Publications

76 entries « 1 of 2 »

2018

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

The ISME Journal, pp. 1-9, 2018.

Abstract | Links | BibTeX

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

Nature Communications, 9 , 2018.

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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

mBio, 8 (6), 2017.

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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

Proceedings of the National Academy of Sciences of the United States of America, 115 , pp. E400-E408, 2017.

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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

The ISME Journal, 12 , pp. 742-755, 2017.

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Becraft ED Woyke T, Jarett Ivanova Godoy-Vitorino Poulton Brown JM Brown Lau Onstott Eisen JA Moser Stepanauskas J N F N J M T D R

Rokubacteria: Genomic giants among the uncultured bacterial phyla Journal Article

Frontiers in Microbiology , 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

Science, 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

Frontiers in Microbiology, 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-Beltrán; K, Mewis; WT, Liu; R, Stepanauskas; T, Woyke; SJ, Hallam

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

Nature Communications, 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

Frontiers in Microbiology , 8 , 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

The ISME Journal, 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

Nature Biotechnology, 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, Fernández-Gómez; 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

Scientific Data, 4 , 2017.

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M, Royo-Llonch; I, Ferrera; FM, Cornejo-Castillo; P, Sánchez; G, Salazar; R, Stepanauskas; JM, González; ME, Sieracki; S, Speich; L, Stemmann; C, Pedrós-Alió; SG, Acinas

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

Frontiers in Microbiology, 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

Nature Communications, 8 (84), 2017.

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

Genome Standards for Single Amplified Genomes and Genomes From Metagenomes of Bacteria and Archaea Journal Article Forthcoming

Nature Biotechnology, Forthcoming.

BibTeX

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

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

Nature Microbiology, 2 (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

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

ISME, 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

mBio, 2017.

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

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

PeerJ, 2017.

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P, Starnawski; T, Bataillon; TJ, Ettema; LM, Jochum; L, Schreiber; X, Chen; MA, Lever; MF, Polz; BB, Jorgensen; A, Schramm; KU, Kjeldsen

Microbial community assembly and evolution in subseafloor sediment Journal Article

PNAS, 114 , pp. 2940-2945, 2017.

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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

Scientific Reports, 7 (41498), 2017.

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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

Scientific Reports, 7 (40579), 2017.

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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

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

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

The ISME Journal, 11 , pp. 186-200, 2016.

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K, Wasmund; M, Cooper; L, Schreiber; KG, Lloyd; BJ, Baker; DJ, Petersen; BB, Jørgensen; 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

mBio, 7 (3), 2016.

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H, Fullerton; CL, Moyer

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

Applied and Environmental Microbiology, 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

Nature Microbiology, 1 (16002), 2016.

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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

ISME, 10 , pp. 1939–1953, 2016.

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

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

Applied and Environmental Microbiology, 82 (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

ISME, 10 , pp. 1902–1914, 2016.

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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

International Microbiology, 19 (39-47), 2015.

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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

ISME, 10 , pp. 1383–1399, 2015.

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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

Applied and Environmental 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

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

Frontiers in Microbiology, 6 , 2015.

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JM, Labonté; EK, Field; M, Lau; D, Chivian; van E, Heerden; 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

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

ISME, 2015.

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R, Stepanauskas

Wiretapping into microbial interactions by single cell genomics Journal Article

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

ISME, 2015.

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Paul BG Bagby SC, Czornyj Arambula Handa Sczyrba Ghosh Miller JF Valentine DL E D S A P

Targeted diversity generation by intraterrestrial archaea and archaeal viruses Journal Article

Nature Communications, 2015.

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R, Stepanauskas

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

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

ISME, 2014.

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M, Martínez-García; F, Santos; M, Moreno-Paz; V, Parro; J, Antón

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

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

ISME, 2014.

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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

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

ISME, 2014.

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76 entries « 1 of 2 »