Tomaso R.R. Bontognali

Microbes produce nanobacteria-like structures, avoiding cell entombment

Microsedimentary structures referred to as nanobacteria-like particles were described from modern carbonate environments, where they form in close spatial association with sulfate-reducing bacteria (SRB). However, the exact mechanism of their formation, as well as their paleontological significance, remains controversial. Here we report on an investigation of microbe-mineral interactions in experimentally produced carbonate globules. The experiments were carried out under anoxic conditions at 30 °C with Desulfovibrio brasiliensis, a SRB known to mediate dolomite formation. We observed that extracellular polymeric substances (EPS) secreted by the microbial community play a key role in the mineralization process. Nanobacteria-like particles represent the early stage of carbonate nucleation within the EPS, which progressively evolve to larger globules displaying a grainy texture. We excluded the possibilities that these structures are fossils of nanobacteria, dissolution surfaces, or artifacts created during sample preparation. D. brasiliensis cells are predominantly located outside of the EPS aggregates where mineral growth takes place. As a result, they remain mobile and are rarely entombed within the mineral. This self-preservation behavior may not be limited to D. brasiliensis. Other microbes may produce, or may have produced during the geological past, biogenic minerals through a similar process. Mineralization within EPS explains why microbial relics are not necessarily present in biogenic carbonates.

Anatomy of Heinrich Layer 1 and its role in the last deglaciation

This research used data acquired at the XRF Core Scanner Lab at the MARUM–Center for Marine Environmental Sciences, University of Bremen, Germany. This research used samples provided by the International Ocean Discovery Program (IODP). Funding for this research was provided by the UK Natural Environmental Research Council (NERC) to Hodell. The NERC Radiocarbon Facility supported two radiocarbon dates, and Wally Broecker generously supported the remainder with funding from the Comer Family Foundation. Research by Rodriguez-Tovar and Dorador was financed by Project CGL2015-66835-P. B.M. acknowledges support from the CSIC-Ramon y Cajal postdoctoral programme RYC-2013-14073. J.F.E. would like to acknowledge funding under ERC Advanced grant 320750- Nanopaleomagnetism.

Microbial mediation of complex subterranean mineral structures

Helictites—an enigmatic type of mineral structure occurring in some caves—differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.

Methanogenesis produces strong 13C enrichment in stromatolites of Lagoa Salgada, Brazil: a modern analogue for Palaeo-/Neoproterozoic stromatolites?

Holocene stromatolites characterized by unusually positive inorganic δ(13) CPDB values (i.e. up to +16‰) are present in Lagoa Salgada, a seasonally brackish to hypersaline lagoon near Rio de Janeiro (Brazil). Such positive values cannot be explained by phototrophic fixation of CO2 alone, and they suggest that methanogenesis was a dominating process during the growth of the stromatolites. Indeed, up to 5xa0mm methane was measured in the porewater. The archaeal membrane lipid archaeol showing δ(13) C values between -15 and 0‰ suggests that archaea are present and producing methane in the modern lagoon sediment. Moreover, (13) C-depleted hopanoids diplopterol and 3β-methylated C32 17β(H),21β(H)-hopanoic acid (both -40‰) are preserved in lagoon sediments and are most likely derived from aerobic methanotrophic bacteria thriving in the methane-enriched water column. Loss of isotopically light methane through the water column would explain the residual (13) C-enriched pool of dissolved inorganic carbon from where the carbonate constituting the stromatolites precipitated. The predominance of methanogenic archaea in the lagoon is most likely a result of sulphate limitation, suppressing the activity of sulphate-reducing bacteria under brackish conditions in a seasonally humid tropical environment. Indeed, sulphate-reduction activity is very low in the modern sediments. In absence of an efficient carbonate-inducing metabolic process, we propose that stromatolite formation in Lagoa Salgada was abiotically induced, while the (13) C-enriched organic and inorganic carbon pools are due to methanogenesis. Unusually, (13) C-enriched stromatolitic deposits also appear in the geological record of prolonged periods in the Palaeo- and Neoproterozoic. Lagoa Salgada represents a possible modern analogue to conditions that may have been widespread in the Proterozoic, at times when low sulphate concentrations in sea water allowed methanogens to prevail over sulphate-reducing bacteria.

Evidence for cavity-dwelling microbial life in 3.22 Ga tidal deposits

Cavities are considered plausible and favorable habitats for life on early Earth. In such microenvironments, organisms may have found an adequate protection against the intense ultraviolet radiation that characterized the Archean ozone-free atmosphere. However, while there is clear evidence that benthic life existed in the Paleoarchean, the oldest traces of cavity-dwelling microbes (coelobionts) have been found in Neoarchean rocks. Here we present the results of a detailed investigation of early silicified cavities occurring in the oldest well-preserved siliciclastic tidal deposits, the 3.22 Ga Moodies Group of the Barberton Greenstone Belt (South Africa). Downward-growing microstromatolitic columns composed of kerogenous laminae are commonly present in planar, bedding-parallel, now silica-filled cavities that formed in sediments of the peritidal zone. In-situ δ13CPDB (PDB—Peedee belemnite) measurements of the kerogen range from –32.3‰ to –21.3‰ and are consistent with a biogenic origin. Scanning electron microscopy analysis of the silicified cavities shows well-preserved chains of cell-sized molds that are interpreted as fossil filamentous microorganisms. The geological context, the morphology of the microstromatolites, the δ13C composition of the kerogen, and the presence of microfossils all suggest that a microbial community inhabited the cavities. These results extend the geological record of coelobionts by ∼500 m.y., supporting the view that cavities were among the first ecological niches to have been occupied by early microorganisms.

The importance of microbial mats for dolomite formation in the Dohat Faishakh sabkha, Qatar

The Dohat Faishakh sabkha in Qatar is one of the rare modern environments where it is possible to study the formation of dolomite, a mineral whose origin has been long debated. In previous studies, dolomite formation in this area was considered to be the result of a penecontemporaneous replacement of aragonite, occurring in the presence of Mg-rich evaporated pore-waters. However, a re-investigation of the sabkha revealed that dolomite is not forming exclusively under the evaporitic conditions that characterize the supratidal zone, but also in microbial mats that colonize the lower intertidal zone, indicating that evaporated pore-waters are not a strict requirement for the mineralization process. Moreover, in the supratidal zone, portions of the sediment that are rich in dolomite are also relatively richer in organic material, which derives from partially degraded microbial mats buried in the sediments. Extracellular polymeric substances (EPS) that constitute microbial mats are recognized as an important component for the formation of Mg-rich carbonates. The presence of living and decaying microbial mats comprising EPS, rather than a replacement process, may be the key factor for dolomite formation in the Dohat Faishakh sabkha.

Mushroom Speleothems: Stromatolites That Formed in the Absence of Phototrophs

Unusual speleothems resembling giant mushrooms occur in Santa Catalina Cave, Cuba. Although these mineral buildups are considered a natural heritage, their composition and formation mechanism remain poorly understood. Here we characterize their morphology and mineralogy and present a model for their genesis. We propose that the mushrooms, which are mainly comprised of calcite and aragonite, formed during four different phases within an evolving cave environment. The stipe of the mushroom is an assemblage of three well-known speleothems: a stalagmite surrounded by calcite rafts that were subsequently encrusted by cave clouds (mammilaries). More peculiar is the cap of the mushroom, which is morphologically similar to cerebroid stromatolites and thrombolites of microbial origin occurring in marine environments. Scanning electron microscopy investigations of this last unit revealed the presence of fossilized extracellular polymeric substances (EPS) – the constituents of biofilms and microbial mats. These organic microstructures are mineralized with Ca-carbonate, suggesting that the mushroom cap formed through a microbially-influenced mineralization process. The existence of cerebroid Ca-carbonate buildups forming in dark caves (i.e., in the absence of phototrophs) has interesting implications for the study of fossil microbialites preserved in ancient rocks, which are today considered as one of the earliest evidence for life on Earth.

Characterization of environmental conditions during microbial Mg-carbonate precipitation and early diagenetic dolomite crust formation: Brejo do Espinho, Rio de Janeiro, Brazil

Abstract For many years, sedimentary dolomite rocks have been considered to be primarily a replacement product of the calcium carbonate components comprising the original limestone, a process known as secondary replacement dolomitization. Although numerous dolomite formations in the geological record are composed of fine-grained crystals of micritic dolomite, an alternative process, that is, direct precipitation, is often excluded because of the absence of visible or geochemical indicators supporting primary precipitation. In this research, we present a study of a modern coastal hypersaline lagoon, Brejo do Espinho, Rio de Janeiro State, Brazil, which is located in a special climatic regime where a well-defined seasonal cycle of wet and dry conditions occur. The direct precipitation of modern high-Mg calcite and Ca-dolomite mud from the lagoonal waters under low-temperature hypersaline conditions is associated with the activity of microbial organisms living in this restricted environment. The mud undergoes an early diagenetic transformation into a 100% dolomite crust on the margins of the lagoon. The biomineralization process, characterized by the variations of the physico-chemical conditions in this environment during the annual hydrological cycle, is integrated with isotopic analysis to define the early diagenetic processes responsible for the formation of both dolomitic mud and crust. The carbon isotope values indicate a contribution of respired organic carbon, which is greater for the crust (δ13C=−9.5‰ Vienna Pee Dee Belemnite (VPDB)) than mud (δ13C=−1.2‰ VPDB). The oxygen isotope values reflect a moderate degree of evaporation during mud formation (δ18O=1.1‰ VPDB), whereas it is greatly enhanced during early diagenetic crust formation (δ18O=4.2‰ VPDB). The clumped isotope formation temperature derived for the Brejo do Espinho mud is 34 °C, whereas it is 32 °C for the crust. These temperatures are consistent with the upper range of measured values during the dry season when the lagoon experiences the most hypersaline conditions.

Evidence of a role for aerobic bacteria in high magnesium carbonate formation in the evaporitic environment of Dohat Faishakh Sabkha in Qatar

Dolomite (MgCa(CO3)2) is an important petroleum reservoir rock mineral common in ancient sedimentary rocks which is infrequently found in modern environments. The mechanism of dolomite formation remains poorly understood, although recent research has focused on the contribution of microbial processes. Sabkha is the Arabic term for saline mudflats occurring in regions characterized by extreme environmental conditions (high temperature, salinity, light intensity, and aridity), where diverse halophilic and extremophilic microorganisms are found. The dynamic evaporitic systems characteristic of sabkhas are crucial for the precipitation of minerals and a role for microorganisms in sabkhas in the process of mineralization has been proposed. In this study the Dohat Faishakh Sabkha in Qatar was investigated for evidence of the role for aerobic bacteria in mediating the formation of high magnesium carbonates and dolomite, two minerals that commonly occur in the sabkha sediments. 29 strains of aerobic microbes were obtained through inoculation on agar plates from two different cores sampled from the sabkha and identified by 16S rRNA gene sequencing as belonging to the genera Bacillus, Salinivibrio, Staphylococcus and, primarily, Virgibacillus. All strains examined caused the pH of an artificial growth medium to increase from 7 to 8.5; however, not all were capable of mediating mineral formation. Only Salinivibrio and Virgibacillus spp. isolates mediated the formation of detectable solid phases within the agar plates. Light microscopy, scanning electron microscopy energy dispersive X-ray (SEM/EDX), and X-ray diffraction (XRD) analyses indicate that the solid phase produced in the presence of these bacterial strains is MgCa(CO3)2 with a MgCO3 mol% varying from 0% to 40%. The results of these laboratory experiments suggested that, in the Dohat Faishakh Sabkha, aerobic bacteria may contribute in the formation of very high Mg calcite, a mineral that is considered the precursor of ordered dolomite.

The Close-Up Imager Onboard the ESA ExoMars Rover: Objectives, Description, Operations, and Science Validation Activities

Abstract The Close-Up Imager (CLUPI) onboard the ESA ExoMars Rover is a powerful high-resolution color camera specifically designed for close-up observations. Its accommodation on the movable drill allows multiple positioning. The science objectives of the instrument are geological characterization of rocks in terms of texture, structure, and color and the search for potential morphological biosignatures. We present the CLUPI science objectives, performance, and technical description, followed by a description of the instruments planned operations strategy during the mission on Mars. CLUPI will contribute to the rover mission by surveying the geological environment, acquiring close-up images of outcrops, observing the drilling area, inspecting the top portion of the drill borehole (and deposited fines), monitoring drilling operations, and imaging samples collected by the drill. A status of the current development and planned science validation activities is also given. Key Words: Mars—Biosignatures—Plane...The Close-Up Imager (CLUPI) onboard the ESA ExoMars Rover is a powerful high-resolution color camera specifically designed for close-up observations. Its accommodation on the movable drill allows multiple positioning. The science objectives of the instrument are geological characterization of rocks in terms of texture, structure, and color and the search for potential morphological biosignatures. We present the CLUPI science objectives, performance, and technical description, followed by a description of the instruments planned operations strategy during the mission on Mars. CLUPI will contribute to the rover mission by surveying the geological environment, acquiring close-up images of outcrops, observing the drilling area, inspecting the top portion of the drill borehole (and deposited fines), monitoring drilling operations, and imaging samples collected by the drill. A status of the current development and planned science validation activities is also given. Key Words: Mars-Biosignatures-Planetary Instrumentation. Astrobiology 17, 595-611.