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The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO 4 2- and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.- and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter., (© 2022. The Author(s).)

Ex situ microelectrode experiments, using cyanobacterial biofilms from karst water creeks, were conducted under various pH, temperature, and constant-alkalinity conditions to investigate the effects of changing environmental parameters on cyanobacterial photosynthesis-induced calcification. Microenvironmental chemical conditions around calcifying sites were controlled by metabolic activity over a wide range of photosynthesis and respiration rates, with little influence from overlying water conditions. Regardless of overlying water pH levels (from 7.8 to 8.9), pH at the biofilm surface was approximately 9.4 in the light and 7.8 in the dark. The same trend was observed at various temperatures (4 degrees C and 17 degrees C). Biological processes control the calcium carbonate saturation state (Omega) in these and similar systems and are able to maintain Omega at approximately constant levels over relatively wide environmental fluctuations. Temperature did, however, have an effect on calcification rate. Calcium flux in this system is limited by its diffusion coefficient, resulting in a higher calcium flux (calcification and dissolution) at higher temperatures, despite the constant, biologically mediated pH. The ability of biological systems to mitigate the effects of environmental perturbation is an important factor that must be considered when attempting to predict the effects of increased atmospheric partial CO(2) pressure on processes such as calcification and in interpreting microfossils in the fossil record.

Calcification of freshwater streams and the involvement of microorganisms in this process are still not fully understood. Here, we report on the metagenomic and metatranscriptomic analyses of bacterial community structures derived from an actively calcifying karst water creek biofilm and underlying tufa by employing next-generation sequencing technologies.The persistent and metabolically active bacterial communities were assessed by DNA-based and RNA-based 16S rRNA gene sequence analysis, respectively. We identified filamentous Cyanobacteria belonging to the Oscillatoriales as the predominant bacterial microorganisms in the biofilm. Cyanobacteria were accompanied by a high diversity of mainly aerobic members affiliated to different bacterial phyla. The second most abundant phylum was Proteobacteria, represented by the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. In addition, Chloroflexi, Planctomycetes, Actinobacteria, Acidobacteria, Bacteroidetes, Spirochaetes, and Verrucomicrobia were present in higher abundances (>0.5%). Several of these phyla included potentially novel subgroups. The tufa stromatolite carbonate one centimeter below the surface exhibited a similar prokaryotic community as the superficial biofilm but showed a lower abundance of Cyanobacteria and a more diverse microbial community. We obtained insights into the in situ microbial metabolism by employing directed sequencing of enriched mRNA (cDNA) and subsequent taxonomic and functional analysis of biofilm-derived reads. High activities in photosynthesis, carbon and protein metabolism were indicated. [ABSTRACT FROM AUTHOR]

Aragonitic microbialites, characterized by a reticulate fabric, were discovered beneath lacustrine microbial mats on the atoll of Kiritimati, Republic of Kiribati, Central Pacific. The microbial mats, with cyanobacteria as major primary producers, grow in evaporated seawater modified by calcium carbonate and gypsum precipitation and calcium influx via surface and/or groundwaters. Despite the high aragonite supersaturation and a high photosynthetic activity, only minor aragonite precipitates are observed in the top parts of the microbial mats. Instead, major aragonite precipitation takes place in lower mat parts at the transition to the anoxic zone. The prokaryotic community shows a high number of phylotypes closely related to halotolerant taxa and/or taxa with preference to oligotrophic habitats. Soil- and plant- inhabiting bacteria underline a potential surface or subsurface influx from terrestrial areas, while chitinase-producing representatives coincide with the occurrence of insect remains in the mats. Strikingly, many of the clones have their closest relatives in microorganisms either involved in methane production or consumption of methane or methyl compounds. Methanogens, represented by the methylotrophic genus Methanohalophilus, appear to be one of the dominant organisms in anaerobic mat parts. All this points to a significant role of methane and methyl components in the carbon cycle of the mats. Nonetheless, thin sections and physicochemical gradients through the mats, as well as the 12C-depleted carbon isotope signatures of carbonates indicate that spherulitic components of the microbialites initiate in the photosynthesis-dominated orange mat top layer, and further grow in the green and purple layer below. Therefore, these spherulites are considered as product of an extraordinary high photosynthesis effect simultaneous to a high inhibition by pristine exopolymers. Then, successive heterotrophic bacterial activity leads to a condensation of the exopolymer framework, and finally to the formation of crevice-like zones of partly degraded exopolymers. Here initiation of horizontal aragonite layers and vertical aragonite sheets of the microbialite occurs, which are considered as a product of high photosynthesis at decreasing degree of inhibition. Finally, at low supersaturation and almost lack of inhibition, syntaxial growth of aragonite crystals at lamellae surfaces leads to thin fibrous aragonite veneers. While sulfate reduction, methylotrophy, methanogenesis and ammonification play an important role in element cycling of the mat, there is currently no evidence for a crucial role of them in CaCO3 precipitation. Instead, photosynthesis and exopolymer degradation sufficiently explain the observed pattern and fabric of microbialite formation. [ABSTRACT FROM AUTHOR]

Abstract: Cyanobacteria-dominated biofilms in a CO2-degassing karst-water creek (Westerhöfer Bach, Germany) were investigated with regard to the effects of microbial activity on CaCO3 precipitation, water chemistry of micro- and macroenvironments, stable isotopic records, and tufa fabric formation. Ex situ microelectrode measurements of pH, O2, Ca2+ and CO3 2− revealed that annually laminated calcified biofilms composed mainly of filamentous cyanobacteria (tufa stromatolites) strongly induced CaCO3 precipitation by photosynthesis under illumination, but inhibited precipitation by respiration in the dark. In contrast, endolithic cyanobacterial biofilms and mosses did not cause photosynthesis-induced precipitation under experimental conditions. No spontaneous precipitation occurred on bare limestone substrates, despite high calcite supersaturation of the ambient water. Mass balance calculations suggest that biofilm photosynthesis was responsible for 10–20% of Ca2+ loss in the creek, while the remaining Ca2+ loss derived from physicochemical precipitation on branches, leaves and as fine-grained calcite particles. Neither analysis of bulk water chemistry nor oxygen nor carbon stable isotopic records of the tufa stromatolites confirmed photosynthetic effects, despite the evident photosynthesis-induced calcite precipitation. Oxygen stable isotopic values reflected seasonal changes in water temperature, and carbon stable isotope values probably recorded carbon isotopic composition of dissolved inorganic carbon in the creek water. Annual lamination and fabric formation of the tufa stromatolites is suggested to vary with photosynthesis-induced calcite precipitation rates that are affected by temperature dependency of diffusion coefficients. Photosynthesis-induced precipitation resulted in encrusted cyanobacterial sheaths, reflecting syntaxial overgrowth of microcrystalline cyanobacterial tubes by microspar, instead of microcrystalline sheath impregnation, which was previously suggested as an indicator of photosynthesis-induced precipitation. Therefore, sheath impregnation or encrustation by CaCO3 cannot be used to distinguish photosynthesis-induced from physicochemically-induced CaCO3 precipitation. [Copyright &y& Elsevier]

The impact of microbial activity on biofilm calcification in aquatic environments is still a matter of debate, especially in settings where ambient water has high CaCO3 mineral supersaturation. In this study, biofilms of two CO2-degassing karst-water creeks in Germany, which attain high calcite supersaturation during their course downstream, were investigated with regard to water chemistry of the biofilm microenvironment. The biofilms mainly consisted of filamentous cyanobacteria (Phormidium morphotype) and heterotrophic bacteria (including sulfate-reducing bacteria), which affect the microenvironment and produce acidic exopolymers. In situ and ex situ microelectrode measurements showed that a strong pH increase, coupled with Ca2 + consumption, occurred in light conditions at the biofilm surface, while the opposite occurred in the dark. Calcite supersaturation at the biofilm surface, calculated from ex situ Ca2 + and CO32- microelectrode measurements, showed that photosynthesis resulted in high omega values during illumination, while respiration slightly lowered supersaturation values in the dark, compared to values in the water column. Dissociation calculation demonstrated that the potential amount of Ca2 + binding by exopolymers would be insufficient to explain the Ca2 + loss observed, although Ca2 + complexation to exopolymers might be crucial for calcite nucleation. No spontaneous precipitation occurred on biofilm-free limestone substrates under the same condition, regardless of high supersaturation. These facts indicate that photosynthesis is a crucial mechanism to overcome the kinetic barrier for CaCO3 precipitation, even in highly supersaturated settings. [ABSTRACT FROM AUTHOR]

Shows that Phanerozoic oceans sustaining calcified cyanobacteria must have had considerably higher calcium concentrations than present-day oceans. Result of high dissolved inorganic carbon concentrations; Lack of calcified cyanobacteria in stromatolite-bearing Precambrian sequences; Paleo-partial pressure curves for carbon dioxide.

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments. [ABSTRACT FROM AUTHOR]

Focuses on the calcification of cyanobacterial filaments. Derivation of Paleozoic carbonate mud from micrite tubes; Mechanism of Girvanella tube formation; Facilitation of calcification by chemical changes in the sheath.