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Marine picocyanobacteria Prochlorococcus and Synechococcus , the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within Prochlorococcus . Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.

Primary AbstractThe euphotic zone of the surface ocean contains distinct physical-chemical regimes that vary inversely in light and nutrient concentrations as a function of depth. The most numerous phytoplankter of the mid- and low-latitude ocean is the picocyanobacteriumProchlorococcus,which consists of ecologically distinct subpopulations (i.e., “ecotypes”). Ecotypes have different temperature, light and nutrient optima and display distinct relative abundances along gradients of these niche dimensions. As a primary producer,Prochlorococcusfixes and releases organic carbon to neighboring microbes as part of the microbial loop. However, little is known about the specific moleculesProchlorococcusaccumulates and releases or how these processes vary among its ecotypes. Here we characterize metabolite diversity ofProchlorococcusby profiling three ecologically-distinct cultured strains: MIT9301, representing a high-light adapted ecotype dominating shallow tropical and sub-tropical waters, MIT0801, representing a low-light adapted ecotype found throughout the euphotic zone and MIT9313, representing a low-light adapted ecotype relatively most abundant at the base of the euphotic zone. In both intracellular and extracellular metabolite profiles, we observe striking differences across strains in the accumulation and release of molecules. Some differences reflect variable genome content across the strains, while others likely reflect variable regulation of genetically-conserved pathways. In the extracellular profiles, we identify molecules that may serve as currencies inProchlorococcus’interactions with neighboring microbes and therefore merit further investigation.ImportanceApproximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacteriumProchlorococcus.Ecologically-distinct subpopulations ofProchlorococcus(or ecotypes) are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. By measuring the chemical profile of three cultured ecotype strains, we observed striking differences in the likely chemical impact ofProchlorococcussubpopulations on their surroundings. Subpopulations differ along gradients of temperature, light and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models ofProchlorococcusphysiology and marine carbon dynamics.

Marine picocyanobacteria (Prochlorococcus and Synechococcus), the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, we find that genes for breaking down chitin - an abundant source of organic carbon that primarily exists as particles - are widespread in this group. We further show that cells with a chitin degradation pathway display chitin degradation activity, attach to chitin particles and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated form of chitin. Marine chitin is largely derived from arthropods, whose roots lie in the early Phanerozoic, 520-535 million years ago, close to when marine picocyanobacteria began colonizing the ocean. We postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Transitioning to a constitutive planktonic life without chitin associations along a major early branch within the Prochlorococcus tree led to cellular and genomic streamlining. Our work highlights how coevolution across trophic levels creates metabolic opportunities and drives biospheric expansions.

Significance Marine microbe growth is limited by iron over about half of the global ocean surface. Dissolved iron is quickly lost from the ocean, but its availability to marine microbes may be enhanced by binding with organic molecules which, in turn, are produced by microbes. We hypothesize this forms a reinforcing cycle between biological activity and iron cycling that locally matches the availability of iron and other nutrients, leading to global-scale resource colimitation between macronutrients and micronutrients, and maximizing biological productivity. Idealized models support this hypothesis, depending on the specific relationships between microbial sources and sinks of organic molecules. An evolutionary selection may have occurred which optimizes these characteristics, resulting in “just enough” iron in the ocean., Iron is the limiting factor for biological production over a large fraction of the surface ocean because free iron is rapidly scavenged or precipitated under aerobic conditions. Standing stocks of dissolved iron are maintained by association with organic molecules (ligands) produced by biological processes. We hypothesize a positive feedback between iron cycling, microbial activity, and ligand abundance: External iron input fuels microbial production, creating organic ligands that support more iron in seawater, leading to further macronutrient consumption until other microbial requirements such as macronutrients or light become limiting, and additional iron no longer increases productivity. This feedback emerges in numerical simulations of the coupled marine cycles of macronutrients and iron that resolve the dynamic microbial production and loss of iron-chelating ligands. The model solutions resemble modern nutrient distributions only over a finite range of prescribed ligand source/sink ratios where the model ocean is driven to global-scale colimitation by micronutrients and macronutrients and global production is maximized. We hypothesize that a global-scale selection for microbial ligand cycling may have occurred to maintain “just enough” iron in the ocean.

Prochlorococcus is one of the most abundant photosynthesizing organisms in the oligotrophic oceans. Gene content variation among Prochlorococcus populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in low-light adapted Prochlorococcus populations from iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower iron flux). Prochlorococcus siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, particularly at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of Prochlorococcus.

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. The marine cyanobacterium Prochlorococcus is a useful model system for understanding how trait variability emerges within microbial species: Its functional diversity is overlaid on measurable environmental gradients, providing a powerful lens into large-scale evolutionary processes. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing the allocation of ecologically important functions within microbial species. We find that nitrate assimilation genes are absent in basal lineages of Prochlorococcus but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, stochastic gene loss, and homologous recombination among closely related cells. By mapping this process onto a model of Prochlorococcus’ macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.

Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing intraspecific allocation of ecologically important functions. Nitrate assimilation genes are absent in basal lineages but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, gene loss, and homologous recombination. By mapping this process onto a model of Prochlorococcus’ macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.

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 self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.

The torsion–rotation spectrum of hydroxyacetone presents a highly challenging analysis problem in molecular physics. Continuing analyses of this species are compelling due to a nascent interest from astronomers, who believe hydroxyacetone may link a variety of organic chemical families observed in the interstellar medium (ISM). Recent work has demonstrated the difficulties in analysis of the millimeter spectrum, and the modestly weaker spectrum in this region has not afforded an ISM detection. We present an extension of the laboratory measurements and analysis up to the room temperature Boltzmann peak near 300 GHz, thus providing sufficient coverage to examine the ISM for the strongest features expected in star-forming hot cores. Even without subsequent detection, searches for the stronger features will produce the lowest possible upper limits of this elusive species.

In order to better characterize the chemistry involving C N groups in regions of star-formation, we have recorded the millimeter-wave rotational spectrum of 2-cyanoethanol. Almost 6000 new transitions were assigned to two separate conformers and three torsionally excited states. The lowest energy conformer, gauche-2-cyanoethanol, its 1 st excited torsion, and the ground state for the anti-I-conformer are best characterized with basic asymmetric rigid-rotor Hamiltonians including distortion. All fit close to experimental uncertainty. Fits for the 2 nd and 3 rd excited torsional states for the gauche-conformer are of somewhat lower quality, which might be explained by a potential interaction between these states. The results of the various fits are discussed in this paper. In all, the present characterization of the spectrum and extensions through prediction should be more than sufficient to guide future millimeter-wave observational studies of this species in the interstellar medium.

Recent detection of the 2C sugar glycolaldehyde in the Sgr B2(N-LMH) hot core source as well as the presence of several sugars and other polyhydroxylated species in the Murchison meteorite have led to interest in observational searches for higher order sugars in the interstellar medium. 1,3-Dihydroxyacetone, the simplest 3C sugar, is one of the species detected in Murchison and is of considerable importance for observational searches as the next step in complexity for interstellar sugars. However, little spectroscopic information is available for this molecule. We present here the Doppler-limited rotational spectrum of 1,3-dihyroxyacetone to 450 GHz. Assignments include the ground state up to J=104 and four additional vibrational states. Standard rotational and quartic centrifugal distortion constants have been determined for each of these states.

Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere., 25 pages, 5 figures, 5 tables, 2 supplementary files

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., Author Summary The existence of the biosphere today depends on its capacity to fix inorganic into living matter. A wide range of evidence also suggests that the earliest life forms on Earth likewise derived their carbon from . From these two observations one can assume that the global biological carbon cycle has always been based on , and we show here that this assumption can be used as a powerful constraint to help organize and explain the deep evolution of life on Earth. Using a novel method that fully integrates aspects of metabolic and phylogenetic analysis, we are able to reconstruct the complete early evolutionary history of biological carbon-fixation, relating all ways in which life today performs this function to a single ancestral form. The diversification in carbon-fixation appears to underpin most of the deepest branches in the tree of life, and this early metabolic diversification – reaching back to the first cells – appears to have been driven not by the contingencies of history, but by direct links to the physical-chemical environment. The ancestral carbon-fixation pathway that we identify is different from any modern form, but better suited to the capabilities of the earliest primitive cells.

Fabry–Perot resonators have tremendous potential to enhance the sensitivity of spectroscopic systems at terahertz (THz) frequencies. Increasing sensitivity will be of benefit in compensating for the relatively low power of current high resolution continuous wave THz radiation techniques, and to fully express the potential of THz spectroscopy as source power increases. Improved sensitivities, and thus scanning speeds, will allow detailed studies of the complex vibration-rotation-tunneling dynamics that large molecules show at THz wavelengths, and will be especially important in studying more elusive, transient species such as those present in planetary atmospheres and the interstellar medium. Coupling radiation into the cavity presents unique challenges at THz frequencies, however, meaning that the cavity configurations common in neighboring frequency domains cannot simply be translated. Instead, novel constructions are needed. Here we present a resonator design in which wire-grid polarizers serve as the input and output coupling mirrors. Using this configuration, Q-factors of a few times 10^5 are achieved near 0.3 THz. To aid future investigations, the parameter space that limits the quality of the cavity is explored and paths to improved performance highlighted. Lastly, the performance of polarizer cavity-based Fourier transform (FT) THz spectrometers is discussed, in particular those design optimizations that should allow for the construction of THz instrumentation that rivals and eventually surpasses the sensitivities achieved with modern FT-microwave cavity spectrometers.

As part of an effort to study gas-grain chemical models in star-forming regions as they relate to molecules containing cyanide (–C≡N) groups, we present here a search for the molecules 2-cyanoethanol (OHCH_2CH_2CN) and methoxyacetonitrile (CH_3OCH_2CN) in the galactic center region SgrB2. These species are structural isomers of each other and are targeted to investigate the cross-coupling of pathways emanating from the photolysis products of methanol and ammonia with pathways involving cyano-containing molecules. Methanol and ammonia ices are two of the main repositories of the elements C, O, and N in cold clouds and understanding their link to cyanide chemistry could give important insights into prebiotic molecular evolution. Neither species was positively detected, but the upper limits we determined allow comparison to the general patterns gleaned from chemical models. Our results indicate the need for an expansion of the model networks to better deal with cyanochemistry, in particular with respect to pathways including products of methanol photolysis. In addition to these results, the two main observational routes for detecting new interstellar molecules are discussed. One route is by decreasing detection limits at millimeter wavelength through spatial filtering with interferometric studies at the Atacama Large Millimeter Array (ALMA), and the second is by searching for intense torsional states at THz frequencies using the Herschel Space Observatory. 2-cyanoethanol and methoxyacetonitrile would both be good test beds for exploring the capabilities of ALMA and Herschel in the study of complex interstellar chemistry.

Stimulated 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 (νt = 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.

Pyruvate is an important “hub” metabolite that is a precursor for amino acids, sugars, cofactors, and lipids in extant metabolic networks. Pyruvate has been produced under simulated hydrothermal vent conditions from alkyl thiols and carbon monoxide in the presence of transition metal sulfides at 250 °C [Cody GD et al. (2000) Science 289(5483):1337–1340], so it is plausible that pyruvate was formed in hydrothermal systems on the early earth. We report here that pyruvate reacts readily in the presence of transition metal sulfide minerals under simulated hydrothermal vent fluids at more moderate temperatures (25–110 °C) that are more conducive to survival of biogenic molecules. We found that pyruvate partitions among five reaction pathways at rates that depend upon the nature of the mineral present; the concentrations of H2S, H2, and NH4Cl; and the temperature. In most cases, high yields of one or two primary products are found due to preferential acceleration of certain pathways. Reactions observed include reduction of ketones to alcohols and aldol condensation, both reactions that are common in extant metabolic networks. We also observed reductive amination to form alanine and reduction to form propionic acid. Amino acids and fatty acids formed by analogous processes may have been important components of a protometabolic network that allowed the emergence of life.

The sulphur chemistry in nine regions in the earliest stages of high-mass star formation is studied through single-dish submillimeter spectroscopy. The line profiles indicate that 10-50% of the SO and SO2 emission arises in high-velocity gas, either infalling or outflowing. For the low-velocity gas, excitation temperatures are 25 K for H2S, 50 K for SO, H2CS, NS and HCS+, and 100 K for OCS and SO2, indicating that most observed emission traces the outer parts (T100 K) of six sources, the SO2 abundance is enhanced by factors of ~100-1000. This region of hot, abundant SO2 has been seen before in infrared absorption, and must be small, ~ 100 K) gas, sulphur-bearing molecules cannot be used as evolutionary tracers during star formation., Comment: Accepted by A&A, 14 pages, 5 figures

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule 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., Comment: 56 pages, 28 figures