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Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy.

McGlynn SE, Chadwick GL, O'Neill A, Mackey M, Thor A, Deerinck TJ, Ellisman MH, Orphan VJ.

Appl Environ Microbiol. 2018 Apr 6. pii: AEM.00399-18. doi: 10.1128/AEM.00399-18. [Epub ahead of print]


Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples.

Zhu Y, Zhao R, Piehowski PD, Moore RJ, Lim S, Orphan VJ, Paša-Tolić L, Qian WJ, Smith RD, Kelly RT.

Int J Mass Spectrom. 2018 Apr;427:4-10. doi: 10.1016/j.ijms.2017.08.016. Epub 2017 Sep 1.


Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment.

Case DH, Ijiri A, Morono Y, Tavormina P, Orphan VJ, Inagaki F.

Front Microbiol. 2017 Dec 19;8:2569. doi: 10.3389/fmicb.2017.02569. eCollection 2017.


Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods.

Pasulka AL, Thamatrakoln K, Kopf SH, Guan Y, Poulos B, Moradian A, Sweredoski MJ, Hess S, Sullivan MB, Bidle KD, Orphan VJ.

Environ Microbiol. 2018 Feb;20(2):671-692. doi: 10.1111/1462-2920.13996. Epub 2017 Dec 14.


Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds.

Trembath-Reichert E, Morono Y, Ijiri A, Hoshino T, Dawson KS, Inagaki F, Orphan VJ.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9206-E9215. doi: 10.1073/pnas.1707525114. Epub 2017 Oct 3.


Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Oct 3;8(5). pii: e01561-17. doi: 10.1128/mBio.01561-17. No abstract available.


Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates.

Marlow JJ, Steele JA, Ziebis W, Scheller S, Case D, Reynard LM, Orphan VJ.

mSphere. 2017 Aug 23;2(4). pii: e00309-17. doi: 10.1128/mSphereDirect.00309-17. eCollection 2017 Jul-Aug.


Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Aug 1;8(4). pii: e00530-17. doi: 10.1128/mBio.00530-17. Erratum in: MBio. 2017 Oct 3;8(5):.


Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis.

Terrado R, Pasulka AL, Lie AA, Orphan VJ, Heidelberg KB, Caron DA.

ISME J. 2017 Sep;11(9):2022-2034. doi: 10.1038/ismej.2017.68. Epub 2017 May 19.


Rapid quantification and isotopic analysis of dissolved sulfur species.

Smith DA, Sessions AL, Dawson KS, Dalleska N, Orphan VJ.

Rapid Commun Mass Spectrom. 2017 May 15;31(9):791-803. doi: 10.1002/rcm.7846.


Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps.

Skennerton CT, Haroon MF, Briegel A, Shi J, Jensen GJ, Tyson GW, Orphan VJ.

ISME J. 2016 Nov;10(11):2679-2692. doi: 10.1038/ismej.2016.55. Epub 2016 Apr 8.


Starvation and recovery in the deep-sea methanotroph Methyloprofundus sedimenti.

Tavormina PL, Kellermann MY, Antony CP, Tocheva EI, Dalleska NF, Jensen AJ, Valentine DL, Hinrichs KU, Jensen GJ, Dubilier N, Orphan VJ.

Mol Microbiol. 2017 Jan;103(2):242-252. doi: 10.1111/mmi.13553. Epub 2016 Nov 22.


Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA.

Miranda PJ, McLain NK, Hatzenpichler R, Orphan VJ, Dillon JG.

Front Microbiol. 2016 Jul 27;7:1163. doi: 10.3389/fmicb.2016.01163. eCollection 2016.


Measurement of rare isotopologues of nitrous oxide by high-resolution multi-collector mass spectrometry.

Magyar PM, Orphan VJ, Eiler JM.

Rapid Commun Mass Spectrom. 2016 Sep 15;30(17):1923-40. doi: 10.1002/rcm.7671.


Members of the methanotrophic genus Methylomarinum inhabit inland mud pots.

Fradet DT, Tavormina PL, Orphan VJ.

PeerJ. 2016 Jul 12;4:e2116. doi: 10.7717/peerj.2116. eCollection 2016.


Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia.

Hatzenpichler R, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E4069-78. doi: 10.1073/pnas.1603757113. Epub 2016 Jun 28.


Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment.

Dawson KS, Scheller S, Dillon JG, Orphan VJ.

Front Microbiol. 2016 May 26;7:774. doi: 10.3389/fmicb.2016.00774. eCollection 2016.


Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities.

Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ.

Front Microbiol. 2016 Apr 29;7:563. doi: 10.3389/fmicb.2016.00563. eCollection 2016.


Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction.

Scheller S, Yu H, Chadwick GL, McGlynn SE, Orphan VJ.

Science. 2016 Feb 12;351(6274):703-7. doi: 10.1126/science.aad7154.


Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation.

Skennerton CT, Ward LM, Michel A, Metcalfe K, Valiente C, Mullin S, Chan KY, Gradinaru V, Orphan VJ.

Front Microbiol. 2015 Dec 23;6:1425. doi: 10.3389/fmicb.2015.01425. eCollection 2015.


Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum.

Kopf SH, Sessions AL, Cowley ES, Reyes C, Van Sambeek L, Hu Y, Orphan VJ, Kato R, Newman DK.

Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E110-6. doi: 10.1073/pnas.1512057112. Epub 2015 Dec 29.


Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages.

Case DH, Pasulka AL, Marlow JJ, Grupe BM, Levin LA, Orphan VJ.

MBio. 2015 Dec 22;6(6):e01348-15. doi: 10.1128/mBio.01348-15.


Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

Pasulka AL, Levin LA, Steele JA, Case DH, Landry MR, Orphan VJ.

Environ Microbiol. 2016 Sep;18(9):3022-43. doi: 10.1111/1462-2920.13185. Epub 2016 Jan 25.


Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW.

Science. 2015 Oct 23;350(6259):434-8. doi: 10.1126/science.aac7745.


Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses.

Dekas AE, Connon SA, Chadwick GL, Trembath-Reichert E, Orphan VJ.

ISME J. 2016 Mar;10(3):678-92. doi: 10.1038/ismej.2015.145. Epub 2015 Sep 22.


Single cell activity reveals direct electron transfer in methanotrophic consortia.

McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ.

Nature. 2015 Oct 22;526(7574):531-5. doi: 10.1038/nature15512. Epub 2015 Sep 16.


Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA.

Mason OU, Case DH, Naehr TH, Lee RW, Thomas RB, Bailey JV, Orphan VJ.

Microb Ecol. 2015 Oct;70(3):766-84. doi: 10.1007/s00248-015-0615-6. Epub 2015 May 7.


Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps.

Dawson KS, Osburn MR, Sessions AL, Orphan VJ.

Geobiology. 2015 Sep;13(5):462-77. doi: 10.1111/gbi.12140. Epub 2015 Apr 28.


Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats.

Kopf SH, McGlynn SE, Green-Saxena A, Guan Y, Newman DK, Orphan VJ.

Environ Microbiol. 2015 Jul;17(7):2542-56. doi: 10.1111/1462-2920.12752. Epub 2015 Mar 27.


A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments.

Bryson SJ, Thurber AR, Correa AM, Orphan VJ, Vega Thurber R.

Environ Microbiol. 2015 Oct;17(10):3708-21. doi: 10.1111/1462-2920.12758. Epub 2015 Mar 25.


Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs.

Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ.

Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):251-9. doi: 10.1099/ijs.0.062927-0. Epub 2014 Oct 23.


Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea.

Marlow JJ, Steele JA, Ziebis W, Thurber AR, Levin LA, Orphan VJ.

Nat Commun. 2014 Oct 14;5:5094. doi: 10.1038/ncomms6094.


Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps.

Sivan O, Antler G, Turchyn AV, Marlow JJ, Orphan VJ.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4139-47. doi: 10.1073/pnas.1412269111. Epub 2014 Sep 22.


The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars.

Marlow JJ, Larowe DE, Ehlmann BL, Amend JP, Orphan VJ.

Astrobiology. 2014 Apr;14(4):292-307. doi: 10.1089/ast.2013.1078. Epub 2014 Mar 31.


Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea.

Sapir A, Dillman AR, Connon SA, Grupe BM, Ingels J, Mundo-Ocampo M, Levin LA, Baldwin JG, Orphan VJ, Sternberg PW.

Front Microbiol. 2014 Feb 10;5:43. doi: 10.3389/fmicb.2014.00043. eCollection 2014.


In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry.

Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ.

Environ Microbiol. 2014 Aug;16(8):2568-90. doi: 10.1111/1462-2920.12436. Epub 2014 Apr 2.


Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh.

Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ.

Environ Microbiol. 2014 Nov;16(11):3398-415. doi: 10.1111/1462-2920.12388. Epub 2014 Feb 26.


Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.

Glass JB, Yu H, Steele JA, Dawson KS, Sun S, Chourey K, Pan C, Hettich RL, Orphan VJ.

Environ Microbiol. 2014 Jun;16(6):1592-611. doi: 10.1111/1462-2920.12314. Epub 2013 Nov 14.


Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea.

Dekas AE, Chadwick GL, Bowles MW, Joye SB, Orphan VJ.

Environ Microbiol. 2014 Oct;16(10):3012-29. doi: 10.1111/1462-2920.12247. Epub 2013 Sep 24.


Whole cell immunomagnetic enrichment of environmental microbial consortia using rRNA-targeted Magneto-FISH.

Trembath-Reichert E, Green-Saxena A, Orphan VJ.

Methods Enzymol. 2013;531:21-44. doi: 10.1016/B978-0-12-407863-5.00002-2.


Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane.

Green-Saxena A, Dekas AE, Dalleska NF, Orphan VJ.

ISME J. 2014 Jan;8(1):150-63. doi: 10.1038/ismej.2013.147. Epub 2013 Sep 5.


Polyphosphate storage during sporulation in the gram-negative bacterium Acetonema longum.

Tocheva EI, Dekas AE, McGlynn SE, Morris D, Orphan VJ, Jensen GJ.

J Bacteriol. 2013 Sep;195(17):3940-6.


Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis.

Bailey JV, Corsetti FA, Greene SE, Crosby CH, Liu P, Orphan VJ.

Geobiology. 2013 Sep;11(5):397-405. doi: 10.1111/gbi.12046. Epub 2013 Jun 21.


Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone.

Tavormina PL, Ussler W 3rd, Steele JA, Connon SA, Klotz MG, Orphan VJ.

Environ Microbiol Rep. 2013 Jun;5(3):414-23. doi: 10.1111/1758-2229.12025. Epub 2013 Jan 29.


Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-Labeling Study.

Yang S, Matsen JB, Konopka M, Green-Saxena A, Clubb J, Sadilek M, Orphan VJ, Beck D, Kalyuzhnaya MG.

Front Microbiol. 2013 Apr 3;4:70. doi: 10.3389/fmicb.2013.00070. eCollection 2013.


Classifying the metal dependence of uncharacterized nitrogenases.

McGlynn SE, Boyd ES, Peters JW, Orphan VJ.

Front Microbiol. 2013 Jan 30;3:419. doi: 10.3389/fmicb.2012.00419. eCollection 2012.


Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan.

Green-Saxena A, Feyzullayev A, Hubert CR, Kallmeyer J, Krueger M, Sauer P, Schulz HM, Orphan VJ.

Environ Microbiol. 2012 Dec;14(12):3271-86. doi: 10.1111/1462-2920.12015. Epub 2012 Nov 1.


Archaea in metazoan diets: implications for food webs and biogeochemical cycling.

Thurber AR, Levin LA, Orphan VJ, Marlow JJ.

ISME J. 2012 Aug;6(8):1602-12. doi: 10.1038/ismej.2012.16. Epub 2012 Mar 8.


A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems.

Levin LA, Orphan VJ, Rouse GW, Rathburn AE, Ussler W 3rd, Cook GS, Goffredi SK, Perez EM, Waren A, Grupe BM, Chadwick G, Strickrott B.

Proc Biol Sci. 2012 Jul 7;279(1738):2580-8. doi: 10.1098/rspb.2012.0205. Epub 2012 Mar 7.

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