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Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

<p>This doctoral research comparatively assesses the biogeochemical properties of suspended aquatic flocs through a integrated field-laboratory approach; providing new insight into the linkages among floc associated bacteria, floc-reactive solid phases and trace metal uptake.</p> <p>Results show flocs to possess a distinct geochemistry, microbiology and composition from bed sedimentary materials in close proximity (III-oxyhydroxide minerals (FeOOH); resulting in localized floc-Fe-mineral precipitates and enhanced reactivity. Further, the Fe-enrichment of floc and of floc bio-mineral constituents in turn provides an important and novel lens through which to examine how environmental microbial communities, microbial metabolism and Fe^III/Fe^IIredox transformations interact. The results were the discovery of floc-hosted, Fe^III/II-redox cycling bacterial consortia across diverse oxygenated (O₂^Sat.=1-103%) aquatic systems, which were not predicted to sustain bacterial Fe-metabolism. Both environmental<em> </em>and experimentally-developed consortial aggregates constituted multiple genera of aero-intolerant Fe^III-reducing and Fe^II-oxidizing bacteria together with oxygen consuming organotrophic species. These findings highlight that the implementation of geochemical thermodynamic constraints alone as a guide to investigating and interpreting microbe-geosphere interactions may not accurately capture processes occurring <em>in situ.</em></p> <p><em> </em> Seasonal investigation of microbial Fe^III/II-redox transformations highlighted the interdependence of floc Fe-redox cycling consortia members, revealing that cold conditions and a turnover in putative Fe-reducing community membership extinguishes the potential for coupled Fe-redox cycling by wintertime floc bacteria. Further, the observed summer-winter seasonal turnover of <em>in situ</em> floc community membership corresponded with an overall shift from dominant Fe to S redox cycling bacterial communities. This significantly impacted observable floc Fe and TE (Cd, Pb) geochemistry, resulting in a shift in floc associated Fe-phases from dominantly Fe^(III)_(s) to Fe^(II)_(s), and, in turn, corresponded to a large decrease of TE uptake by flocs under ice.</p> / Doctor of Science (PhD)

Les effondrements miniers en Lorraine (France) ont pour origine la rupture des piliers de soutien constitués de minerai de fer. Leur rupture n'est pas seulement due aux seules contraintes mécaniques qu’exerce le recouvrement mais également aux différentes transformations minéralogiques du minerai de fer, compromettant sa cohésion et sa résistance et par conséquent, la stabilité des piliers. On parle alors d’altération/vieillissement minéralogique du minerai de fer. Les mécanismes chimiques qui entrainent ces transformations minéralogiques sont désormais bien connus mais l’influence de l’activité bactérienne n’est pas encore bien comprise. Des travaux préliminaires ayant soulevé le rôle possible des activités microbiennes, ce travail de thèse s'est alors appliqué à identifier les métabolismes bactériens susceptibles de réagir avec le minerai de fer en conditions aérobie et anaérobie, et à en caractériser les effets physico-chimiques, minéralogiques et mécaniques. Les groupes métaboliques bactériens suspectés d’être impliqués dans ces réactions (activités ferri-réductrices, ferro-oxydantes et sulfato-réductrices) ont été identifiés dans les eaux de mine et incubés en présence du minerai de fer, en souche pure ou avec un consortium issu de l’eau de mine. Les bactéries ferri-réductrices (IRB), sulfato-réductrices (BSR) et acidophiles ferro-oxydantes ont été les seules qui, dans les conditions de laboratoire, ont impacté significativement le minerai en modifiant le ratio Fe(II)/Fe(III). Une phase ferro-carbonatée et de la pyrite se sont formées respectivement au cours des incubations avec les IRB et BSR, et ont été caractérisées par analyse du solide (spectroscopies infrarouge en réflexion diffuse (DRIFTS) et Mössbauer et par diffraction aux rayons X). Des bactéries nitrate-réductrices ont aussi été testées et aucune modification significative du ratio Fe(II)/Fe(III) du minerai de fer n’a été observée. Enfin, les propriétés mécaniques du minerai de fer ont été mesurées après les réactions d’oxydo-réduction biologiques et purement chimiques. Des modifications sensibles de ces propriétés mécaniques par rapport à l’état initial ont ainsi pu être mises en évidence. Sur la base de ces résultats, l’hypothèse de l’altération mécanique du minerai de fer par des activités microbiennes est donc tout à fait réaliste. / Mine collapses occurred in Lorraine (France) because of the failure of safety pillars made of iron ore. Their failure is not only due to the mechanic stresses applied by the overburden, but also due to the various mineralogical transformations in iron ore which decrease material cohesion and resistance and thus stability of pillars. This is called mineralogical alteration/ageing of iron ore. Chemical mechanisms inducing these mineralogical transformations are now well known but the influence of microbial activity is not well understood yet. Preliminary works have raised the possible role of microbial activity, then the focus of this work was to identify the various bacterial metabolisms capable of reacting with iron ore and to characterize the physico-chemical, mineralogical and mechanical effects. The bacterial metabolism groups possibly implied in these reactions (iron-reducing (IRB), iron-oxidizing and sulfate-reducing bacteria (SRB)) were identified from the mine water. As pure strain or as consortium, these bacteria were incubated with iron ore. Under laboratory conditions, only iron-reducing, sulfate-reducing and acidophilic iron-oxidizing bacteria impacted iron ore samples by modifying the Fe(II)/Fe(III) ratio. A ferrous-carbonate phase and pyrite were formed during incubations with IRB and SRB, respectively. These minerals were characterized from analysis of the solid phase (Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), Mössbauer spectroscopy and X-ray diffraction). The impact nitrate-reducing bacteria was also tested but the Fe(II)/Fe(III) ratio of iron ore was not modified significantly. Finally, mechanical properties of iron ore were measured after microbial and purely chemical redox reactions. Discernible modifications of these mechanical properties were observed. From these results, the alteration of iron ore mechanical properties by bacterial activities is a realistic assumption.