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Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.

Song HS, Lee JY, Haruta S, Nelson WC, Lee DY, Lindemann SR, Fredrickson JK, Bernstein HC.

Front Microbiol. 2019 Jun 11;10:1264. doi: 10.3389/fmicb.2019.01264. eCollection 2019.


Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Mar 7;9(1):1034. doi: 10.1038/s41467-018-03572-7.


Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Feb 8;9(1):585. doi: 10.1038/s41467-018-02922-9. Erratum in: Nat Commun. 2018 Mar 7;9(1):1034.


Harnessing the Periplasm of Bacterial Cells To Develop Biocatalysts for the Biosynthesis of Highly Pure Chemicals.

Yang Y, Wu Y, Hu Y, Wang H, Guo L, Fredrickson JK, Cao B.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01693-17. doi: 10.1128/AEM.01693-17. Print 2018 Jan 1.


Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process.

Song HS, Thomas DG, Stegen JC, Li M, Liu C, Song X, Chen X, Fredrickson JK, Zachara JM, Scheibe TD.

Front Microbiol. 2017 Sep 29;8:1866. doi: 10.3389/fmicb.2017.01866. eCollection 2017.


Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat.

Bernstein HC, Brislawn CJ, Dana K, Flores-Wentz T, Cory AB, Fansler SJ, Fredrickson JK, Moran JJ.

FEMS Microbiol Ecol. 2017 Oct 1;93(10). doi: 10.1093/femsec/fix121.


Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.

Hou Z, Nelson WC, Stegen JC, Murray CJ, Arntzen E, Crump AR, Kennedy DW, Perkins MC, Scheibe TD, Fredrickson JK, Zachara JM.

Sci Rep. 2017 Sep 20;7(1):12006. doi: 10.1038/s41598-017-12275-w.


Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.


Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C.

Environ Microbiol Rep. 2017 Oct;9(5):512-521. doi: 10.1111/1758-2229.12558. Epub 2017 Jul 13.


Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.

Liu Y, Liu C, Nelson WC, Shi L, Xu F, Liu Y, Yan A, Zhong L, Thompson C, Fredrickson JK, Zachara JM.

Environ Sci Technol. 2017 May 2;51(9):4877-4886. doi: 10.1021/acs.est.6b05018. Epub 2017 Apr 18.


Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership.

Bernstein HC, McClure RS, Thiel V, Sadler NC, Kim YM, Chrisler WB, Hill EA, Bryant DA, Romine MF, Jansson JK, Fredrickson JK, Beliaev AS.

mSystems. 2017 Mar 7;2(2). pii: e00181-16. doi: 10.1128/mSystems.00181-16. eCollection 2017 Mar-Apr.


Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.

Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC.

Environ Microbiol. 2017 Apr;19(4):1552-1567. doi: 10.1111/1462-2920.13720. Epub 2017 Mar 28.


Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC.

Front Microbiol. 2016 Dec 16;7:1949. doi: 10.3389/fmicb.2016.01949. eCollection 2016.


Syntrophic anaerobic photosynthesis via direct interspecies electron transfer.

Ha PT, Lindemann SR, Shi L, Dohnalkova AC, Fredrickson JK, Madigan MT, Beyenal H.

Nat Commun. 2017 Jan 9;8:13924. doi: 10.1038/ncomms13924.


Trade-offs between microbiome diversity and productivity in a stratified microbial mat.

Bernstein HC, Brislawn C, Renslow RS, Dana K, Morton B, Lindemann SR, Song HS, Atci E, Beyenal H, Fredrickson JK, Jansson JK, Moran JJ.

ISME J. 2017 Feb;11(2):405-414. doi: 10.1038/ismej.2016.133. Epub 2016 Nov 1.


Extracellular electron transfer mechanisms between microorganisms and minerals.

Shi L, Dong H, Reguera G, Beyenal H, Lu A, Liu J, Yu HQ, Fredrickson JK.

Nat Rev Microbiol. 2016 Oct;14(10):651-62. doi: 10.1038/nrmicro.2016.93. Epub 2016 Aug 30. Review.


Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies.

Stegen JC, Konopka A, McKinley JP, Murray C, Lin X, Miller MD, Kennedy DW, Miller EA, Resch CT, Fredrickson JK.

Sci Rep. 2016 Jul 29;6:30553. doi: 10.1038/srep30553.


Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth.

Bernstein HC, McClure RS, Hill EA, Markillie LM, Chrisler WB, Romine MF, McDermott JE, Posewitz MC, Bryant DA, Konopka AE, Fredrickson JK, Beliaev AS.

MBio. 2016 Jul 26;7(4). pii: e00949-16. doi: 10.1128/mBio.00949-16.


Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

Stegen JC, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Danczak RE, Fansler SJ, Kennedy DW, Resch CT, Tfaily M.

Nat Commun. 2016 Apr 7;7:11237. doi: 10.1038/ncomms11237.


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):930-41. doi: 10.1099/mic.0.000285. Epub 2016 Mar 23.


Engineering microbial consortia for controllable outputs.

Lindemann SR, Bernstein HC, Song HS, Fredrickson JK, Fields MW, Shou W, Johnson DR, Beliaev AS.

ISME J. 2016 Sep;10(9):2077-84. doi: 10.1038/ismej.2016.26. Epub 2016 Mar 11.


Editorial: Systems Biology and Ecology of Microbial Mat Communities.

Klotz MG, Bryant DA, Fredrickson JK, Inskeep WP, Kühl M.

Front Microbiol. 2016 Feb 9;7:115. doi: 10.3389/fmicb.2016.00115. eCollection 2016. No abstract available.


Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.

Song HS, Renslow RS, Fredrickson JK, Lindemann SR.

Front Microbiol. 2015 Dec 1;6:1298. doi: 10.3389/fmicb.2015.01298. eCollection 2015.


Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA.

Liu Y, Fredrickson JK, Zachara JM, Shi L.

Front Microbiol. 2015 Oct 1;6:1075. doi: 10.3389/fmicb.2015.01075. eCollection 2015.


Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling.

Liu Y, Fredrickson JK, Sadler NC, Nandhikonda P, Smith RD, Wright AT.

Biotechnol Biofuels. 2015 Sep 25;8:156. doi: 10.1186/s13068-015-0343-7. eCollection 2015. Review.


Regulation of electron transfer processes affects phototrophic mat structure and activity.

Ha PT, Renslow RS, Atci E, Reardon PN, Lindemann SR, Fredrickson JK, Call DR, Beyenal H.

Front Microbiol. 2015 Sep 3;6:909. doi: 10.3389/fmicb.2015.00909. eCollection 2015.


Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer.

Edwards MJ, White GF, Norman M, Tome-Fernandez A, Ainsworth E, Shi L, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA.

Sci Rep. 2015 Jul 1;5:11677. doi: 10.1038/srep11677.


ECOLOGY. Ecological communities by design.

Fredrickson JK.

Science. 2015 Jun 26;348(6242):1425-7. doi: 10.1126/science.aab0946. No abstract available.


Estimating and mapping ecological processes influencing microbial community assembly.

Stegen JC, Lin X, Fredrickson JK, Konopka AE.

Front Microbiol. 2015 May 1;6:370. doi: 10.3389/fmicb.2015.00370. eCollection 2015.


Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms.

Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO.

Front Microbiol. 2015 Apr 17;6:209. doi: 10.3389/fmicb.2015.00209. eCollection 2015.


An autotrophic H2 -oxidizing, nitrate-respiring, Tc(VII)-reducing Acidovorax sp. isolated from a subsurface oxic-anoxic transition zone.

Lee JH, Fredrickson JK, Plymale AE, Dohnalkova AC, Resch CT, McKinley JP, Shi L.

Environ Microbiol Rep. 2015 Jun;7(3):395-403. doi: 10.1111/1758-2229.12263. Epub 2015 Apr 8. Erratum in: Environ Microbiol Rep. 2018 Apr;10 (2):228.


Genomic analyses of bacterial porin-cytochrome gene clusters.

Shi L, Fredrickson JK, Zachara JM.

Front Microbiol. 2014 Nov 26;5:657. doi: 10.3389/fmicb.2014.00657. eCollection 2014.


Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum.

Rodionova IA, Li X, Plymale AE, Motamedchaboki K, Konopka AE, Romine MF, Fredrickson JK, Osterman AL, Rodionov DA.

Environ Microbiol Rep. 2015 Apr;7(2):204-10. doi: 10.1111/1758-2229.12227. Epub 2014 Dec 17.


Trends and future challenges in sampling the deep terrestrial biosphere.

Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO.

Front Microbiol. 2014 Sep 12;5:481. doi: 10.3389/fmicb.2014.00481. eCollection 2014.


Spatially tracking (13) C-labelled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry.

Moran JJ, Doll CG, Bernstein HC, Renslow RS, Cory AB, Hutchison JR, Lindemann SR, Fredrickson JK.

Environ Microbiol Rep. 2014 Dec;6(6):786-91. doi: 10.1111/1758-2229.12211. Epub 2014 Oct 27.


A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA.

Liu Y, Wang Z, Liu J, Levar C, Edwards MJ, Babauta JT, Kennedy DW, Shi Z, Beyenal H, Bond DR, Clarke TA, Butt JN, Richardson DJ, Rosso KM, Zachara JM, Fredrickson JK, Shi L.

Environ Microbiol Rep. 2014 Dec;6(6):776-85. doi: 10.1111/1758-2229.12204. Epub 2014 Sep 24.


Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.

Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Markillie LM, Isern NG, Chrisler WB, Kucek LA, Hill EA, Pinchuk GE, Bryant DA, Wiley HS, Fredrickson JK, Konopka A.

ISME J. 2014 Nov;8(11):2243-55. doi: 10.1038/ismej.2014.69. Epub 2014 Apr 29.


Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.

Cole JK, Hutchison JR, Renslow RS, Kim YM, Chrisler WB, Engelmann HE, Dohnalkova AC, Hu D, Metz TO, Fredrickson JK, Lindemann SR.

Front Microbiol. 2014 Apr 7;5:109. doi: 10.3389/fmicb.2014.00109. eCollection 2014.


The X-ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe-mineral interface.

Edwards MJ, Baiden NA, Johs A, Tomanicek SJ, Liang L, Shi L, Fredrickson JK, Zachara JM, Gates AJ, Butt JN, Richardson DJ, Clarke TA.

FEBS Lett. 2014 May 21;588(10):1886-90. doi: 10.1016/j.febslet.2014.04.013. Epub 2014 Apr 18.


Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.

Stolyar S, Liu Z, Thiel V, Tomsho LP, Pinel N, Nelson WC, Lindemann SR, Romine MF, Haruta S, Schuster SC, Bryant DA, Fredrickson JK.

Genome Announc. 2014 Jan 30;2(1). pii: e01060-13. doi: 10.1128/genomeA.01060-13.


Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer.

Wilkins MJ, Kennedy DW, Castelle CJ, Field EK, Stepanauskas R, Fredrickson JK, Konopka AE.

Microbiology. 2014 Feb;160(2):362-372. doi: 10.1099/mic.0.073965-0.


Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

Babauta JT, Atci E, Ha PT, Lindemann SR, Ewing T, Call DR, Fredrickson JK, Beyenal H.

Front Microbiol. 2014 Jan 27;5:11. doi: 10.3389/fmicb.2014.00011. eCollection 2014.


Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria.

Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA.

Front Microbiol. 2013 Dec 23;4:407. doi: 10.3389/fmicb.2013.00407. eCollection 2013.


Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer.

Wilkins MJ, Kennedy DW, Castelle CJ, Field EK, Stepanauskas R, Fredrickson JK, Konopka AE.

Microbiology. 2014 Feb;160(Pt 2):362-72. doi: 10.1099/mic.0.073965-0. Epub 2013 Dec 9.


The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.

Lindemann SR, Moran JJ, Stegen JC, Renslow RS, Hutchison JR, Cole JK, Dohnalkova AC, Tremblay J, Singh K, Malfatti SA, Chen F, Tringe SG, Beyenal H, Fredrickson JK.

Front Microbiol. 2013 Nov 13;4:323. doi: 10.3389/fmicb.2013.00323. eCollection 2013.



Renslow R, Babauta J, Dohnalkova A, Boyanov M, Kemner K, Majors P, Fredrickson J, Beyenal H.

Energy Environ Sci. 2013 Jun 1;6(6):1827-1836.


Quantifying community assembly processes and identifying features that impose them.

Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, Rockhold ML, Konopka A.

ISME J. 2013 Nov;7(11):2069-79. doi: 10.1038/ismej.2013.93. Epub 2013 Jun 6.


Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals.

White GF, Shi Z, Shi L, Wang Z, Dohnalkova AC, Marshall MJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA.

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6346-51. doi: 10.1073/pnas.1220074110. Epub 2013 Mar 28.


Persistence of uranium groundwater plumes: contrasting mechanisms at two DOE sites in the groundwater-river interaction zone.

Zachara JM, Long PE, Bargar J, Davis JA, Fox P, Fredrickson JK, Freshley MD, Konopka AE, Liu C, McKinley JP, Rockhold ML, Williams KH, Yabusaki SB.

J Contam Hydrol. 2013 Apr;147:45-72. doi: 10.1016/j.jconhyd.2013.02.001. Epub 2013 Feb 15.


Feedback-controlled LED photobioreactor for photophysiological studies of cyanobacteria.

Melnicki MR, Pinchuk GE, Hill EA, Kucek LA, Stolyar SM, Fredrickson JK, Konopka AE, Beliaev AS.

Bioresour Technol. 2013 Apr;134:127-33. doi: 10.1016/j.biortech.2013.01.079. Epub 2013 Feb 10.


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