Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry.

Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.

Deconvolving microbial and environmental controls on marine sedimentary pyrite sulfur isotope ratios.

Reconstructions of past environmental conditions and biological activity are often based on bulk stable isotope proxies, which are inherently open to multiple interpretations. This is particularly true of the sulfur isotopic composition of sedimentary pyrite (δ34Spyr), which is used to reconstruct ocean-atmosphere oxidation state and track the evolution of several microbial metabolic pathways. We present a microanalytical approach to deconvolving the multiple signals that influence δ34Spyr, yielding both the unambiguous determination of microbial isotopic fractionation (εmic) and new information about depositional conditions. We applied this approach to recent glacial-interglacial sediments, which feature over 70‰ variations in bulk δ34Spyr across these environmental transitions. Despite profound environmental change, εmic remained essentially invariant throughout this interval and the observed range in δ34Spyr was instead driven by climate-induced variations in sedimentation.

Sedimentary parameters control the sulfur isotope composition of marine pyrite.

Reconstructions of coupled carbon, oxygen, and sulfur cycles rely heavily on sedimentary pyrite sulfur isotope compositions (δ34Spyr). With a model of sediment diagenesis, paired with global datasets of sedimentary parameters, we show that the wide range of δ34Spyr (~100 per mil) in modern marine sediments arises from geographic patterns in the relative rates of diffusion, burial, and microbial reduction of sulfate. By contrast, the microbial sulfur isotope fractionation remains large and relatively uniform. Over Earth history, the effect of increasing seawater sulfate and oxygen concentrations on sulfate and sulfide transport and reaction may explain the corresponding increase observed in the δ34S offset between sulfate and pyrite. More subtle variations may be related to changes in depositional environments associated with sea level fluctuations and supercontinent cycles.

Oxidation of the Ediacaran ocean.

Oxygenation of the Earth's surface is increasingly thought to have occurred in two steps. The first step, which occurred approximately 2,300 million years (Myr) ago, involved a significant increase in atmospheric oxygen concentrations and oxygenation of the surface ocean. A further increase in atmospheric oxygen appears to have taken place during the late Neoproterozoic period ( approximately 800-542 Myr ago). This increase may have stimulated the evolution of macroscopic multicellular animals and the subsequent radiation of calcified invertebrates, and may have led to oxygenation of the deep ocean. However, the nature and timing of Neoproterozoic oxidation remain uncertain. Here we present high-resolution carbon isotope and sulphur isotope records from the Huqf Supergroup, Sultanate of Oman, that cover most of the Ediacaran period (approximately 635 to approximately 548 Myr ago). These records indicate that the ocean became increasingly oxygenated after the end of the Marinoan glaciation, and they allow us to identify three distinct stages of oxidation. When considered in the context of other records from this period, our data indicate that certain groups of eukaryotic organisms appeared and diversified during the second and third stages of oxygenation. The second stage corresponds with the Shuram excursion in the carbon isotope record and seems to have involved the oxidation of a large reservoir of organic carbon suspended in the deep ocean, indicating that this event may have had a key role in the evolution of eukaryotic organisms. Our data thus provide new insights into the oxygenation of the Ediacaran ocean and the stepwise restructuring of the carbon and sulphur cycles that occurred during this significant period of Earth's history.

Strong local, not global, controls on marine pyrite sulfur isotopes.

Understanding variation in the sulfur isotopic composition of sedimentary pyrite (δ34Spyr) is motivated by the key role of sulfur biogeochemistry in regulating Earth's surface oxidation state. Until recently, the impact of local depositional conditions on δ34Spyr has remained underappreciated, and stratigraphic variations in δ34Spyr were interpreted mostly to reflect global changes in biogeochemical cycling. We present two coeval δ34Spyr records from shelf and basin settings in a single sedimentary system. Despite their proximity and contemporaneous deposition, these two records preserve radically different geochemical signals. Swings of ~65‰ in shelf δ34Spyr track short-term variations in local sedimentation and are completely absent from the abyssal record. In contrast, a long-term ~30‰ decrease in abyssal δ34Spyr reflects regional changes in ocean circulation and/or sustained pyrite formation. These results highlight strong local controls on δ34Spyr, calling for reevaluation of the current practice of using δ34Spyr stratigraphic variations to infer global changes in Earth's surface environment.

Direct Observation of the Dynamics of Single-Cell Metabolic Activity during Microbial Diauxic Growth.

Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology's most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.IMPORTANCE Understanding how genetic information is realized as the behavior of individual cells is a long-term goal of biology but represents a significant technological challenge. In clonal microbial populations, variation in gene regulation is often interpreted as metabolic heterogeneity. This follows the central dogma of biology, in which information flows from DNA to RNA to protein and ultimately manifests as activity. At present, DNA and RNA can be characterized in single cells, but the abundance and activity of proteins cannot. Inferences about metabolic activity usually therefore rely on the assumption that transcription reflects activity. By tracking the atoms from which they build their biomass, we make direct observations of growth rate and substrate specialization in individual cells throughout a period of growth in a changing environment. This approach allows the flow of information from DNA to be constrained from the distal end of the regulatory cascade and will become an essential tool in the rapidly advancing field of single-cell metabolism.

Environmental insights from high-resolution (SIMS) sulfur isotope analyses of sulfides in Proterozoic microbialites with diverse mat textures.

In modern microbial mats, hydrogen sulfide shows pronounced sulfur isotope (δ34 S) variability over small spatial scales (~50‰ over <4 mm), providing information about microbial sulfur cycling within different ecological niches in the mat. In the geological record, the location of pyrite formation, overprinting from mat accretion, and post-depositional alteration also affect both fine-scale δ34 S patterns and bulk δ34 Spyrite values. We report µm-scale δ34 S patterns in Proterozoic samples with well-preserved microbial mat textures. We show a well-defined relationship between δ34 S values and sulfide mineral grain size and type. Small pyrite grains (<25 µm) span a large range, tending toward high δ34 S values (-54.5‰ to 11.7‰, mean: -14.4‰). Larger pyrite grains (>25 µm) have low but equally variable δ34 S values (-61.0‰ to -10.5‰, mean: -44.4‰). In one sample, larger sphalerite grains (>35 µm) have intermediate and essentially invariant δ34 S values (-22.6‰ to -15.6‰, mean: -19.4‰). We suggest that different sulfide mineral populations reflect separate stages of formation. In the first stage, small pyrite grains form near the mat surface along a redox boundary where high rates of sulfate reduction, partial closed-system sulfate consumption in microenvironments, and/or sulfide oxidation lead to high δ34 S values. In another stage, large sphalerite grains with low δ34 S values grow along the edges of pore spaces formed from desiccation of the mat. Large pyrite grains form deeper in the mat at slower sulfate reduction rates, leading to low δ34 Ssulfide values. We do not see evidence for significant 34 S-enrichment in bulk pore water sulfide at depth in the mat due to closed-system Rayleigh fractionation effects. On a local scale, Rayleigh fractionation influences the range of δ34 S values measured for individual pyrite grains. Fine-scale analyses of δ34 Spyrite patterns can thus be used to extract environmental information from ancient microbial mats and aid in the interpretation of bulk δ34 Spyrite records.

Sulphur cycling in a Neoarchaean microbial mat.

Multiple sulphur (S) isotope ratios are powerful proxies to understand the complexity of S biogeochemical cycling through Deep Time. The disappearance of a sulphur mass-independent fractionation (S-MIF) signal in rocks <~2.4 Ga has been used to date a dramatic rise in atmospheric oxygen levels. However, intricacies of the S-cycle before the Great Oxidation Event remain poorly understood. For example, the isotope composition of coeval atmospherically derived sulphur species is still debated. Furthermore, variation in Archaean pyrite δ34 S values has been widely attributed to microbial sulphate reduction (MSR). While petrographic evidence for Archaean early-diagenetic pyrite formation is common, textural evidence for the presence and distribution of MSR remains enigmatic. We combined detailed petrographic and in situ, high-resolution multiple S-isotope studies (δ34 S and Δ33 S) using secondary ion mass spectrometry (SIMS) to document the S-isotope signatures of exceptionally well-preserved, pyritised microbialites in shales from the ~2.65-Ga Lokammona Formation, Ghaap Group, South Africa. The presence of MSR in this Neoarchaean microbial mat is supported by typical biogenic textures including wavy crinkled laminae, and early-diagenetic pyrite containing <26‰ µm-scale variations in δ34 S and Δ33 S = -0.21 ± 0.65‰ (±1σ). These large variations in δ34 S values suggest Rayleigh distillation of a limited sulphate pool during high rates of MSR. Furthermore, we identified a second, morphologically distinct pyrite phase that precipitated after lithification, with δ34 S = 8.36 ± 1.16‰ and Δ33 S = 5.54 ± 1.53‰ (±1σ). We propose that the S-MIF signature of this secondary pyrite does not reflect contemporaneous atmospheric processes at the time of deposition; instead, it formed by the influx of later-stage sulphur-bearing fluids containing an inherited atmospheric S-MIF signal and/or from magnetic isotope effects during thermochemical sulphate reduction. These insights highlight the complementary nature of petrography and SIMS studies to resolve multigenerational pyrite formation pathways in the geological record.

Carbon isotopes and lipid biomarkers from organic-rich facies of the Shuram Formation, Sultanate of Oman.

The largest recorded carbon isotopic excursion in Earth history is observed globally in carbonate rocks of middle Ediacaran age. Known from the Sultanate of Oman as the 'Shuram excursion', this event records a dramatic, systematic shift in δ(13) Ccarbonate values to ca. -12‰. Attempts to explain the nature, magnitude and origin of this excursion include (i) a primary signal resulting from the protracted oxidation of a large dissolved organic carbon reservoir in seawater, release of methane from sediment-hosted clathrates, or water column stratification; and (ii) a secondary signal from diagenetic processes. The compositions and isotope ratios of organic carbon phases during the excursion are critical to evaluating these ideas; however, previous work has focused on localities that are low in organic carbon, hindering straightforward interpretation of the observed time-series trends. We report carbon isotope data from bulk organic carbon, extracted bitumen and kerogen, in addition to lipid biomarker data, from a subsurface well drilled on the eastern flank of the South Oman Salt Basin, Sultanate of Oman. This section captures Nafun Group strata through the Ediacaran-Cambrian boundary in the Ara Group and includes an organic-rich, deeper-water facies of the Shuram Formation. Despite the high organic matter contents, the carbon isotopic compositions of carbonates - which record a negative δ(13) C isotope excursion similar in shape and magnitude to sections elsewhere in Oman - do not covary with those of organic phases (bulk TOC, bitumen and kerogen). Paired inorganic and organic δ(13) C data only display coupled behaviour during the latter part of the excursion's recovery. Furthermore, lipid biomarker data reveal that organic matter composition and source inputs varied stratigraphically, reflecting biological community shifts in non-migrated, syngenetic organic matter deposited during this interval.