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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. 2019 Sep 27. doi: 10.1089/ast.2018.1892. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


Oxygen consumption rates of bacteria under nutrient-limited conditions.

Riedel TE, Berelson WM, Nealson KH, Finkel SE.

Appl Environ Microbiol. 2013 Aug;79(16):4921-31. doi: 10.1128/AEM.00756-13. Epub 2013 Jun 14.


Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.


Rate enhancement of bacterial extracellular electron transport involves bound flavin semiquinones.

Okamoto A, Hashimoto K, Nealson KH, Nakamura R.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7856-61. doi: 10.1073/pnas.1220823110. Epub 2013 Apr 1.


Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS.

Genome Res. 2013 May;23(5):867-77. doi: 10.1101/gr.150433.112. Epub 2013 Apr 5.


A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.

Ishii S, Suzuki S, Norden-Krichmar TM, Tenney A, Chain PS, Scholz MB, Nealson KH, Bretschger O.

Nat Commun. 2013;4:1601. doi: 10.1038/ncomms2615.


Shewanella oneidensis MR-1 chemotaxis proteins and electron-transport chain components essential for congregation near insoluble electron acceptors.

Harris HW, El-Naggar MY, Nealson KH.

Biochem Soc Trans. 2012 Dec 1;40(6):1167-77. doi: 10.1042/BST20120232.


Adaptation of soil microbes during establishment of microbial fuel cell consortium fed with lactate.

Futamata H, Bretschger O, Cheung A, Kan J, Owen R, Nealson KH.

J Biosci Bioeng. 2013 Jan;115(1):58-63. doi: 10.1016/j.jbiosc.2012.07.016. Epub 2012 Aug 16.


Electricity generation from a floating microbial fuel cell.

Huang Y, He Z, Kan J, Manohar AK, Nealson KH, Mansfeld F.

Bioresour Technol. 2012 Jun;114:308-13. doi: 10.1016/j.biortech.2012.02.142. Epub 2012 Mar 7.


Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment.

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

PLoS One. 2012;7(2):e30495. doi: 10.1371/journal.pone.0030495. Epub 2012 Feb 7.

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