Isotopic clumping in wood as a proxy for photorespiration in trees.

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

The origin of carbonate mud and implications for global climate.

Carbonate mud represents one of the most important geochemical archives for reconstructing ancient climatic, environmental, and evolutionary change from the rock record. Mud also represents a major sink in the global carbon cycle. Yet, there remains no consensus about how and where carbonate mud is formed. Here, we present stable isotope and trace-element data from carbonate constituents in the Bahamas, including ooids, corals, foraminifera, and algae. We use geochemical fingerprinting to demonstrate that carbonate mud cannot be sourced from the abrasion and mixture of any combination of these macroscopic grains. Instead, an inverse Bayesian mixing model requires the presence of an additional aragonite source. We posit that this source represents a direct seawater precipitate. We use geological and geochemical data to show that "whitings" are unlikely to be the dominant source of this precipitate and, instead, present a model for mud precipitation on the bank margins that can explain the geographical distribution, clumped-isotope thermometry, and stable isotope signature of carbonate mud. Next, we address the enigma of why mud and ooids are so abundant in the Bahamas, yet so rare in the rest of the world: Mediterranean outflow feeds the Bahamas with the most alkaline waters in the modern ocean (>99.7th-percentile). Such high alkalinity appears to be a prerequisite for the nonskeletal carbonate factory because, when Mediterranean outflow was reduced in the Miocene, Bahamian carbonate export ceased for 3-million-years. Finally, we show how shutting off and turning on the shallow carbonate factory can send ripples through the global climate system.

Nitrogen isotope evidence for expanded ocean suboxia in the early Cenozoic.

The million-year variability of the marine nitrogen cycle is poorly understood. Before 57 million years (Ma) ago, the 15N/14N ratio (δ15N) of foraminifera shell-bound organic matter from three sediment cores was high, indicating expanded water column suboxia and denitrification. Between 57 and 50 Ma ago, δ15N declined by 13 to 16 per mil in the North Pacific and by 3 to 8 per mil in the Atlantic. The decline preceded global cooling and appears to have coincided with the early stages of the Asia-India collision. Warm, salty intermediate-depth water forming along the Tethys Sea margins may have caused the expanded suboxia, ending with the collision. From 50 to 35 Ma ago, δ15N was lower than modern values, suggesting widespread sedimentary denitrification on broad continental shelves. δ15N rose at 35 Ma ago, as ice sheets grew, sea level fell, and continental shelves narrowed.

Neoproterozoic to early Phanerozoic rise in island arc redox state due to deep ocean oxygenation and increased marine sulfate levels.

A rise in atmospheric O2 levels between 800 and 400 Ma is thought to have oxygenated the deep oceans, ushered in modern biogeochemical cycles, and led to the diversification of animals. Over the same time interval, marine sulfate concentrations are also thought to have increased to near-modern levels. We present compiled data that indicate Phanerozoic island arc igneous rocks are more oxidized (Fe3+/ΣFe ratios are elevated by 0.12) vs. Precambrian equivalents. We propose this elevation is due to increases in deep-ocean O2 and marine sulfate concentrations between 800 and 400 Ma, which oxidized oceanic crust on the seafloor. Once subducted, this material oxidized the subarc mantle, increasing the redox state of island arc parental melts, and thus igneous island arc rocks. We test this using independently compiled V/Sc ratios, which are also an igneous oxybarometer. Average V/Sc ratios of Phanerozoic island arc rocks are elevated (by +1.1) compared with Precambrian equivalents, consistent with our proposal for an increase in the redox state of the subarc mantle between 800 and 400 Ma based on Fe3+/ΣFe ratios. This work provides evidence that the more oxidized nature of island arc vs. midocean-ridge basalts is related to the subduction of material oxidized at the Earth's surface to the subarc mantle. It also indicates that the rise of atmospheric O2 and marine sulfate to near-modern levels by the late Paleozoic influenced not only surface biogeochemical cycles and animal diversification but also influenced the redox state of island arc rocks, which are building blocks of continental crust.

A record of deep-ocean dissolved O2 from the oxidation state of iron in submarine basalts.

The oxygenation of the deep ocean in the geological past has been associated with a rise in the partial pressure of atmospheric molecular oxygen (O2) to near-present levels and the emergence of modern marine biogeochemical cycles. It has also been linked to the origination and diversification of early animals. It is generally thought that the deep ocean was largely anoxic from about 2,500 to 800 million years ago, with estimates of the occurrence of deep-ocean oxygenation and the linked increase in the partial pressure of atmospheric oxygen to levels sufficient for this oxygenation ranging from about 800 to 400 million years ago. Deep-ocean dissolved oxygen concentrations over this interval are typically estimated using geochemical signatures preserved in ancient continental shelf or slope sediments, which only indirectly reflect the geochemical state of the deep ocean. Here we present a record that more directly reflects deep-ocean oxygen concentrations, based on the ratio of Fe3+ to total Fe in hydrothermally altered basalts formed in ocean basins. Our data allow for quantitative estimates of deep-ocean dissolved oxygen concentrations from 3.5 billion years ago to 14 million years ago and suggest that deep-ocean oxygenation occurred in the Phanerozoic (541 million years ago to the present) and potentially not until the late Palaeozoic (less than 420 million years ago).

Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide.

The zinc finger protein EVI1 is causally associated with acute myeloid leukemogenesis, and inhibition of its function with a small molecule therapeutic may provide effective therapy for EVI1-expressing leukemias. In this paper we describe the development of a pyrrole-imidazole polyamide to specifically block EVI1 binding to DNA. We first identify essential domains for leukemogenesis through structure-function studies on both EVI1 and the t(3;21)(q26;q22)-derived RUNX1-MDS1-EVI1 (RME) protein, which revealed that DNA binding to the cognate motif GACAAGATA via the first of two zinc finger domains (ZF1, encompassing fingers 1-7) is essential transforming activity. To inhibit DNA binding via ZF1, we synthesized a pyrrole-imidazole polyamide 1, designed to bind to a subsite within the GACAAGATA motif and thereby block EVI1 binding. DNase I footprinting and electromobility shift assays revealed a specific and high affinity interaction between polyamide 1 and the GACAAGATA motif. In an in vivo CAT reporter assay using NIH-3T3-derived cell line with a chromosome-embedded tet-inducible EVI1-VP16 as well as an EVI1-responsive reporter, polyamide 1 completely blocked EVI1-responsive reporter activity. Growth of a leukemic cell line bearing overexpressed EVI1 was also inhibited by treatment with polyamide 1, while a control cell line lacking EVI1 was not. Finally, colony formation by RME was attenuated by polyamide 1 in a serial replating assay. These studies provide evidence that a cell permeable small molecule may effectively block the activity of a leukemogenic transcription factor and provide a valuable tool to dissect critical functions of EVI1 in leukemogenesis.

Aerobic growth at nanomolar oxygen concentrations.

Molecular oxygen (O(2)) is the second most abundant gas in the Earth's atmosphere, but in many natural environments, its concentration is reduced to low or even undetectable levels. Although low-oxygen-adapted organisms define the ecology of low-oxygen environments, their capabilities are not fully known. These capabilities also provide a framework for reconstructing a critical period in the history of life, because low, but not negligible, atmospheric oxygen levels could have persisted before the "Great Oxidation" of the Earth's surface about 2.3 to 2.4 billion years ago. Here, we show that Escherichia coli K-12, chosen for its well-understood biochemistry, rapid growth rate, and low-oxygen-affinity terminal oxidase, grows at oxygen levels of ≤ 3 nM, two to three orders of magnitude lower than previously observed for aerobes. Our study expands both the environmental range and temporal history of aerobic organisms.