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UMR 6197

Microbiology of  Extreme Environments



En - Fr

Loïs Maignien
Associate Professor / CNRS chair
Microbial EcoGenomics
University of Western Brittany


October 2019

Postdoctoral position opening  in our lab  microbial ecogenomics of the Southern Ocean plankton. Read More here

July 2019

We have four six-month Master II internships for 2020!

"Coastal Marine Archaea ecology and genomics"
supervised by Clarisse Lemonnier (postdoc)

"Deep Terrestrial subseafloor  microorganisms feedback on CO2 injection and storage"
Supervised by Ashley Grosche (postdoc)

"Southern Ocean plankton metagenomics"
Supervised by Loïs Maignien

"Ecology of unusual Archaeal phyla in the microbenthos of abyssal plains"
Supervised by Blandine Trouche

Interested microbiology and bioinformtics MSc. students, don't hesistate to contact us for more info.

April 2019
Congratulation to Florian Trigodet for the succesful defense of his PhD on the Role of electroactive Bacteria in stainless steel ennoblement

(photo credit: Yann Moalic)

April 2019
Congratulation to Clarisse Lemonnier for the succesful defense of her PhD on Dynamics and control of coastal bacterioplankton community structure in the bay of Brest

(photo credit: Feriel Bouderka)

March 2019
Application is now open for the EBAME5 workshop:
"Emerging Bioinformatics Applications for Microbial Ecogenomics" with similar program than last year, with a two weeks format for more hands on participant's data...
Apply untill May 13 to participate. More info here

(photo credit: Damien Courtine)

October 2018
Welcome to Ashley Grosche in our group! Ashley just finished her PhD in geomicrobiology of hydrothermal vents at Rutgers U.  As a postdoc in our group, she will investigate the  terrestrial biosphere, deep under the surface, as part of the  Science for clean energy H2020 project
Ashley started with collecting sample from  CarbFix monitoring wells in Iceland!

(photo credit: Ashley)

May 2018
Application is now open for the EBAME4 workshop:
"Emerging Bioinformatics Applications for Microbial Ecogenomics"
Apply untill June 25 to participate. More info here
(photo credit: Meren)

April 2018
Blandine is onboard the R/V Sonne to sample deep-sea sediments from the Atacama trench! Follow the expedition blog here

(photo Manfred Schlosser)

March 2018
Florian Trigodet presented his doctoral work during the regional final of "Ma These en 180s"

December 2017
Damien Courtine defended his PhD thesis "Comparative genomics of closely related Thermococcus". First PhD graduation of the Microbial Ecogenomics group. Congrats Damien!
PhD defense Damien Courtine

October 2017
Great group of instructors and participants for the 2017 edition of the EBAME workshop!
ebame 3 group  picture
photo credit: meren

October 2017
New paper out!

Septempber 2017
Welcome to Blandine Trouche in the group and congaratulation for her PhD fellowship. Blandine will work on biogeography of deep-sea microorganisms using 'omics approaches as part of THE ABYSS project with IFREMER and the Genoscope.

June 2017
Workshop annoucement: the third EBAME workshop will take place in Brest, October 21-27, 2017. Join us for a week of bioinformatics for microbial ecogenomics!! Apply until June 26.

May 2017
New PhD fellowship available in the lab on ecology and biogeography of deep sea microorganisms. Apply before May 29.

May 2017

Documentary about our ACE expedition on the French TV!

March 2017
Damien Courtine is going to the source (code), as visiting PhD student in Merenlab at UChicago!

February 2017
Epic interview for the Swiss Radio RTS (in french) while sampling the Mertz Glacier during our Antarctic Journey.

(image credit: François Bernard)

January 18, 2017

I'm on board the R/V Akademik Treshnikov for ACE leg 2: 40 days of sampling between Hobart and Punta Arenas!

December 16, 2016
The lab boards the R/V Akademik Treschnikov for an amazing Antarctic Circumnavigation Expedition, with the aim to better understand planktonic microorganisms involved in carbon cycling in the Southern Ocean. Follow the ACE science here, and ship route here

ACE antarctic

September 28, 2016

Emerging Bioinformatics Applications for Microbial EcoGenomics
We are hosting the 2nd EBAME workshop at IUEM on October 7, from 13:00 to 16:00. Entrance is free! IUEM amphi D. Program is here

August 29, 2016
New paper out! see the publication section

August 9, 2016

The editorial that finalizes our "Frontiers in Microbiology" Research Topic: New insights into microbial ecology through subtle nucleotide variations. A great collection of papers highlighting the importance of high-resolution methods for amplicon studies!

August 1, 2016
New paper out! see the publication section

July 20, 2016
New paper out! The complete genome of a remarkable deep-sea archaeon:

Summer 2016
Exited and honored to carry a research program at the MBL as a 2016 Whitman scientist.

July 5, 2016
With Damien Eveillard, teaching the environnemental genomic session at the 2016 Anger Bioinformatics summer school.

June 21, 2016
Florian Trigodet is presenting the first results of his PhD projects at the 18th international congress on marine corrosion and fouling in Toulon, France:  Marine electroactive biofilms responsible for stainless steel ennoblement - An EcoGenomic approach

May 20, 2016
Sabrina Belendis is on board the R/V Minerva Uno for the MicroMare2015 Cruise led by Violetta la Conno at IAMC. She is sampling Deep Hypersaline Anoxic Basins and mud volcanoes in the Mediterranean  Sea.
minerva uno

March 14, 2016

Welcome to Dr. Sabrina Berlendis in the LM2E. Sabrina will carry research on Deep Hypersaline Anoxic Lakes as a postdoc research associate, together with colleagues at IAMC in Messina. She is the recipient of the Postdoctoral fellowship in EcoGenomics of deep-sea Archaea and Bacteria from the Region Bretagne.

January 31, 2016
Congratulation to Florian Trigodet for his Academia-Industry PhD scholarship!
Florian will use our Ecogenomics toolbox to study electron transfer in marine electroactive biofilms during biocorrosion, a joint project with the French Corrosion Institute

September 14, 2015
EBAME Workshop on September 24. Program now available here! Free attendance thanks to the support of the IUEM and the EUROPOLE MER consortium.

September 9, 2015
 "Emerging Bioinformatics Approaches in Microbial Ecogenomics" (EBAME) workshop at IUEM on September 24, with MerenChris Quince, Damien Eveillard, Dominique Lavennier, Gaetan Benoit, ....  Be on the look for a program anouncement!

September 2015
Welcome to Dr. A. M. Eren (a.k.a. Meren) from the  Marine Biological Laboratory / U. Chicago as an EBAME Europole Mer invited researcher.

July 27, 2015
At the Marine Biological Laboratory of Woods Hole for a month to integrate new methods to our EcoGenomics toolbox.

July 25, 2015
Co-PI on a five year ANR grant to study microbial communites colonizing and altering marine nanoplastic particles in coastal waters.

July 15, 2015
Co-PI on a five year NSF Grant (as  MBL adjunct scientist) to develop genome-centric metagenomic approaches and apply them  to the study of rhizosphere microbes.

July 9, 2015

Lecturing introductory course on molecular methods for microbial community analysis at the Bioinformatics Summer School in University of Angers, together with with Damien Eveillard

July 8, 2015
Congratulations to Clarisse Lemonnier for her new PhD scholarship! Clarisse will carry out research for the next three years on coastal marine microbial communities dynamics.

May 22, 2015
Postdoctoral fellowship in EcoGenomics of deep-sea Archaea and Bacteria available at the LM2E. See here for Job description and application

May 9, 2015
Just embarked on the R/V "Pourquoi pas ?" for the MoMARsat 2015 campaign until May 1st. With the ROV VICTOR, we will sample the "Lucky Strike" hydrothermal vent field and perform maintenance of the deep-sea long term observatory sensor/samplers. Follow the science blog here!

March 27, 2015
LM2E seminar: welcome to Fréderic Mahé, author (et al.) of SWARM and VSEARCH, who is visiting us for a presentation of his recent work on marker gene amplicon  analysis.

March 25, 2015
New postdoc opportunity to work on ecology of extremophiles using amplicon/genomics/metagenomics approaches.  Interested candidate should apply before May 1st 2015! Appointment starting on June 1st 2015 at the latest.

March 20, 2015
Welcome to Maria-Antonietta Nisi, researcher at IAMC, Napples! Maria-Antonietta will join our lab for two weeks to work on amplicon data from the Mediteranean deep anoxic hypersaline basins. 

March 9-16, 2015
Participation to the Ocean Sampling Day jamboree. The MicroB3 project gathered an amazing scientific party at EBI (Hinxton, UK) to analyze the Ocean Sampling Day data. Results soon!

October 22, 2014

I embark on board the R/V Urania for the Saline2014 cruise. We will explore Deep Hypersaline Lakes of East Mediterranean Sea. Follow our science at sea here and with #saline2014

October 10, 2014
New paper online in Environmental Microbiology:
The effects of variable sample biomass on comparative metagenomics
Preprint in the publications section

October 1, 2014
Welcome to Damien Courtine at the LM2E and congratulation for his new PhD scholarship! Damien will use comparative genomics to get insights on extremophile ecology, evolution and phylogeography.

May 13, 2014
New application deadline for the PhD project on genomics of extremophiles. Last day for application is June 3, 2014. Online application on the doctoral school portal is mandatory.

April 27, 2014
PhD scholarship  available for  three years to work on comparative and functional genomics of  Extremophiles!  See here for more info and how to apply.

March 27, 2014

Adjunct Scientist appointment at the Marine Biological Laboratory for the next 3 years. Really looking forward to continue collaborations initiated during the postdoctoral position at the Bay Paul center and Co-PI new projects!

March 7, 2014
Frontiers in Microbiology, Special issue on "Oligotyping". Last week to submit an abstract! A very interesting way to (re)visit your 16s gene amplicon data!

Feb 01, 2014
First release of this home page at IUEM! This site will present my scientific, teaching and mentoring activities at the IUEM (European Academic Insitute for the Sea, in Brest- France).

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