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Although biomineralization of CaCO 3 is widespread in Bacteria and Archaea, the molecular mechanisms involved in this process remain less known than those used by Eukaryotes. A better understanding of these mechanisms is crucial for a broad diversity of studies including those (i) aiming at assessing the role of bacteria in the geochemical cycles of Ca and C, (ii) investigating the process of fossilization, and (iii) engineering applications using bacterially mediated CaCO 3 mineralization. Different types of bacterially-mediated mineralization modes have been distinguished depending on whether they are influenced (by extracellular organic molecules), induced (by metabolic activity) or controlled (by specific genes). In the first two types, mineralization is usually extracellular, while it is intracellular for the two ascertained cases of controlled bacterial mineralization. In this review, we list a large number of cases illustrating the three different modes of bacterially-mediated CaCO 3 mineralization. Overall, this shows the broad diversity of metabolic pathways, organic molecules and thereby microorganisms that can biomineralize CaCO 3 . Providing an improved understanding of the mechanisms involved and a good knowledge of the molecular drivers of carbonatogenesis, the increasing number of (meta)-omics studies may help in the future to estimate the significance of bacterially mediated CaCO 3 mineralization.

Mn(II)-oxidizing organisms promote the biomineralization of manganese oxides with specific textures, under ambient conditions. Controlling the phases formed and their texture on a larger scale may offer environmentally relevant routes to manganese oxide synthesis, with potential technological applications, for example, for energy storage. In the present study, we sought to use biofilms to promote the formation of electroactive minerals and to control the texture of these biominerals down to the electrode scale (i.e., cm scale). We used the bacterium Pseudomonas putida strain MnB1 which can produce manganese oxide in a biofilm. We characterized the biofilm–mineral assembly using a combination of electron microscopy, synchrotron-based X-ray absorption spectroscopy, X-ray diffraction, thermogravimetric analysis and electron paramagnetic resonance spectroscopy. Under optimized conditions of biofilm growth on the surface of current collectors, mineralogical characterizations revealed the formation of several minerals including a slightly crystalline MnOx birnessite. Electrochemical measurements in a half-cell against Li(0) revealed the electrochemical signature of the Mn4+/Mn3+ redox couple indicating the electroactivity of the biomineralized biofilm without any post-synthesis chemical, physical or thermal treatment. These results provide a better understanding of the properties of biomineralized biofilms and their possible use in designing new routes for one-pot electrode synthesis.

In the context of the ecological sustainability of phosphorus, emerging evidence for the ubiquitous presence of polyphosphate-accumulating bacteria in natural environments invites efforts to reveal their roles in the biogeochemical cycle of phosphorus. This requires high-throughput methods to characterize their structure and dynamics in ecosystems. A promising strategy is to combine the staining of intracellular polyphosphate granules and their subsequent detection by flow cytometry, enabling rapid data acquisition. In this study, we evaluated the potential of this approach by testing various factors that could affect the efficiency and specificity of polyphosphate labeling. Most of our experiments were performed using the 4′,6-diamidino-2-phenylindole dye (DAPI). However, we also carried out a preliminary study using the synthetic fluorochrome JC-D7, a new selective fluorescent dye used for the specific labeling of endogenous polyphosphate in living cells. The assays were performed on Tetrasphaera elongata, a Gram-positive bacterium known to accumulate large amounts of intracellular polyphosphates. We also used six bacterial strains belonging to different phyla, in particular a Gram-negative bacterial strain belonging to the genus Pseudomonas, which is characterized by low levels of cellular polyphosphate. The potential of flow cytometry to quantify and sort polyphosphate-accumulating bacteria in complex environmental samples, including soil, freshwater and sediments, was also examined. Our tests provide useful information for the design of future experiments and highlight the potential pitfalls and limitations of detecting polyphosphate-accumulating bacteria using the cytometric approach. We also show that JC-D7 is a promising dye for achieving these objectives, particularly for enumerating polyphosphate-accumulating bacteria from environmental samples.

Iron and manganese are poorly soluble elements in oxic and alkaline solutions, whereas they are much more soluble under anoxic conditions. As a result, the formation of authigenic mineral phases rich in Fe and/or Mn has traditionally been viewed as diagnostic of global or local anoxic conditions. Here we reveal that some specific cyanobacteria of very small size (< 2 µm, i.e., picocyanobacteria) can biomineralize abundant, authigenic Fe(III)-, Mn(IV)- and Si-rich amorphous phases under oxic conditions in an alkaline lake in Mexico. The resulting biominerals cluster as small globules arranged as rings around the division septum of cyanobacterial cells. These rings are enveloped within an organic, likely polysaccharidic envelope and are partially preserved, at least morphologically, upon sedimentation. Based on their 16S rDNA sequence, these cyanobacteria were affiliated with the Synechococcales order. The high Fe and Mn enrichment of the biominerals questions the systematic inference of anoxic conditions based on their detection. Moreover, this process scavenges iron from the water column, an overlooked biological contribution to the Fe cycle. Finally, it reveals a new case of controlled biomineralization of Si-rich phases by bacteria.

As biominerals are good tracers of microbial interactions with the environment, they may provide signatures of microbial evolution and paleoenvironmental conditions. Since modern analogues of past environments help with defining proxies and biosignatures, we explored microbe mineral interactions in the water column of a maar lake, located in France: Lake Pavin. This lake is considered as a potential Precambrian ocean analogue, as it is ferruginous and meromictic, i.e., stratified with a superficial O2-rich layer (mixolimnion) and a deeper permanently anoxic layer (monimolimnion). We combined bulk chemical analyses of dissolved and particulate matter in combination with electron microscopy analyses of the particulate matter at different depths along the water column. The mineralogy changed along with water chemistry, and most of the minerals were intimately associated with microorganisms. Evolution of the redox conditions with depth leads to the successive precipitation of silica and carbonates, Mn-bearing, Fe-bearing and S-containing phases, with a predominance of phosphates in the monimolimnion. This scheme parallels the currently-assessed changes of microbial diversity with depth. The present results corroborate previous studies that suggested a strong influence of microbial activity on mineralogical diversity through extracellular and intracellular biomineralization. This paper reports detailed data on mineralogical profiles of the water column and encourages extended investigation of these processes.

Cyanobacteria have played a significant role in the formation of past and modern carbonate deposits at the surface of the Earth using a biomineralization process that has been almost systematically considered induced and extracellular. Recently, a deep-branching cyanobacterial species, Candidatus Gloeomargarita lithophora, was reported to form intracellular amorphous Ca-rich carbonates. However, the significance and diversity of the cyanobacteria in which intracellular biomineralization occurs remain unknown. Here, we searched for intracellular Ca-carbonate inclusions in 68 cyanobacterial strains distributed throughout the phylogenetic tree of cyanobacteria. We discovered that diverse unicellular cyanobacterial taxa form intracellular amorphous Ca-carbonates with at least two different distribution patterns, suggesting the existence of at least two distinct mechanisms of biomineralization: (i) one with Ca-carbonate inclusions scattered within the cell cytoplasm such as in Ca. G. lithophora, and (ii) another one observed in strains belonging to the Thermosynechococcus elongatus BP-1 lineage, in which Ca-carbonate inclusions lie at the cell poles. This pattern seems to be linked with the nucleation of the inclusions at the septum of the cells, showing an intricate and original connection between cell division and biomineralization. These findings indicate that intracellular Ca-carbonate biomineralization by cyanobacteria has been overlooked by past studies and open new perspectives on the mechanisms and the evolutionary history of intra- and extracellular Ca-carbonate biomineralization by cyanobacteria.

Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.

Iron and manganese are poorly soluble elements in oxic and alkaline solutions, whereas they are much more soluble under anoxic conditions. As a result, the formation of authigenic mineral phases rich in Fe and/or Mn has traditionally been viewed as diagnostic of global or local anoxic conditions. Here we reveal that some specific cyanobacteria of very small size (< 2 µm, i.e., picocyanobacteria) can biomineralize abundant, authigenic Fe(III)-, Mn(IV)- and Si-rich amorphous phases under oxic conditions in an alkaline lake in Mexico. The resulting biominerals cluster as small globules arranged as rings around the division septum of cyanobacterial cells. These rings are enveloped within an organic, likely polysaccharidic envelope and are partially preserved, at least morphologically, upon sedimentation. Based on their 16S rDNA sequence, these cyanobacteria were affiliated with the Synechococcales order. The high Fe and Mn enrichment of the biominerals questions the systematic inference of anoxic conditions based on their detection. Moreover, this process scavenges iron from the water column, an overlooked biological contribution to the Fe cycle. Finally, it reveals a new case of controlled biomineralization of Si-rich phases by bacteria.

Iron and manganese are poorly soluble elements in oxic and alkaline solutions, whereas they are much more soluble under anoxic conditions. As a result, the formation of authigenic mineral phases rich in Fe and/or Mn has traditionally been viewed as diagnostic of global or local anoxic conditions. Here we reveal that some specific cyanobacteria of very small size (< 2 µm, i.e., picocyanobacteria) can biomineralize abundant, authigenic Fe(III)-, Mn(IV)- and Si-rich amorphous phases under oxic conditions in an alkaline lake in Mexico. The resulting biominerals cluster as small globules arranged as rings around the division septum of cyanobacterial cells. These rings are enveloped within an organic, likely polysaccharidic envelope and are partially preserved, at least morphologically, upon sedimentation. Based on their 16S rDNA sequence, these cyanobacteria were affiliated with the Synechococcales order. The high Fe and Mn enrichment of the biominerals questions the systematic inference of anoxic conditions based on their detection. Moreover, this process scavenges iron from the water column, an overlooked biological contribution to the Fe cycle. Finally, it reveals a new case of controlled biomineralization of Si-rich phases by bacteria.