Publications

131 entries « 2 of 3 »

2018

DK, Ngugi; U, Stingl

High-quality draft single-cell genome sequence of the NS5 marine group from the coastal Red Sea Journal Article

In: Genome Announcements, vol. 6, no. 25, 2018.

Abstract | Links | BibTeX

AM, Plominsky; N, Trefault; and Blanton JM, Podell S; la Iglesia R, De; EE, Allen; von Dassow P and Ulloa O,

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones Journal Article

In: Enviornmental Microbiology, 2018.

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SL, Garcia; SLR, Stevens; B, Crary; M, Martinez-Garcia; R, Stepanauskas; T, Woyke; SG, Tringe; SGE, Andersson; S, Bertilsson; RR, Malmstrom; KD, McMahon

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations Journal Article

In: The ISME Journal, vol. 12, no. 3, pp. 742-755, 2018.

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JH, Munson-McGee; S, Peng; S, Dewerff; R, Stepanauskas; RJ, Whitaker; JS, Weitz; MJ, Young

A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments Journal Article

In: The ISME Journal, vol. 12, no. 7, pp. 1706-1714, 2018.

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Y, Seeleuthner; S, Mondy; V, Lombard; Q, Carradec; E, Pelletier; M, Wessner; J, Leconte; JF, Mangot; J, Poulain; K, Labadie; R, Logares; S, Sunagawa; V, De Berardinis; M, Salanoubat; C, Dimier; S, Kandels-Lewis; M, Picheral; S, Searson; SG, Acinas; E, Boss; M, Follows; G, Gorsky; N, Grimsley; L, Karp-Boss; U, Krzic; F, Not; H, Ogata; J, Raes; EG, Reynaud; C, Sardet; S, Speich; L, Stemmann; D, Velayoudon; J, Weissenbach; S, Pesant; N, Poulton; R, Stepanauskas; P, Bork; C, Bowler; P, Hingamp; MB, Sullivan; D, Iudicone; R, Massana; JM, Aury; B, Henrissat; E, Karsenti; O, Jaillon; M, Sieracki; C, De Vargas; P, Wincker

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans Journal Article

In: Nature Communications, vol. 9, 2018.

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K, Bergauer; A, Fernandez-Guerra; JAL, Garcia; RR, Sprenger; R, Stepanauskas; MG, Pachiadaki; ON, Jensen; GJ, Herndl

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 3, pp. E400-E408, 2018.

Abstract | Links | BibTeX

2017

HL, Sewell; AK, Kaster; AM, Spormann

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes Journal Article

In: mBio, vol. 8, no. 6, 2017.

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Woyke T Becraft ED, Jarett J

Rokubacteria: Genomic giants among the uncultured bacterial phyla Journal Article

In: Frontiers in Microbiology , vol. 8, 2017.

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MG, Pachiadaki; E, Sintes; K, Bergauer; JM, Brown; NR, Record; BK, Swan; ME, Mathyer; SJ, Hallam; P, Lopez-Garcia; Y, Takaki; T, Nunoura; T, Woyke; GJ, Herndl; R, Stepanauskas

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation Journal Article

In: Science, vol. 358, pp. 1046-1051, 2017.

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D, Ceccarelli; G, Garriss; SY, Choi; NA, Hasan; R, Stepanauskas; M, Pop; A, Huq; RR, Colwell

Characterization of two cryptic plasmids isolated in Haiti from clinical Vibrio cholerae non-O1/non-O139 Journal Article

In: Frontiers in Microbiology, vol. 8, 2017.

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AK, Hawley; MK, Nobu; JJ, Wright; WE, Durno; C, Morgan-Lang; B, Sage; P, Schwientek; BK, Swan; C, Rinke; M, Torres-BeltrĂĄn; K, Mewis; WT, Liu; R, Stepanauskas; T, Woyke; SJ, Hallam

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients Journal Article

In: Nature Communications, vol. 8, 2017.

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ED, Becraft; JA, Dodsworth; SK, Murugapiran; SC, Thomas; JI, Ohlsson; R, Stepanauskas; BP, Hedlund; WD, Swingley

Genomic comparison of two family-level groups of the uncultivated NAG1 archaeal lineage from chemically and geographically disparate hot springs Journal Article

In: Frontiers in Microbiology , vol. 8, 2017.

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J.J, Hamilton; S.L, Garcia; B.S, Brown; B.O, Oyserman; Moya-Flores F,; S, Bertilsson; R.R, Malmstrom; K, Forest; K, McMahon

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI Journal Article

In: American Society for Microbiology, vol. 2, no. 4, pp. e00091-17, 2017.

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JF, Mori; JJ, Scott; KW, Hager; CL, Moyer; K, Kusel; D, Emerson

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov Journal Article

In: The ISME Journal, vol. 11, pp. 2624-2636, 2017.

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RM, Bowers; NC, Kyrpides; R, Stepanauskas; M, Harmon-Smith; D, Doud; TBK, Reddy; F, Schulz; J, Jarett; AR, Rivers; EA, Eloe-Fadrosh; SG, Tringe; NN, Ivanova; A, Copeland; A, Clum; ED, Becraft; RR, Malmstrom; B, Birren; M, Podar; P, Bork; GM, Weinstock; GM, Garrity; JA, Dodsworth; S, Yooseph; G, Sutton; FO, Glöckner; JA, Gilbert; WC, Nelson; SJ, Hallam; SP, Jungbluth; TJG, Ettema; S, Tighe; KT, Konstantinidis; WT, Liu; BJ, Baker; T, Rattei; JA, Eisen; B, Hedlund; KD, McMahon; N, Fierer; R, Knight; R, Finn; G, Cochrane; I, Karsch-Mizrachi; GW, Tyson; C, Rinke; A, Lapidus; F, Meyer; P, Yilmaz; DH, Parks; AM, Eren; L, Schriml; JF, Banfield; P, Hugenholtz; T, Woyke

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Journal Article

In: Nature Biotechnology, vol. 35, pp. 725-731, 2017.

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A, Alberti; J, Poulain; S, Engelen; K, Labadie; S, Romac; I, Ferrera; G, Albini; JM, Aury; C, Belser; A, Bertrand; C, Cruaud; C, Da Silva; C, Dossat; F, Gavory; S, Gas; J, Guy; M, Haquelle; E, Jacoby; O, Jaillon; A, Lemainque; E, Pelletier; G, Samson; M, Wessner; SG, Acinas; M, Royo-Llonch; FM, Cornejo-Castillo; R, Logares; B, FernĂĄndez-GĂłmez; C, Bowler; G, Cochrane; C, Amid; PT, Hoopen; C, De Vargas; N, Grimsley; E, Desgranges; S, Kandels-Lewis; H, Ogata; N, Poulton; ME, Sieracki; R, Stepanauskas; MB, Sullivan; JR, Brum; MB, Duhaime; BT, Poulos; BL, Hurwitz; S, Pesant; E, Karsenti; P, Wincker; P, Bazire; O, Beluche; L, Bertrand; M, Besnard-Gonnet; I, Bordelais; M, Boutard; M, Dubois; C, Dumont; E, Ettedgui; P, Fernandez; E, Garcia; NG, Aiach; T, Guerin; C, Hamon; E, Brun; S, Lebled; P, Lenoble; C, Louesse; E, Mahieu; B, Mairey; N, Martins; C, Megret; C, Milani; J, Muanga; C, Orvain; E, Payen; P, Perroud; E, Petit; D, Robert; M, Ronsin; B, Vacherie; P, Bork; E, Boss; M, Follows; G, Gorsky; P, Hingamp; D, Iudicone; L, Karp-Boss; F, Not; J, Raes; C, Sardet; S, Speich; L, Stemmann; S, Sunagawa

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition Journal Article

In: Scientific Data, vol. 4, 2017.

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M, Royo-Llonch; I, Ferrera; FM, Cornejo-Castillo; P, SĂĄnchez; G, Salazar; R, Stepanauskas; JM, GonzĂĄlez; ME, Sieracki; S, Speich; L, Stemmann; C, PedrĂłs-AliĂł; SG, Acinas

Exploring microdiversity in novel Kordia sp. (Bacteroidetes) with proteorhodopsin from the tropical Indian Ocean via Single Amplified Genomes Journal Article

In: Frontiers in Microbiology, vol. 8, 2017.

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R, Stepanauskas; EA, Fergusson; J, Brown; NJ, Poulton; B, Tupper; JM, Labonté; ED, Becraft; JM, Brown; MJ, Pachiadaki; T, Povilaitis; BP, Thompson; CJ, Mascena; WK, Bellows; A, Lubys

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles Journal Article

In: Nature Communications, vol. 8, no. 84, 2017.

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A, Collingro; S, Köstlbacher; M, Mussmann; R, Stepanauskas; S, Hallam; M, Horn

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae Journal Article

In: ISME, 2017.

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Luo, Haiwei; Huang, Yongjie; Stepanauskas, Ramunas; Tang, Jijun

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes Journal Article

In: Nature Microbiology, vol. 2, no. 17091, 2017.

Abstract | Links | BibTeX

N, Kashtan; SE, Roggensack; JW, Berta-Thompson; M, Grinberg; R, Stepanauskas; SW, Chisholm

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus Journal Article

In: ISME, 2017.

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WH, Wilson; IC, Gilg; M, Moniruzzaman; EK, Field; S, Koren; GR, LeCleir; J, Martínez Martínez; NJ, Poulton; BK, Swan; R, Stepanauskas; SW, Wilhelm

Genomic exploration of individual giant ocean viruses Journal Article

In: ISME, 2017.

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Y, Guan; MF, Haroon; I, Alam; JG, Ferry; U, Stingl

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1 Journal Article

In: vol. 9, no. 4, pp. 404-410, 2017.

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Z, Landry; BK, Swan; GJ, Herndl; R, Stepanauskas; SJ, Giovannoni

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter Journal Article

In: mBio, 2017.

Abstract | Links | BibTeX

SP, Jungbluth; del Rio TG,; SG, Tringe; R, Stepanauskas; MS, Rappé

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems Journal Article

In: PeerJ, 2017.

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P, Starnawski; T, Bataillon; T.J.G, Ettema; L.M, Jochum; Schreiber L,; X, Chen; Ploz M Lever M, JÞrgensen B; A, Schramm; K, Kjeldsen

Microbial community assembly and evolution in subseafloor sediment Journal Article

In: PNAS, vol. 114, no. 11, pp. 2940-2945, 2017.

Abstract | Links | BibTeX

JF, Mangot; R, Logares; P, Sanchez; F, Latorre; Y, Seeleuthner; S, Mondy; ME, Sieracki; O, Jaillon; P, Wincker; C, Vargas; R, Massana

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells Journal Article

In: Scientific Reports, vol. 7, no. 41498, 2017.

Abstract | Links | BibTeX

MJ, Neave; CT, Michell; A, Apprill; CR, Voolstra

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts Journal Article

In: Scientific Reports, vol. 7, no. 40579, 2017.

Abstract | Links | BibTeX

2016

J, Choi; F, Yang; R, Stepanauskas; E, Cardenas; A, Garoutte; R, Williams; J, Flater; JM, Tiedje; KS, Hofmockel; 6,; B, Gelder; A, Howe

Strategies to improve reference databases for soil microbiomes Journal Article

In: ISME, 2016.

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T, Vannier; J, Leconte; Y, Seeleuthner; S, Mondy; E, Pelletier; JM, Aury; C, De Vargas; M, Sieracki; D, Iudicone; D, Vaulot; P, Wincker; O, Jaillon

Survey of the green picoalga Bathycoccus genomes in the global ocean Journal Article

In: Scientific Reports, vol. 6, 2016.

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MJ, Neave; R, Rachmawati; L, Xun; CT, Michell; DG, Bourne; A, Apprill; CR, Voolstra

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales Journal Article

In: ISME, 2016.

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MJ, Neave; R, Rachmawati; L, Xun; CT, Michell; DG, Bourne; A, Apprill; CR, Voolstra

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales Journal Article

In: The ISME Journal, vol. 11, pp. 186-200, 2016.

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K, Wasmund; M, Cooper; L, Schreiber; KG, Lloyd; BJ, Baker; DJ, Petersen; BB, JĂžrgensen; R, Stepanauskas; R, Reinhardt; A, Schramm; A, Loy; L, Adrian

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling Journal Article

In: mBio, vol. 7, no. 3, 2016.

Abstract | Links | BibTeX

H, Fullerton; CL, Moyer

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep Subsurface Biosphere Journal Article

In: Applied and Environmental Microbiology, vol. 82, pp. 3000-3008, 2016.

Abstract | Links | BibTeX

BJ, Baker; JH, Saw; AE, Lind; CS, Lazar; KU, Hinrichs; AP, Teske; TJ, Ettema

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea Journal Article

In: Nature Microbiology, vol. 1, no. 16002, 2016.

Abstract | Links | BibTeX

S, Dyksma; K, Bischof; BM, Fuchs; K, Hoffmann; D, Meier; A, Meyerdierks; P, Pjevac; D, Probandt; M, Richter; R, Stepanauskas; M, Mußmann

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments Journal Article

In: ISME, vol. 10, pp. 1939–1953, 2016.

Abstract | Links | BibTeX

Y, Zhang; Y, Sun; N, Jiao; R, Stepanauskas; H, Luo

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5 Journal Article

In: Applied and Environmental Microbiology, vol. 82, no. 7, 2016.

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A, Eiler; R, Mondav; L, Sinclair; L, Fernandez-Vidal; DG, Scofield; P, Schwientek; M, Martinez-Garcia; D, Torrents; KD, McMahon; SGE, Andersson; R, Stepanauskas; T, Woyke; S, Bertilsson

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria Journal Article

In: ISME, vol. 10, pp. 1902–1914, 2016.

Abstract | Links | BibTeX

2015

A, Srivastava; KD, McMahon; R, Stepanauskas; HP, Grossart

De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany) Journal Article

In: International Microbiology, vol. 19, no. 39-47, 2015.

Abstract | Links | BibTeX

DK, Ngugi; J, Blom; R, Stepanauskas; U, Stingl

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines Journal Article

In: ISME, vol. 10, pp. 1383–1399, 2015.

Abstract | Links | BibTeX

JH, Munson-McGee; EK, Field; M, Bateson; C, Rooney; R, Stepanauskas; MJ, Young

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs Journal Article

In: Applied and Environmental Microbiology, 2015.

Abstract | Links | BibTeX

SA, Carr; BN, Orcutt; KW, Mandernack; JR, Spear

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica Journal Article

In: Frontiers in Microbiology, 2015.

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SA, Carr; BN, Orcutt; KW, Mandernack; JR, Spear

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica Journal Article

In: Frontiers in Microbiology, vol. 6, 2015.

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JM, Labonté; EK, Field; M, Lau; D, Chivian; van Heerden E,; KE, Wommack; TL, Kieft; TC, Onstott; R, Stepanauskas

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population Journal Article

In: Frontiers in Microbiology, 2015.

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JM, Labonté; BK, Swan; B, Poulos; H, Luo; S, Koren; SJ, Hallam; MB, Sullivan; T, Woyke; KE, Wommack; R, Stepanauskas

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton Journal Article

In: ISME, 2015.

Abstract | Links | BibTeX

R, Stepanauskas

Wiretapping into microbial interactions by single cell genomics Journal Article

In: Frontiers in Microbiology, 2015.

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J, Martijn; F, Schullz; K, Zaremba-Niedzwiedzka; J, Viklund; R, Stepanauskas; SGE, Andersson; M, Horn; L, Guy; TJG, Ettema

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution Journal Article

In: ISME, 2015.

Abstract | Links | BibTeX

Bagby SC Paul BG, Czornyj E

Targeted diversity generation by intraterrestrial archaea and archaeal viruses Journal Article

In: Nature Communications, 2015.

Abstract | Links | BibTeX

R, Stepanauskas

Crystal Ball: Re-defining microbial diversity from its single-celled building blocks Journal Article

In: Environmental Microbiology Reports, 2015.

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2014

EK, Field; A, Sczyrba; AE, Lyman; CC, Harris; T, Woyke; R, Stepanauskas; D, Emerson

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount Journal Article

In: ISME, 2014.

Abstract | Links | BibTeX

131 entries « 2 of 3 »