- - Physiology and metabolism of microorganisms
- - Ecology of microorganisms
- - Archaea and Bacteria
- - Biogeochemical cycling of carbon and nitrogen
Dr. Pierre Offre
Searching for the bacteria that escaped notice for so long
Marine microbiologist Pierre Offre investigates bacteria that are found in every sea and on almost every beach and sand flat. ‘They probably represent one-quarter of all bacteria you can find on any sand grain in the tidal zone. However, this group of bacteria is still relatively unknown to science. For some reason, these bacteria managed to escape the attention of microbiologists for a long time.’
Unknown reservoir of biodiversity
‘The fact that these bacteria were first described only recently is the reason that their name is not familiar to most, including members of the microbiology research community. Initially, they were referred to by the code name JTB255. Nowadays, they are referred to as Candidatus Woeseiales, after the American molecular evolutionary biologist Carl Woese who passed away in 2012. Yet we do not currently know much about the biodiversity of these microorganisms. We do not even know how many distinct types of microorganisms are included in the candidate order Woeseiales. As for now, we can only say that it includes a minimum of 15 major lineages.’
Organic food
‘I try to understand how these bacteria live. What do they eat? With whom or what do they live? And in particular, how do they influence the breakdown of organic matter in marine environments? The latter question is meant to elucidate the ecological significance of these bacteria that seemingly have the capability to live from the breakdown of organic material, such as proteins. The first individual species that was isolated in 2016 was found to break down proteins into various substances, including ammonia. Other members of the family seem to gain their energy by breaking down sulphur compounds.’
Useful enzymes
‘My interest in these bacteria is mainly fundamental in nature. With a group that so widely occurs in all marine environments, I am genuinely working at the basis of the figurative ecological iceberg. These bacteria exert an influence on all marine environments in which oxygen occurs and likely play important roles in nutrient cycles. They even occur on land, in relatively saline areas. It could well be the case that this fundamental knowledge will one day yield practical applications. For example, the enzymes that these bacteria use to break down proteins might one day arouse the interest of biotechnology companies.’
Read more +Research interests
The astounding diversity of metabolisms, physiologies and ecological strategies in both extent and past life forms is at the center of my motivation for biological sciences. I have a particular interest in microorganisms, especially Bacteria and Archaea, because of the incredible variety of their primary and secondary metabolisms, which fascinates me. The variety of those metabolisms is key to the (re)cycling of nutrients essential to all life forms and is therefore a central component of the biogeochemical engine that enabled life to thrive and diversify on Earth for up to 4 billion years. The overall aim of my research is to characterize metabolic and physiological traits of microorganisms, determine their molecular basis and understand how those traits drive the cycling of nutrients in ecosystems and the assembly of biological communities. I address those overarching goals in two distinct lines of research:
Ecological niche and life strategies of archaeal ammonia oxidizers in dark ocean waters: The ammonia-oxidizing archaea (AOA) are chemo-litho-autotrophic aerobes that conserve energy and produce reducing equivalents from the oxidation of ammonia into nitrite. Those microorganisms are thought to play a major role in the ocean nitrogen cycle and uncultivated relatives of those microorganisms account for up to 40% of all bacteria and archaea in dark ocean waters. The large proportion of those putative autotrophs in deep waters challenges the idea that most deep-sea microorganisms are heterotrophs depending on the vertical flux of particulate organic matter. Those observations challenge as well our knowledge of the lifestyle of AOA and their deep-water relatives and question our understanding of nitrogen cycling in the ocean. Using a combination of physiological experiments on cultivated AOA strains, enrichment cultures, isotopic tracer studies and ‘omics approaches, my team investigates the physiological and metabolic traits enabling relatives of cultivated AOA to thrive in the deep ocean and clarify models of deep-water nitrogen cycling.
Metabolic and physiological diversity of JTB255 bacteria: JTB255 is a group of Gammaproteobacteria, which was recently shown to be widely distributed in marine benthic environments, including both coastal and deep-sea sediments. Sequencing surveys suggest that JTB255 could account for a large fraction of all bacteria and archaea in sediments and may indeed represent one of the core groups of the global sediment microbiome. Until recently JTB255 was only known as a cluster of 16S rRNA gene sequences but several partial genomes and one complete genome have now been obtained. Investigations of those genomes suggested that JTB255 bacteria include some chemo-organo-heterotrophs both strict and facultative (some have a potential for hydrogen and sulfur-based chemo-litho-autotrophy). My research team aims at characterizing the metabolic and physiological diversity of those bacteria using growth experiments on a cultivated strain, enrichment cultures and ‘omics investigations in order to further our knowledge of the ecological role of JTB255.
Research Experience
Since 09/2017: Tenure Track Scientist at NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry (MMB)
04/2015 – 09/2017: Senior Scientist at Max-Planck Institute for Marine Microbiology (Germany), HGF MPG Joint Research Group for Deep-Sea Ecology and Technology
01/2015 – 03/2015: Visiting Scientist at University of Uppsala (Sweden), Department of Limnology
08/2010 – 12/2014: Postdoctoral Researcher at University of Vienna (Austria), Department of Ecogenomics and Systems Biology
05/2008 – 08/2010: Postdoctoral Researcher at University of Aberdeen (United Kingdom), Institute of Biological and Environmental Sciences
01/2008 – 04/2008: Researcher at INRA-Dijon (France), Department ‘Plants, Microbes and Environments’
12/2003 – 06/2007: PhD student at INRA-Dijon (France), Department ‘Soil and Environmental Microbiology’
09/2002 – 07/2003: Master student at INRA-Dijon (France), Department ‘Soil and Environmental Microbiology’
Publications
Google Scholar: https://scholar.google.nl/citations?user=i9rHLcYAAAAJ&hl=en
Linked news
Linked blogs
NIOZ publications
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2024
Timmis, K.; Hallsworth, J.E.; McGenity, T.J.; Armstrong, R.; Colom, M.F.; Karahan, Z.C.; Chavarría, M.; Bernal, P.; Boyd, E.S.; Ramos, J.L.; Kaltenpoth, M.; Pruzzo, C.; Clarke, G.; López‐Garcia, P.; Yakimov, M.M.; Perlmutter, J.; Greening, C.; Eloe‐Fadrosh, E.; Verstraete, W.; Nunes, O.C.; Kotsyurbenko, O.; Nikel, P.I.; Scavone, P.; Häggblom, M.M.; Lavigne, R.; Le Roux, F.; Timmis, J.K.; Parro, V.; Michán, C.; García, J.L.; Casadevall, A.; Payne, S.M.; Frey, J.; Koren, O.; Prosser, J.I.; Lahti, L.; Lal, R.; Anand, S.; Sood, U.; Offre, P.; Bryce, C.C.; Mswaka, A.Y.; Jores, J.; Kaçar, B.; Blank, L.M.; Maaßen, N.; Pope, P.B.; Banciu, H.L.; Armitage, J.; Lee, S.Y.; Wang, F.; Makhalanyane, T.P.; Gilbert, J.A.; Wood, T.K.; Vasiljevic, B.; Soberón, M.; Udaondo, Z.; Rojo, F.; Tamang, J.P.; Giraud, T.; Ropars, J.; Ezeji, T.; Müller, V.; Danbara, H.; Averhoff, B.; Sessitsch, A.; Partida‐Martínez, L.P.; Huang, W.; Molin, S.; Junier, P.; Amils, R.; Wu, X.; Ron, E.; Erten, H.; de Martinis, E.C.P.; Rapoport, A.; Öpik, M.; Pokatong, W.D.R.; Stairs, C.; Amoozegar, M.A.; Serna, J.G. (2024). A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society. Microbial Biotechnology 17(5): e14456. https://dx.doi.org/10.1111/1751-7915.14456
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2023
Molari, M.; Hassenrueck, C.; Laso-Pérez, R.; Wegener, G.; Offre, P.; Scilipoti, S.; Boetius, A. (2023). A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nature Microbiology 8(4): 651-665. https://dx.doi.org/10.1038/s41564-023-01342-w
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2022
Martijn, J.; Vosseberg, J.; Guy, L.; Offre, P.; Ettema, T.J.G. (2022). Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nature Ecology & Evolution 6: 1829-1831. https://dx.doi.org/10.1038/s41559-022-01871-3Moody, E.R.R.; Mahendrarajah, T.A.; Dombrowski, N.; Clark, J.W.; Petitjean, C.; Offre, P.; Szöllosi, G.J.; Spang, A.; Williams, T.A. (2022). An estimate of the deepest branches of the tree of life from ancient vertically evolving genes. eLIFE 11: e66695. https://dx.doi.org/10.7554/elife.66695Patterson, M.O.; Levy, R.H.; Kulhanek, D.K.; van de Flierdt, T.; Horgan, H.; Dunbar, G.B.; Naish, T.R.; Ash, J.; Pyne, A.; Mandeno, D.; Winberry, P.; Harwood, D.M.; Florindo, F.; Jimenez-Espejo, F.J.; Läufer, A.; Yoo, K.-C.; Seki, O.; Stocchi, P.; Klages, J.P.; Lee, J.I.; Colleoni, F.; Suganuma, Y.; Gasson, E.; Ohneiser, C.; Flores, J.-A.; Try, D.; Kirkman, R.; Koch, D.; the SWAIS 2C Science Team (2022). Sensitivity of the West Antarctic Ice Sheet to +2 °C (SWAIS 2C). Sci. Drill. 30: 101-112. https://dx.doi.org/10.5194/sd-30-101-2022Spang, A.; Mahendrarajah, T.A.; Offre, P.; Stairs, C.W. (2022). Evolving perspective on the origin and diversification of cellular life and the virosphere. Genome Biology and Evolution 14(6): evac034. https://dx.doi.org/10.1093/gbe/evac034
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2020
Hoffmann, K.; Bienhold, C.; Buttigieg, P.L.; Knittel, K.; Laso-Pérez, R.; Rapp, J.Z.; Boetius, A.; Offre, P. (2020). Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. ISME J. 14: 1042-1056. https://dx.doi.org/10.1038/s41396-020-0588-4
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2019
Bayer, B.; Pelikan, C.; Bittner, M.J.; Reinthaler, T.; Könneke, M.; Herndl, G.; Offre, P. (2019). Proteomic response of three marine ammonia-oxidizing archaea to hydrogen peroxide and their metabolic interactions with a heterotrophic alphaproteobacterium. mSystems 4(4): e00181-19. https://dx.doi.org/10.1128/msystems.00181-19Dombrowski, N.; Lee, J.-H.; Williams, T.A.; Offre, P.; Spang, A. (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol. Lett. 366(2): 1-12. https://dx.doi.org/10.1093/femsle/fnz008Spang, A.; Offre, P. (2019). Towards a systematic understanding of differences between archaeal and bacterial diversity. Environmental Microbiology Reports 11(1): 9-12. https://dx.doi.org/10.1111/1758-2229.12701
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2018
Buttigieg, P.L.; Fadeev, E.; Bienhold, C.; Hehemann, L.; Offre, P.; Boetius, A. (2018). Marine microbes in 4D - using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Curr. Opin. Microbiol. 43: 169-185. https://dx.doi.org/10.1016/j.mib.2018.01.015Kellner, S.; Spang, A.; Offre, P.; Szöllosi; Petitjean, C.; Williams, T.A. (2018). Genome size evolution in the Archaea. Emerging Topics in Life Sciences 2(4): ETLS20180021. https://dx.doi.org/10.1042/etls20180021Martijn, J.; Vosseberg, J.; Guy, L.; Offre, P.; Ettema, T.J. G. (2018). Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature (Lond.) 557(7703): 101-105. https://doi.org/10.1038/s41586-018-0059-5
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