石良，博士，教授，博士生导师，2016年引进到中国地质大学（武汉）环境学院的全职特聘教授。

联系方式：湖北省武汉市洪山区鲁磨路388号，430074，中国地质大学（武汉）环境学院生物科学与技术系，Email：liang.shi@cug.edu.cn

研究方向：地质微生物学，主要包括以下两个方面：

A.  微生物-矿物之间的胞外电子传导机理（Extracellular electron transfer mechanisms between microorganisms and minerals）。 作为一个非常重要的生物地球化学反应，微生物-矿物之间的电子传导直接影响到矿物的形成和风化,以及环境中污染物的转化,迁移和降解。另外，与常见的、位于细胞内的电子传递链不同，微生物-矿物之间的电子传导涉及到电子由细胞内传导到位于细胞外矿物表面的独特过程。这一特殊的电子传导过程可用来修复环境中污染物；低品位贵金属（铜、金等）的提取；生产电、氢气和生物燃料；室温合成新型的纳米材料和防治钢锈蚀。正是由于其在生物地球化学过程中的重要性，在生物电子传导过程中的特殊性和在生物技术中的多种应用性，微生物-矿物之间的电子传导近年来已成为地质微生物学、生物地球化学和多个基础学科以及应用科学研究的焦点和热点。因此，开展微生物-矿物之间胞外电子传导机理的研究，对提升从分子水平上认识微生物胞外电子传导过程、传导后对矿物的影响和开发利用与微生物胞外电子传导相关的生物技术，均具有重要意义。

B . 地质微生物群系：地表下微生物种群的组分和功能（Geomicrobiome: the microbial composition and function in subsurface environment）。目前，微生物学领域正经历由单分子、单菌株研究到群系研究的演变。这场革命性的转变将为有效利用微生物扭转全球暖化、防治人类疾病、增加粮食产量、保障饮水安全、治理环境污染和发展生物经济提供科学依据和技术保证。正是这些原因，世界各发达国家都在积极主导和推动与微生物群系相关的研究。在地表下，生活着数量庞大（>5×1029 和20%地球生物总量）、种类众多和尚未发现的微生物。它们是全球微生物群系的一个重要组成部分，并且直接参与多种重要的地质化学反应。因此，地表下微生物种群的组分和功能正成为地质微生物学界关注的热点和前沿领域，其研究成果对准确预测微生物种群与地质环境之间的相互作用、建立精确的污染物反应迁移模型和科学应用地质微生物群系，都有着极其重要的意义。

石良教授已在国际一流期刊发表专著1篇和SCI论文103篇，包括1篇Nature Reviews Microbiology (微生物学领域排名第一，影响因子=24.747)。论文总引用次数超过3715次，H-指数是33。

Publications

Peer-reviewed Scientific Journal Articles

1.  L Shi*, H Dong*, G Reguera, H Beyenal, A Lu, J Liu, HQ Yu and JK Fredrickson. 2016. Extracellular electron transfer mechanisms between microorganisms and minerals. Nature Reviews Microbiology 14: 651-662.

2.  J Liu, CI Pierce, L Shi, Z Wang, Z Shi, E Arenholz and KM Rosso. 2016. Particle size effect and the mechanism of hematite reduction by the outer membrane cytochrome OmcA of Shewanella oneidensis MR-1. Geochimica et Cosochimica Acta(doi.org/10.1016/j.gca.2016.08.022).

3.  A Sheng, F Liu, L Shi and J Liu. 2016. Aggregation kinetics of hematite particles in the presence of outer membrane cytochrome OmcA of Shewanella oneidenesis MR-1. Environmental Science & Technology (DOI: 10.1021/acs.est.6b02963).

4.  Y Ding, Y Zhou, J Yao, C Szymanski, J Fredrickson, L Shi, B Cao, Z Zhu, and X-Y Yu. 2016. In situ molecular imaging of the biofilm and its matrix. Analytical Chemistry (DOI: 10.1021/acs.analchem.6b03909).

5.  AH Tanzil, ST Sultana, SR Saunders, AC Dohnalkova, L Shi, Emily Davenport, P Ha, and H Beyenal.  2016. Production of gold nanoparticles by electrode-respiring Geobacter sulfurreducens biofilms. Enzyme and Microbial Technology(accepted).

6. AH Tanzil, ST Sultana, SR Saunders, L Shi, E Marsili and H Beyenal1. 2016. Biological synthesis of nanoparticles in biofilms。Enzyme and Microbial Technology (accepted).

7. H Wei, J Dai, M Xia, MF Romine, L Shi, A Beliaev, JM Tiedje, KH Nealson, JK Fredrickson, J Zhou and D Qiu. 2016. Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1. Microbiology16: 930-941.

8. S Yang, Y Liu, Liu C, L Shi, J Shang, H Shan, JM Zachara, JK Fredrickson, D Kennedy, CT Resch, C Thompson and S Fansler. 2016. Nitrate bioreduction in redox-variable low permeability sediments. Science of the Total Environment539:186-195.

9. Y Liu, JK Fredrickson, JM Zachara and L Shi*. 2015. Direct involvement of ombB, omaB and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA. Frontier in Microbiology 6: 1075.

10. Z Wang, Z Shi, L Shi, GF White, DJ Richardson, TA Clarke, JK Fredrickson and JM Zachara. 2015. Effects of soluble flavin on heterogeneous electron transfer between surface-exposed bacterial cytochromes and iron oxides. 2015.Geochimica et Cosmochimica Acta 163: 299-310.

11. M Edwards, G White, M Norman, A Tome-Fernandez, E Ainsworth, L Shi, JK Fredrickson, JM Zachara, J Butt, DJ Richardson and TA Clarke. 2015. Redox linked flavin sites in extracellular decaheme proteins involved in microbe-mineral electron transfer. Scientific Reports 5: 11677.

12. C Beckwith, MJ Edwards, M Lawes, L Shi, JN Butt, DJ Richardson and TA Clarke. 2015. Characterisation of MtoD fromSideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth. Frontier in Microbiology6:332.

13. J Lee, JK Fredrickson, AE Plymale, AC Dohnalkova, CT Resch, JP McKinley and L Shi. 2015. An autotrophic H2-oxidizing, nitrate-respiring, Tc(VII)-reducing Acidovorax sp. isolated from a subsurface oxic-anoxic transition zone.Environmental Microbiology Reports 7: 395-403.

14.  L Shi*, JK Fredrickson and JM Zachara. 2014. Genomic analyses of bacterial porin-cytochrome gene clusters.Frontier in Microbiology 5: 657.

15. Y Liu, Z Wang, J Liu, C Levar, MJ Edwards, JT Babauta, DW Kennedy, Z Shi, H Beynal, DR Bond, TA Clarke, JN Butt, DJ Richardson, KM Rosso, JM Zachara, JK Fredrickson and L Shi*. 2014. A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA. Environmental Microbiology Reports 6: 776-785.

16. S Pirbandian, SE Barchinger, KM Leung, HS Byun, Y Jangir, RA Bouhenni, SB Reed, MF Romine, DA Saffarini, L Shi, YA Gorby, JH Golbeck, and MY El-Naggar. 2014. Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components. Proceedings of the National Academy of Sciences of the United States of America 111: 12883-12888. (http://www.pnnl.gov/science/highlights/highlight.asp?id=3779).    

17.  MJ Edwards, N Baiden, A Johs, ST Tomanicek, L Liang, L Shi, JK Fredrickson, JM Zachara, AJ Gates, JN Butt, DJ Richardson and TA Clarke. 2014. The X-ray structure of Shewanella oneidensis OmcA reveals new insight at microbe-mineral interface. FEBS Letter 588: 1886-1890.

18. HS Byun, S. Pirbadian, A Nakano, L Shi and MY El-Naggar. 2014. Kinetic Monte Carlo simulations and molecular conductance measurements of the bacterial decaheme cytochrome MtrF. ChemElectroChem 1:1932-1939.

19. GF White, Z Shi, L Shi, Z Wang, AC  Dohnalkova, MJ Marshall, JK Fredrickson, JM Zachara, JN Butt, DJ Richardson and TA Clarke. 2013. Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals. Proceedings of the National Academy of Sciences of the United States of America 110(16): 6346-6351. (http://news.sciencemag.org/sciencenow/2013/03/scienceshot-the-original-iron-lu.html).

20. J Liu, CI Pearce, C Liu, Z Wang, L Shi, E Arenholz and KM Rosso. 2013. Fe3-xTixO4 nanoparticles as tunable probes of microbial metal oxidation. Journal of the American Chemical Society 135(24): 8896-8907.

21. DGG McMillan, SJ Marritt, MA Firer-Sherwood, L Shi, DJ Richardson, SD Evans, SJ Elliott, JN Butt and LJC Jeuken. 2013. Protein-protein interaction regulates the direction of catalysis and electron transfer in a redox enzyme complex.Journal of the American Chemical Society 135(28): 10650-10656.

22. V Kodali, MH Littke, SC Tilton, JG Teeguarden, L Shi, CW Frevert, W Wang, JG Pounds and BD Thrall. 2013. Dysregulation of macrophage activation profiles by engineered nanoparticles. ACS Nano 7(8): 6997–7010.

23. Z Shi, JM. Zachara, Z Wang, L Shi and JK Fredrickson. 2013. Reductive dissolution of goethite and hematite suspended particles by reduced flavins. Geochimica et Cosmochimica Acta 121: 139-154.

24. Y Wang, PC Sevinc, SM Belchik, JK Fredrickson, L Shi and HP Lu. 2013. Single-cell imaging and spectroscopic analyses of Cr(VI) reduction on the surface of bacterial cells. Langmuir 29(3): 950-956.

25. AJ Gates, SJ Marritt, JM Bradley, L Shi, DG McMillan, LJ Jeuken, DJ Richardson and JN Butt. 2013. Electrode assemblies composed of redox cascades from microbial respiratory electron transfer chains. Biochemical Society Transactions 41(5):1249-1253.

26.  L Shi*, KM Rosso, JM Zachara and JK Fredrickson. 2012. Mtr extracellular electron transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective. Biochemical Society Transactions 40(6): 1261-1267.

27. L Shi*, KM Rosso, TA Clarke, DJ Richardson, JM Zachara and JK Fredrickson. 2012. Molecular underpinnings of Fe(III) oxide reduction by Shewanella oneidensis MR-1. Frontiers in Microbiology 3: 50. doi: 10.3389/fmicb.2012.00050.

28. J Liu, Z Wang, SM Belchik, MJ Edwards, C Liu, DW Kennedy, ED Merkley, MS Lipton, JN Butt, DJ Richardson, JM Zachara, JK Fredrickson, KM Rosso and L Shi*. 2012. Identification and characterization of MtoA: a decaheme c-type cytochrome of the neutrophilic Fe(II)-oxidizing bacterium Sideroxydans lithotrophicus ES-1. Frontiers in Microbiology 3: 37. doi: 10.3389/fmicb.2012.00037.

29.  MJ Edwards, A Hall, L Shi, JK Fredrickson, JM Zachara, JN Butt, DJ Richardson and  TA Clarke. 2012. The crystal structure of the extracellular 11-heme cytochrome UndA reveals a conserved 10-heme motif and defined binding site for soluble iron chelates. Structure 20: 1275-1284.

30. Z Shi, JM Zachara, L Shi, Z Wang, DA Moore, DW Kennedy and JK Fredrickson. 2012. Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite.Environmental Science & Technology 46: 11644-11652.

31. S Marritt, TG Lowe, J Bye, DGG McMillan, L Shi, J Fredrickson, J Zachara, DJ Richardson, MR Cheesman, LJC Jeuken and JN Butt. 2012. A functional description of CymA, the key-stone for anaerobic respiratory flexibility in Shewanella.Biochemical Journal 444: 465–474.

32. B Cao, PD. Majors, B Ahmed, RS Renslow, A Dohnalkova, CP Sylvia, L Shi, S Kjelleberg, JK Fredrickson and Haluk Beyenal. 2012. Biofilm shows spatially stratified metabolic responses to contaminant exposure. Environmental Microbiology 14: 2901-2910.

33. DJ Richardson, JN Butt, JK Fredrickson, JM Zachara, L Shi, MJ Edwards, G White, N Baiden, AJ Gates, SJ Marritt and TA Clarke. 2012. ‘Porin-cytochrome’ model for microbe-to-mineral electron transfer. Molecular Microbiology 85: 201-212.

34. BM Fonseca, M Tien, M. Rivera, L Shi and RO Louro. 2012. Efficient and selective isotopic labeling of hemes to facilitate the study of multiheme proteins. BioTechniques: doi: 10.2144/000113859.

35. E Merkley, B Anderson, J Park, S Belchik, L Shi, M Monroe, R Smith and M Lipton. 2012. Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching. Journal of Proteome Research 11(12): 6147-6158.

36. GF White, Z Shi, L Shi, AC Dohnakova, JK Fredrickson, JM Zachara, JN Butt, DJ Richardson and TA Clarke. 2012. Development of a proteoliposome model to probe transmembrane electron-transfer reactions. Biochemical Society Transactions 40(6): 1257-1260.

37.  S Marritt, DGG McMillan, L Shi, JK Fredrickson, JM Zachara, DJ Richardson, LJC Jeuken and JN Butt. 2012. The roles of CymA in support of the respiratory flexibility of Shewanella oeidensis MR-1. Biochemical Society Transactions 40(6): 1217-1221.

38. M Breuer, P Zaezycki, L Shi, TA Clarke, MJ Marcus, JN Butt, DJ Richardson, JK Fredrickson, JM Zachara, J Blumberger and KM Rosso. 2012. Molecular structure and free energy landscape from electron transport in the decahaem cytochrome MtrF. Biochemical Society Transactions 40(6): 1198-12603.

39.  DJ Richardson, M Edwards, G White, N Baiden, RS Hartshorne, J Fredrickson, L Shi, J Zachara, A Gates, JN Butt and TA Clarke. 2012. Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration. Biochemical Society Transactions 40(3): 493-500.

40.  H Yang, H Gandhi, L Shi, HW Kreuzer, NE Ostrom and EL Hegg. 2012. Using gas chromatography-isotope ratio mass spectrometry to determine the fractionation factor for H2 production by hydrogenases. Rapid Communications in Mass Spectrometry 26: 61-68.

41. AE Plymale, V Bailey, JK Fredrickson, S Heald, E Buck, L Shi, Z Wang, C Resch, D Moore and H Bolton. 2012. Biotic and abiotic reduction and solubilization of Pu(IV)O2•xH2O(am) as affected by AQDS and EDTA.  Environmental Science & Technology 46(4): 2132-2140.

42. SJ Tomanicek, A Johs, MS Sawhney, A Gardberg, L Shi and L Liang. 2012. Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA of Shewanella oneidensis MR-1. Acta Crystallographica Section F Structural Biology and Crystallization Communications 68 (Pt1): 53-55.

43.  L Shi*, SM Belchik, AE Plymale, S Heald, AC Dohnalkova, K Sybirna, H Bottin, TC Squier, JM Zachara and JK Fredrickson. 2011. Purification and characterization of [NiFe]-hydrogenase of Shewanella oneidensis MR-1. Applied and Environmental Microbiology 77: 5584-5590.

44.  L Shi*, SM Belchik, Z Wang, DW Kennedy, AC Dohnalkova, MJ Marshall, JM Zachara and JK Fredrickson. 2011. Identification and characterization of UndAHRCR-6, an outer membrane endecaheme c-type cytochrome of Shewanella sp. strain HRCR-6. Applied and Environmental Microbiology 77: 5521-5523.

45.  SM Belchik, DW Kennedy, AC Dohnalkova, Y Wang, PC Sevinc, H Wu, Y Lin, HP Lu, JK Fredrickson and L Shi*. 2011. Extracellular reduction of hexavalent chromium by cytochromes MtrC and OmcA of Shewanella oneidensis MR-1. Applied and Environmental Microbiology 77: 4035-4011.

46. Y Qian, L Shi and M Tien. 2011. SO2907, a putative TonB-dependent receptor, is involved in dissimilatory iron reduction by Shewanella oneidensis MR-1. Journal of Biological Chemistry 286: 33973-33980.

47.  TA Clarke, M Edwards, AJ Gates, A Hall, G White, J Bradley, C Reardon, L Shi, A Beliaev, M Marshall, Z Wang, N. Watmough, J Fredrickson, J Zachara, Julea N Butt and DJ Richardson. 2011. The structure of a bacterial cell surface deca-heme electron conduit. Proceedings of National Academy of Science of the United States of America  108: 9384-9389.(http://www.nature.com/nchembio/journal/v7/n7/full/nchembio.606.html).

48.  B Cao, B Ahmed, DW Kennedy, Z Wang, L Shi, MJ Marshall, JK Fredrickson, NG Isern, PD Majors and H Beyenal. 2011. Contribution of extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms to U(VI) immobilization.Environmental Science & Technology 45: 5483-5490.

49. B Cao, L Shi, R Brown, Y Xiong, JK Fredrickson, MF Romine, MJ Marshall, MS Lipton and H Beyenal.. 2011. Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics. Environmental Microbiology 13: 1018-1031.

50. Y Xiong, B Chen, L Shi, J Fredrickson, D Bigelow and T Squier. 2011. Targeted protein degradation of outer membrane decaheme cytochrome MtrC metal reductase in Shewanella oneidensis MR-1 measured using biarsenical probe CrAsH-EDT2.Biochemistry 50: 9738-9751.

51. H Zhang, F Yang, W Qian, RN Brown, Y Wang, ME Monroe, SO Purvine, RJ Moore, L Shi, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2011. Identification of c-type heme-containing peptides using non-activated IMAC resin enrichment and higher-energy collisional dissociation. Analytical Chemistry 83: 7260-7268.

52.  A Johs, L Shi, T Droubay, JF Ankner and L Liang. 2010. Characterization of the decaheme c-type cytochrome OmcA in solution and on hematite surfaces by small angle X-ray scattering and neutron reflectometry. Biophysical Journal 98: 3035-4043.

53. H Zhang, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton.  2010.  Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling. Journal of Proteome Research 9:2160-2169.

54.  CL Reardon, AC Dohalkova, P Nachimuthu, DW Kennedy, DA Saffarini, BW Arey, L Shi, Z Wang, D Moore, JS McLean, D Moyles, MJ Marshall, JM Zachara, JK Fredrickson, AS Beliaev. 2010. Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1. Geobiology 8: 56-68.

55.  L Shi*, DJ Richardson, Z Wang, SN Kerisit, KM Rosso, JM Zachara and JK Fredrickson*. 2009. The roles of outer membrane cytochromes of Shewanella and Geobacter in extracellular electron transfer. Environmental Microbiology Reports. 1: 220-227.

56. L Shi*, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith and J Adkins*. 2009. Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella entrica. Infection and Immunity 77: 3227–3233.

57.  L Shi*, C Ansong, HS Smallwood, L Rommereim, JE McDermott, HM Brewer, AD Norbeck, R Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins*. 2009. Proteome of Salmonella enterica serotype Typhimurium grown in a low Mg2+/pH medium. Journal of Proteome and Bioinformatics 2(9): 388-397.

58. RS Hartshorne, CL Reardon, D Ross, J Nuester, TA Clarke, AJ  Gates, PC Mills, JK Fredrickson, JM Zachara, L Shi, AS Beliaev, MJ Marshall, M Tien, S Brantley, JN Butt and DJ  Richardson. 2009. Characterization of an electron conduit between bacteria and the extracellular environment. Proceedings of National Academy of Science of the United States of America 106(52): 22169-22174. (http://sciencenow.sciencemag.org/cgi/content/full/2009/1217/3).

59.  SM Chowdhury, L Shi, H Yoon, LM Rommereim, AD Norbeck, KJ Auberry, JN Adkins, F Heffron, and RD Smith. 2009. A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis. Journal of Proteome Research. 8: 1504-1514.

60.  L Meitl, CM Eggleston, N Khare, PJS Colberg, CL Reardon and L Shi. 2009. Electrochemical interaction of Shewanella oneidensis MR-1 and its outer membrane cytochromes OmcA and MtrC with hematite electrodes. Geochimica et Cosmochimica Acta. 73: 5292-5307.

61.  BH Lower, R Yongsunthon, L Shi, L Wildling, HJ Gruber, CL Reardon, GE Pinchuk, TC Droubay, JF Boily, and SK Lower.  2009. Antibody-recognition force microscopy shows that OmcA and MtrC cytochromes are expressed on the outer surface of Shewanella oneidensis MR-1. Applied and Environmental Microbiology. 75: 2931-2935 (Cover of May 1st issue of AEM).

62.  RC Taylor, M Singhal, J Weller, S Khoshnevis, L Shi, J McDermott. 2009. A network inference workflow applied to virulence-related processes in Salmonella typhimurium. Annals of the NY Academy of Sciences. 1158:143-158.

63.  Z Wang*, C Liu, X Wang, MJ Marshall, JM Zachara, KM Rosso, M Dupuis, JK Fredrickson, Steve Heald, and L Shi*. 2008. Reduction kinetics of Fe(III) complexes by outer membrane cytochromes MtrC and OmcA of Shewanella oneidensis MR-1.Applied and Environmental Microbiology. 74: 6746-6755.

64.  KD Rodland, JN Adkins, CK Ansong, SM Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, and F Heffron.  2008.  Elucidating host pathogen interactions using high-throughput mass spectrometry. Future Microbiology. 3: 625–634.

65.  HM Mottaz, AD Norbeck, JN Adkins, NP Manes, CK Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008.  Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems. Journal of Biomolecular Techniques. 19: 285-295.

66.  TA Clarke, T Holley, RS Hartshorne, JK Fredrickson, JM Zachara, L Shi, and DJ Richardson. 2008. The role of multihaem cytochromes in the respiration of nitrite in Escherichia coli and Fe(III) in Shewanella oneidensis.Biochemical Society Transaction. 36(Pt 5):1005-1010.

67.  L Shi*, S Deng, MJ Marshall, Z Wang, DW Kennedy, AC Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara and JK Fredrickson*. 2008. Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA. Journal of Bacteriology 190: 5512-5516.

68.  BH Lower, RD Lins, Z Oestreicher, TP Straatsma, MF Hochella Jr., L Shi and SK Lower. 2008. In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype. Environmental Science & Technology. 42: 3821-3827.

69.   H Zhang, X Tang, G Munske, N Zakharova, .Yang, C Zheng, M Wolff, N Tolic, G Anderson, L Shi, M Marshall, JK Fredrickson and J Bruce. 2008. In vivo identification of outer membrane protein OmcA-MtrC interaction network inShewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers. Journal of Proteome Research. 7: 1712-1720.

70.  CM Eggleston, J Voros, L Shi, BH Lower, TC Droubay and PJS Colberg. 2008. Binding and direct electrochemistry of OmcA, an outer-membrane cytochrome from an iron reducing bacterium, with oxide electrodes: A candidate biofuel cell system. Inorganica Chimica Acta. 361: 769-777.

71.  MJ Marshall, AE Plymale, DW Kennedy, L Shi, Z Wang, S Reed, A Dohnalkova, CJ Simonson, C Liu, D Saffarini, MF Romine, JM Zachara, AS Beliaev and JK Fredrickson. 2008. Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium (VII) by Shewanella oneidensis MR-1. Environmental Microbiology. 10: 125-136.

72.  RS Hartshorne RS, BN Jepson, TA Clarke, SJ Field, JK Fredrickson, J Zachara, L Shi, JN Butt and DJ Richardson. 2007. Characterization of Shewanella oneidensis MtrC: a cell surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors. Journal of Biological Inorganic Chemistry 12: 1083-1094.

73.  L Shi*, TC Squier, JM Zachara and JK Fredrickson*. 2007. Respiration of metal (hydr)oxides by Shewanella andGeobacter: A key role for multiheme c-type cytochromes. Molecular Microbiology 65: 12-20.

74.  BH Lower, L Shi, R Yongsunthon, TC Droubay, DE McCready, and SK Lower. 2007.  Dynamic force spectroscopy of specific bonds that form between an iron oxide surface and outer membrane cytochromes OmcA and MtrC from Shewanella oneidensis. Journal of Bacteriology 189: 4944-4952.

75.  NS Wigginton, KM Rosso, BH Lower, L Shi and MF Hochella, Jr. 2007. Electron tunneling properties of outer-membrane decaheme cytochromes from Shewanella oneidensis. Geochimica et Cosmochimica Acta. 71: 543-555.

76.   Y Xiong, L Shi, B Chen, MU Mayer, BH Lower, Y Londer, S Bose, MF Hochella, JK Fredrickson, and TC Squier. 2006. High-affinity binding and direct electron transfer to solid metals by purified metal reducing protein OmcA decaheme cytochrome. Journal of the American Chemical Society. 128: 13978-13979. (http://www.pnl.gov/biology/highlights/2006111706.stm)

77.   L Shi*, JN Adkins, JR Coleman, A Dohnalkova, AA Schepmoes, HM Mottaz, AD Norbeck, SO Purvine, HS Smallwood, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith and TC Squier. 2006. Proteomic analysis of Salmonella entericaserovar Typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages. Journal of Biological Chemistry. 281:29131-29140. (also featured in ASM's MicrobeWorld Radio: http://www.flpradio.com/microbeworld/audio/061225-070119/070102.mp3).

78.  L Shi*, B Chen, Z Wang, DA Elias, MU Mayer YA Gorby, S Ni, BH Lower, DW Kennedy, DS Wunschel, HM Mottaz, MJ Marshall, EA Hill, AS Beliaev, JM Zachara, JK Fredrickson and TC Squier.  2006.  Isolation of a high-affinity functional protein complex between OmcA and MtrC: two decaheme c-type cytochromes of Shewanella oneidensis MR-1. Journal of Bacteriology. 188: 4705-4714.

79.   HS Smallwood, L Shi and TC Squier. 2006. Increases in calmodulin abundance and stabilization of activated iNOS mediate bacterial killing in RAW 264.7 macrophages. Biochemistry 45: 9717-9726.

80.  YA Gorby, S Yanina, JS McLean, KM Rosso, D Moyles, A Dohnalkova, TJ Beveridge, IS Chang,  A Korenevski, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, DA Saffarini, EA Hill, L Shi, DA Elias, DW Kennedy, G Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson and JK Fredrickson. 2006. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proceedings of National Academy of Science of the United States of America. 103:11358-11363.

81.  MJ Marshall, AS Beliaev, AC Dohnalkaova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM Kemner, JS Mclean, SB Reed, DE Culley, VL Bailey, CJ Simonson, DA Saffarini, MF Romine, JM Zachara and JK Fredrickson. 2006. c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis. PLoS Biology. 4: 1324-1333.

82.  R Li, MB Potters, L Shi and PJ Kennelly. 2005. The protein phosphatases of Synechocystis sp. strain PCC 6803: open reading frames sll1033 and sll1387 encode enzymes that exhibit both protein-serine and protein-tyrosine phosphatase activity in vitro. Journal of Bacteriology. 187: 5877-5884.

83.  W Zhang* and L Shi*. 2005. Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases. Microbiology 151: 2159-2173.

84.  UU Mayer-Cumblidge, L Shi and TC Squier.  2005. One-step, non-denaturing pull-down of an RNA polymerase core enzyme complex using an improved multi-affinity probe resin. Molecular BioSystems 1: 53-56. (Also featured in Chemical Science, an online publication of the Royal Society of Chemistry, a European organization dedicated to advancing the chemical sciences).

85.  F Yang, B Bogdanov, EF Strittmatter, AN Vilkov, MA Gritsenko, L Shi, DA Elias, S Ni, MF Romine, L Pasa-Tolic, MS. Lipton and RD Smith. 2005. Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry. Journal of Proteome Research 4: 846-854.

86.  LM Markillie, J-T Lin, JN Adkins, DL Auberry, E Hill, BS Hooker, PA Moore, RJ Moore, L Shi, S Wiley and V Kery. 2005. A simple protein complex purification and identification method for high throughput mapping of protein interaction networks. Journal of Proteome Research 4: 268-274. (Also highlighted as the most-accessed articles in 2005 in theJournal of Proteome Research).

87.  L Shi*, J-T Lin, LM Markillie, TC Squier and BS Hooker. 2005. Over-expression of multi-heme c-type cytochromes.BioTechniques 38: 297-299.

88.  W Zhang* and L Shi*. 2004. Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains. Microbiology 150: 4189-4197.

89.  L Shi* and W Zhang*. 2004. Comparative analysis of eukaryotic-type protein phosphatases in two streptomycete genomes. Microbiology 150: 2247-2256.

90.  M A Warren, LM Kucharski, A Veenstra, L Shi, PF Grulich and ME Maguire. 2004. The CorA Mg2+ transporter is a homotetramer. Journal of Bacteriology 186: 4605-4612.

91.  L Shi. 2004. Manganese-dependent protein O-phosphatases in prokaryotes and their biological functions. Frontiers in Bioscience 9:1382-1397.

92.  L Shi, R Kishore, MR McMullen and LE Nagy. 2002. Chronic ethanol increases LPS-stimulated Egr-1 expression in RAW 264.7 macrophages: contribution to enhanced TNFa production.  Journal of Biological Chemistry 277:14777-14785.

93.  L Shi, R Kishore, MR McMullen and LE Nagy. 2002. Lipopolysaccharide stimulation of ERK1/2 increases TNFa production via Egr-1. American Journal of Physiology-Cell Physiology 282: C1205-C1211.

94.  L Shi*, DG Kehres and ME Maguire.  2001.  The PPP-family protein phosphatases PrpA and PrpB of Salmonella entericaserovar Typhimurium possess distinct biochemical properties. Journal of Bacteriology 183:7053-7057.

95.  L Shi, KM Bischoff and PJ Kennelly. 1999. The IcfG gene cluster of Synechocystis sp PCC6803 encodes an Rsb/Spo-like protein kinase, protein phosphatase, and two phosphoproteins. Journal of Bacteriology 181: 4761-4767.

96.  L Shi, WW Carmichael and PJ Kennelly. 1999. Cyanobacterial PPP-family protein phosphatases possess multifunctional capabilities and are resistant to microcystin-LR. Journal of Biological Chemistry 274: 10039-10046.

97.  L Shi, M Potts and PJ Kennelly. 1998. The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. FEMS Microbiology Reviews 22: 229-253.

98.  KM Bischoff, L Shi and PJ Kennelly. 1998. The detection of enzyme activity following SDS-polyacrylamide gel electrophoresis. Analytical Biochemistry 260: 1-17.

99.  L Shi and WW Carmichael. 1997. pp1-cyano2, a protein serine/threonine phosphatase 1 gene from the cyanobacteriumMicrocystis aeruginosa UTEX 2063. Archives of Microbiology 168: 528-531.

100.  L Shi, WW Carmichael and I Miller. 1995. Immuno-gold localization of hepatotoxin in cyanobacterial cells.Archives of Microbiology 163: 7-15.

101.   L Shi, I Miller and R Moore. 1993. Immunocytochemical localization of indole-3-acetic acid in primary root ofZea mays. Plant, Cell & Environment 16: 967-973.

102.   L Shi and MG Cline. 1992. Shoot inversion-induced ethylene production in the diageotropica tomato mutant. Annals of Botany 69: 119-122.

103.   Z Hosokowa, L Shi, TK Prasad and MG Cline. 1990. Apical dominance control in Ipomoea nil: the influence of the shoot apex, leaves and stem. Annals of Botany 65:547-556.

*Corresponding author

Book chapter

L. Shi, M Tien, JK Fredrickson, JM Zachara and KM Rosso. 2016. Microbial redox proteins and protein complexes for extracellular respiration., pp 187–216 .In “Redox Proteins in Supercomplexes and Signalosomes” (Ricardo Louro and Irene Diaz Moreno, Eds, CRC Press).

Workshop report

L. Shi, G. Reguera, H. Beyenal, A. Lu and J. Liu. 2015. Workshop Report of US-China Collaborative Research on Microbe-Mineral Interaction: Microbial Extracellular Electron Transfer with Minerals as Electron Sources and Sinks. Prepared for the US NSF.