CIVIL STATUS

Family name : ALAIN
First name : Karine
Date of birth : January 4th 1976
Marital status : married, one child
Professional address : Institut Universitaire Européen de la Mer (IUEM)
EMR6002 BIOMEX (UBO-CNRS-Ifremer)
Laboratory of Biology and Ecology of Deep Sea Ecosystems (BEEP)
Technopôle Brest Iroise, 29280 Plouzané
Tél. (+33) 02 98 49 88 53
E-mail : Karine.Alain@univ-brest.fr

ORCID ID: 0000-0002-8812-9081
 

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CURRENT POSITION

CNRS research director (DR2), HDR. Section 29 (Biodiversity, evolution and biological adaptations: from macromolecules to communities).

Director of the EMR6002 Biology, Interactions and adaptations of Organisms in EXtreme environments (BIOMEX)(Website: www.umr-beep.fr/EMR-BIOMEX)

Director of the Sino-French laboratory (IRP 1211) MicrobSea.
Expertise: Microbiology, Microbial ecology of extreme marine environments.

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SYNOPTIC : COURSE

-Since January 2024/Research director (DR2) at CNRS, EMR6002 Biology, Interactions and adaptations of Organisms in EXtreme environments (BIOMEX)

-Since January 2022/ Research director (DR2) at CNRS, Unité de Biologie et d'Ecologie des Ecosystèmes marins Profonds (BEEP) UMR6197

- July 2021- December2021 / Research director (DR2) at CNRS, LM2E UMR6197

- 2007 -2021/ CRCN Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, IUEM, Brest.

- 2006-2007 / ATER Observatoire Océanologique (Director : P. Lebaron), Banyuls-sur-mer.

- 2004-2006 / Post-doc at Max Planck Institute for Marine Microbiology, Department of Microbiology (Director : F. Widdel), Bremen, Germany.

- 2000-2003 / PhD Université de Bretagne Occidentale, Brest, France – Ifremer, laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles (Director : J. Querellou), Brest.
 

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EDUCATION AND ACADEMIC QUALIFICATIONS

- June 2014 : Habilitation to supervise research (HDR), Université de Bretagne Occidentale, Brest, France.
Topic : « Microbial biosphere of extreme marine habitats: Contribution to the study of diversity, functions, geographical limits and interactions with the environment».

- Oct. 2000/Oct. 2003 PhD in Fundamental and Applied Microbiology, Université de Bretagne Occidentale, BREST (29). PhD thesis carried out at Ifremer, in the laboratory of Microbiology and Biotechnology of Extremophiles(DRV/VP/MBE ancien CMM), in Plouzané (29). PhD thesis director : Prof. F. Duchiron (Université de Reims). Ifremer grant.
Topic « Cultural and molecular approaches of microbial assemblages associated with hydrothermal polychaetes of the family Alvinellidae». PhD thesis defended on 03/10/2003. Honorable mention with congratulations of the jury.

- 1999/2000 Diplôme d'Etudes Approfondies de microbiologie fondamentale et appliquée - DEA co-habilitated by the universities of CAEN, RENNES and BREST. "Isolation and characterization of a new type of baro-thermophilic abyssal bacteria". Mention Bien.

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COLLECTIVE RESPONSIBILITIES

Local administrative responsibilities

-2021-2025: Nominated member of the scientific council of IUEM (European Institute for Sea Sciences)

-2022-2026: Elected member of the administrative council of IUEM (rank A)

- 2016-2022: Leader of the theme 2 "Characterization and activities of microbial actors in deep extreme ecosystems" of UMR6197.

-2018-2021: Elected member of the administrative council of IUEM (rank B)
- 2015-2022 : Elected member of the UMR6197 laboratory council
- 2009-2015 : Prevention assistant of the UMR6197

 National administrative responsibilities

- Since 2024: Director of the EMR6002 Biology, Interactions and adaptations of Organisms in EXtreme environments (BIOMEX)

- 2023: Chair of the professional selection examination for CNRS senior research engineers (IRHC)

- 2016-2019: Co-coordinator of the axis 3 "Geobiological interactions in extreme environments" of the laboratory of excellence LabexMER "The ocean in the change" grouping 11 units of excellence in the west.

 - Since 2010: Member of the board of directors of AFEM (Association Francophone d'Ecologie Microbienne). Secretary of the AFEM since 2013. Co-editor of the e-monthly newsletter "La Lettre de l'AFEM" (4-5 pages) since September 2015.

- 2010-2012: Appointed member of section 29 (Biodiversity, evolution and biological adaptations:
From macromolecules to communities) of the CNRS (NOR: ESRR1000407A, order of 24-11-2010, ESR - DGRI-SPFCO-B2)

- 2008-2010 : Substitute member of the national commission 'Fleet and devices', committee 'Evaluation' : Evaluation of oceanographic campaigns of the French fleet.

 International administrative responsibilities

- 2018-2026 : French Director of the International Associated Laboratory MICROBSEA, Franco-Chinese Laboratory of Deep Sea Microbiology". This Franco-Chinese laboratory is focused on the microbiology of hydrothermal springs. It associates 2 laboratories:
- LM2E Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197 CNRS/Ifremer/Université de Bretagne Occidentale, IUEM, Plouzané, France. French director: Dr. K. ALAIN
- KLMBR State Key Laboratory of Marine Biogenetic Resources; Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, Xiamen, China. Chinese Director: Prof. Z. SHAO

20 à 95h d'enseignement par an en microbiologie et écologie microbienne, dans les filières suivantes:

- Licence 2 en Biologie Cellulaire et Physiologie, faculté des Sciences de Brest

- Licence 2 en Biologie des Populations, faculté des Sciences de Brest

- Licence 3 en Biologie Cellulaire et Physiologie, faculté des Sciences de Brest

- Master 1 et Biologie et Santé, faculté des Sciences de Brest

- Master 1 en sciences de la mer et du Littoral, Institut Universitaire Européen de la Mer, Brest-Plouzané

- Master 2 Biologie et Santé, spécialité Microbiologie Fondamentale et Appliquée de l’Université de Bretagne Occidentale (Brest)

2024

69/ Pouder, E., Vince, E., Jacquot, K., Traoré, M. B., Grosche, A., Ludwig, M., Jebbar, M., Maignien, L., Alain, K. & Mieszkin, S. (in press). Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland. Systematic and Applied Microbiology. (IF 3,3; Q2)

68/ Wang, S., Jiang, L., Zhao, Z., Chen, Z., Wang, J., Alain, K., Cui, L., Zhong, Y., Peng, Y., Lai, Q., Dong, X., & Shao, Z. (2024). Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments. ISME Journal. 18(1): wrae19. https://doi.org/10.1093/ismejo/wrae119 (IF 10,8; Q1)

2023

67/ Cozannet, M., Le Guellec, S. & Alain, K. (2023). A variety of substrates for methanogenesis. Case Studies in Chemical and Environmental Engineering. 8, 100533. https://doi.org/10.1016/j.cscee.2023.100533 (IF: 7,93; Q1)

66/ Wang, S., Jiang, L., Cui, L., Alain, K., Xie, S. & Shao, Z. (2023). Insights into the mechanism of cyclooctasulfur oxidation and reduction by the neutrophilic chemolithoautotrophic Sulfurovum indicum from deep-sea hydrothermal ecosystem. Antioxidants. 12, 627. https://doi.org/10.3390/antiox12030627 (IF: 7,68; Q1)

65/ Wang, S., Jiang, L., Xie, S., Alain, K., Wang, Z., Wang, J., Liu, D.  & Shao, Z. (2023). Disproportionation of inorganic sulfur compounds by mesophilic chemolithoautotrophic Campylobacterota. mSystems. 8(1), e0095422. https://doi.org/10.1128/msystems 00954-22 (IF: 7,33; Q1)

64/ Mieszkin, S., Trouche, B., Ancousture, J., Raouf, Y., Uroz, S. & Alain, K. (2023). Scleromatobacter humisilvae gen., nov., sp. nov., a novel bacterium isolated from an oak forest soil. International Journal of Systematic and Evolutionary Microbiology. 73, 005793. https://doi.org/10.1099/ijsem.0.005793 (IF: 2,68; Q4)

2022

63/ Allioux, M., Yvenou, S., Merkel, A., Cozannet, M., Aube, J., Pommellec, J., Le Romancer, M., Lavastre, V., Guillaume, D. & Alain, K. (2022). A metagenomic insight into the microbiomes of geothermal springs in the subantarctic Kerguelen Islands. Scientific Reports. 12, 22243. https://www.nature.com/articles/s41598-022-26299-4 (IF: 4,99; Q2)

62/ Allioux, M., Yvenou, S., Godfroy, A., Shao, Z., Jebbar, M. & Alain, K. (2022). Genome analysis of a new sulphur disproportionating species Thermosulfurimonas strain F29 and comparative genomics of sulfur-disproportionating bacteria from marine hydrothermal vents. Microbial Genomics. 8, 000865. https://doi.org/10.1099/mgen.0.000865 (IF: 5,24; Q1)

61/ Cario, A., Larzilliere, M., Nguyen, O., Alain, K. & Marre, S. (2022). High-pressure microfluidics for ultra-fast microbial phenotyping. Frontiers in Microbiology. 13, 866681. https://www.frontiersin.org/articles/10.3389/fmicb.2022.866681/full (IF: 6,06; Q1).

60/ Alain, K., Aronson, H.D., Allioux, M., Yvenou, S. & Amend, A. (2022). Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents. Environmental Microbiology. 24(5), 2210-2219.  https://doi.org/10.1111/1462-2920.15975. (IF: 5,48; Q2)

59/ Yvenou, S., Allioux, M., Slobodkin, A., Slobodkina, G., Jebbar, M. & Alain, K. (2022). Genetic potential of Dissulfurimicrobium hydrothermale, an obligate sulfur-disproportionating thermophilic microorganism. Microorganisms. 10, 60. https://doi.org/10.3390/microorganisms10010060. (IF: 4,93; Q2)

2021

58/ Moalic, Y., Dalmasso, C., Courtine, D., Hartunians, J., Georges, M., Oger, P., Zeng, X., Shao, Z., Jebbar, M. & Alain, K. (2021). The piezo-hyperthermophilic archaeon Thermococcus piezophilus regulates its energy efficiency system to cope with large hydrostatic pressure variations. Frontiers in Microbiology, 12, 730231. https://doi.org/10.3389/fmicb.2021.730231 (IF: 6,06; Q1).

57/ Mieszkin, S., Pouder, E., Uroz, S., Simon-Colin, C. & Alain, K. (2021). Acidisoma silvae sp. nov. and Acidisoma cellulosilytica sp. nov., two acidophilic bacteria isolated from decaying wood, hydrolyzing cellulose and producing poly-3-hydroxybutyrate. Microorganisms, 9, 2053. https://doi.org/10.3390/microorganisms9102053. (IF: 4,93; Q2)

56/ Slobodkina, G., Allioux, M., Merkel, A., Cambon, M.-A., Alain, K. Jebbar, M. & Slobodkin, A. (2021). Physiological and genomic characterization of Archaeoglobus neptunius sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent and proposal to reclassify three species of the genus Archaeoglobus into novel genera. Frontiers in Microbiology, 12, 679245. #: 10.3389/fmicb.2021.679245. (IF: 6,06; Q1).

55/ Alain, K., Vince, E., Courtine, D., Maignien, L., Zeng, X., Shao, Z. & Jebbar, M. (2021). Thermococcus henrietii sp. nov., a novel extreme thermophilic and piezophilic sulfur-reducing archaeon isolated from a deep-sea hydrothermal chimney (EPR 9°N). International Journal of Systematic and Evolutionary Microbiology, 71, 004895. DOI 10.1099/ijsem.0.004895 (IF: 2,40; Q3)
 
54 / Courtine, D., Vince, E., Maignien, L., Philippon, X., Gayet, N., Shao, Z., Jebbar, M. & Alain, K.  (2021). Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge. International Journal of Systematic and Evolutionary Microbiology, 71, 004853. DOI 10.1099/ijsem.0.004853 (IF: 2,40; Q3)

53/ Zeng, X., Alain, K., & Shao, Z. (2021). Microorganisms inhabiting deep-sea hydrothermal vents. Marine Life Science & Technology, 3, 204-230. https://doi.org/10.1007/s42995-020-00086-4 (IF: 5,70; Q1)

52/ Cozannet, M., Borrel, G., Roussel, E., Moalic, Y., Allioux, M., Sanvoisin, A., Toffin, L., & Alain, K. (2021). New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Microorganisms, 9(1), 30. https://doi.org/10.3390/microorganisms9010030. (IF: 4,93) 

51/ Allioux, M., Jebbar, M., Slobodkina, G., Slobodkin, A., Moalic, Y., Frolova, A., Shao, Z. & Alain, K. (2021). Complete genome sequence of Thermosulfurimonas marina sp. nov., an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a shallow hydrothermal vent. Marine Genomics, 55, 100800. https://doi.org/10.1016/j.margen.2020.100800 (IF: 1,67) 

2020

50/ Allioux, M., Yvenou, S., Slobodkina, G., Slobodkin, A., Shao, Z., Jebbar, M., & Alain, K. (2020). Genomic characterization and environmental distribution of a thermophilic anaerobe Dissulfurirhabdus thermomarina SH388^T involved in disproportionation of sulfur compounds in shallow sea hydrothermal vents. Microorganisms, 8(1132), 1-14. https://doi.org/10.3390/microorganisms8081132  (IF: 4,15) 

49/ Slobodkina, G., Allioux, M., Merkel, A., Alain, K. Jebbar, M. & Slobodkin, A. (2020). Genome analysis of Thermosulfuriphilus ammonigenes ST65^T, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a shallow hydrothermal vent. Marine Genomics, 54: 100786. DOI: 10.1016/j.margen.2020.100786  (IF: 1,67)

48/ Wang, L., Lai, Q., Jebbar, M., Shao, Z. & Alain, K. (2020). Complete genome sequence of Methanofervidicoccus sp. A16, a thermophilic methanogen isolated from a Mid Cayman Rise hydrothermal vent. Marine Genomics, 53:100768. DOI: 10.1016/j.margen.2020.100768  (IF: 1,87) 

47/ Jiang, L., Liu, X., Dong, C., Huang, Z., Cambon-Bonavita, M.-A., Alain, K., Gu, L., Wang, S. & Shao, Z. (2020). Candidatus ‘Desulfobulbus rimicarensis’, an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata. Applied and Environmental Microbiology, 86(8), e02549-19, 1-16. doi:10.1128/AEM.02549-19. (IF: 4,08) 

2019

46/ Slobodkin, A., Slobodkina, G., Allioux, M., Alain, K., Jebbar, M., Shadrin, V., Kublanov, I., Toshchakov, S. & Bonch-Osmolovskaya, E. (2019). Genomic insights into carbon and energy metabolism of a thermophilic deep-sea bacterium Deferribacter autotrophicus revealed new metabolic traits in the phylum Deferribacteres. Genes, 10, 849, 1-21, doi:10.3390/genes10110849. (IF: 3,48) 

2017

45/ Jiang, L., L’Haridon, S., Jebbar, M., Xu, H., Alain, K. & Shao, Z. (2017). Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1^T from an East Pacific hydrothermal sediment. Standards in Genomic Sciences. 12:3. (IF: 3,17) 

44/ Zhang, X., Zeng, X., Alain, K., Jebbar, M. & Shao, Z. (2017). Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment from the West Pacific. International Journal of Systematic and Evolutionary Microbiology. 67:1462–1467. (IF: 2,44) 

43/ Cao, J., Birien, T., Gayet, N., Huang, Z., Shao, Z., Jebbar, M. & Alain, K. (2017). Desulfurobacterium indicum sp. nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean. International Journal of Systematic and Evolutionary Microbiology. 67:1665–1668. (IF: 2,44) 

42/ Gaboyer, F., Maignien, L., Jebbar, M. & Alain, K. (2017). Draft genome of Halomonas lionensis, a stress-tolerant gammaproteobacterium isolated from Mediterranean Sea sediments. Genome Announcements. 5(23):e00311-17. 

41/ Gaboyer, F., Maignien, L., Jebbar, M. & Alain, K. (2017). Draft genome of Phaeobacter leonis type strain 306^T, an alphaproteobacterium isolated from Mediterranean Sea sediments. Genome Announcements. 5(26):e00312-17. 

40/ Courtine, D., Alain, K., Georges, M., Morrison, H.G., Murat, E. & Maignien, L. (2017). Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. EXT12c, isolated from the East Pacific Rise 9°N. Genome Announcements, 5:doi:10.1128/genomeA.01385-17. 

2016

39/ Cao, J., Maignien, L., Shao, Z., Alain, K. & Jebbar, M. (2016). Genome sequence of the piezophilic, mesophilic sulfate-reducing bacterium, Desulfovibrio indicus J2^T. Microbiol Resour Ann. 4(2): e00214-16.

38/ Dalmasso, C., Oger, P., Courtine, D., Georges, M., Takai, K., Maignien, L. & Alain, K. (2016). Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus piezophilus CDGS^T, able to grow under Extreme Hydrostatic Pressures. Genome Announcements. 4(4): e00610-16. Doi: 10.1128/genomeA.00610-16.

37/ Cao, J., Jebbar, M., Gayet, N., Zeng, X., Shao, Z. & Alain, K. (2016). Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of five Desulfovibrio spp. International Journal of Systematic and Evolutionary Microbiology. 66:3904-3911. (IF: 2,44) 

36/ Lai, Q., Cao, J., Dupont, S., Shao, Z., Jebbar, M. & Alain, K. (2016). Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean. International Journal of Systematic and Evolutionary Microbiology 66:3985–3989. (IF: 2,44) 

35/ Dalmasso, C., Oger, P., Selva, G., Courtine, D., L’Haridon, S., Garlaschelli, A., Roussel, E., Miyazaki, J., Reveillaud, J., Jebbar, M., Takai, K., Maignien, L. & Alain, K. (2016). Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise. Systematic and Applied Microbiology. 39:440-444. (IF: 3,89) 

2015

34/ Zeng, X., Zhang, Z., Li, X., Zhang, X., Cao, J., Jebbar, M., Alain, K. & Shao, Z. (2015). Anoxybacter fermentans gen. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology. 65:710-715. (IF: 2,51) 

33/ Zeng, X., Zhang, Z., Li, X., Jebbar, M., Alain, K. & Shao, Z. (2015). Caloranaerobacter ferrireducens sp. nov., an anaerobic thermophilic iron(III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits. International Journal of Systematic and Evolutionary Microbiology. 65:1714-1718. (IF: 2,51) 

32/ Gaboyer, F., Burgaud, G. & Alain, K. (2015). Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic approach. FEMS Microbiology and Ecology. 91(5): 1-13. (IF: 3,88) 

2014

31/ L’Haridon, S., Jiang, L., Alain, K., Chalopin, M., Rouxel, O., Beauverger, M., Xu, H., Shao, Z. & Jebbar, M. (2014). Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment. Extremophiles 18: 81-88. (IF: 2,21) 

30/ Ciobanu, M.-C., Burgaud, G., Dufresne, A., Breuker, A., Redou, V., Ben Maamar, S., Gaboyer, F., Vandenabeele-Trambouze, O., Lipp, J.S., Schippers, A., Vandenkoornhuyse, P., Barbier, G., Jebbar, M., Godfroy, A. & Alain, K. (2014). Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. The ISME Journal. 8: 1370-1380. https://doi.org/10.1038/ismej.2013.250 (IF: 9,27) 

29/ Gaboyer, F., Vandenabeele-Trambouze, O., Cao, J., Ciobanu, M.-C., Jebbar, M., Le Romancer, M. & Alain, K. (2014). Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment. Research in Microbiology 165: 490-500. (IF: 2,83) 

28/ Rédou, V., Ciobanu, M.-C., Pachiadaki, M.G., Edgcomb, V., Alain, K., Barbier, G., Burgaud, G. (2014). In-depth analyses of subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths. FEMS Microbiology Ecology 90: 908-921. (IF: 3,88) 

2013

27/ Zeng, X., Zhang, X., Jiang, L., Alain, K., Jebbar, M. & Shao, Z. (2013). Palaeococcus pacificus sp. nov., a novel archaeon from a deep-sea hydrothermal sediment. International Journal of Systematic and Evolutionary Microbiology 63: 2155-2159. (IF: 2,80) 

26/ Gorlas, A., Bienvenu, N., Alain, K. & Geslin, C. (2013). Thermococcus prieurii sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent at the East Pacific Rise. International Journal of Systematic and Evolutionary Microbiology 63:2920-2926. (IF: 2,80) 

25/ Theodorakopoulos, N., Bachar, D., Christen, R., Alain, K. & Chapon, V. (2013). Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers. Microbiology Open doi: 10.1002/mbo3.119. (IF: 3,14) 

24/ Gaboyer, F., Tindall, B.J., Ciobanu, M.C., Duthoit, F. & Alain, K. (2013). Phaeobacter leonis sp. nov., a novel alphaproteobacterium from Mediterranean Sea sediments. International Journal of Systematic and Evolutionary Microbiology 63: 3301-3306.  (IF: 2,80) 

2012

23/ Ciobanu, M.-C., Rabineau, M., Droz, L., Révillon, S., Ghiglione, J.-F., Dennielou, B., Jorry, S., Kallmeyer, J., Etoubleau, J., Pignet, P., Crassous, P., Laugier, J., Guégan, M., Godfroy, A. & Alain, K. (2012). Sedimentological imprint on subseafloor bacterial and archaeal communities in Mediterranean Sea Quaternary sediments. Biogeosciences 9: 3491-3512. (IF: 3,86) 

22/ Alain, K., Harder, J., Widdel, F. & Zengler, K. (2012). Anaerobic utilization of toluene by marine Alpha- and Gammaproteobacteria reducing nitrate. Microbiology 158: 2946-2957. (IF: 3,06) 

21/ Aslanian. D., Moulin, M., Schnurle, P., Klingelhoefer, F., Leroux, E., Rabineau, M., Gailler, A., Bache, F., Gorini, C., Kuroda, J., Eguchi, N., Droxler, A., Alain, K., Roure, F., Haq. B. (2012). Structure and evolution of the Gulf of Lions: The Sardinia seismic experiment and the GOLD (Gulf of Lions Drilling) project. The Leading Edge 31(7): 786-792. (IF: 0,94)

2011

20/ Alain, K., Callac, N., Ciobanu, M.-C., Reynaud, Y., Duthoit, F. & Jebbar, M. (2011). DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols. Journal of Microbiological Methods 87: 355-362. (IF: 2,43) 

2010

19/ Alain, K., Postec, A., Grinsard, E., Lesongeur, F., Prieur, D. & Godfroy, A. (2010a). Thermodesulfatator atlanticus sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 60: 33-38. (IF: 2,27) 

18/ Alain, K., Tindall, B.J., Catala, P., Intertaglia, L. & Lebaron, P. (2010b). Ekhidna lutea gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from the South East Pacific Ocean. International Journal of Systematic and Evolutionary Microbiology 60: 2972-2978. (IF: 2,11) 

17/ Sayeh, R., Birrien, J.-L., Alain, K., Barbier, G., Hamdi, M. & Prieur, D. (2010). Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches. Extremophiles 14: 501-514. (IF: 2,94) 

2009

16/ Alain, K., Callac, N., Guégan, M., Lesongeur, F., Crassous, P., Cambon-Bonavita, M.-A., Querellou, J. & Prieur, D. (2009a). Nautilia abyssi sp. nov., a novel thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 59: 1310-1315. (IF: 2,27) 

15/ Alain, K. & Querellou, J. (2009b). Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13: 583-594. (IF: 2,94) 

14/ Byrne, N., Lesongeur, F., Bienvenu, N., Geslin, C., Alain, K., Prieur, D. & Godfroy, A. (2009). Effect of variation of environmental conditions on the microbial communities of deep-sea vent chimneys, cultured in a bioreactor. Extremophiles 13:595-608. (IF: 2,94) 

13/ Simon-Colin, C., Alain, K., Raguénès, G., Schmitt, S., Kervarec, N., Gouin, C., Crassous, P., Costa, B. & Guézennec, J.G. (2009). Biosynthesis of medium chain length poly(3-hydroxyalkanoates) (mcl-PHAs) from cosmetic co-products by Pseudomonas raguenesii sp. nov., isolated from Tetiaroa, French Polynesia. Bioresource Technology 100: 6033-6039. (IF: 4,98) 

2008

12/ Simon-Colin, C., Alain, K., Colin, S., Cozien, J., Costa, B., Guézennec, J.G. & Raguénès, G.H. (2008). A novel mcl PHA-producing bacterium, Pseudomonas guezennei sp. nov., isolated from a ‘kopara’ mat located in Rangiroa, an atoll of French Polynesia. Journal of Applied Microbiology 104: 581-586. (IF: 2,50) 

11/ Alain, K., Tindall, B.J., Intertaglia, L., Catala, P. & Lebaron, P. (2008a). Hellea balneolensis gen. nov. sp. nov., a novel prosthecate alphaproteobacterium from the Mediterranean Sea. International Journal of Systematic and Evolutionary Microbiology 58: 2511-2519. (IF: 2,27) 

10/ Alain, K., Intertaglia, L., Catala, P. & Lebaron, P. (2008b). Eudoraea adriatica gen. nov. sp. nov., a novel marine bacterium of the family Flavobacteriaceae. International Journal of Systematic and Evolutionary Microbiology 58: 2275-2281. (IF: 2,27) 

2006

9/ Alain, K., Holler, T., Musat, F., Elvert, M., Treude, T. & Krüger, M. (2006). Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environmental Microbiology 8: 574-590. (IF: 5,84) 

2005

8/ Pagé, A., Juniper, S.K.J., Olagnon, M., Alain, K., Desrosiers, G., Querellou, J. & Cambon-Bonavita, M.-A. (2005). Microbial diversity associated with a Paralvinella sulfincola tube and the adjacent substratum on an active deep-sea vent chimney. Geobiology 2: 225-238. (IF: 4,29) 

2004

7/ Alain, K., Zbinden, M., Le Bris, N., Lesongeur, F., Querellou, J., Gaill, F. & Cambon-Bonavita, M.-A. (2004). Early steps in microbial colonisation processes at deep-sea hydrothermal vents. Environmental Microbiology 6 : 227-241. (IF: 5,84) 

2003

6/ Alain, K., Rolland, S., Lesongeur, F., Pignet, P., Le Gall, C., Crassous, P. & Querellou, J. (2003). Desulfurobacterium crinifex sp. nov., a novel thermophilic, pinkish-streamers forming, chemolithoautotrophic bacterium isolated from a Juan de Fuca Ridge hydrothermal vent and amendment of the genus Desulfurobacterium. Extremophiles, 7: 361-370. (IF: 2,68) 

2002

5/ Alain, K., Marteinsson, V.T., Miroshnichenko, M., Bonch-Osmolovskaya, E., Prieur, D. & Birrien, J.-L. (2002a). Marinitoga piezophila, sp. nov., a rod-shaped thermo-piezophilic bacterium isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 52:1331-1339. (IF: 2,87) 

4/ Alain, K., Querellou, J., Lesongeur, F., Pignet, P., Crassous, P., Raguénès, G., Cueff, V. & Cambon-Bonavita, M.-A. (2002b). Caminibacter hydrogeniphilus, gen. nov., sp. nov., a novel thermophilic hydrogen-oxidising bacterium isolated from an East-Pacific rise hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 52:1317-1323. (IF: 2,87) 

3/ Alain, K., Pignet, P., Zbinden, M., Quillévéré, M., Duchiron, F., Donval, J.-P., Lesongeur, F., Raguénès, G., 3. Crassous, P., Querellou, J. & Cambon-Bonavita, M.-A. (2002c). Caminicella sporogenes, gen. nov., sp. nov., a novel thermophilic spore-forming bacterium isolated from an East-Pacific rise hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 52: 1621-1628. (IF: 2,87) 

2/ Alain, K., Olagnon, M., Desbruyères, D., Pagé, A., Barbier, G., Juniper, S.K., Querellou, J. & Cambon-Bonavita, M.-A. (2002d). Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiology Ecology, 42: 463-476. (IF: 3,41) 

2001

1/ Querellou, J., Alain, K., Cambon-Bonavita, M.-A. (2001). Thermophiles from deep-sea hydrothermal vents. Vie Milieu, 51(4) : 161-172. 
 

BOOKS
3. Kallmeyer, J. & Wagner, D. (Ed.). Authors: Alain, K., Alawi, M., Amend, J., Biddle, J., Borgomano, J., Cockell, C., Cragg, B., DiPrimio, R., Edgcomb, V., Inagaki, F., Ito, M., Jungbluth, S., LaRowe, D., Lever, M., Lloyd, K.G., Morono, Y., Oger, P., Ollivier, B., Orsi, W., Parkes, R.J., Pedersen, K., Rappe, M., Roussel, E., Røy, H., Sass, H., Teske, A.P., Toffin, L., Webster, G., Weightman, A. Microbial Life of the Deep Biosphere. Berlin, Boston: De Gruyter, 2014.

2 . Prévot-Julliard, A.-C., Maris, V., Alain, K., Aumeeruddy-Thomas, Y., Devictor, V., Langlais, A., Not F., Puijalon, S., Pujol, B. (Ed.). BiodiversitéS : Nouveaux regards sur le vivant. Editions Le Cherche-Midi, coll. Beau livre, Paris, 2010. ISBN 978-2-7491-1862-8. 176 pages.
 
1. Alain, K. Les communautés microbiennes des sources hydrothermales du Pacifique : Approches culturales et moléculaires des assemblages microbiens associés aux polychètes hydrothermaux de la famille Alvinellidae. Éditions universitaires européennes, VDM Verlagsservicegesellschaft mbH, Saarbrücken, 2010. ISBN 978-613-1-55077-5. 197 pages.
 
 
BOOK CHAPTERS
 
1.     Toffin, T. & Alain, K. (2014). Cultivation of marine sub-seafloor microorganisms: state-of-the-art solutions and major issues. In Kallmeyer, J., Wagner, D. (Ed.), Microbial Life of the deep biosphere. Editions De Gruyter, Berlin/Boston. pp. 83-99.
 
2.     Bertrand, J.-C., Bonin, P., Ollivier, B., Alain, K., Godfroy, A., Pradel, N., Normand, P. (2018). Chapter 4: Evolutionary success of prokaryotes. In Bertrand, J.-C., Normand, P., Ollivier, B., Sime-Ngando, T. (Eds.), Prokaryotes and Evolution. Editions Springer International, Switzerland. ISBN 978-3-319-99784-1, pp. 131-214.
 
3.     Alain, K., Vandenkoornhuyse, P. (2019). Chapitre 7 : Paléogénomique et histoires évolutives ; secret 86 : De la vie à plusieurs kilomètres dans les sédiments marins. In Faure, D., Joly, D., Salamitou, S. (Ed.), 101 secrets de l’ADN. Editions CNRS, Paris. pp. 281-283.

4. Alain, K., Cozannet, M., Allioux, M., Thiroux, S., Hartunians J. (2024). Archées : habitats et physiologies associées. In Les archées, micro-organismes du troisième domaine du vivant 1. Découverte, évolution et diversité des archées. B. Clouet-d'Orval, B. Franzetti, P. Oger (Dir.). Collections classiques, Encyclopédie SCIENCES, Biologie, microbiologie ISBN 978789481686 / 9781789491685, chap.4, pp.161-215 (ISTE Editions Ltd).
 
4.     Godfroy, A., François, D., Hartunians, J., Moalic, Y. & Alain, K. (in press). Physiology, metabolism and ecology of thermophiles from deep-sea vents. In Vetriani, C., Giovannelli, D. (eds.), The Microbiology of Deep-Sea. Editions Springer International.