Publications

127 entries « 2 of 3 »

2018

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.

Abstract | Links | BibTeX

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.

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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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

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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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Links | BibTeX

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.

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M, MartĂ­nez-GarcĂ­a; F, Santos; M, Moreno-Paz; V, Parro; J, AntĂłn

Unveiling viral–host interactions within the ‘microbial dark matter’ Journal Article

In: Nature Communications, 2014.

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DK, Ngugi; J, Blom; I, Alam; M, Rashid; W, Ba-Alawi; G, Zhang; T, Hikmawan; Y, Guan; A, Antunes; R, Siam; H, El Dorry; V, Bajic; U, Stingl

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea Journal Article

In: ISME, 2014.

Abstract | Links | BibTeX

NH, Youssef; C, Rinke; R, Stepanauskas; I, Farag; T, Woyke; MS, Elshahed

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’ Journal Article

In: ISME, 2014.

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M, Gomariz; M, Martinez-Garcia; F, Santos; F, Rodriguez; S, Capella-Gutierrez; T, Gabaldon; R, Rosello-Mora

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists Journal Article

In: ISME, 2014.

Abstract | Links | BibTeX

127 entries « 2 of 3 »