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Unravelling the microbial carbon pump in the ocean: Linkage between gene expression and RDOM generation by marine bacteria (CARAMBA)

Periodic Reporting for period 1 - CARAMBA (Unravelling the microbial carbon pump in the ocean: Linkage between gene expression and RDOM generation by marine bacteria (CARAMBA))

Reporting period: 2017-03-06 to 2019-03-05

The increase of carbon dioxide (CO2) in the atmosphere due to human activities has consequences for global change that have sparked substantial interest in the study of the planetary carbon cycle. The ocean is one of the largest carbon reservoirs on Earth and therefore plays a key role in the global carbon cycle. At present, the ocean absorbs 30% of anthropogenic CO2. The ocean contains an amount of carbon in the form of oceanic dissolved organic matter (DOM; 660 Gt) similar to that in atmospheric CO2 (829 Gt). A net oxidation of only 1% of the seawater DOM pool in one year would be enough to produce a CO2 flux larger than that coming annually from fossil fuel combustion. Even though the importance of oceanic DOM for the global carbon cycles is well recognized, major gaps in our understanding of the chemical composition and the cycling of individual compounds persist.

Bacteria play a key role in DOM processing in the ocean. For example, one half of carbon fixed by phytoplankton through photosynthesis, the main source of DOM in the ocean, are processed by bacteria. They use this DOM for respiration, thus transforming it back into CO2, or for production of new bacterial biomass that then enters the trophic web (i.e. is consumed by ciliates and flagellates that will be then grazed by higher trophic levels). However, it was only recently discovered that marine bacteria also release DOM. Part of bacterially-derived DOM is largely resistant to further utilization and persists in the ocean’s interior through thousands of years. This mechanism of carbon sequestration in the ocean mediated by bacteria is what we know as the microbial carbon pump.

However, how and why marine bacteria produce DOM and why this DOM is not further degraded in the ocean is still under investigation, and getting the answers are essential to predict climate change effects: If all this pool of recalcitrant DOM was respired and the carbon released to the atmosphere, it would double the atmospheric CO2 inventory.

The main objective of the CARAMBA project was to better understand the ultimate reasons, for bacterial DOM production and its persistence in the ocean. The specific objectives were to elucidate whether bacterial taxonomical composition affected DOM production and tis quality, and whether environmental conditions would affect the bioavailability of this produced DOM.
To achieve the scientific questions proposed in CARAMBA, we chose to combine the work with model bacterial organisms in culture with experimental incubations using natural microbial communities from the Mediterranean Sea. We chose bacterial strains originating from contrasting marine environments and lifestyles: Coastal vs. open sea, oligotrophs vs. copiotrophs, different taxonomical groups. These model strains were grown in the laboratory under a single and measurable carbon source (glucose). Once the strains grew and achieved the stationary phase, DOM from the cultures was extracted, quantified and characterized. This allowed us to estimate the amount of DOM produced by marine bacteria and to assess the differences in DOM quality associated with the differences in bacterial taxonomy, that ranged from 9 to 23% of initial carbon. Finally, we conducted experimental incubations with natural marine communities sampled from the Mediterranean Sea. In those, we assessed how much of the DOM produced in the cultures could be up taken by natural microbial communities (labile DOM) and how much of it would persist as refractory. We could evidence that DOM produced by the different bacterial strains was not equally available: DOM produced by Photobacterium angustum, a fast-growing gammaproteobacteria, was enriched in labile compounds and induced high activity of the enzyme aminopeptidase in natural communities. In contrast, DOM produced by the slow-growing alphaproteobacteria Sphingopyxis alaskensis induced a slower uptake by natural communities and mostly mediated by the enzyme alkaline phosphatase. The stimulation of different metabolisms in natural bacteria suggested a change in carbon cycles linked to the differences in bacterial composition. These results are presented principally to the scientific community during the participation in international meetings and through the publication of SCI papers, but also to the broader audience through social media and outreach activities.
Understanding how DOM in the ocean is created and maintained is key in the efforts for managing the increasing carbon humans are introducing into the atmosphere. The data provided by the CARAMBA project will set the basis to re-consider the role of bacteria through the carbon cycle: While carbon fluxes through bacteria are usually included in models as the sum of bacterial production and respiration, DOM transformation and release by bacteria are poorly represented in them. Further steps in the field should be oriented to go “from bench to boat”, this is to get better estimations of bacterial DOM production patterns and their persistence in natural conditions, as well as the impact of climate change stressors (temperature, UV, presence of contaminants, changing nutrient fields) on the microbial carbon pump in the ocean.
Our model strains: Photobacterium angustum, Sphingopyxis alaskensis, Eudoraea adriatica
Nawal Bouchachi, Master student on the Caramba Project, extracting bacterial DOM in solid phase
Quentin Devresse, Master student on the Caramba Project, sampling for bacterial DOM stoichiometry