Dynamique et rôle des microorganismes dans l'écosystème bois coulé en milieu profond

When wood sinks to the deep-sea floor it creates a new ecosystem that does not depend directly on energy from sunlight. This ecosystem is called chemosynthetic because of the presence of a fauna associated with symbiotic bacteria that can assimilate inorganic carbon from seawater. Furthermore this system is colonized by specialized fauna that use symbiotic bacteria to digest the wood matrix. Previous studies mostly focused on these symbiotic macroorganisms and the role played by non-symbiotic microorganisms in the sunken wood ecosystem remains unknown. We demonstrate in this thesis the important role played by non symbiotic microorganisms during the sunken wood ecosystem establishment. We reveal the ecological succession of microorganisms driven by time and wood structure. The first step of this succession is characterized by a microbial population able to produce hydrogen sulfide after one month of immersion. This hydrogen sulfide production is the basis for (1) a chemolithoautotroph biofilm development on the wood surface and (2) a recruitment of species associated with chemoautotrophic bacteria. Our results suggest a succession of different phases that transform a terrigeneous substrate into an environment that may have helped, million years ago, the colonization of the deep sea by chemosynthetic species.Lorsqu’un morceau de bois atteint le fond de l’océan, il provoque la mise en place d’un écosystème capable de se développer en absence de lumière. Cet écosystème est qualifié de chimiosynthétique du fait de la présence d’une faune pouvant fixer le carbone inorganique présent dans l’eau de mer. De plus, ce système attire une faune ultra-specialisée qui utilise des symbiontes bactériens pour digèrer le bois. Avant ces travaux, la plupart des études s’interressaient principalement à la macrofaune et le rôle des microorganismes libres demeurait inconnu. Nous avons pu démontrer dans cette thèse le rôle essentiel que jouent les microorganismes libres dans la mise en place de cet écosystème. Nous avons prouvé que des communautés de microorganismes se succédaient au cours de la première année de colonisation et que cette succession était influencée par le type de bois et l’environment dans lequel il se trouve. La première phase de cette succession aboutit au développement après un mois, d’une population de bactéries sulfato-réductrices produisant de l’hydrogène sulfuré et ce, même en l’absence d’organismes foreurs. Cette production d’hydrogène sulfuré est à la base (1) du développement rapide d’un biofilm chimiolithoautotrophe et (2) du recrutement d’espèces possédants des symbiontes chimiosynthétiques. Nos résultats ont permis d’aboutir à la proposition d’une succession d’étapes clés liées permettant la transformation d’un substrat térrigène en un écosysteme qui, il y a plusieurs millions d’années, aurait permis à la faune chimiosynthétique de coloniser les grands fonds

HgCl2 addition to pore water samples from cold seeps can affect the geochemistry of dissolved inorganic carbon ([DIC], δ13CDIC)

The conventional use of mercuric chloride (HgCl2) as an antimicrobial agent in water samples for dissolved inorganic carbon (DIC) analysis poses health and environmental risks related to its handling and disposal. Even though there is an increasing interest in quantifying pore water DIC contribution to the ocean carbon cycle and deep-sea acidification, the paucity of comparative studies on marine pore waters prevents the modification of sampling protocols and HgCl2 still remains widely used. Here, we compared DIC concentrations and δ13CDIC composition in pore water samples from methane seepage areas in the Barents Sea and offshore N. Svalbard. Samples were extracted using 0.15 μm rhizon filters and split into two aliquots with 2–3 replicates each. Only one aliquot was treated with 10 μL saturated HgCl2(aq) and all samples were stored in the dark at 4 ◦C, prior to measurements ~30 days later. The samples yielded extremely wide ranges of DIC concentrations, from 1.8 mM to 20.1 mM, and δ13CDIC values, from − 36.0‰ to − 1.6‰ (VPDB), due to variable contributions of methane-derived DIC to the pore water system. Overall, we obtained lower [DIC] (77% samples; N = 26) and heavier δ13C values (79% samples; N = 42) in Hg-treated samples. Isotopic and concentration differences larger than the uncertainties on the mean of replicated measurements (±0.2–0.5‰; ± 0.5 mM) and analytical precision (0.15‰; 0.71 mM) represent the 38% and 19% of the samples, with offsets of up to 7.4‰ and 1.9 mM, respectively. The largest offsets are in agreement with our CO2-degassing model, suggesting an interaction between mercuric chloride and dissolved hydrogen sulfide released by sulfate-driven methane oxidation. We therefore caution against further use of HgCl2 for DIC studies of marine pore waters from cold seeps

Hand-written letters and photo albums linking geoscientists with school classes

Do we miss something about &laquo;traditional&rdquo; media such as handwritten letters and photography before the digital age? Some of the authors remember this age fondly, and we wanted to see if this fondness could be translated into a science dialogue project with school classes. We designed and carried out a communication process with 4 classes at different schools across Europe. During this process, each class would interact with a single scientist primarily via hand-written questions &amp; letters, and a Polaroid photo album. The scientists would make this unique, one-of-a-kind album whilst on board a research expedition in the Barents Sea. We asked the question whether this process might show any benefits to the school students involved. To answer this, we asked the students to write up their thoughts on communicating with a scientist in this way. We analysed the texts and found that most students thought the letters and polaroid albums were a &ldquo;beautiful experience&rdquo;. Others commented on how important it is to actually put pen to paper and write, since they use (almost) only digital media these days. Most importantly, the students learnt different elements of the science connected to the research expedition, but also about the scientific process in general. And, equally important, some of the students were surprised and thankful that the scientists took the time to communicate with them in such a personal way. These results could possibly have been achieved using other media, however the hand-written letters and Polaroids worked very well. They also seemed to conjure up some of the personal memories that we have about communication not so long ago. Maybe there is something to be said for slowing things down with our science communication projects and making them more personal and unique. This is something that snail-mail and making photo albums forces us to do.</p

The Impact of Methane on Microbial Communities at Marine Arctic Gas Hydrate Bearing Sediment

Cold seeps are characterized by high biomass, which is supported by the microbial oxidation of the available methane by capable microorganisms. The carbon is subsequently transferred to higher trophic levels. South of Svalbard, five geological mounds shaped by the formation of methane gas hydrates, have been recently located. Methane gas seeping activity has been observed on four of them, and flares were primarily concentrated at their summits. At three of these mounds, and along a distance gradient from their summit to their outskirt, we investigated the eukaryotic and prokaryotic biodiversity linked to 16S and 18S rDNA. Here we show that local methane seepage and other environmental conditions did affect the microbial community structure and composition. We could not demonstrate a community gradient from the summit to the edge of the mounds. Instead, a similar community structure in any methane-rich sediments could be retrieved at any location on these mounds. The oxidation of methane was largely driven by anaerobic methanotrophic Archaea-1 (ANME-1) and the communities also hosted high relative abundances of sulfate reducing bacterial groups although none demonstrated a clear co-occurrence with the predominance of ANME-1. Additional common taxa were observed and their abundances were likely benefiting from the end products of methane oxidation. Among these were sulfide-oxidizing Campilobacterota, organic matter degraders, such as Bathyarchaeota, Woesearchaeota, or thermoplasmatales marine benthic group D, and heterotrophic ciliates and Cercozoa

Seasonal shifts of microbial methane oxidation in Arctic shelf waters above gas seeps

The Arctic Ocean subseabed holds vast reservoirs of the potent greenhouse gas methane (CH4), often seeping into the ocean water column. In a continuously warming ocean as a result of climate change an increase of CH4 seepage from the seabed is hypothesized. Today, CH4 is largely retained in the water column due to the activity of methane-oxidizing bacteria (MOB) that thrive there. Predicted future oceanographic changes, bottom water warming and increasing CH4 release may alter efficacy of this microbially mediated CH4 sink. Here we investigate the composition and principle controls on abundance and activity of the MOB communities at the shallow continental shelf west of Svalbard, which is subject to strong seasonal changes in oceanographic conditions. Covering a large area (364 km2), we measured vertical distribution of microbial methane oxidation (MOx) rates, MOB community composition, dissolved CH4 concentrations, temperature and salinity four times throughout spring and summer during three consecutive years. Sequencing analyses of the pmoA gene revealed a small, relatively uniform community mainly composed of type-Ia methanotrophs (deep-sea 3 clade). We found highest MOx rates (7 nM d−1) in summer in bathymetric depressions filled with stagnant Atlantic Water containing moderate concentrations of dissolved CH4 (d−1) due to lower temperatures and mixing of Transformed Atlantic Water flushing MOB with the Atlantic Water out of the depressions. Our results show that MOB and MOx in CH4-rich bottom waters are highly affected by geomorphology and seasonal conditions

Elevated methane alters dissolved organic matter composition in the Arctic Ocean cold seeps

Cold seeps release methane (CH4) from the seafloor to the water column, which fuels microbially mediated aerobic methane oxidation (MOx). Methane-oxidising bacteria (MOB) utilise excess methane, and the MOB biomass serves as a carbon source in the food web. Yet, it remains unclear if and how MOx modifies the composition of dissolved organic matter (DOM) in cold seeps. We investigated MOx rates, DOM compositions and the microbial community during ex-situ incubations of seawater collected from a cold seep site at Norskebanken (north of the Svalbard archipelago) in the Arctic Ocean. Samples were incubated with and without methane amendments. Samples amended with methane (∼1 µM final concentration) showed elevated rates of MOx in both seep and non-seep incubations. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses showed that the number of DOM formulas (i.e., molecular diversity) increased by up to 39% in these incubations. In contrast, the number of formulas decreased by 20% in samples not amended with methane, both from non-seep and seep locations. DOM composition was thus altered towards a more diverse and heterogeneous composition along with elevated methanotrophic activity in methane-amended conditions. In addition to microbial DOM production, abating microbial diversity indicates that elevated DOM diversity was potentially related to grazing pressure on bacteria. The diversity of DOM constituents, therefore, likely increased with the variety of decaying cells contributing to DOM production. Furthermore, based on a principal coordinate analysis, we show that the final DOM composition of non-seep samples amended with methane became more resemblant to that of seep samples. This suggests that methane intrusions will affect water column DOM dynamics similarly, irrespective of the water column’s methane history

Dynamics and role of microorganisms in the deep-sea sunken wood ecosystem

Lorsqu’un morceau de bois atteint le fond de l’océan, il provoque la mise en place d’un écosystème capable de se développer en absence de lumière. Cet écosystème est qualifié de chimiosynthétique du fait de la présence d’une faune pouvant fixer le carbone inorganique présent dans l’eau de mer. De plus, ce système attire une faune ultra-specialisée qui utilise des symbiontes bactériens pour digèrer le bois. Avant ces travaux, la plupart des études s’interressaient principalement à la macrofaune et le rôle des microorganismes libres demeurait inconnu. Nous avons pu démontrer dans cette thèse le rôle essentiel que jouent les microorganismes libres dans la mise en place de cet écosystème. Nous avons prouvé que des communautés de microorganismes se succédaient au cours de la première année de colonisation et que cette succession était influencée par le type de bois et l’environment dans lequel il se trouve. La première phase de cette succession aboutit au développement après un mois, d’une population de bactéries sulfato-réductrices produisant de l’hydrogène sulfuré et ce, même en l’absence d’organismes foreurs. Cette production d’hydrogène sulfuré est à la base (1) du développement rapide d’un biofilm chimiolithoautotrophe et (2) du recrutement d’espèces possédants des symbiontes chimiosynthétiques. Nos résultats ont permis d’aboutir à la proposition d’une succession d’étapes clés liées permettant la transformation d’un substrat térrigène en un écosysteme qui, il y a plusieurs millions d’années, aurait permis à la faune chimiosynthétique de coloniser les grands fonds.When wood sinks to the deep-sea floor it creates a new ecosystem that does not depend directly on energy from sunlight. This ecosystem is called chemosynthetic because of the presence of a fauna associated with symbiotic bacteria that can assimilate inorganic carbon from seawater. Furthermore this system is colonized by specialized fauna that use symbiotic bacteria to digest the wood matrix. Previous studies mostly focused on these symbiotic macroorganisms and the role played by non-symbiotic microorganisms in the sunken wood ecosystem remains unknown. We demonstrate in this thesis the important role played by non symbiotic microorganisms during the sunken wood ecosystem establishment. We reveal the ecological succession of microorganisms driven by time and wood structure. The first step of this succession is characterized by a microbial population able to produce hydrogen sulfide after one month of immersion. This hydrogen sulfide production is the basis for (1) a chemolithoautotroph biofilm development on the wood surface and (2) a recruitment of species associated with chemoautotrophic bacteria. Our results suggest a succession of different phases that transform a terrigeneous substrate into an environment that may have helped, million years ago, the colonization of the deep sea by chemosynthetic species

Phylogenetic_distance_matrix

The file contains the phylogenetic distance matrix calculated with the comdistnt function in the Picante R package

Historical contingency impacts on community assembly and ecosystem function in chemosynthetic marine ecosystems

Predicting ecosystem functioning requires an understanding of the mechanisms that drive microbial community assembly. Many studies have explored microbial diversity extensively and environmental factors are thought to be the principal drivers of community composition. Community assembly is, however, also influenced by past conditions that might affect present-day assemblages. Historical events, called legacy effects or historical contingencies, remain poorly studied in the sea and their impact on the functioning of the communities is not known. We tested the influence, if any, of historical contingencies on contemporary community assembly and functions in a marine ecosystem. To do so, we verified if different inoculum communities colonizing the same substrate led to communities with different compositions. We inoculated wood with sea water microbes from different marine environments that differ in ecological and evolutionary history. Using 16S rRNA and metagenomic sequencing, it was demonstrated that historical contingencies change the composition and potential metabolisms of contemporary communities. The effect of historical events was transient, dominated by environmental selection as, over time, species sorting was a more important driver of community assembly. Our study shows not only that historical contingencies affect marine ecosystems but takes the analysis a step further by characterizing this effect as strong but transient

OTU_table

The file contains the annotated and resampled OTU table