Oxygen isotope effects during microbial sulfate reduction: applications to sediment cell abundances

Marine sulphate captures a Paleozoic transition to a modern terrestrial weathering environment

The triple oxygen isotope composition of sulphate minerals has been used to constrain the evolution of Earth's surface environment (e.g., pO2, pCO2 and gross primary productivity) throughout the Proterozoic Eon. This approach presumes the incorporation of atmospheric O2 atoms into riverine sulphate via the oxidative weathering of pyrite. However, this is not borne out in recent geological or modern sulphate records, where an atmospheric signal is imperceptible and where terrestrial pyrite weathering occurs predominantly in bedrock fractures that are physically more removed from atmospheric O2. To better define the transition from a Proterozoic to a modern-like weathering regime, here we present new measurements from twelve marine evaporite basins spanning the Phanerozoic. These data display a step-like transition in the triple oxygen isotope composition of evaporite sulphate during the mid-Paleozoic (420 to 387.7 million years ago). We propose that the evolution of early root systems deepened the locus of pyrite oxidation and reduced the incorporation of O2 into sulphate. Further, the early Devonian proliferation of land plants increased terrestrial organic carbon burial, releasing free oxygen that fueled increased redox recycling of soil-bound iron and resulted in the final rise in pO2 to modern-like levels.

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption-impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01-4.7 fmol SO42- cell-1 h-1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23-40 nmol h-1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris

Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earth's surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here, we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell-specific sulfate respiration rates and net sulfur isotope fractionation inversely covary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.

The triple oxygen isotope composition of marine sulfate and 130 million years of microbial control

The triple oxygen isotope composition (Δ'¹⁷O) of sulfate minerals is widely used to constrain ancient atmospheric pO₂/pCO₂ and rates of gross primary production. The utility of this tool is based on a model that sulfate oxygen carries an isotope fingerprint of tropospheric O₂ incorporated through oxidative weathering of reduced sulfur minerals, particularly pyrite. Work to date has targeted Proterozoic environments (2.5 billion to 0.542 billion years ago) where large isotope anomalies persist; younger timescale records, which would ground ancient environmental interpretation in what we know from modern Earth, are lacking. Here we present a high-resolution record of the [Formula: see text]O and Δ'¹⁷O in marine sulfate for the last 130 million years of Earth history. This record carries a Δ'¹⁷O close to 0o, suggesting that the marine sulfate reservoir is under strict control by biogeochemical cycling (namely, microbial sulfate reduction), as these reactions follow mass-dependent fractionation. We identify no discernible contribution from atmospheric oxygen on this timescale. We interpret a steady fractional contribution of microbial sulfur cycling (terrestrial and marine) over the last 100 million years, even as global weathering rates are thought to vary considerably.

Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events.IMPORTANCE Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.