Publications

127 entries « 1 of 3 »

2023

A, Srivastava; D, De Corte; JAL, Garcia; BK, Swan; R, Stepanauskas; GJ, Herndl; E, Sintes

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses Journal Article

In: Microbiome, vol. 11, no. 239, 2023, ISSN: 2049-2618.

Abstract | Links | BibTeX

JM, Haro-Moreno; M, López-Pérez; A, Alekseev; E, Podoliak; K, Kovalev; V, Gordeliy; R, Stepanauskas; F, Rodriguez-Valera

Flotillin-associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes Journal Article

In: mSystems, vol. 8, iss. 3, no. e0000823, 2023.

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AE, Booker; T, D’Angelo; A, Adams-Beyea; JM, Brown; O, Nigro; MS, Rappé; R, Stepanauskas; BN, Orcutt

Life strategies for Aminicenantia in subseafloor oceanic crust Journal Article

In: The ISME Journal, vol. 17, pp. 1406-1415, 2023, ISSN: 1751-7370 (online).

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J, Anstett; AM, Plominsky; EF, DeLong; A, Kiesser; K, Jürgens; C, Morgan-Lang; R, Stepanauskas; FJ, Stewart; O, Ulloa; T, Woyke; R, Malmstrom; SJ, Hallam

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters Journal Article

In: Scientific Data, vol. 10, no. 332, 2023, ISSN: 2052-4463 (online).

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T, D'Angelo; J, Goordial; MR, Lindsay; J, McGonigle; A, Booker; D, Moser; R, Stepanauskas; BN, Orcutt

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota Journal Article

In: The ISME Journal, vol. 17, pp. 891-902, 2023, ISSN: 1751-7370 (online).

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CO, Seymour; M, Palmer; ED, Becraft; R, Stepanauskas; AD, Friel; F, Schulz; T, Woyke; E, Eloe-Fadrosh; D, Lai; J-Y, Jiao; Z-S, Hua; L, Liu; Z-H, Lian; W-J, Li; M, Chuvochina; BK, Finley; BJ, Koch; E, Schwartz; P, Dijkstra; DP, Moser; BA, Hungate; BP, Hedlund

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota Journal Article

In: Nature Microbiology, 2023.

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T, Hackl; R, Laurenceau; MJ, Ankenbrand; C, Bliem; Z, Cariani; E, Thomas; KD, Dooley; AA, Arellano; SL, Hogle; P, Berube; GE, Leventhal; E, Luo; JM, Eppley; AA, Zayed; J, Beaulaurier; R, Stepanauskas; MB, Sullivan; EF, DeLong; SJ, Biller; SW, Chisholm

Novel integrative elements and genomic plasticity in ocean ecosystems Journal Article

In: Cell, vol. 186, iss. 1, pp. 47-62.e16, 2023, ISSN: 0092-8674.

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2022

J.H., Munson-McGee; M.R., Lindsay; E, Sintes; J.M., Brown; T, D'Angelo; J, Brown; L.C., Lubelczyk; P, Tomko; D, Emerson; B.N., Orcutt; N.J., Poulton; G.J., Herndl; R, Stepanauskas

Decoupling of respiration rates and abundance in marine prokaryoplankton Journal Article

In: Nature, vol. 612, pp. 764-770, 2022.

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BJ, Fremin; AS, Bhatt; NC, Kyrpides; C, Global Phage Small Open Reading Frame

Thousands of small, novel genes predicted in global phage genomes Journal Article

In: Cell Reports, vol. 39, iss. 12, no. 110984, 2022.

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S, Lyalina; R, Stepanauskas; F, Wu; S, Sanjabi; KS, Pollard

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community Journal Article

In: PLoS One , vol. 17, iss. 4, no. e0261795, 2022.

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Magnuson, E; Altshuler, I; Fernández-Martínez, M. Á.; Chen, Y; Maggiori, C; Goordial, J; Whyte, L. G. (Ed.)

Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring Journal Article

In: ISME Journal, vol. 16, pp. 1798-1808, 2022.

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M, Acker; SL, Hogle; PM, Berube; T, Hackl; A, Coe; R, Stepanauskas; SW, Chisholm; DJ, Repeta

Phosphonate production by marine microbes: Exploring new sources and potential function Journal Article

In: PNAS, vol. 119, no. 11, pp. e2113386119, 2022.

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T, D’Angelo; J, Goordial; N, Poulton; L, Seyler; JA, Huber; R, Stepanauskas; BN, Orcutt

Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume Journal Article

In: Frontiers in Microbiology, vol. 12, no. 738231, 2022.

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C, Martínez-Pérez; C, Greening; SK, Bay; RJ, Lappan; Z, Zhao; D, De Corte; C, Hulbe; C, Ohneiser; C, Stevens; B, Thomson; R, Stepanauskas; JM, González; R, Logares; GJ, Herndl; SE, Morales; F, Baltar

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf Journal Article

In: Nature Communications, vol. 13, no. 117, 2022.

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C, Martínez-Pérez; C, Greening; SK, Bay; RJ, Lappan; Z, Zhao; D, De Corte; C, Hulbe; C, Ohneiser; C, Stevens; B, Thomson; R, Stepanauskas; JM, González; R, Logares; GJ, Herndl; SE, Morales; F, Baltar

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf Journal Article

In: Nature Communications, vol. 13, no. 117, 2022.

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2021

RM, Bowers; S, Nayfach; F, Schulz; SP, Jungbluth; IA, Ruhl; A, Sheremet; J, Lee; D, Goudeau; EA, Eloe-Fadrosh; R, Stepanauskas; RR, Malmstrom; NC, Kyrpides; PF, Dunfield; T, Woyke

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution Journal Article

In: The ISME Journal, vol. 16, pp. 1337-1347, 2021.

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RM, Bowers; S, Nayfach; F, Schulz; SP, Jungbluth; IA, Ruhl; J, Lee; D, Goudeau; EA, Eloe-Fadrosh; R, Stepanauskas; RR, Malmstrom; NC, Krypides; PF, Dunfield; T, Woyke

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell resolution Journal Article

In: ISME Journal, 2021.

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R, Hendrickson; C, Urbaniak; JJ, Minich; HS, Aronson; C, Martino; R, Stepanauskas; R, Knight; K, Venkateswaran

Clean room microbiome complexity impacts planetary protection bioburden Journal Article

In: Microbiome, vol. 9, no. 238, 2021, ISBN: 2049-2618.

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Hoffert, M.; Anderson, R. E.; Reveillaud, J.; Murphy, L. G.; Stepanauskas, R.; Huber, J. A.

Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems Journal Article

In: Frontiers in Microbiology, vol. 12, pp. 714920, 2021.

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Goordial, J.; D’angelo, T.; Labonté, J. M.; Poulton, N. J.; Brown, J. M.; Stepanauskas, R.; Früh-Green, G. L.; Orcutt, B. N.

Microbial diversity and function in shallow subsurface sediment and oceanic lithosphere of the atlantis massif Journal Article

In: mBio, vol. 12, no. 4, pp. e00490-21, 2021.

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Šulčius, S.; Alzbutas, G.; Juknevičiūtė, V.; Šimoliūnas, E.; Venckus, P.; Šimoliūnienė, M.; Paškauskas, R.

Exploring viral diversity in a gypsum karst lake ecosystem using targeted single-cell genomics Journal Article

In: Genes, vol. 12, no. 6, pp. 886, 2021.

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Murphy, C. L.; Sheremet, A.; Dunfield, P. F.; Spear, J. R.; Stepanauskas, R.; Woyke, T.; Elshahed, M. S.; Youssef, N. H.

Genomic analysis of the yet-uncultured binatota reveals broad methylotrophic, alkane-degradation, and pigment production capacities Journal Article

In: mBio, vol. 12, no. 3, pp. e00985-21, 2021.

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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, vol. 39, pp. 499-509, 2021.

Abstract | Links | BibTeX

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, vol. 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, vol. 118, no. 11, 2021, ISSN: 1091-6490.

Abstract | Links | BibTeX

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, vol. 11, no. 524828, 2020.

Abstract | Links | BibTeX

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, vol. 11, no. 1848, 2020.

Abstract | Links | BibTeX

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, vol. 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, vol. 11, no. 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, vol. 11, no. 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, vol. 179, no. 7, pp. 1623-1635, 2019.

Abstract | Links | BibTeX

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, vol. 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, vol. 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, vol. 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, vol. 9, pp. 6025, 2019.

Abstract | Links | BibTeX

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, vol. 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, vol. 8, pp. e01249-18, 2019.

Abstract | Links | BibTeX

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, vol. 13, pp. 1457-1468, 2019, ISSN: 1751-7370.

Abstract | Links | BibTeX

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, vol. 8, 2019.

Abstract | Links | BibTeX

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 , vol. 21, no. 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, vol. 10, no. 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, vol. 9, 2018.

Abstract | Links | BibTeX

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, vol. 6, no. 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, vol. 5, 2018, ISSN: 2052-4463.

Abstract | Links | BibTeX

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.

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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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

127 entries « 1 of 3 »