Microbialite taphonomy and biogenicity: new insights from NanoSIMS

Tracking Organomineralization Processes from Living Microbial Mats to Fossil Microbialites

Geneses of microbialites and, more precisely, lithification of microbial mats have been studied in different settings to improve the recognition of biogenicity in the fossil record. Living microbial mats and fossil microbialites associated with older paleoshorelines have been studied in the continental Maquinchao Basin in southernmost South America. Here, we investigate carbonate crusts from a former pond where active mineralizing microbial mats have been previously studied. Petrographic observations revealed the presence of abundant erect and nonerect microfilaments and molds with diameters varying from 6 to 8 micrometers. Additionally, smaller pores and organic matter (OM) remains have been identified in areas containing less filaments and being dominated by carbonate. A Mg, Al and Si-rich phase has also been identified in the carbonate matrix associated with the dominant micritic calcite. Moreover, mineralized sheaths contain mixed carbonate (calcite) with Mg, Al and Si, where the latter elements are associated with authigenic clays. The presence of mineralized sheaths further attests to biologically induced processes during the uptake of CO2 by photosynthetic microorganisms. Additionally, the high density of the micritic phase supports the subsequent mineralization by nonphotosynthetic microorganisms and/or physicochemical processes, such as evaporation. Since the micritic filament microstructure of these recent crusts is very similar to that observed in fossil microbialites, they can be used to bridge the gap between living mats and fossil buildups.

Global distribution of a chlorophyll f cyanobacterial marker

Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.

The Taphonomy of Proterozoic Microbial Mats and Implications for Early Diagenetic Silicification

The complex nature of growth and decomposition in microbial mats results in a broad range of microbial preservation. Such taphonomic variability complicates both the description of microbial elements preserved within geologic materials and the potential interpretation of microbial biomarkers. This study uses a taphonomic assessment to explore the preservation of different microbial components within silicified microbial mats of the late Mesoproterozoic (~1.0 Ga) Angmaat Formation, Bylot Supergroup, Baffin Island. The Angmaat Formation consists of unmetamorphosed and essentially undeformed strata that represent intertidal to supratidal deposition within an evaporative microbial flat. Early diagenetic silicification preserved microbial communities across a range of environments, from those episodically exposed to persistently submerged. Here, we present the development of a new methodology involving the use of high-resolution image mosaics to investigate the taphonomy of microfossils preserved in these mats. A taphonomic grade is assigned using a modified classification that accounts for both the taphonomic preservation state (good, fair, poor) of individual microfossils, as well as the degree of compaction of the overall mat. We show that although various taphonomic states occur within each of the silicified mats, the overall taphonomic assessment differentiates between well-preserved mats that are interpreted to have been silicified during active growth, to highly degraded and compacted mats that are interpreted to represent preservation during later stages of biological decomposition. These data indicate that even small changes in the timing of silicification may have substantial implications on our identification of microbial biomarkers and, therefore, our interpretation of early Earth ecosystems.

A microbial role in the construction of Mono Lake carbonate chimneys?

Lacustrine carbonate chimneys are striking, metre-scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano-, micro- and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre-thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life.

Chemical and Optical Identification of Micrometer-Sized 1.9 Billion-Year-Old Fossils by Combining a Miniature Laser Ablation Ionization Mass Spectrometry System with an Optical Microscope

The recognition of biosignatures on planetary bodies requires the analysis of the putative microfossil with a set of complementary analytical techniques. This includes localized elemental and isotopic analysis of both, the putative microfossil and its surrounding host matrix. If the analysis can be performed with spatial resolution at the micrometer level and ppm detection sensitivities, valuable information on the (bio)chemical and physical processes that influenced the sample material can be gained. Our miniaturized laser ablation ionization mass spectrometry (LIMS)-time-of-flight mass spectrometer instrument is a valid candidate for performing the required chemical analysis in situ. However, up until now it was limited by the spatial accuracy of the sampling. In this contribution, we introduce a newly developed microscope system with micrometer accuracy for Ultra High Vacuum application, which allows a significant increase in the measurement capabilities of our miniature LIMS system. The new enhancement allows identification and efficient and accurate sampling of features of micrometer-sized fossils in a host matrix. The performance of our system is demonstrated by the identification and chemical analysis of signatures of micrometer-sized fossil structures in the 1.9 billion-year-old Gunflint chert.

Mineralisation of filamentous cyanobacteria in Lake Thetis stromatolites, Western Australia

Stromatolites are cited as some of the earliest evidence for life on Earth, but problems remain in reconciling the paucity of microfossils in ancient carbonate examples with the abundance of microbes that help construct modern analogues. Here, we trace the mineralisation pathway of filamentous cyanobacteria within stromatolites from Lake Thetis, Western Australia, providing new insights into microfossil preservation in carbonate stromatolites. Lake Thetis cyanobacteria exhibit a spectrum of mineralisation processes that include early precipitation of Mg-silicates, largely controlled by the morphochemical features of the cyanobacteria, followed by aragonite formation that is inferred to be driven by heterotrophic activity. Fossilised cyanobacteria with high-quality morphological preservation are characterised by a significant volume of authigenic Mg-silicates, which have preferentially nucleated in/on extracellular organic material and on cell walls, and now replicate the region once occupied by the cyanobacterial sheath. In such specimens, aragonite is restricted to the outer sheath margin and parts of the cell interior. Cyanobacteria that display more significant degradation appear to possess a higher ratio of aragonite to Mg-silicate. In these specimens, aragonite forms micronodules in the sheath zone and is spatially associated with the inferred remains of heterotrophic bacteria. Aragonite also occurs as an advancing front from the outer margin of the sheath where it is commonly intergrown with Mg-silicates. Where there is no evidence of Mg-silicates within filaments, the fidelity of microfossil preservation is poor. In these cases, individual filaments may no longer be visible under light microscopy, and little organic material remains, but filament traces remain detectable using electron microscopy due to variations in aragonite texture. These data provide further evidence that authigenic silicate minerals play a crucial role in the fossilisation of micro-organisms; in their absence, carbonate crystal growth potentially mediated by heterotrophic microbial decay may largely obliterate morphological evidence for life within stromatolites, although mineralogical traces may still be detectable using electron microscopy.

Alteration of rocks by endolithic organisms is one of the pathways for the beginning of soils on Earth

Subaerial endolithic systems of the current extreme environments on Earth provide exclusive insight into emergence and development of soils in the Precambrian when due to various stresses on the surfaces of hard rocks the cryptic niches inside them were much more plausible habitats for organisms than epilithic ones. Using an actualistic approach we demonstrate that transformation of silicate rocks by endolithic organisms is one of the possible pathways for the beginning of soils on Earth. This process led to the formation of soil-like bodies on rocks in situ and contributed to the raise of complexity in subaerial geosystems. Endolithic systems of East Antarctica lack the noise from vascular plants and are among the best available natural models to explore organo-mineral interactions of a very old “phylogenetic age” (cyanobacteria-to-mineral, fungi-to-mineral, lichen-to-mineral). On the basis of our case study from East Antarctica we demonstrate that relatively simple endolithic systems of microbial and/or cryptogamic origin that exist and replicate on Earth over geological time scales employ the principles of organic matter stabilization strikingly similar to those known for modern full-scale soils of various climates.

Carbonate ooids of the Mesoarchaean Pongola Supergroup, South Africa

Ooids from the Mesoarchaean Chobeni Formation, Pongola Supergroup, KwaZulu-Natal, South Africa are older than any ooids reported to date. They are made of dolomite and ankerite and show concentric, radial-concentric, micritic, and radial fabrics. Radial ooids are interpreted to have originated from high-Mg-calcite and probably formed by microbial activity in a low-energy regime, while concentric ooids had an aragonite precursor and formed biotically under agitated/high-energy environmental conditions. Micritic ooids formed via the recrystallization of concentric ooids. Ooids and other allochems, such as intraclasts and peloids, contain carbonaceous matter. The close association of carbonaceous matter within ooid cortices with metabolically important elements, such as N, S and P, as identified by nano-scale secondary ion mass spectrometry analysis, allows us to propose a biologically induced origin for some ooids. By analogy with modern examples, a variety of microbial communities probably played a role in carbonate precipitation and ooid formation. Shale-normalized rare earth element (REE) distribution patterns of ooids and other allochems show positive La_SN , Gd_SN and Y_SN anomalies, superchondritic Y/Ho ratios and depleted light rare earth elements (LREEs) relative to the heavy rare earth elements (HREEs), which resemble those of seawater. These anomalies are less pronounced than expected for an open marine setting, which is interpreted as evidence for deposition in restricted shallow marine environments. Non-seawater REE patterns in recrystallized matrix and pore- and vein-filling carbonate likely reflect redistribution of rare earth elements during post-depositional alteration and/or reflect differences in the elemental and REE compositions of diagenetic fluids.

Carbon and sulfur isotopic signatures of ancient life and environment at the microbial scale: Neoarchean shales and carbonates

An approach to coordinated, spatially resolved, in situ carbon isotope analysis of organic matter and carbonate minerals, and sulfur three- and four-isotope analysis of pyrite with an unprecedented combination of spatial resolution, precision, and accuracy is described. Organic matter and pyrite from eleven rock samples of Neoarchean drill core express nearly the entire range of δ(13) C, δ(34) S, Δ(33) S, and Δ(36) S known from the geologic record, commonly in correlation with morphology, mineralogy, and elemental composition. A new analytical approach (including a set of organic calibration standards) to account for a strong correlation between H/C and instrumental bias in SIMS δ(13) C measurement of organic matter is identified. Small (2-3 μm) organic domains in carbonate matrices are analyzed with sub-permil accuracy and precision. Separate 20- to 50-μm domains of kerogen in a single ~0.5 cm(3) sample of the ~2.7 Ga Tumbiana Formation have δ(13) C = -52.3 ± 0.1‰ and -34.4 ± 0.1‰, likely preserving distinct signatures of methanotrophy and photoautotrophy. Pyrobitumen in the ~2.6 Ga Jeerinah Formation and the ~2.5 Ga Mount McRae Shale is systematically (13) C-enriched relative to co-occurring kerogen, and associations with uraniferous mineral grains suggest radiolytic alteration. A large range in sulfur isotopic compositions (including higher Δ(33) S and more extreme spatial gradients in Δ(33) S and Δ(36) S than any previously reported) are observed in correlation with morphology and associated mineralogy. Changing systematics of δ(34) S, Δ(33) S, and Δ(36) S, previously investigated at the millimeter to centimeter scale using bulk analysis, are shown to occur at the micrometer scale of individual pyrite grains. These results support the emerging view that the dampened signature of mass-independent sulfur isotope fractionation (S-MIF) associated with the Mesoarchean continued into the early Neoarchean, and that the connections between methane and sulfur metabolism affected the production and preservation of S-MIF during the first half of the planet's history.

Determination of oral uptake and biodistribution of platinum and chromium by the garden snail (Helix aspersa) employing nano-secondary ion mass-spectrometry

Environmental heavy metal contamination is a case of concern for both animal and human health. Studying the fate of metals in plant or animal tissues may provide information on pollution. In the present study, we investigated the possibility to follow the biological fate of chromium and platinum uptake in common garden snails (Helix aspersa), typically accumulating high concentrations of metals from their environment. Chromium and platinum were administered orally to snails in 5 groups (n=25/group): control, food contaminated by ca. 2.5 μg g(-1) and 19 μg g(-1) chromium and 2.5 μg g(-1) and 25 μg g(-1) platinum, for 8 weeks. Following exposure, surviving snails were sacrificed, shell and remaining tissue investigated by ICP-MS, and shell, midgut gland and mantle by nano-secondary ion mass-spectrometry (Nano-SIMS). (12)C(14)N-normalized platinum and (40)Ca-normalized chromium measurements indicated highest enrichments in cellular vesicles of the midgut gland, and lower concentrations in mantle and shell, with significantly higher platinum and chromium concentrations in the 2 exposure groups vs. control (P<0.05), with somewhat differing distribution patterns for chromium and platinum. Comparable results were obtained by ICP-MS, with both chromium and platinum fed snails showing drastically elevated concentrations of metals in shell (up to 78 and 122 μg g(-1) dw platinum and chromium, respectively) and in other tissues (up to 200 and 1125 μg g(-1) dw platinum and chromium, respectively). Nano-SIMS allowed for semi-quantitative comparison of metal fate in snail tissues, making this an interesting technique for future studies in the area of environmental pollution.