceed those of O2 and Cl2 produced during decomposition of oxychlorines. This suggests that the abundance of compounds observed by the Sample Analysis at Mars (SAM) instruments in Sheepbed samples (CB-3, CB5, and CB6) may be controlled by an increase in the reduced-carbon/oxychlorine ratio of these samples. To increase chances of in situ detection of Martian organics during pyrolysis-GC-MS, we propose that the derivatization agents stored on SAM may be used as an external source of reduced carbon, increasing artificially the reduced-carbon to perchlorate ratio during pyrolysis, allowing the expression of more abundant and perhaps more diverse Martian organic matter.

Published
2016

34. Environmental vulnerability of the global ocean epipelagic plankton community interactome

Author

Chaffron, Samuel, Delage, Erwan, Budinich, Marko, Vintache, Damien, Henry, Nicolas, Nef, Charlotte, Ardyna, Mathieu, Zayed, Ahmed A., Junger, Pedro C., Galand, Pierre E., Lovejoy, Connie, Murray, Alison E., Sarmento, Hugo, Acinas, Silvia G., Babin, Marcel, Iudicone, Daniele, Jaillon, Olivier, Karsenti, Eric, Wincker, Patrick, Karp-Boss, Lee, Sullivan, Matthew B., Bowler, Chris, de Vargas, Colomban, Eveillard, Damien, Galand, Pierre, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, 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 (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Federal University of São Carlos (UFSCar), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Division of Earth and Ecosystem Sciences (DEES), Desert Research Institute (DRI), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), 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), Université de Nantes (UN), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Microbiology [Columbus], Ohio State University [Columbus] (OSU), Department of Marine Biology and Oceanography, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), University of Maine, Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Project: 862923,AtlantECO, European Project: 835067,DIATOMIC, IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-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), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Adaptation et diversité en milieu marin (ADMM), and Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR)

Subjects
[SDE] Environmental Sciences, changement climatique, Ecology, Systems Biology, fungi, SciAdv r-articles, réseau écologique, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], plancton océanique, [SDE]Environmental Sciences, Bio-informatique, sense organs, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Research Articles, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS, Research Article, modélisation
Abstract

A global photic-ocean plankton ecological network predicts distinct vulnerabilities to environmental change across marine biomes., Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network—the community interactome—and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.

Published
2021
Full Text
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35. 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
Full Text
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36. 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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37. Antarctic ecosystem responses following ice‐shelf collapse and iceberg calving: Science review and future research

Author

Ingels, Jeroen, Aronson, Richard B, Smith, Craig R, Baco, Amy, Bik, Holly M, Blake, James A, Brandt, Angelika, Cape, Mattias, Demaster, David, Dolan, Emily, Domack, Eugene, Fire, Spencer, Geisz, Heidi, Gigliotti, Michael, Griffiths, Huw, Halanych, Kenneth M, Havermans, Charlotte, Huettmann, Falk, Ishman, Scott, Kranz, Sven A, Leventer, Amy, Mahon, Andrew R, McClintock, James, McCormick, Michael L, Mitchell, B Greg, Murray, Alison E, Peck, Lloyd, Rogers, Alex, Shoplock, Barbara, Smith, Kathryn E, Steffel, Brittan, Stukel, Michael R, Sweetman, Andrew K, Taylor, Michelle, Thurber, Andrew R, Truffer, Martin, Putte, Anton, Vanreusel, Ann, Zamora‐Duran, Maria Angelica, Ingels, Jeroen, Aronson, Richard B, Smith, Craig R, Baco, Amy, Bik, Holly M, Blake, James A, Brandt, Angelika, Cape, Mattias, Demaster, David, Dolan, Emily, Domack, Eugene, Fire, Spencer, Geisz, Heidi, Gigliotti, Michael, Griffiths, Huw, Halanych, Kenneth M, Havermans, Charlotte, Huettmann, Falk, Ishman, Scott, Kranz, Sven A, Leventer, Amy, Mahon, Andrew R, McClintock, James, McCormick, Michael L, Mitchell, B Greg, Murray, Alison E, Peck, Lloyd, Rogers, Alex, Shoplock, Barbara, Smith, Kathryn E, Steffel, Brittan, Stukel, Michael R, Sweetman, Andrew K, Taylor, Michelle, Thurber, Andrew R, Truffer, Martin, Putte, Anton, Vanreusel, Ann, and Zamora‐Duran, Maria Angelica

Abstract

The calving of A-68, the 5,800-km2, 1-trillion-ton iceberg shed from the Larsen C Ice Shelf in July 2017, is one of over 10 significant ice-shelf loss events in the past few decades resulting from rapid warming around the Antarctic Peninsula. The rapid thinning, retreat, and collapse of ice shelves along the Antarctic Peninsula are harbingers of warming effects around the entire continent. Ice shelves cover more than 1.5 million km2 and fringe 75% of Antarctica's coastline, delineating the primary connections between the Antarctic continent, the continental ice, and the Southern Ocean. Changes in Antarctic ice shelves bring dramatic and large-scale modifications to Southern Ocean ecosystems and continental ice movements, with global-scale implications. The thinning and rate of future ice-shelf demise is notoriously unpredictable, but models suggest increased shelf-melt and calving will become more common. To date, little is known about sub-ice-shelf ecosystems, and our understanding of ecosystem change following collapse and calving is predominantly based on responsive science once collapses have occurred. In this review, we outline what is known about (a) ice-shelf melt, volume loss, retreat, and calving, (b) ice-shelf-associated ecosystems through sub-ice, sediment-core, and pre-collapse and post-collapse studies, and (c) ecological responses in pelagic, sympagic, and benthic ecosystems. We then discuss major knowledge gaps and how science might address these gaps. This article is categorized under: Climate, Ecology, and Conservation > Modeling Species and Community Interactions.

Published
2021

38. 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

39. Respiratory nitrate ammonification by Shewanella oneidensis MR-1

Author

Cruz-Garcia, Claribel, Murray, Alison E., Klappenbach, Joel A., Stewart, Valley, and Tiedje, James M.

Subjects
Ammonium nitrate -- Usage, Shewanella -- Genetic aspects, Shewanella -- Research, Gene mutations -- Research, Biological sciences
Abstract

Anaerobic cultures of Shewanella oneidensis MR-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. Little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. A mutant with the napA gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the NapA enzyme is the sole nitrate reductase. Hence, S. oneidensis MR-1 conducts respiratory nitrate ammonification, also termed dissimilatory nitrate reduction to ammonium, but not respiratory denitrification.

Published
2007

40. Genomics: applications to Antarctic ecosystems

Author

Peck, Lloyd S., Clark, Melody S., Clarke, Andrew, Cockell, Charles S., Convey, Peter, Detrich, III, H. William, Fraser, Keiron P. P., Johnston, Ian A., Methe, Barbara A., Murray, Alison E., Römisch, Karin, and Rogers, Alex D.

Published
2005
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41. On the Past, Present, and Future Role of Biology in NASA’s Exploration of our Solar System

Author

Hand, Kevin, primary, Phillips, Cynthia B., additional, Chyba, Christopher F., additional, Toner, Brandy, additional, Katija, Kakani, additional, Orphan, Victoria, additional, Huber, Julie, additional, Cavanaugh, Colleen M., additional, Carlson, Marian, additional, Christner, Brent, additional, Templeton, Alexis, additional, Seewald, Jeffrey, additional, Hofgartner, Jason D., additional, Amend, Jan P., additional, Orcutt, Beth N., additional, Bartlett, Douglas H., additional, Falkowski, Paul, additional, Anderson, Rika, additional, Spear, John R., additional, Shank, Tim, additional, Fischer, Woodward W., additional, Hazen, Robert M., additional, Hoehler, Tori, additional, D'Hondt, Steven, additional, Pitesky, Jo, additional, Lynch, Kennda, additional, Shock, Everett L., additional, Craft, Kate, additional, Boyd, Eric, additional, House, Christopher H., additional, Reysenbach, Anna-Louise, additional, Glass, Jennifer, additional, Fike, David, additional, Baross, John A., additional, Gogarten, Johann Peter, additional, Kaçar, Betül, additional, El-Naggar, Moh, additional, Murray, Alison E., additional, Dupont, Christopher, additional, Scully, Jennifer, additional, Rothschild, Lynn, additional, Trembath-Reichert, Elizabeth, additional, Klein, Frieder, additional, Cohen, Phoebe A., additional, Gile, Gillian H., additional, Lloyd, Karen, additional, Dekas, Anne, additional, Delaney, John R., additional, Skidmore, Mark, additional, Buongiorno, Joy, additional, Rogers, Karyn, additional, Hofmann, Amy, additional, Brazelton, William J., additional, Anbar, Ariel, additional, Manalang, Dana Ann, additional, Stevenson, Bradley, additional, Neuer, Susanne, additional, Hara, Ellie, additional, Nordheim, Thomas, additional, Shapiro, Russell, additional, Bradley, Alexander S., additional, Mikucki, Jill, additional, Brown, Michael E., additional, Glamoclija, Mihaela, additional, Reyes, Carolina, additional, Sánchez-Román, Mónica, additional, Farmer, Jack D., additional, Giovannelli, Donato, additional, Suel, Gurol, additional, Trumbo, Samantha, additional, Cameron, Marissa, additional, Osburn, Magdalena, additional, Bradley, James Andrew, additional, Garcia-Pichel, Ferran, additional, Steen, Andrew D., additional, Marlow, Jeffrey, additional, Trubl, Gareth, additional, Robinson, Kirtland, additional, Caro, Tristan, additional, Fulfer, Victoria, additional, Parker, Ceth W., additional, Feyhl-Buska, Jayme, additional, and Roussel, Anaïs, additional

Published
2021
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43. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

Author

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

Published
2020
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44. Antarctic ecosystem responses following ice‐shelf collapse and iceberg calving: Science review and future research

Author

Ingels, Jeroen, primary, Aronson, Richard B., additional, Smith, Craig R., additional, Baco, Amy, additional, Bik, Holly M., additional, Blake, James A., additional, Brandt, Angelika, additional, Cape, Mattias, additional, Demaster, David, additional, Dolan, Emily, additional, Domack, Eugene, additional, Fire, Spencer, additional, Geisz, Heidi, additional, Gigliotti, Michael, additional, Griffiths, Huw, additional, Halanych, Kenneth M., additional, Havermans, Charlotte, additional, Huettmann, Falk, additional, Ishman, Scott, additional, Kranz, Sven A., additional, Leventer, Amy, additional, Mahon, Andrew R., additional, McClintock, James, additional, McCormick, Michael L., additional, Mitchell, B. Greg, additional, Murray, Alison E., additional, Peck, Lloyd, additional, Rogers, Alex, additional, Shoplock, Barbara, additional, Smith, Kathryn E., additional, Steffel, Brittan, additional, Stukel, Michael R., additional, Sweetman, Andrew K., additional, Taylor, Michelle, additional, Thurber, Andrew R., additional, Truffer, Martin, additional, Putte, Anton, additional, Vanreusel, Ann, additional, and Zamora‐Duran, Maria Angelica, additional

Published
2020
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45. 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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47. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel

Author

Massana, Ramon, Murray, Alison E., Preston, Christina M., and DeLong, Edward F.

Subjects
Santa Barbara Channel -- Natural history, Marine plankton -- Research, Marine bacteria -- Genetic aspects, Biological sciences
Abstract

The waters of the Santa Barbara Channel contain archaeal rRNA and rDNA whose relative abundance is lower in surface waters as compared to deep waters. The bacteria are an active, abundant and dynamic component of the picoplankton. The rRNA of the euryarchaeal group of marine Archaea are present in surface waters, while the rRNA from the crenarchaeal group are present in the deeper waters. The members of the crenarchaeal group form a large part of the prokaryotic biomass in subsurface coastal waters. The archaeal rDNA clones belong to two groups.

Published
1997

48. 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. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, 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, Pedros-Alio, 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. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, 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, Pedros-Alio, 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. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.

Published
2020
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49. Author 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. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, 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, 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. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, 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, 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

Abstract

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online.

Published
2020

50. Editorial: Antarctic Biology: Scale Matters.

Author

Danis, Bruno, Van de Putte, Anton, Convey, Peter, Griffiths, Huw, Linse, Katrin, Murray, Alison E., Danis, Bruno, Van de Putte, Anton, Convey, Peter, Griffiths, Huw, Linse, Katrin, and Murray, Alison E.

Abstract

A founding principle of the Antarctic Treaty is that, in the interests of all humankind, Antarctica should continue to be used exclusively for peaceful purposes and should not become the scene or object of international discord. From many standpoints, Antarctica is considered as a sanctuary, and plays a pivotal role in the global system. From an ecological point of view, Antarctica and the surrounding Southern Ocean harbor exceptional levels of biodiversity. Its ecosystems are, however, facing rapid climatic and environmental changes, and the scientific community, embodied by the Scientific Committee on Antarctic Research (SCAR), have identified the urgent need to understand the potential responses of these ecosystems. Such questions are extremely complex, as biodiversity, here defined as “the variability among living organisms from all sources, including inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems” (Convention on Biological Diversity, 1992), can vary at many different spatio-temporal scales and levels of biological organization, from molecules to entire ecosystems.

Published
2020

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