Short- and Long-Range Attractive Forces That Influence the Structure of Montmorillonite Osmotic Hydrates

Clay swelling is a colloidal phenomenon that has a large influence on flow and solute migration in soils and sediments. While models for clay swelling have been proposed over many years, debate remains as to the interaction forces that combine to produce the observed swelling behavior. Using cryogenic transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering, we study the influence of salinity, in combination with layer charge, interlayer cation, and particle size, on montmorillonite swelling. We observe a decrease in swelling with increased layer charge, increased cation charge, and decreased cation hydration, each indicative of the critical influence of Coulombic attraction between the negatively charged layers and interlayer cations. Cryo-TEM images of individual montmorillonite particles also reveal that swelling is dependent upon the number of layers in a particle. Calculations of the van der Waals (vdW) interaction based on new measurements of Hamaker coefficients confirm that long-range vdW interactions extend beyond near-neighbor layer interactions and result in a decrease in layer spacing with a larger number of layers. This work clarifies the short- and long-range attractive interactions that govern clay structure and ultimately the stability and permeability of hydrated clays in the environment

Mechanism of Ferric Oxalate Photolysis

Iron­(III) oxalate, Fe³⁺(C₂O₄)₃^3–, is a photoactive metal organic complex found in natural systems and used to quantify photon flux as a result of its high absorbance and reaction quantum yield. It also serves as a model complex to understand metal carboxylate complex photolysis because the mechanism of photolysis and eventual production of CO₂ is not well understood for any system. We employed pump/probe mid-infrared transient absorption spectroscopy to study the photolysis reaction of the iron­(III) oxalate ion in D₂O and H₂O up to 3 ns following photoexcitation. We find that intramolecular electron transfer from oxalate to iron occurs on a sub-picosecond time scale, creating iron­(II) complexed by one oxidized and two spectator oxalate ligands. Within 40 ps following electron transfer, the oxidized oxalate molecule dissociates to form free solvated CO_2(aq) and a species inferred to be CO₂^• ^– based on the appearance of a new vibrational absorption band and <i>ab initio</i> simulation. This work provides direct spectroscopic evidence for the first mechanistic steps in the photolysis reaction and presents a technique to analyze other environmentally relevant metal carboxylate photolysis reactions

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories

Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

The fractionation of hydrogen stable isotopes during lipid biosynthesis is larger in autotrophic than in heterotrophic microorganisms, possibly due to selective incorporation of hydrogen from water into NAD­(P)­H, resulting in D-depleted lipids. An analogous fractionation should occur during amino acid biosynthesis. Whereas these effects are traditionally measured using gas-phase isotope ratio on 1H-1H and 1H-2H, using an electrospray mass spectrometry-based technique on the original biomolecular structure and fitting of isotopic patterns we measured the hydrogen isotope compositions of proteins from an acidophilic microbial community with organism specificity and compared values with those for lipids. We showed that lipids were isotopically light by −260 ‰ relative to water in the growth solution; alternatively protein isotopic composition averaged −370 ‰. This difference suggests that steps in addition to NAD­(P)H formation contribute to D/H fractionation. Further, autotrophic bacteria sharing 94% 16S rRNA gene sequence identity displayed statistically significant differences in protein hydrogen isotope fractionation, suggesting different metabolic traits consistent with distinct ecological niches or incorrectly annotated gene function. In addition, it was found that heterotrophic, archaeal members of the community had isotopically light protein (−323 ‰) relative to growth water and were significantly different from coexisting bacteria. This could be attributed to metabolite transfer from autotrophs and unknown aspects of fractionation associated with iron reduction. Differential fractionation of hydrogen stable isotopes into metabolites and proteins may reveal trophic levels of members of microbial communities. The approach developed here provided insights into the metabolic characteristics of organisms in natural communities and may be applied to analyze other systems

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories

A Model for Nucleation When Nuclei Are Nonstoichiometric: Understanding the Precipitation of Iron Oxyhydroxide Nanoparticles

Despite years of study, quantitative models for the nucleation and growth of metal oxyhydroxide nanoparticles from aqueous solution have remained elusive. The problem is complicated by surface adsorption, which causes the stoichiometry of the nucleus to differ from that of the bulk precipitate and causes the surface tension of the precipitate-water interface to depend upon solution chemistry. Here we present a variation of classical nucleation theory that can accommodate surface adsorption, and apply it to understand the nucleation of β-FeOOH (akaganeite) nanoparticles from aqueous FeCl₃ solutions. We use small-angle X-ray scattering (SAXS) to quantify nucleation rates over a range of concentrations (5–200 mM FeCl₃) and temperatures (47–80 °C), then apply our model to estimate the critical nucleus size and surface tension at each condition. The surface tension varies from 0.07 J/m² in 200 mM solutions to 0.16 J/m² in 5 mM solutions. This behavior indicates that the nuclei contain an excess of Cl^– and H⁺ relative to the ideal FeOOH stoichiometry, and the coadsorption of Cl^– and H⁺ is critical for reducing surface tension into a range where classical nucleation pathways can operate. Furthermore, we find that the surface tension can be roughly estimated from aqueous solubility data alone, which may help to understand systems where surface tension data is unavailable

Consensus population genome properties.

§<p>Marker gene detection details are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061692#pone.0061692.s006" target="_blank">Table S6</a>.</p>*<p>Parenthetical values indicate cases where locally elevated depth of coverage suggests that assembly software may have compressed multiple 16S gene copies into a single locus.</p

Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

<div><p>Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative <i>de novo</i> assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.</p></div