The fixation of into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a “phylometabolic” tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.

Abstract. The sulphur chemistry in nine regions in the earliest stages of high-mass star formation is studied through singledish submillimeter spectroscopy. The line profiles indicate that 10-50% of the SO and SO 2 emission arises in high-velocity gas, either infalling or outflowing. For the low-velocity gas, excitation temperatures are 25 K for H 2 S, 50 K for SO, H 2 CS, NS and HCS + , and 100 K for OCS and SO 2 , indicating that most observed emission traces the outer parts (T < 100 K) of the molecular envelopes, except high-excitation OCS and SO 2 lines. Abundances in the outer envelopes, calculated with a Monte Carlo program, using the physical structures of the sources derived from previous submillimeter continuum and CS line data, are ∼10 −8 for OCS, ∼10 −9 for H 2 S, H 2 CS, SO and SO 2 , and ∼10 −10 for HCS + and NS. In the inner envelopes (T > 100 K) of six sources, the SO 2 abundance is enhanced by a factor of ∼100-1000. This region of hot, abundant SO 2 has been seen before in infrared absorption, and must be small, < ∼ 0. 2 (180 AU radius). The derived abundance profiles are consistent with models of envelope chemistry which invoke ice evaporation at T ∼ 100 K. Shock chemistry is unlikely to contribute. A major sulphur carrier in the ices is probably OCS, not H 2 S as most models assume. The source-to-source abundance variations of most molecules by factors of ∼10 do not correlate with previous systematic tracers of envelope heating. Without observations of H 2 S and SO lines probing warm ( > ∼ 100 K) gas, sulphur-bearing molecules cannot be used as evolutionary tracers during star formation.

Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus. To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and selforganization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen. metabolic evolution | Prochlorococcus | microbial oceanography | mutualism | Earth history M etabolism sustains the nonequilibrium chemical order of the biosphere by continually supplying the energy and building blocks of all cells on Earth (1-5). Here we ask: How does cellular metabolic evolution shape the mass and energy flows of ecosystems? The oceanic phytoplankter Prochlorococcus (6), the most abundant photosynthetic cell on Earth (7,8), provides an ideal model system for addressing this question. Prochlorococcus and its deeper-branching sister lineage marine Synechococcus make up the marine picocyanobacteria and have a characteristic biogeography (9). Prochlorococcus "ecotypes" have geographically (10, 11) and seasonally (12) dynamic populations that in warm, stable stratified water columns always return to the same general structure: Recently diverging highlight-adapted (HL) ecotypes are most abundant toward the surface, whereas deeper branching low-light-adapted (LL) ecotypes are most abundant at depth (10-14) (Fig. 1).What selective forces drove this niche partitioning in Prochlorococcus, and what were the consequences for the ocean ecosystem in general? To address these questions, we reconstructed (15, 16) (Fig. 2) the evolution of core metabolism in strains representing the major clades of Prochlorococcus. To interpret the observed patterns, we developed an evolutionary framework that illuminates the driving forces that produc...

a b s t r a c tStimulated by recent THz measurements of the methanol spectrum in one of our laboratories, undertaken in support of NASA programs related to the Herschel Space Observatory (HSO) and the Atacama Large Millimeter Array (ALMA), we have carried out a global analysis of available microwave and high-resolution infrared data for the first three torsional states (m t = 0, 1, 2), and for J values up to 30. This global fit of approximately 5600 frequency measurements and 19 000 Fourier transform far infrared (FTFIR) wavenumber measurements to 119 parameters reaches the estimated experimental measurement accuracy for the FTFIR transitions, and about twice the estimated experimental measurement accuracy for the microwave, submillimeter-wave, and terahertz transitions. The present fit is essentially a continuation of our earlier work, but we have greatly expanded our previous data set and have added a large number of new torsion-rotation interaction terms to the Hamiltonian in our previously used computer program. The results, together with a number of calculated (but unmeasured) transitions, including their line strength, estimated uncertainty, and lower state energy, are made available in the supplementary material as a database formatted to be useful for astronomical searches. Some discussion of several open spectroscopic problems, e.g., (i) an improved notation for the numerous parameters in the torsion-rotation Hamiltonian, (ii) possible causes of the failure to fit frequency measurements to the estimated measurement uncertainty, and (iii) pitfalls to be avoided when intercomparing apparently identical parameters from the internal axis method and the rho axis method are also given.

Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. We identify as modules, either subsets of chemicals and reactions, or subsets of functions, that are re-used in many contexts with a conserved internal structure. At the small molecule substrate level, module boundaries are often associated with the most complex reaction mechanisms, catalyzed by highly conserved enzymes. Cofactors form a biosynthetically and functionally distinctive control layer over the small-molecule substrate. The most complex members among the cofactors are often associated with the reactions at module boundaries in the substrate networks, while simpler cofactors participate in widely generalized reactions. The highly tuned chemical structures of cofactors (sometimes exploiting distinctive properties of the elements of the periodic table) thereby act as 'keys' that incorporate classes of organic reactions within biochemistry. Module boundaries provide the interfaces where change is concentrated, when we catalogue extant diversity of metabolic phenotypes. The same modules that organize the compositional diversity of metabolism are argued, with many explicit examples, to have governed long-term evolution. Early evolution of core metabolism, and especially of carbon-fixation, appears to have required very few innovations, and to have used few rules of composition of conserved modules, to produce adaptations to simple chemical or energetic differences of environment without diverse solutions and without historical contingency. We demonstrate these features of metabolism at each of several levels of hierarchy, beginning with the small-molecule metabolic substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Content from this work may be used under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 licence.