Karine Alain

KAlain

Karine Alain

Research Director DR2 (CNRS)
Microbiologist
Director of the EMR6002 BIOMEX Biology, Interactions and adaptations of Organisms in EXtreme environments
Head of the Sino-French associated laboratory IRP MicrobSea
Karine.Alain@univ-brest.fr
02 98 49 88 53

My research is devoted to the study of microbial communities living at deep-sea hydrothermal vents, and those living in geographically isolated and poorly anthropised terrestrial hot springs in the Southern and Antarctic polar regions. They aim to provide insights into the functioning of these unique ecosystems, the microbial diversity, the catabolic pathways implemented and some of the adaptive mechanisms used by microorganisms growing in these extreme environments, sometimes close to the physico-chemical limits of life. I am particularly interested in under-documented microbial metabolisms (sulfur and iron cycles), as well as in phylogenetic branches of life (bacteria and archaea) that are largely unexplored and without cultivated representatives. For the past few years, I have been particularly interested in the disproportionation of inorganic sulfur compounds, in the taxa that implement it, the molecular pathways involved, the place of this catabolism in the sulfur cycle, its emergence on Earth and the geomicrobiological interactions associated with it.

 

Major ongoing research projects :

  • ANR PRC ANR-22-CE02-0001 (2022-2026), MISD “Deciphering the pathways of microbial sulfur disproportionation in hydrothermal taxa” (P.I. K. ALAIN) (Website: anr.fr/Project-ANR-22-CE02-0001)
    IPEV n°1231 (2022-2025), SEKMET “Sub-antarctic hot Environments of Kerguelen and Saint Paul: Microbial diversity and ExtraTerrestrial analogues” (P.Is. K. ALAIN, M. LE ROMANCER)                (Website: https://www.researchgate.net/project/SEKMET-Sub-antarctic-hot-Environments-of-Kerguelen-and-Saint-Paul-Microbial-diversity-and-ExtraTerrestrial-analogues)
    ANR JCJC ANR-22-CE01-0013 (2022-2026), IRON2MI “The IRON cycle in deep-sea hydrothermal vents: contribution of iron-reducing and iron-oxidizing MIcroorganisms and impact on MInerals alteration” (P.I. S. MIESZKIN) (Website: anr.fr/Projet-ANR-22-CE01-0013)
    ANR PRC ANR-22-CE02-0017 (2023-2027), HOT-DOG “New insights into hydrothermal deep-sea vents microbial ecosystems” (P.I. S. MARRE) (Website: anr.fr/Projet-ANR-22-CE02-0017)
    PPR Ocean-Climate (2022-2028), LIFEDEEPER “LIving together in the Future: vulnErability of DEEP sea Ecosystems facing potential mineral Resources exploitation” (P.I. M.-A. CAMBON) (Website: lifedeeper.ifremer.fr)
  • EUR ISblue flagship project ISLAB (2024-2028) "Linking earthquakes to life evolution: The Icelandic laboratory" (P.I.s L. GEOFFROY & K. ALAIN)

 

Keywords: Deep biosphere / Microbial ecology / ‘Extreme’ habitats / Cultivation / Molecular biology / Sulfur disproportionation / Methanogenesis / Iron cycle / Taxonomy, species concept / Relationships between the microbial activities and the biogeochemical cycles / Ecosystem functioning / High-pressure.

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)

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

 

70 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)

 

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://authors.elsevier.com/sd/article/S2666-0164(23)00238-4. (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. (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 SH388T 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 ST65T, 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 SLHLJ1T 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 306T, 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 J2T. 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 CDGST, 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.     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.