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

NanoSIMS (Nanoscale Secondary-Ion Mass Spectrometry) is a powerful analytical technique that allows quantitative, subcellular imaging of incorporation and transfer of isotopically labeled compounds and metabolites in biological tissue (Hoppe et al., 2013). This technique is well adapted to study small organisms such as foraminifera. Recent studies have successfully applied NanoSIMS analysis of foraminifera to study the localization of labeled compounds incorporated into their calcium carbonate test and into the cell itself. In the test, it was applied to better understand the microdistribution of different elements (e.g. Mg/Ca ratio) used as proxies for paleoclimate reconstruction (e.g. Kunioka et al., 2006; Nehrke et al., 2013; Tachikawa et al., 2013). One study correlated NanoSIMS with TEM imaging to study the incorporation of isotopically labeled nitrate and sulfate in benthic foraminifera cell (Nomaki et al., 2016). In a series of individual experiments, we have used NanoSIMS in combination with TEM to study metabolic processes in foraminifera: 1) Heterotrophic feeding was investigated in the benthic species A. tepida under oxic and anoxic conditions (Lekieffre et al., 2016). 2) The spatio-temporal dynamics of assimilation and translocation of 13C-bicarbonate and 15N-ammonium/nitrate was investigated in both benthic (kleptoplastidy) and planktonic (symbiotic) foraminifera with pulse-chase experiments. In a benthic species containing sequestered chloroplasts, these were demonstrated to play a significant role in the incorporation of both inorganic carbon and nitrogen into the cytoplasm (Jauffrais et al., 2016 TMS oral presentation). Symbiotic planktonic foraminifera showed rapid uptake of bicarbonate and ammonium through the symbionts, whereas uptake of nitrate was less efficient.

NanoSIMS applied to the study of foraminifera

The nature of early life on Earth is difficult to assess because potential Early Archean biosignatures are commonly poorly preserved. Interpretations of such materials have been contested, and abiotic or epigenetic derivations have been proposed (summarized in [1]). Yet, an understanding of Archean life is of astrobiological importance, as knowledge of early evolutionary processes on Earth could provide insight to development of life on other planets. A recently-discovered assemblage of organic microstructures in approx.3 Ga charts of the Farrel Quartzite (FQ) of Australia [2-4] includes unusual spindle-like forms and a variety of spheroids. If biogenicity and syngeneity of these forms could be substantiated, the FQ assemblage would provide a new view of Archean life. Our work uses NanoSIMS to further assess the biogenicity and syngeneity of FQ microstructures. In prior NanoSIMS studies [5-6], we gained an understanding of nano-scale elemental distributions in undisputed microfossils from the Neoproterozoic Bitter Springs Formation of Australia. Those results provide a new tool with which to evaluate poorly preserved materials that we might find in Archean sediments and possibly in extraterrestrial materials. We have applied this tool to the FQ forms.

/pdf/diversification-in-the-archean-biosphere-insights-from-2mb02i5ftf.pdf

Diversification in the Archean biosphere: Insights from NanoSIMS of Microstructures in the Farrel Quartzite of Australia

Nitrogen and sulfur are key elements in the biogeochemical cycles of marine ecosystems to which benthic foraminifera contribute significantly. Yet, cell-specific assimilation of ammonium, nitrate and sulfate by these protists is poorly characterized and understood across their wide range of species-specific trophic strategies. For example, detailed knowledge about ammonium and sulfate assimilation pathways is lacking and although some benthic foraminifera are known to maintain intracellular pools of nitrate and/or to denitrify, the potential use of nitrate-derived nitrogen for anabolic processes has not been systematically studied. In the present study, NanoSIMS isotopic imaging correlated with transmission electron microscopy was used to trace the incorporation of isotopically labeled inorganic nitrogen (ammonium or nitrate) and sulfate into the biomass of twelve benthic foraminiferal species from different marine environments. On timescales of twenty hours, no detectable 15N-enrichments from nitrate assimilation were observed in species known to perform denitrification, indicating that, while denitrifying foraminifera store intra-cellular nitrate, they do not use nitrate-derived nitrogen to build their biomass. Assimilation of both ammonium and sulfate, with corresponding 15N and 34S-enrichments, were observed in all species investigated (with some individual exceptions for sulfate). Assimilation of ammonium and sulfate thus can be considered widespread among benthic foraminifera. These metabolic capacities may help to underpin the ability of benthic foraminifera to colonize highly diverse marine habitats.

/pdf/ammonium-and-sulfate-assimilation-is-widespread-in-benthic-1exhx5ls.pdf

Ammonium and Sulfate Assimilation Is Widespread in Benthic Foraminifera

abundances of 86 Sr. The distribution of 86 Sr in the skeleton was imaged with the NanoSIMS ion microprobe with a spatial resolution of 200 nm and combined with images of the skeletal ultra-structure. Importantly, the distribution of the 86 Sr label in the P. porites skeleton was found to be strongly heterogeneous. This constrains the physical dimensions of the hypothetical Extracellular Calcifying Fluid (ECF) reservoir at the surface of the growing skeleton, which is implicit in most geochemical models for coral biomineralization. These new experimental capabilities allow for a much more detailed view of the growth dynamics for a wide range of marine organisms that

/pdf/strontium-86-labeling-experiments-show-spatially-588vpyeb3l.pdf

Anders Meibom

Papers

NanoSIMS applied to the study of foraminifera

Diversification in the Archean biosphere: Insights from NanoSIMS of Microstructures in the Farrel Quartzite of Australia

Ammonium and Sulfate Assimilation Is Widespread in Benthic Foraminifera

Strontium-86 labeling experiments show spatially heterogeneous skeletal formation in the scleractinian coral Porites porites

Beryllium and Boron Measurements in QUE 94411 Chondrules: Possible Constraints on Formation Temperature