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A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index.

Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D.

mBio. 2020 Jan 14;11(1). pii: e02475-19. doi: 10.1128/mBio.02475-19.


Detecting Endogenous Microbial Metabolism and Differentiating Between Abiotic and Biotic Signals Observed by Bioelectrochemical Systems in Soils.

Lam BR, Barge LM, Noell AC, Nealson KH.

Astrobiology. 2020 Jan;20(1):39-52. doi: 10.1089/ast.2018.1892. Epub 2019 Sep 27.


Genome Sequence of Mariprofundus sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral.

Lopez A, Albino D, Beraki S, Broomell S, Canela R, Dingmon T, Estrada S, Fernandez M, Savalia P, Nealson K, Emerson D, Barco R, Tully BJ, Amend JP.

Microbiol Resour Announc. 2019 Sep 26;8(39). pii: e00995-19. doi: 10.1128/MRA.00995-19.


Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment.

Lam BR, Barr CR, Rowe AR, Nealson KH.

Front Microbiol. 2019 Aug 28;10:1979. doi: 10.3389/fmicb.2019.01979. eCollection 2019.


The kinetics of siderophore-mediated olivine dissolution.

Torres MA, Dong S, Nealson KH, West AJ.

Geobiology. 2019 Jul;17(4):401-416. doi: 10.1111/gbi.12332. Epub 2019 Feb 7.


Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater.

Suzuki S, Nealson KH, Ishii S.

Front Microbiol. 2018 Dec 18;9:3141. doi: 10.3389/fmicb.2018.03141. eCollection 2018.


Methane on Mars and Habitability: Challenges and Responses.

Yung YL, Chen P, Nealson K, Atreya S, Beckett P, Blank JG, Ehlmann B, Eiler J, Etiope G, Ferry JG, Forget F, Gao P, Hu R, Kleinböhl A, Klusman R, Lefèvre F, Miller C, Mischna M, Mumma M, Newman S, Oehler D, Okumura M, Oremland R, Orphan V, Popa R, Russell M, Shen L, Sherwood Lollar B, Staehle R, Stamenković V, Stolper D, Templeton A, Vandaele AC, Viscardy S, Webster CR, Wennberg PO, Wong ML, Worden J.

Astrobiology. 2018 Oct;18(10):1221-1242. doi: 10.1089/ast.2018.1917. Epub 2018 Sep 19. Review.


Self-standing Electrochemical Set-up to Enrich Anode-respiring Bacteria On-site.

Okamoto A, Rowe A, Deng X, Nealson KH.

J Vis Exp. 2018 Jul 24;(137). doi: 10.3791/57632.


Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.

Ishii S, Suzuki S, Tenney A, Nealson KH, Bretschger O.

ISME J. 2018 Dec;12(12):2844-2863. doi: 10.1038/s41396-018-0238-2. Epub 2018 Jul 26.


Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments.

Lam BR, Rowe AR, Nealson KH.

Environ Microbiol. 2018 Jun;20(6):2270-2287. doi: 10.1111/1462-2920.14275. Epub 2018 Aug 8.


Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments.

Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A.

Int J Syst Evol Microbiol. 2018 May;68(5):1652-1658. doi: 10.1099/ijsem.0.002723. Epub 2018 Mar 23.


Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors.

Rowe AR, Rajeev P, Jain A, Pirbadian S, Okamoto A, Gralnick JA, El-Naggar MY, Nealson KH.

mBio. 2018 Feb 27;9(1). pii: e02203-17. doi: 10.1128/mBio.02203-17.


Multi-heme cytochromes provide a pathway for survival in energy-limited environments.

Deng X, Dohmae N, Nealson KH, Hashimoto K, Okamoto A.

Sci Adv. 2018 Feb 16;4(2):eaao5682. doi: 10.1126/sciadv.aao5682. eCollection 2018 Feb.


Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions.

Robador A, LaRowe DE, Finkel SE, Amend JP, Nealson KH.

Front Microbiol. 2018 Feb 1;9:109. doi: 10.3389/fmicb.2018.00109. eCollection 2018.


Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer.

Neely C, Bou Khalil C, Cervantes A, Diaz R, Escobar A, Ho K, Hoefler S, Smith HH, Abuyen K, Savalia P, Nealson KH, Emerson D, Tully B, Barco RA, Amend J.

Genome Announc. 2018 Feb 1;6(5). pii: e01581-17. doi: 10.1128/genomeA.01581-17.


Redox Sensing within the Genus Shewanella.

Harris HW, Sánchez-Andrea I, McLean JS, Salas EC, Tran W, El-Naggar MY, Nealson KH.

Front Microbiol. 2018 Jan 25;8:2568. doi: 10.3389/fmicb.2017.02568. eCollection 2017.


Quantifying Microorganisms at Low Concentrations Using Digital Holographic Microscopy (DHM).

Bedrossian M, Barr C, Lindensmith CA, Nealson K, Nadeau JL.

J Vis Exp. 2017 Nov 1;(129). doi: 10.3791/56343.


A metabolic-activity-detecting approach to life detection: Restoring a chemostat from stop-feeding using a rapid bioactivity assay.

Li SL, Bai MD, Hsiao CJ, Cheng SS, Nealson KH.

Bioelectrochemistry. 2017 Dec;118:147-153. doi: 10.1016/j.bioelechem.2017.08.001. Epub 2017 Aug 9.


Bioelectricity (electromicrobiology) and sustainability.

Nealson KH.

Microb Biotechnol. 2017 Sep;10(5):1114-1119. doi: 10.1111/1751-7915.12834. Epub 2017 Aug 14.


Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.

Suzuki S, Ishii S, Hoshino T, Rietze A, Tenney A, Morrill PL, Inagaki F, Kuenen JG, Nealson KH.

ISME J. 2017 Nov;11(11):2584-2598. doi: 10.1038/ismej.2017.111. Epub 2017 Jul 21.


Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources.

Ishii S, Suzuki S, Yamanaka Y, Wu A, Nealson KH, Bretschger O.

Bioelectrochemistry. 2017 Oct;117:74-82. doi: 10.1016/j.bioelechem.2017.06.003. Epub 2017 Jun 15.


Outer membrane cytochromes/flavin interactions in Shewanella spp.-A molecular perspective.

Babanova S, Matanovic I, Cornejo J, Bretschger O, Nealson K, Atanassov P.

Biointerphases. 2017 May 31;12(2):021004. doi: 10.1116/1.4984007.


In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring.

Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A.

Environ Microbiol. 2017 Jun;19(6):2272-2285. doi: 10.1111/1462-2920.13723. Epub 2017 May 5.


Nanoelectronic Investigation Reveals the Electrochemical Basis of Electrical Conductivity in Shewanella and Geobacter.

Ding M, Shiu HY, Li SL, Lee CK, Wang G, Wu H, Weiss NO, Young TD, Weiss PS, Wong GC, Nealson KH, Huang Y, Duan X.

ACS Nano. 2016 Nov 22;10(11):9919-9926. Epub 2016 Nov 8.


Evolution of Cell Size Homeostasis and Growth Rate Diversity during Initial Surface Colonization of Shewanella oneidensis.

Lee CK, Kim AJ, Santos GS, Lai PY, Lee SY, Qiao DF, Anda J, Young TD, Chen Y, Rowe AR, Nealson KH, Weiss PS, Wong GCL.

ACS Nano. 2016 Oct 25;10(10):9183-9192. doi: 10.1021/acsnano.6b05123. Epub 2016 Sep 6.


Electromicrobiology: realities, grand challenges, goals and predictions.

Nealson KH, Rowe AR.

Microb Biotechnol. 2016 Sep;9(5):595-600. doi: 10.1111/1751-7915.12400. Epub 2016 Aug 10. Review.


Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

Blatter M, Sugnaux M, Comninellis C, Nealson K, Fischer F.

ChemSusChem. 2016 Jul 7;9(13):1570-4. doi: 10.1002/cssc.201600459. Epub 2016 Jun 6.


Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids.

Robador A, LaRowe DE, Jungbluth SP, Lin HT, Rappé MS, Nealson KH, Amend JP.

Front Microbiol. 2016 Apr 5;7:454. doi: 10.3389/fmicb.2016.00454. eCollection 2016.


Real-Time Manganese Phase Dynamics during Biological and Abiotic Manganese Oxide Reduction.

Johnson JE, Savalia P, Davis R, Kocar BD, Webb SM, Nealson KH, Fischer WW.

Environ Sci Technol. 2016 Apr 19;50(8):4248-58. doi: 10.1021/acs.est.5b04834. Epub 2016 Mar 28.


Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1.

Wei H, Dai J, Xia M, Romine MF, Shi L, Beliav A, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J, Qiu D.

Microbiology. 2016 Jun;162(6):930-941. doi: 10.1099/mic.0.000285. Epub 2016 Mar 23.


Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.

Kan J, Clingenpeel S, Dow CL, McDermott TR, Macur RE, Inskeep WP, Nealson KH.

Front Microbiol. 2016 Feb 29;7:210. doi: 10.3389/fmicb.2016.00210. eCollection 2016.


Species-dependent hydrodynamics of flagellum-tethered bacteria in early biofilm development.

Bennett RR, Lee CK, De Anda J, Nealson KH, Yildiz FH, O'Toole GA, Wong GC, Golestanian R.

J R Soc Interface. 2016 Feb;13(115):20150966. doi: 10.1098/rsif.2015.0966.


Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function.

Inskeep WP, Jay ZJ, Macur RE, Clingenpeel S, Tenney A, Lovalvo D, Beam JP, Kozubal MA, Shanks WC, Morgan LA, Kan J, Gorby Y, Yooseph S, Nealson K.

Front Microbiol. 2015 Oct 26;6:1044. doi: 10.3389/fmicb.2015.01044. eCollection 2015.


Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach.

Ishii S, Suzuki S, Tenney A, Norden-Krichmar TM, Nealson KH, Bretschger O.

Sci Rep. 2015 Oct 7;5:14840. doi: 10.1038/srep14840.


Ignimbrite textural properties as determinants of endolithic colonization patterns from hyper-arid Atacama Desert.

Cámara B, Suzuki S, Nealson KH, Wierzchos J, Ascaso C, Artieda O, de los Ríos A.

Int Microbiol. 2014 Dec;17(4):235-47. doi: 10.2436/20.1501.01.226.


Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes.

Li SL, Nealson KH.

Front Microbiol. 2015 Feb 17;6:111. doi: 10.3389/fmicb.2015.00111. eCollection 2015.


Ex-phot: a new take on primitive utilization of solar energy.

Nealson KH.

Environ Microbiol Rep. 2015 Feb;7(1):33-5. doi: 10.1111/1758-2229.12256. No abstract available.


Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism.

Rowe AR, Chellamuthu P, Lam B, Okamoto A, Nealson KH.

Front Microbiol. 2015 Jan 14;5:784. doi: 10.3389/fmicb.2014.00784. eCollection 2014.


Woody Hastings: 65 years of fun.

Greenberg EP, Nealson KH, Johnson CH.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):14964-5. doi: 10.1073/pnas.1415972111. Epub 2014 Sep 30. No abstract available.


Flavin redox bifurcation as a mechanism for controlling the direction of electron flow during extracellular electron transfer.

Okamoto A, Hashimoto K, Nealson KH.

Angew Chem Int Ed Engl. 2014 Oct 6;53(41):10988-91. doi: 10.1002/anie.201407004. Epub 2014 Aug 26.


Cell-secreted flavins bound to membrane cytochromes dictate electron transfer reactions to surfaces with diverse charge and pH.

Okamoto A, Kalathil S, Deng X, Hashimoto K, Nakamura R, Nealson KH.

Sci Rep. 2014 Jul 11;4:5628. doi: 10.1038/srep05628.


Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.

Suzuki S, Kuenen JG, Schipper K, van der Velde S, Ishii S, Wu A, Sorokin DY, Tenney A, Meng X, Morrill PL, Kamagata Y, Muyzer G, Nealson KH.

Nat Commun. 2014 May 21;5:3900. doi: 10.1038/ncomms4900.


An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome.

Edlund A, Yang Y, Hall AP, Guo L, Lux R, He X, Nelson KE, Nealson KH, Yooseph S, Shi W, McLean JS.

Microbiome. 2013 Oct 2;1(1):25. doi: 10.1186/2049-2618-1-25.


Microbial population and functional dynamics associated with surface potential and carbon metabolism.

Ishii S, Suzuki S, Norden-Krichmar TM, Phan T, Wanger G, Nealson KH, Sekiguchi Y, Gorby YA, Bretschger O.

ISME J. 2014 May;8(5):963-78. doi: 10.1038/ismej.2013.217. Epub 2013 Dec 19.


Electricity generation by microbial fuel cell using microorganisms as catalyst in cathode.

Jang JK, Kan J, Bretschger O, Gorby YA, Hsu L, Kim BH, Nealson KH.

J Microbiol Biotechnol. 2013 Dec;23(12):1765-73.


Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells.

Ishii S, Suzuki S, Norden-Krichmar TM, Wu A, Yamanaka Y, Nealson KH, Bretschger O.

Water Res. 2013 Dec 1;47(19):7120-30. doi: 10.1016/j.watres.2013.07.048. Epub 2013 Oct 20.


Yellowstone lake nanoarchaeota.

Clingenpeel S, Kan J, Macur RE, Woyke T, Lovalvo D, Varley J, Inskeep WP, Nealson K, McDermott TR.

Front Microbiol. 2013 Sep 11;4:274. doi: 10.3389/fmicb.2013.00274. eCollection 2013.


Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem.

Suzuki S, Ishii S, Wu A, Cheung A, Tenney A, Wanger G, Kuenen JG, Nealson KH.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15336-41. doi: 10.1073/pnas.1302426110. Epub 2013 Sep 3.


Isotope ratios of H, C, and O in CO2 and H2O of the martian atmosphere.

Webster CR, Mahaffy PR, Flesch GJ, Niles PB, Jones JH, Leshin LA, Atreya SK, Stern JC, Christensen LE, Owen T, Franz H, Pepin RO, Steele A; MSL Science Team, Achilles C, Agard C, Alves Verdasca JA, Anderson R, Anderson R, Archer D, Armiens-Aparicio C, Arvidson R, Atlaskin E, Aubrey A, Baker B, Baker M, Balic-Zunic T, Baratoux D, Baroukh J, Barraclough B, Bean K, Beegle L, Behar A, Bell J, Bender S, Benna M, Bentz J, Berger G, Berger J, Berman D, Bish D, Blake DF, Blanco Avalos JJ, Blaney D, Blank J, Blau H, Bleacher L, Boehm E, Botta O, Böttcher S, Boucher T, Bower H, Boyd N, Boynton B, Breves E, Bridges J, Bridges N, Brinckerhoff W, Brinza D, Bristow T, Brunet C, Brunner A, Brunner W, Buch A, Bullock M, Burmeister S, Cabane M, Calef F, Cameron J, Campbell J, Cantor B, Caplinger M, Caride Rodríguez J, Carmosino M, Carrasco Blázquez I, Charpentier A, Chipera S, Choi D, Clark B, Clegg S, Cleghorn T, Cloutis E, Cody G, Coll P, Conrad P, Coscia D, Cousin A, Cremers D, Crisp J, Cros A, Cucinotta F, d'Uston C, Davis S, Day M, de la Torre Juarez M, DeFlores L, DeLapp D, DeMarines J, DesMarais D, Dietrich W, Dingler R, Donny C, Downs B, Drake D, Dromart G, Dupont A, Duston B, Dworkin J, Dyar MD, Edgar L, Edgett K, Edwards C, Edwards L, Ehlmann B, Ehresmann B, Eigenbrode J, Elliott B, Elliott H, Ewing R, Fabre C, Fairén A, Farley K, Farmer J, Fassett C, Favot L, Fay D, Fedosov F, Feldman J, Feldman S, Fisk M, Fitzgibbon M, Floyd M, Flückiger L, Forni O, Fraeman A, Francis R, François P, Freissinet C, French KL, Frydenvang J, Gaboriaud A, Gailhanou M, Garvin J, Gasnault O, Geffroy C, Gellert R, Genzer M, Glavin D, Godber A, Goesmann F, Goetz W, Golovin D, Gómez Gómez F, Gómez-Elvira J, Gondet B, Gordon S, Gorevan S, Grant J, Griffes J, Grinspoon D, Grotzinger J, Guillemot P, Guo J, Gupta S, Guzewich S, Haberle R, Halleaux D, Hallet B, Hamilton V, Hardgrove C, Harker D, Harpold D, Harri AM, Harshman K, Hassler D, Haukka H, Hayes A, Herkenhoff K, Herrera P, Hettrich S, Heydari E, Hipkin V, Hoehler T, Hollingsworth J, Hudgins J, Huntress W, Hurowitz J, Hviid S, Iagnemma K, Indyk S, Israël G, Jackson R, Jacob S, Jakosky B, Jensen E, Jensen JK, Johnson J, Johnson M, Johnstone S, Jones A, Joseph J, Jun I, Kah L, Kahanpää H, Kahre M, Karpushkina N, Kasprzak W, Kauhanen J, Keely L, Kemppinen O, Keymeulen D, Kim MH, Kinch K, King P, Kirkland L, Kocurek G, Koefoed A, Köhler J, Kortmann O, Kozyrev A, Krezoski J, Krysak D, Kuzmin R, Lacour JL, Lafaille V, Langevin Y, Lanza N, Lasue J, Le Mouélic S, Lee EM, Lee QM, Lees D, Lefavor M, Lemmon M, Lepinette Malvitte A, Léveillé R, Lewin-Carpintier É, Lewis K, Li S, Lipkaman L, Little C, Litvak M, Lorigny E, Lugmair G, Lundberg A, Lyness E, Madsen M, Maki J, Malakhov A, Malespin C, Malin M, Mangold N, Manhes G, Manning H, Marchand G, Marín Jiménez M, Martín García C, Martin D, Martin M, Martínez-Frías J, Martín-Soler J, Martín-Torres FJ, Mauchien P, Maurice S, McAdam A, McCartney E, McConnochie T, McCullough E, McEwan I, McKay C, McLennan S, McNair S, Melikechi N, Meslin PY, Meyer M, Mezzacappa A, Miller H, Miller K, Milliken R, Ming D, Minitti M, Mischna M, Mitrofanov I, Moersch J, Mokrousov M, Molina Jurado A, Moores J, Mora-Sotomayor L, Morookian JM, Morris R, Morrison S, Mueller-Mellin R, Muller JP, Muñoz Caro G, Nachon M, Navarro López S, Navarro-González R, Nealson K, Nefian A, Nelson T, Newcombe M, Newman C, Newsom H, Nikiforov S, Nixon B, Noe Dobrea E, Nolan T, Oehler D, Ollila A, Olson T, de Pablo Hernández MÁ, Paillet A, Pallier E, Palucis M, Parker T, Parot Y, Patel K, Paton M, Paulsen G, Pavlov A, Pavri B, Peinado-González V, Peret L, Perez R, Perrett G, Peterson J, Pilorget C, Pinet P, Pla-García J, Plante I, Poitrasson F, Polkko J, Popa R, Posiolova L, Posner A, Pradler I, Prats B, Prokhorov V, Purdy SW, Raaen E, Radziemski L, Rafkin S, Ramos M, Rampe E, Raulin F, Ravine M, Reitz G, Rennó N, Rice M, Richardson M, Robert F, Robertson K, Rodriguez Manfredi JA, Romeral-Planelló JJ, Rowland S, Rubin D, Saccoccio M, Salamon A, Sandoval J, Sanin A, Sans Fuentes SA, Saper L, Sarrazin P, Sautter V, Savijärvi H, Schieber J, Schmidt M, Schmidt W, Scholes D, Schoppers M, Schröder S, Schwenzer S, Sebastian Martinez E, Sengstacken A, Shterts R, Siebach K, Siili T, Simmonds J, Sirven JB, Slavney S, Sletten R, Smith M, Sobrón Sánchez P, Spanovich N, Spray J, Squyres S, Stack K, Stalport F, Stein T, Stewart N, Stipp SL, Stoiber K, Stolper E, Sucharski B, Sullivan R, Summons R, Sumner D, Sun V, Supulver K, Sutter B, Szopa C, Tan F, Tate C, Teinturier S, ten Kate I, Thomas P, Thompson L, Tokar R, Toplis M, Torres Redondo J, Trainer M, Treiman A, Tretyakov V, Urqui-O'Callaghan R, Van Beek J, Van Beek T, VanBommel S, Vaniman D, Varenikov A, Vasavada A, Vasconcelos P, Vicenzi E, Vostrukhin A, Voytek M, Wadhwa M, Ward J, Weigle E, Wellington D, Westall F, Wiens RC, Wilhelm MB, Williams A, Williams J, Williams R, Williams RB, Wilson M, Wimmer-Schweingruber R, Wolff M, Wong M, Wray J, Wu M, Yana C, Yen A, Yingst A, Zeitlin C, Zimdar R, Zorzano Mier MP.

Science. 2013 Jul 19;341(6143):260-3. doi: 10.1126/science.1237961.

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