Publications

105 entries « 1 of 3 »

2021

WE, Kim; K, Charov; M, Dzunkova; ED, Becraft; J, Brown; F, Schulz; T, Woyke; JJ, La Clair; R, Stepanauskas; MD, Burkart

Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics Journal Article

In: 2021.

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S, Nayfach; A, Roux; R, Seshadri; D, Udwary; N, Varghese; F, Schulz; D, Wu; D, Paez-Espino; I-M, Chen; M, Huntemann; K, Palaniappan; J, Ladau; S, Mukherjee; TBK, Reddy; T, Nielsen; E, Kirton; EP, Faria; JN, Edirisinghe; CS, Henry; SP, Jungbluth; D, Chivian; P, Dehal; EM, Wood-Charlson; AP, Arkin; S, Tringe; A, Visel; Consortium, IMG/M Data; T, Woyke; NJ, Mouncey; NN, Ivanova; NC, Kyrpides; EA, Eloe-Fadrosh

A Genomic Catalogue of Earth’s Microbiomes Journal Article

In: Nature Biotechnology, 39 , pp. 499-509, 2021.

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ED, Becraft; MCY, Lau; OKI, Bezuidt; JM, Brown; JM, Labonté; K, Kauneckaite-Griguole; R, Salkauskaite; G, Alzbutas; JD, Sackett; BR, Kruger; V, Kadnikov; E, Van Heerden; D, Moser; N, Ravin; T, Onstott; R, Stepanauskas

Evolutionary stasis of a deep subsurface microbial lineage Journal Article

In: The ISME Journal, 2021.

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EM, Fones; DR, Colman; EA, Kraus; R, Stepanauskas; AS, Templeton; JR, Spear; ES, Boyd

Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation Journal Article

In: The ISME Journal, 15 , pp. 1121-1135, 2021.

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O, Ulloa; C, Henríquez-Castillo; S, Ramírez-Flandes; AM, Plominsky; AA, Murillo; C, Morgan-Lang; SJ, Hallam; R, Stepanauskas

The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean Journal Article

In: PNAS, 118 (11), 2021, ISSN: 1091-6490.

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2020

JM, Brown; JM, Labonté; J, Brown; NR, Record; NJ, Poulton; ME, Sieracki; R, Logares; R, Stepanauskas

Single Cell Genomics Reveals Viruses Consumed by Marine Protists Journal Article

In: Frontiers in Microbiology, 11 (524828), 2020.

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JP, Beam; ED, Becraft; JM, Brown; F, Schulz; JK, Jarett; O, Bezuidt; NJ, Poulton; K, Clark; PF, Dunfield; NV, Ravin; JR, Spear; BP, Hedlund; KA, Kormas; SM, Sievert; MS, Elshahed; HA, Barton; MB, Stott; JA, Eisen; DP, Moser; TC, Onstott; T, Woyke; R, Stepanauskas

Ancestral absence of electron transport chains in Patescibacteria and DPANN Journal Article

In: Frontiers in Microbiology, 11 (1848), 2020.

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JK, Jarett; M, Džunková; F, Schulz; S, Roux; D, Paez-Espino; E, Eloe-Fadrosh; SP, Jungbluth; N, Ivanova; JR, Spear; SA, Carr; CB, Trivedi; FA, Corsetti; HA, Johnson; E, Becraft; N, Kyrpides; R, Stepanauskas; T, Woyke

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat Journal Article

In: The ISME Journal, 14 , pp. 2527-2541, 2020.

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ML, Chen; ED, Becraft; M, Pachiadaki; JM, Brown; JK, Jarett; JM, Gasol; NV, Ravin; DP, Moser; T, Nunoura; GJ, Herndl; T, Woyke; R, Stepanauskas

Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f Journal Article

In: Frontiers in Microbiology, 11 (376), 2020.

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JHW, Saw; T, Nunoura; M, Hirai; Y, Takaki; R, Parsons; M, Michelsen; K, Longnecker; EB, Kujawinski; R, Stepanauskas; Z, Landry; CA, Carlson; SJ, Giovannoni

Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria Journal Article

In: mBio, 11 (1), pp. e02975-19, 2020.

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2019

MG, Pachiadaki; JM, Brown; J, Brown; O, Bezuidt; PM, Berube; SJ, Biller; NJ, Poulton; MD, Burkart; JJ, La Clair; SW, Chisholm; R, Stepanauskas

Charting the complexity of the marine microbiome through single cell genomics Journal Article

In: Cell, 179 (7), pp. 1623-1635, 2019.

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JM, Labonté; M, Pachiadaki; E, Fergusson; J, McNichol; A, Grosche; LK, Gulmann; C, Vetriani; SM, Sievert; R, Stepanauskas

Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system Journal Article

In: Frontiers in Microbiology, 10 , pp. 1262, 2019.

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LR, Thompson; MF, Haroon; AA, Shibl; MJ, Cahill; DK, Ngugi; GJ, Williams; JT, Morton; R, Knight; KD, Goodwin; U, Stingl

Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes Journal Article

In: Applied and Environmental Microbiology, 85 , 2019.

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M, Ren; X, Feng; Y, Huang; H, Wang; Z, Hu; S, Clingenpeel; BK, Swan; MM, Fonseca; D, Posada; R, Stepanauskas; JT, Hollibaugh; PG, Foster; T, Woyke; H, Luo

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution Journal Article

In: ISME, 13 , pp. 2150-2161, 2019.

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ME, Sieracki; NJ, Poulton; O, Jaillon; P, Wincker; de Vargas C,; L, Rubinat-Ripoll; R, Stepanauskas; R, Logares; R, Massana

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems Journal Article

In: Scientific Reports, 9 , pp. 6025, 2019.

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NH, Youssef; IF, Farag; CR, Hahn; J, Jarett; E, Becraft; E, Eloe-Fadrosh; J, Lightfoot; A, Bourgeois; T, Cole; S, Ferrante; M, Truelock; W, Marsh; M, Jamaleddine; S, Ricketts; R, Simpson; A, McFadden; W, Hoff; NV, Ravin; S, Sievert; R, Stepanauskas; T, Woyke; M, Elshahed

Genomic characterization of candidate division LCP-89 reveals an atypical cell wall structure, microcompartment production, and dual respiratory and fermentative capacities Journal Article

In: Applied and Environmental Microbiology, 85 , pp. e00110-19, 2019.

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JD, Sackett; BR, Kruger; ED, Becraft; JK, Jarett; R, Stepanauskas; T, Woyke; DP, Moser

Four draft single-cell genome sequences of novel, nearly identical Kiritimatiellaeota strains isolated from the continental deep subsurface Journal Article

In: Microbiology Resource Announcements, 8 , pp. e01249-18, 2019.

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SA, Carr; SP, Jungbluth; EA, Eloe-Fadrosh; R, Stepanauskas; T, Woyke; MS, Rappé; BN, Orcutt

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere Journal Article

In: The ISME Journal, 13 , pp. 1457-1468, 2019, ISSN: 1751-7370.

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PM, Berube; A, Rasmussen; R, Braakman; R, Stepanauskas; SW, Chisholm

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus Journal Article

In: eLife, 8 , 2019.

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Y, Wang; JM, Huang; GJ, Cui; T, Nunoura; Y, Takaki; WL, Li; J, Li; ZM, Gao; K, Takai; AQ, Zhang; R, Stepanauskas

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean Journal Article

In: Environmental Microbiology , 21 (2), pp. 716-729, 2019.

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PB, Matheus Carnevali; F, Schulz; CJ, Castelle; RS, Kantor; PM, Shih; I, Sharon; JM, Santini; MR, Olm; Y, Amano; BC, Thomas; K, Anantharaman; D, Burstein; ED, Becraft; R, Stepanauskas; T, Woyke; JF, Banfield

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria Journal Article

In: Nature Communications, 10 (463), 2019, ISSN: 2041-1723.

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2018

YM, Lee; K, Hwang; JI, Lee; M, Kim; CY, Hwang; HJ, Noh; H, Choi; HK, Lee; J, Chun; SG, Hong; SC, Shin

Genomic insight into the predominance of candidate phylum Atribacteria JS1 lineage in marine sediments Journal Article

In: Frontiers in Microbiology, 9 , 2018.

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JK, Jarett; S, Nayfach; M, Podar; W, Inskeep; NN, Ivanova; J, Munson-Mcgee; F, Schulz; M, Young; ZJ, Jay; JP, Beam; NC, Kyrpides; RR, Malmstrom; R, Stepanauskas; T, Woyke

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis Journal Article

In: Microbiome, 6 (161), 2018, ISSN: 2049-2618.

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PM, Berube; SJ, Biller; T, Hackl; SL, Hogle; BM, Satinsky; JW, Becker; R, Braakman; SB, Collins; L, Kelly; J, Berta-Thompson; A, Coe; K, Bergauer; HA, Bouman; TJ, Browning; D, De Corte; C, Hassler; Y, Hulata; JE, Jacquot; EW, Maas; T, Reinthaler; E, Sintes; T, Yokokawa; D, Lindell; R, Stepanauskas; SW, Chisholm

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments Journal Article

In: Scientific Data, 5 , 2018, ISSN: 2052-4463.

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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, 6 (25), 2018.

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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, 12 (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, 12 (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, 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, 115 (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, 8 (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 , 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, 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, 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

In: 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

In: Frontiers in Microbiology , 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, 2 (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, 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, 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

In: 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

In: 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

In: Nature Communications, 8 (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, 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

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: 9 (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.

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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, Jørgensen B; A, Schramm; K, Kjeldsen

Microbial community assembly and evolution in subseafloor sediment Journal Article

In: PNAS, 114 (11), pp. 2940-2945, 2017.

Abstract | Links | BibTeX

105 entries « 1 of 3 »