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 Cacarbonate 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.calcification | amorphous calcium carbonate | polyphosphate

The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0–14 m depth) and long-term-maintained laboratory aquaria. Using small subunit (SSU) rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota), Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than in field samples, possibly due to more stable and favorable laboratory conditions. The maintenance of highly diverse natural microbialites in laboratory aquaria holds promise to study the role of different metabolisms in the formation of these structures under controlled conditions.

The structure, mineralogy, and accretion processes of the modern and subfossil cyanobacterial microbialites from the alkaline crater lake Alchichica (Puebla, Mexico) were studied, along the lake's bathymetry and hydrochemistry. The recent lowering of the lake level had exposed microbialitic carbonate mounds and crusts, which emerged up to 2 m above the water surface, while accreting cyanobacterial microbialites were present down to a depth of *15 m. Morphological and molecular analysis found that the living cyanobacterial mats were composed of diverse filamentous and coccoid cyanobacteria

International audienceMicrobialitesareorgano-sedimentaryrocksfoundinabundancethroughoutthegeologicalrecordbackto∼3.5Ga.Interpretationsofthebiologicalandenvironmentalconditionsunderwhichtheyformedrelyoncomparisonswithmodernmicrobialites.Therefore,abettercharacterizationofdiversemodernmicrobialitesiscrucialtoimprovesuchinterpretations.Here,westudiedmodernmicrobialitesfromthreeMexicanalkalinecraterlakes:Quechulac,LaPreciosaandAtexcac.Thegeochemicalanalysesofwatersolutionsshowedthattheyweresupersaturatedtovaryingextentswithseveralmineralphases,includingaragonite,calcite,hydromagnesite,aswellashydratedMg-silicates.Consistently,X-raydiffraction(XRD)andFouriertransforminfraredspectroscopy(FTIR)analysesrevealedthatmicrobialitesarecomposedofadiversityofmineralphasesincludingaragoniteandsometimescalcite,hydromagnesite,andmoreinterestingly,apoorly-crystallinehydratedsilicatephase.Couplingofscanningelectronmicroscopy(SEM)withenergydispersiveX-rayspectrometrymicroanalysesonpolishedsectionsshowedthatthislatterphaseisabundant,authigenic,magnesium-richandsometimesassociatedwithironandmanganese.Thismineralphaseissimilartokerolite,ahydratedpoorlycrystallinetalc-likephase(Mg3Si4O10(OH)2·nH2O).Diversemicrofossilswerepermineralizedbythissilicatephase.Someofthemwereimagedin3DbyFIB-tomographyshowingthattheirmorphologywasexquisitelypreserveddowntothefewnm-scale.ThestructuralandchemicalfeaturesofthesefossilswerefurtherstudiedusingacombinationoftransmissionelectronmicroscopyandscanningtransmissionX-raymicroscopy(STXM)atthecarbonandmagnesiumK-edgesandironL2,3-edges.Theseresultsshowedthatorganiccarbonispervasivelyassociatedwithkerolite.Overall,itissuggestedthatthepoorly-crystallinehydratedmagnesium-richsilicateformsinmanyalkalinelakesandhasastrongpotentialforfossilizationofmicrobesandorganicmatter.Moreover,thefrequentoccurrenceofsuchanauthigenicsilicatephaseinmodernlacustrinemicrobialitescallsforareappraisalofitspotentialpresenceinancientrocks

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.