The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The solar chemical composition is an important ingredient in our understanding of the formation, structure, and evolution of both the Sun and our Solar System. Furthermore, it is an essential refer ...

The Chemical Composition of the Sun

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.

/pdf/ocean-acidification-the-other-co-2-problem-4h18mw2cpj.pdf

Ocean Acidification: The Other CO 2 Problem

Climate change 2014 - Synthesis Report

About Supramolecular Assemblies of π-Conjugated Systems

Mineralogy and petrography of Ca-Fe-rich silicate rims around heavily altered Allende dark inclusions

Nutrients from the host diet and microbial cross-feeding allow diverse bacteria to colonize the animal gut. Less is known about the role of host-derived nutrients in enabling gut bacterial colonization. We examined metabolic interactions within the evolutionary ancient symbiosis between the honey bee (Apis mellifera) and the core gut microbiota member Snodgrassella alvi. This Betaproteobacteria is incapable of metabolizing saccharides, yet colonizes the honey bee gut in the presence of only a sugar diet. Using comparative metabolomics, 13C tracers, and Nanoscale secondary ion mass spectrometry (NanoSIMS), we show in vivo that S. alvi grows on host-derived organic acids, including citrate, glycerate and 3-hydroxy-3-methylglutarate which are actively secreted by the host into the gut lumen. S. alvi additionally modulates tryptophan metabolism in the gut, primarily by converting kynurenine to anthranilate. These results suggest that Snodgrassella is adapted to a specific metabolic niche in the gut that depends on host-derived nutritional resources.

https://www.biorxiv.org/content/biorxiv/early/2023/01/23/2023.01.23.524906.full.pdf

Foraging on host synthesized metabolites enables the bacterial symbiont Snodgrassella alvi to colonize the honey bee gut

Introduction: Hydrogen isotopes in extraterrestrial materials provide unique insights on the origin of organic matter (OM) in the solar system. Large deuterium (D) enrichments have been reported in micrometer-sized regions (“hotspots”) of interplanetary dust particles [1, 2], and insoluble organic matter (IOM) extracted from primitive meteorites (carbonaceous and ordinary chondrites) [3]. Although an heritage from cold interstellar chemistry has often been favoured to explain these isotopic anomalies, both the origin of the organic matter (OM) and the location of its deuteration remain largely undetermined [4, 5]. Samples and methods: Since the pioneering work of M. Maurette in Adelie Land [6], large collections of micrometeorites (MMs, interplanetary dust particles with sizes ranging from ~ 20 to 1000 μm) have been collected in Antarctic ice and snow [7, 8]. Since 2000, we have collected unaltered micrometeorites from central Antarctic surface snow in the vicinity of the permanent French-Italian CONCORDIA station located at Dome C [9]. MMs studied here were extracted from ultra-clean snow in a trench at depths ranging from 3.3 m to 4.3 m, corresponding to fall on Earth between 1955 and 1970. Among the recovered finegrained micrometeorites, we selected particles exhibiting a fluffy fine-grained texture with no evidence of heating during atmospheric entry (i.e. vesicles and/or magnetite rim) [10]. A scanning electron microscope survey of this subgroup revealed 6 particles with sizes between 40 x 80 μm and 110 x 275 μm that are exceptionally rich in carbon, hereafter referred as UltraCarbonaceous Antarctic MicroMeteorites (UCAMMs) [11, 12]. We characterrized the structure and mineralogy of two UCAMMs, DC06-09-19 and DC06-09-119 (hereafter quoted #19 and #119) by field emission gun scanning electron microscopy and Transmission Electron Microscopy (TEM). Using the NanoSIMS-50 National Facility at LEME-MNHN (Paris), we performed isotopic imaging of their C, H and O isotopic compositions. Results: UCAMMs # 19 and # 119 consist of fine scale assemblages of OM and submicron to micron mineral phases including Mg-rich olivines and pyroxenes, Fe-sulphides and Mg-rich carbonates [13]. Carbon is dominantly present in the form of OM and represents from 60% up to 80% of the particle's volume. The presence of both Fe-sulphides and carbonates in UCAMMs indicate that they experienced little to no modification upon atmospheric entry and during their terrestrial residence at low temperature (-75°C 10 (δD > 6400 ‰) extend over 139 μm2 and 208 μm2 in #19 and #119, respectively, accounting for 27% and 83% of the analyzed surface. It is, to our knowledge, the first time that such deuterium enrichments are observed over such large areas.

https://www.lpi.usra.edu/meetings/lpsc2009/pdf/1724.pdf

Extreme deuterium enrichment in organic matter from cometary antarctic

Calcitic Scleractinian Corals: When, where and why?

Introduction: Recently it has been demonstrated that some metal grains in CH chondrites and the bencubbinites QUE94411 and Hammadah al Hamra 237 display compositionally zoned concentration profiles that are interpreted to originate by condensation from a gas of solar composition [1]. It has been estimated that these grains grew on a timescale of days [1]. The persistence of these profiles, and the lack of kamacite/taenite phase exsolution, indicates further that these grains have not undergone significant thermal processing (>300 C) since their formation. Here we report spatially resolved trace element concentration measurements in metal grains in the bencubbinite QUE94411, for the platinum group elements (PGEs: Ru, Rh, Pd, Os, Ir, Pt) and other siderophiles. The siderophile element profiles measured in these grains are compared to models of the condensation process to elucidate possible grain growth processes at high temperatures in the solar nebula. Experimental: The thick section QUE94411,6 was X-ray mapped in Ni Kα using an electron microprobe. Large (>100 μm) chemically zoned and unzoned metal grains were selected for trace element microanalysis by laser ablation ICP-MS. Prior to laser ablation the P, Cr, Fe, Co, and Ni compositional profiles of these grains were measured by electron microprobe. A CETAC LSX-200 laser ablation peripheral was used for solid sample introduction into a magnetic sector ICP mass spectrometer, the Finnigan ElementTM [2]. Each point on the sample was analyzed with 30pulse laser bursts; the laser-ablated pit produced was approximately 30 μm in diameter and 15 μm deep. A series of analyses were performed across each grain in ~30 μm steps. The isotopes monitored were P, V, Cr, Fe, Co, Ni, Mo, Ru, Rh, Pd, W, Re, Os, Ir, Pt. Instrumental sensitivity factors for each isotope were determined by measuring signal intensity from the ataxite Hoba, which has known concentrations of the elements of interest [3]. Precision of the LA-ICP-MS measurements was typically 10% (1σ). Results and Discussion: Figure 1 shows siderophile element profiles across a representative zoned FeNi metal grain in QUE94411. The data in this figure are normalized to Fe and CI abundances [4]. As shown, those siderophiles that are more refractory than Fe display a radial gradient in this grain that mimics that of Ni and Co. The PGEs (with the exception of Pd) are present at maximum normalized concentrations of two to four times that of CI chondrites; this enrichment diminishes toward the rims of the grain, where the abundance is 0.0 0.5 1.0 1.5 2.0 2.5 3.0

/pdf/platinum-group-element-distributions-in-bencubbinite-metal-1r7f43s1tf.pdf

Anders Meibom

Papers

Mineralogy and petrography of Ca-Fe-rich silicate rims around heavily altered Allende dark inclusions

Foraging on host synthesized metabolites enables the bacterial symbiont Snodgrassella alvi to colonize the honey bee gut

Extreme deuterium enrichment in organic matter from cometary antarctic

Calcitic Scleractinian Corals: When, where and why?

Platinum group element distributions in Bencubbinite metal grains