Balance and imbalance in biogeochemical cycles reflect the operation of closed, exchange, and open sets.

Biogeochemical reactions modulate the chemical composition of the oceans and atmosphere, providing feedbacks that sustain planetary habitability over geological time. Here, we mathematically evaluate a suite of biogeochemical processes to identify combinations of reactions that stabilize atmospheric carbon dioxide by balancing fluxes of chemical species among the ocean, atmosphere, and geosphere. Unlike prior modeling efforts, this approach does not prescribe functional relationships between the rates of biogeochemical processes and environmental conditions. Our agnostic framework generates three types of stable reaction combinations: closed sets, where sources and sinks mutually cancel for all chemical reservoirs; exchange sets, where constant ocean-atmosphere conditions are maintained through the growth or destruction of crustal reservoirs; and open sets, where balance in alkalinity and carbon fluxes is accommodated by changes in other chemical components of seawater or the atmosphere. These three modes of operation have different characteristic timescales and may leave distinct evidence in the rock record. To provide a practical example of this theoretical framework, we applied the model to recast existing hypotheses for Cenozoic climate change based on feedbacks or shared forcing mechanisms. Overall, this work provides a systematic and simplified conceptual framework for understanding the function and evolution of global biogeochemical cycles.

The proteome is a terminal electron acceptor.

Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance.

Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO2 through geologic time should be reevaluated.

The history of Earth's carbon cycle reflects trends in atmospheric composition convolved with the evolution of photosynthesis. Fortunately, key parts of the carbon cycle have been recorded in the carbon isotope ratios of sedimentary rocks. The dominant model used to interpret this record as a proxy for ancient atmospheric CO2 is based on carbon isotope fractionations of modern photoautotrophs, and longstanding questions remain about how their evolution might have impacted the record. Therefore, we measured both biomass (εp) and enzymatic (εRubisco) carbon isotope fractionations of a cyanobacterial strain (Synechococcus elongatus PCC 7942) solely expressing a putative ancestral Form 1B rubisco dating to ≫1 Ga. This strain, nicknamed ANC, grows in ambient pCO2 and displays larger εp values than WT, despite having a much smaller εRubisco (17.23 ± 0.61‰ vs. 25.18 ± 0.31‰, respectively). Surprisingly, ANC εp exceeded ANC εRubisco in all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. Such models can be rectified by introducing additional isotopic fractionation associated with powered inorganic carbon uptake mechanisms present in Cyanobacteria, but this amendment hinders the ability to accurately estimate historical pCO2 from geological data. Understanding the evolution of rubisco and the CO2 concentrating mechanism is therefore critical for interpreting the carbon isotope record, and fluctuations in the record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2.

A Bacterial Form I' Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart.

Form I rubiscos evolved in Cyanobacteria ≥ 2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) capping both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I'; L8) demonstrates that the L8 complex can assemble without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in 13C relative to 12C. In Cyanobacteria, only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I' (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L8 rubisco (16.25 ± 1.36‱ vs. 22.42 ± 2.37‱, respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.

Response to comment on "Reexamination of 2.5-Ga 'whiff' of oxygen interval points to anoxic ocean before GOE".

Sedimentological, textural, and microscale analyses of the Mount McRae Shale revealed a complex postdepositional history, previously unrecognized in bulk geochemical studies. We found that metal enrichments in the shale do not reside with depositional organic carbon, as previously proposed by Anbar et al., but with late-stage pyrite, compromising claims for a "whiff" of oxygen ~50 million years before the Great Oxygenation Event.

Trajectories for the evolution of bacterial CO2-concentrating mechanisms.

Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form-i.e., lacking a single gene-cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3-, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.

Oceanic nutrient rise and the late Miocene inception of Pacific oxygen-deficient zones.

The modern Pacific Ocean hosts the largest oxygen-deficient zones (ODZs), where oxygen concentrations are so low that nitrate is used to respire organic matter. The history of the ODZs may offer key insights into ocean deoxygenation under future global warming. In a 12-My record from the southeastern Pacific, we observe a >10‰ increase in foraminifera-bound nitrogen isotopes (15N/14N) since the late Miocene (8 to 9 Mya), indicating large ODZs expansion. Coinciding with this change, we find a major increase in the nutrient content of the ocean, reconstructed from phosphorus and iron measurements of hydrothermal sediments at the same site. Whereas global warming studies cast seawater oxygen concentrations as mainly dependent on climate and ocean circulation, our findings indicate that modern ODZs are underpinned by historically high concentrations of seawater phosphate.

Compositionally and density stratified igneous terrain in Jezero crater, Mars.

Before Perseverance, Jezero crater's floor was variably hypothesized to have a lacustrine, lava, volcanic airfall, or aeolian origin. SuperCam observations in the first 286 Mars days on Mars revealed a volcanic and intrusive terrain with compositional and density stratification. The dominant lithology along the traverse is basaltic, with plagioclase enrichment in stratigraphically higher locations. Stratigraphically lower, layered rocks are richer in normative pyroxene. The lowest observed unit has the highest inferred density and is olivine-rich with coarse (1.5 millimeters) euhedral, relatively unweathered grains, suggesting a cumulate origin. This is the first martian cumulate and shows similarities to martian meteorites, which also express olivine disequilibrium. Alteration materials including carbonates, sulfates, perchlorates, hydrated silicates, and iron oxides are pervasive but low in abundance, suggesting relatively brief lacustrine conditions. Orbital observations link the Jezero floor lithology to the broader Nili-Syrtis region, suggesting that density-driven compositional stratification is a regional characteristic.

Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA.

Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O2 concentrations were lower and sulfide was more prevalent in Earth surface environments. We identified a new site at Santa Paula Creek (SPC) in Ventura County, CA-a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.

Early impacts of climate change on a coastal marine microbial mat ecosystem.

Among the earliest consequences of climate change are extreme weather and rising sea levels-two challenges to which coastal environments are particularly vulnerable. Often found in coastal settings are microbial mats-complex, stratified microbial ecosystems that drive massive nutrient fluxes through biogeochemical cycles and have been important constituents of Earth's biosphere for eons. Little Ambergris Cay, in the Turks and Caicos Islands, supports extensive mats that vary sharply with relative water level. We characterized the microbial communities across this variation to understand better the emerging threat of sea level rise. In September 2017, the eyewall of category 5 Hurricane Irma transited the island. We monitored the impact and recovery from this devastating storm event. New mat growth proceeded rapidly, with patterns suggesting that storm perturbation may facilitate the adaptation of these ecosystems to changing sea level. Sulfur cycling, however, displayed hysteresis, stalling for >10 months after the hurricane and likely altering carbon storage potential.

Challenges of Measuring Soluble Mn(III) Species in Natural Samples.

Soluble Mn(III)-L complexes appear to constitute a substantial portion of manganese (Mn) in many environments and serve as critical high-potential species for biogeochemical processes. However, the inherent reactivity and lability of these complexes-the same chemical characteristics that make them uniquely important in biogeochemistry-also make them incredibly difficult to measure. Here we present experimental results demonstrating the limits of common analytical methods used to quantify these complexes. The leucoberbelin-blue method is extremely useful for detecting many high-valent Mn species, but it is incompatible with the subset of Mn(III) complexes that rapidly decompose under low-pH conditions-a methodological requirement for the assay. The Cd-porphyrin method works well for measuring Mn(II) species, but it does not work for measuring Mn(III) species, because additional chemistry occurs that is inconsistent with the proposed reaction mechanism. In both cases, the behavior of Mn(III) species in these methods ultimately stems from inter- and intramolecular redox chemistry that curtails the use of these approaches as a reflection of ligand-binding strength. With growing appreciation for the importance of high-valent Mn species and their cycling in the environment, these results underscore the need for additional method development to enable quantifying such species rapidly and accurately in nature.

Reexamination of 2.5-Ga "whiff" of oxygen interval points to anoxic ocean before GOE.

Transient appearances of oxygen have been inferred before the Great Oxygenation Event (GOE) [∼2.3 billion years (Ga) ago] based on redox-sensitive elements such as Mo and S­most prominently from the ∼2.5-Ga Mount McRae Shale in Western Australia. We present new spatially resolved data including synchrotron-based x-ray spectroscopy and secondary ion mass spectrometry to characterize the petrogenesis of the Mount McRae Shale. Sediments were primarily composed of organic matter and volcanic ash (a potential source of Mo), with U-Pb ages revealing extremely low sedimentation rates. Catagenesis created bedding-parallel microfractures, which subsequently acted as fluid pathways for metasomatic alteration and recent oxidative weathering. Our collective observations suggest that the bulk chemical datasets pointing toward a "whiff" of oxygen developed during postdepositional events. Nonzero Δ33S in trace-metal­poor, early diagenetic pyrite and the unusually enriched organic carbon at low sedimentation rates instead suggest that environmental oxygen levels were negligible ∼150 million years before the GOE.

Prebiotic photoredox synthesis from carbon dioxide and sulfite.

Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.

Formation of Magnesium Carbonates on Earth and Implications for Mars.

Magnesium carbonates have been identified within the landing site of the Perseverance rover mission. This study reviews terrestrial analog environments and textural, mineral assemblage, isotopic, and elemental analyses that have been applied to establish formation conditions of magnesium carbonates. Magnesium carbonates form in five distinct settings: ultramafic rock-hosted veins, the matrix of carbonated peridotite, nodules in soil, alkaline lake, and playa deposits, and as diagenetic replacements within lime-and dolostones. Dominant textures include fine-grained or microcrystalline veins, nodules, and crusts. Microbial influences on formation are recorded in thrombolites, stromatolites, crinkly, and pustular laminites, spheroids, and filamentous microstructures. Mineral assemblages, fluid inclusions, and carbon, oxygen, magnesium, and clumped isotopes of carbon and oxygen have been used to determine the sources of carbon, magnesium, and fluid for magnesium carbonates as well as their temperatures of formation. Isotopic signatures in ultramafic rock-hosted magnesium carbonates reveal that they form by either low-temperature meteoric water infiltration and alteration, hydrothermal alteration, or metamorphic processes. Isotopic compositions of lacustrine magnesium carbonate record precipitation from lake water, evaporation processes, and ambient formation temperatures. Assessment of these features with similar analytical techniques applied to returned Martian samples can establish whether carbonates on ancient Mars were formed at high or low temperature conditions in the surface or subsurface through abiotic or biotic processes. The timing of carbonate formation processes could be constrained by 147Sm-143Nd isochron, U-Pb concordia, 207Pb-206Pb isochron radiometric dating as well as 3He, 21Ne, 22Ne, or 36Ar surface exposure dating of returned Martian magnesium carbonate samples.

Impact of River Channel Lateral Migration on Microbial Communities across a Discontinuous Permafrost Floodplain.

Permafrost soils store approximately twice the amount of carbon currently present in Earth's atmosphere and are acutely impacted by climate change due to the polar amplification of increasing global temperature. Many organic-rich permafrost sediments are located on large river floodplains, where river channel migration periodically erodes and redeposits the upper tens of meters of sediment. Channel migration exerts a first-order control on the geographic distribution of permafrost and floodplain stratigraphy and thus may affect microbial habitats. To examine how river channel migration in discontinuous permafrost environments affects microbial community composition, we used amplicon sequencing of the 16S rRNA gene on sediment samples from floodplain cores and exposed riverbanks along the Koyukuk River, a large tributary of the Yukon River in west-central Alaska. Microbial communities are sensitive to permafrost thaw: communities found in deep samples thawed by the river closely resembled near-surface active-layer communities in nonmetric multidimensional scaling analyses but did not resemble floodplain permafrost communities at the same depth. Microbial communities also displayed lower diversity and evenness in permafrost than in both the active layer and permafrost-free point bars recently deposited by river channel migration. Taxonomic assignments based on 16S and quantitative PCR for the methyl coenzyme M reductase functional gene demonstrated that methanogens and methanotrophs are abundant in older permafrost-bearing deposits but not in younger, nonpermafrost point bar deposits. The results suggested that river migration, which regulates the distribution of permafrost, also modulates the distribution of microbes potentially capable of producing and consuming methane on the Koyukuk River floodplain. IMPORTANCE Arctic lowlands contain large quantities of soil organic carbon that is currently sequestered in permafrost. With rising temperatures, permafrost thaw may allow this carbon to be consumed by microbial communities and released to the atmosphere as carbon dioxide or methane. We used gene sequencing to determine the microbial communities present in the floodplain of a river running through discontinuous permafrost. We found that the river's lateral movement across its floodplain influences the occurrence of certain microbial communities-in particular, methane-cycling microbes were present on the older, permafrost-bearing eroding riverbank but absent on the newly deposited river bars. Riverbank sediment had microbial communities more similar to those of the floodplain active-layer samples than permafrost samples from the same depth. Therefore, spatial patterns of river migration influence the distribution of microbial taxa relevant to the warming Arctic climate.

An ecophysiological explanation for manganese enrichment in rock varnish.

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese-over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant-a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

Non-lithifying microbial ecosystem dissolves peritidal lime sand.

Microbialites accrete where environmental conditions and microbial metabolisms promote lithification, commonly through carbonate cementation. On Little Ambergris Cay, Turks and Caicos Islands, microbial mats occur widely in peritidal environments above ooid sand but do not become lithified or preserved. Sediment cores and porewater geochemistry indicated that aerobic respiration and sulfide oxidation inhibit lithification and dissolve calcium carbonate sand despite widespread aragonite precipitation from platform surface waters. Here, we report that in tidally pumped environments, microbial metabolisms can negate the effects of taphonomically-favorable seawater chemistry on carbonate mineral saturation and microbialite development.

Isotopic analyses of Ordovician-Silurian siliceous skeletons indicate silica-depleted Paleozoic oceans.

The Phanerozoic Eon marked a major transition from marine silica deposition exclusively via abiotic pathways to a system dominated by biogenic silica sedimentation. For decades, prevailing ideas predicted this abiotic-to-biogenic transition were marked by a significant decrease in the concentration of dissolved silica in seawater; however, due to the lower perceived abundance and uptake affinity of sponges and radiolarians relative to diatoms, marine dissolved silica is thought to have remained elevated above modern values until the Cenozoic radiation of diatoms. Studies of modern marine silica biomineralizers demonstrated that the Si isotope ratios (δ30 Si) of sponge spicules and planktonic silica biominerals produced by diatoms or radiolarians can be applied as quantitative proxies for past seawater dissolved silica concentrations due to differences in Si isotope fractionations among these organisms. We undertook 446 ion microprobe analyses of δ30 Si and δ18 O of sponge spicules and radiolarians from Ordovician-Silurian chert deposits of the Mount Hare Formation in Yukon, Canada. These isotopic data showed that sponges living in marine slope and basinal environments displayed small Si isotope fractionations relative to coeval radiolarians. By constructing a mathematical model of the major fluxes and reservoirs in the marine silica cycle and the physiology of silica biomineralization, we found that the concentration of dissolved silica in seawater was less than ~150 µM during early Paleozoic time-a value that is significantly lower than previous estimates. We posit that the topology of the early Paleozoic marine silica cycle resembled that of modern oceans much more closely than previously assumed.

Coal fly ash is a major carbon flux in the Chang Jiang (Yangtze River) basin.

Fly ash-the residuum of coal burning-contains a considerable amount of fossilized particulate organic carbon (FOCash) that remains after high-temperature combustion. Fly ash leaks into natural environments and participates in the contemporary carbon cycle, but its reactivity and flux remained poorly understood. We characterized FOCash in the Chang Jiang (Yangtze River) basin, China, and quantified the riverine FOCash fluxes. Using Raman spectral analysis, ramped pyrolysis oxidation, and chemical oxidation, we found that FOCash is highly recalcitrant and unreactive, whereas shale-derived FOC (FOCrock) was much more labile and easily oxidized. By combining mass balance calculations and other estimates of fly ash input to rivers, we estimated that the flux of FOCash carried by the Chang Jiang was 0.21 to 0.42 Mt C⋅y-1 in 2007 to 2008-an amount equivalent to 37 to 72% of the total riverine FOC export. We attributed such high flux to the combination of increasing coal combustion that enhances FOCash production and the massive construction of dams in the basin that reduces the flux of FOCrock eroded from upstream mountainous areas. Using global ash data, a first-order estimate suggests that FOCash makes up to 16% of the present-day global riverine FOC flux to the oceans. This reflects a substantial impact of anthropogenic activities on the fluxes and burial of fossil organic carbon that has been made less reactive than the rocks from which it was derived.

Microbial succession and dynamics in meromictic Mono Lake, California.

Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.