Earth-Life Science Institute

To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinomonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on 1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); 2) clades amended since the 2007 proposal with recently described new species; 3) orphan clades of genomospecies F6 and F10; 4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and 5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.

The inability to resolve the exact temporal relationship between two pivotal events in Earth history, the Paleoproterozoic Great Oxidation Event (GOE) and the first “snowball Earth” global glaciation, has precluded assessing causality between changing atmospheric composition and ancient climate change. Here we present temporally resolved quadruple sulfur isotope measurements (δ 34 S, ∆ 33 S, and ∆ 36 S) from the Paleoproterozoic Seidorechka and Polisarka Sedimentary Formations on the Fennoscandian Shield, northwest Russia, that address this issue. Sulfides in the former preserve evidence of mass-independent fractionation of sulfur isotopes (S-MIF) falling within uncertainty of the Archean reference array with a ∆ 36 S/∆ 33 S slope of −1.8 and have small negative ∆ 33 S values, whereas in the latter mass-dependent fractionation of sulfur isotopes (S-MDF) is evident, with a ∆ 36 S/∆ 33 S slope of −8.8. These trends, combined with geochronological constraints, place the S-MIF/S-MDF transition, the key indicator of the GOE, between 2,501.5 ± 1.7 Ma and 2,434 ± 6.6 Ma. These are the tightest temporal and stratigraphic constraints yet for the S-MIF/S-MDF transition and show that its timing in Fennoscandia is consistent with the S-MIF/S-MDF transition in North America and South Africa. Further, the glacigenic part of the Polisarka Formation occurs 60 m above the sedimentary succession containing S-MDF signals. Hence, our findings confirm unambiguously that the S-MIF/S-MDF transition preceded the Paleoproterozoic snowball Earth. Resolution of this temporal relationship constrains cause-and-effect drivers of Earth’s oxygenation, specifically ruling out conceptual models in which global glaciation precedes or causes the evolution of oxygenic photosynthesis.

We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshop's talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE-it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1 .

Earth possesses a persistent, internally-generated magnetic field, whereas no trace of a dynamo has been detected on Venus, at present or in the past, although a high surface temperature and recent resurfacing events may have removed paleomagnetic evidence. Whether or not a terrestrial body can sustain an internally generated magnetic field by convection inside its metallic fluid core is determined in part by its initial thermodynamic state and its compositional structure, both of which are in turn set by the processes of accretion and differentiation. Here we show that the cores of Earth- and Venus-like planets should grow with stable compositional stratification unless disturbed by late energetic impacts. They do so because higher abundances of light elements are incorporated into the liquid metal that sinks to form the core as the temperatures and pressures of metal-silicate equilibration increase during accretion. We model this process and determine that this establishes a stable stratification that resists convection and inhibits the onset of a geodynamo. However, if a late energetic impact occurs, it could mechanically stir the core creating a single homogenous region within which a long-lasting geodynamo would operate. While Earth's accretion has been punctuated by a late giant impact with likely enough energy to mix the core (e.g. the impact that formed the Moon), we hypothesize that the accretion of Venus is characterized by the absence of such energetic giant impacts and the preservation of its primordial stratifications.

BACKGROUND: Jasmonates are plant lipid-derived oxylipins that act as key signaling compounds when plants are under oxidative stress, but little is known about their functions in mammalian cells. Here we investigated whether jasmonates could protect human neuroblastoma SH-SY5Y cells against oxidative stress-induced toxicity. METHODS: The cells were pretreated with individual jasmonates for 24h and exposed to hydrogen peroxide (H2O2) for 24h. Before the resulting cytotoxicity, intracellular reactive oxygen species (ROS) levels, and mitochondrial membrane potential were measured. We also measured intracellular glutathione (GSH) levels and investigated changes in the signaling cascade mediated by nuclear factor erythroid 2-related factor 2 (Nrf2) in cells treated with 12-oxo phytodienoic acid (OPDA). RESULTS: Among the jasmonates, only OPDA suppressed H2O2-induced cytotoxicity. OPDA pretreatment also inhibited the H2O2-induced ROS increase and mitochondrial membrane potential decrease. In addition, OPDA induced the nuclear translocation of Nrf2 and increased intracellular GSH level and the expression of the Nrf2-regulated phase II antioxidant enzymes heme oxygenase-1, NADPH quinone oxidoreductase 1, and glutathione reductase. Finally, the cytoprotective effects of OPDA were reduced by siRNA-induced knockdown of Nrf2. CONCLUSIONS: These results demonstrated that among jasmonates, only OPDA suppressed oxidative stress-induced death of human neuroblastoma cells, which occurred via activation of the Nrf2 pathway. GENERAL SIGNIFICANCE: Plant-derived oxylipin OPDA may have the potential to provide protection against oxidative stress-related diseases.

Significance Anomalous sulfur isotopic compositions preserved in sedimentary rocks older than ∼2.5 billion years have been widely interpreted as the products of UV photolysis of sulfur dioxide in an anoxic atmosphere and used to track the history of primitive Earth and evolution of early life. In this study, we present strong observational evidence that there is an additional process that produces similar anomalous sulfur isotope signatures. This previously unknown origin not only offers a tool for quantifying the present-day atmospheric sulfur budget and evaluating its influences on climate and public health but also implies that anomalous sulfur isotopic compositions in some of the oldest rocks on Earth might have been produced in a way different from that previously thought.

Micron-sized diamond anvils with a 3 μm culet were successfully processed using a focused ion beam (FIB) system and the generation of high pressures was confirmed using the double stage diamond anvil cell technique. The difficulty of aligning two second-stage micro-anvils was solved via the paired micro-anvil method. Micro-manufacturing using a FIB system enables us to control anvil shape, process any materials, including nano-polycrystalline diamond and single crystal diamond, and assemble the sample exactly in a very small space between the second-stage anvils. This method is highly reproducible. High pressures over 300 GPa were achieved, and the pressure distribution around the micro-anvil culet was evaluated by using a well-focused synchrotron micro-X-ray beam.

Abstract The Martian mantle probably experienced an early global magma ocean stage. The crystallization and the fractionation and overturn of such a magma ocean likely led to the formation of a compositionally distinct layer at the bottom of the mantle. This layer would have been heavily enriched in iron and in heat‐producing elements (HPE). The significant iron enrichment can lead to long‐term stability with little mixing between the layer and the overlying mantle. We studied the influence of such an enriched basal layer on the thermal and chemical evolution of the Martian mantle using both 2‐D finite‐volume modeling at mantle scale, and a parameterized convection approach at the entire planetary scale. The basal layer is most likely stably stratified because of its moderate thickness and/or its gradual enrichment in iron with depth that prevents the development of convection in this region. We explored a wide parameter space in our parameterized models, including the layer thickness and the mantle rheology. We show that the presence of an enriched basal layer has a dramatic influence on the thermo‐chemical evolution of Mars, strongly delaying deep cooling, and significantly affecting nearly all present‐day characteristics of the planet (heat flux, thermal state, crustal and lithospheric thickness, Love number and tidal dissipation). In particular, the enrichment of the layer in iron and HPE generates large volumes of stable melt near the core‐mantle boundary. Due to their intrinsic low viscosity and seismic velocities, these regions of silicate melt could be erroneously interpreted as core material.

From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth. There may have been mixed formamide-water solutions, but even in the presence of catalyst, solutions with >20 weight% water in formamide would not have produced significant amounts of prebiotic compounds. It might be feasible to produce relatively pure formamide by a rare occurrence of freezing formamide/water mixtures at temperatures lower than formamide's freezing point (2.55 °C) but greater than the freezing point of water. Because of the high density of formamide ice it would have sunk and accumulated at the bottom of the solution. If the remaining water froze on the surface of this ice, and was then removed by a sublimation-ablation process, a small amount of pure formamide ice might have been produced. In addition a recent report suggested that ∼85 weight% formamide could be prepared by a geochemical type of fractional distillation process, offering another possible route for prebiotic formamide production.

orbital. In addition to directly increasing the overpotential through the generation of an unstable intermediate, charge disproportionation inhibits charge accumulation by dissipating the total oxidative energy of the system. A favorable charge accumulation process may also be beneficial for electrode kinetics due to the enhanced coupling between reaction rates and electrochemical driving force. The model proposed in this study may help explain why low-spin 4d/5d rare metals are often more active than the abundant high-spin 3d materials for multi-electron transfer reactions in general, and provides new insight into how active 3d-metal catalysts can be synthesized by optimizing the energetics of both bond formation and charge accumulation.

Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here, we demonstrate that two residues of λ's J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses.

Mercury's metallic core is expected to have formed under highly reducing conditions, resulting in the presence of significant quantities of silicon alloyed to iron. Here we present the phase diagram of the Fe-FeSi system, reconstructed from in situ X-ray diffraction measurements at pressure and temperature conditions spanning over those expected for Mercury's core, and ex situ chemical analysis of recovered samples. Under high pressure, we do not observe a miscibility gap between the cubic fcc and B2 structures, but rather the formation of a re-entrant bcc phase at temperatures close to melting. Upon melting, the investigated alloys are observed to evolve towards two distinct Fe-rich and Fe-poor liquid compositions at pressures below 35-38 GPa. The evolution of the phase diagram with pressure and temperature prescribes a range of possible core crystallization regimes, with strong dependence on the Si abundance of the core.

Jasmonates have crucial roles in plant responses to biotic and abiotic stresses. Given the importance of transcriptional regulation in jasmonate-mediated stress responses, transcription factors are key regulators of jasmonate signaling. The transcription factors JASMONATE-ASSOCIATED MYC2-LIKE 1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate signaling, although the mechanisms that control the activities of these transcription factors remain unclear. To understand the regulatory mechanisms of JAM proteins, we used a yeast two-hybrid assay to screen for protein interaction partners of JAM1 and found that JAM1 interacted with JAZ proteins.

Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.

The Azores Archipelago is located near the Mid-Atlantic Ridge (MAR) and consists of nine islands, resting on both sides of the ridge. Various methods including seismic reflection, gravity and passive seismic imaging have previously been used to investigate the crustal thickness beneath the islands. They have yielded thickness estimates that range between roughly 10 and 30 km, but until now models of the more fine-scale crustal structure have been lacking. Pending questions include the thickness of the volcanic edifice beneath the islands and whether crustal intrusions or even underplating can be observed beneath any island. In this study, we use data from nine seismic stations located on the Azores Islands to investigate the crustal structure with teleseismic P-wave receiver functions. Our results indicate that the base of the volcanic edifice is located approximately 1 to 4 km depth beneath the different islands and that the crust–mantle boundary has an average depth of ∼17 km. There is strong evidence for magmatic underplating beneath the island of São Jorge, and indications that the underplating is also present beneath São Miguel and possibly Santa Maria. Additionally, the seismological lithosphere–asthenosphere boundary, defined as a seismic velocity drop in the uppermost mantle, seems to deepen with increasing distance from the MAR. It has a depth of ∼45 km beneath the islands close to the MAR, compared to depths >70 km beneath the more distal islands.

We report the syntheses of ribonucleoside 5'-monophosphates activated with imidazole, using a mechanism which relies on the in situ generation of cyanogen chloride from the reaction of cyanide anion with hypochlorous acid. Cyanogen chloride reacts rapidly with imidazole to form diimidazole imine as the major product, a species which affords the activation of ribonucleoside 5'-monophosphates to their 5'-phosphorimidazolides.

The lunar cratering record is used to constrain the bombardment history of both the Earth and the Moon. However, it is suggested from different perspectives, including impact crater dating, asteroid dynamics, lunar samples, impact basin-forming simulations, and lunar evolution modelling, that the Moon could be missing evidence of its earliest cratering record. Here we report that impact basins formed during the lunar magma ocean solidification should have produced different crater morphologies in comparison to later epochs. A low viscosity layer, mimicking a melt layer, between the crust and mantle could cause the entire impact basin size range to be susceptible to immediate and extreme crustal relaxation forming almost unidentifiable topographic and crustal thickness signatures. Lunar basins formed while the lunar magma ocean was still solidifying may escape detection, which is agreeing with studies that suggest a higher impact flux than previously thought in the earliest epoch of Earth-Moon evolution.

The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.

We present TempDAC, a 3-D numerical model for calculating the steady-state temperature distribution for continuous wave laser-heated experiments in the diamond anvil cell. TempDAC solves the steady heat conduction equation in three dimensions over the sample chamber, gasket, and diamond anvils and includes material-, temperature-, and direction-dependent thermal conductivity, while allowing for flexible sample geometries, laser beam intensity profile, and laser absorption properties. The model has been validated against an axisymmetric analytic solution for the temperature distribution within a laser-heated sample. Example calculations illustrate the importance of considering heat flow in three dimensions for the laser-heated diamond anvil cell. In particular, we show that a “flat top” input laser beam profile does not lead to a more uniform temperature distribution or flatter temperature gradients than a wide Gaussian laser beam.

Electronics waste production has been fueled by economic growth and the demand for faster, more efficient consumer electronics. The glass and metals in end-of-life electronics components can be reused or recycled; however, conventional extraction methods rely on energy-intensive processes that are inefficient when applied to recycling e-waste that contains mixed materials and small amounts of metals. To make e-waste recycling economically viable and competitive with obtaining raw materials, recovery methods that lower the cost of metal reclamation and minimize environmental impact need to be developed. Microbial surface adsorption can aid in metal recovery with lower costs and energy requirements than traditional metal-extraction approaches. We introduce a novel method for metal recovery by utilizing metal-binding peptides to functionalize fungal mycelia and enhance metal recovery from aqueous solutions such as those found in bioremediation or biomining processes. Using copper-binding as a proof-of-concept, we compared binding parameters between natural motifs and those derived in silico, and found comparable binding affinity and specificity for Cu. We then combined metal-binding peptides with chitin-binding domains to functionalize a mycelium-based filter to enhance metal recovery from a Cu-rich solution. This finding suggests that engineered peptides could be used to functionalize biological surfaces to recover metals of economic interest and allow for metal recovery from metal-rich effluent with a low environmental footprint, at ambient temperatures, and under circumneutral pH.