Effects of salinity on the adsorption of nucleotides onto phyllosilicates

Major evolutionary transitions before cells: A journey from molecules to organisms

Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.

Plasmid size determines adsorption to clay and breakthrough in a saturated sand column

Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.

Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

Features of DNA-Montmorillonite Binding Visualized by Atomic Force Microscopy

In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg²⁺ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg²⁺, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.

Gamma irradiation of adenine and guanine adsorbed into hectorite and attapulgite

This study focuses on the radiolysis (up to 36 kGy) of guanine and adenine (nitrogenous bases) adsorbed in hectorite and attapulgite to highlight the potential role of clays as protective agents against ionizing radiation in prebiotic processes. In this framework, the study investigated the nitrogenous bases' behavior in two types of systems: a) aqueous suspension of adenine-clay systems and b) guanine-clay systems in the solid state. This research utilized spectroscopic and chromatographic techniques for its analytical purposes. Regardless of the reaction medium conditions, the results reveal that nitrogenous bases are stable under ionizing irradiation when adsorbed on both clays.

Adenine imprinted beads as a novel selective extracellular DNA extraction method reveals underestimated prevalence of extracellular antibiotic resistance genes in various environments

Despite severe threats of extracellular antibiotic resistance genes (eARGs) towards public health in various environments, advanced studies have been hindered mainly by ineffective extracellular DNA (exDNA) extraction methods, which is challenged by trace levels of exDNA and inference from abundant coexisting compounds. This study developed a highly selective exDNA extraction method based on molecular imprinting technology (MIT) by using adenine as the template for the first time. Results suggested that adenine imprinted beads were rough spheres at an average size of 0.39 ± 0.07 μm. They effectively adsorbed DNA in the absence of chaotropic agents, with superior capacity (796.2 mg/g), rate (0.0066/s) and regarding DNA of variable lengths, even the ultra-short DNA (<100 bp). They were also highly selective towards DNA, circumventing the interference of competitive compounds' interference. These properties contribute to efficient exDNA extraction (71 %-119 %) from various environmental samples. Specifically, adenine imprinted beads enabled significantly higher extraction rates of eARGs from river, air and vegetable samples (69 %-95 %) compared to that by commercial DNA extraction products (16 %-62 %). The adenine imprinted beads-based method reveals underestimated eARG levels in the environment and the corresponding risks, and thus will thus be a powerful tool for advanced exDNA research.

Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces

The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO₂ particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO₂ surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.

Testing Abiotic Reduction of NAD+ Directly Mediated by Iron/Sulfur Minerals

Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD⁺) under anaerobic prebiotic conditions, observing the NAD⁺/NADH redox transition by using ultraviolet-visible spectroscopy and ¹H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD⁺/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The ability of an iron sulfide mineral to transfer electrons to a biochemical cofactor that is found in every living cell demonstrates how geologic materials could have played a direct role in the evolution of certain cofactor-driven metabolic pathways.

Nucleotide Adsorption on Iron(III) Oxide Nanoparticle Surfaces: Insights into Nano-Geo-Bio Interactions Through Vibrational Spectroscopy

Molecular processes at geochemical interfaces impact many environmental processes that are critical to the fate and transport of contaminants in water systems. Often these interfaces are coated with natural organic matter, oxyanions, or biological components, yet little is understood about these coatings. Herein, we are interested in better understanding the interaction of biological components with nanoscale iron oxide minerals. In particular, we use attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to investigate the adsorption behavior of deoxyadenosine monophosphate (dAMP) on hematite nanoparticle surfaces as a function of pH and in the presence and absence of adsorbed phosphate. These results show that fewer nucleotides adsorb at higher pH. Additionally, when phosphate anions are preadsorbed, nucleotide adsorption is significantly limited due to site-blocking by adsorbed inorganic phosphate. The pH dependence provides insights into the adsorption process and the importance of electrostatic interactions. Preadsorbed phosphate affects the binding mode of dAMP, suggesting synergistic interactions between the coadsorbates. Two-dimensional correlation spectroscopy was used to further analyze the infrared spectra. Based on this analysis, a dAMP adsorption pathway onto a preadsorbed phosphate-hematite surface was proposed, suggesting the displacement of adsorbed phosphate by dAMP. Overall, this study provides some insights into geochemical-biological interactions on nanoscale iron oxide surfaces using vibrational spectroscopy.

In situ polymerization of styrene–clay nanocomposites and their properties

Abstract

This work focuses on the preparation and characterization of polystyrene/organoclay nanocomposites. The effects of the nature of the organoclays and the method of preparation were studied in order to evaluate their morphological, thermal and mechanical properties. X-ray diffraction (SAXS), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning and transmission electron microscopy (SEM, TEM), atomic force microscope (AFM) were used to determine the characteristics of the resulting materials. Initially, cetyltrimethylammonium bromide was used as an organomodifier to modify the clay to form an organic clay. After that, polystyrene/organoclay nanocomposites were synthesized by an in situ mass polymerization process in which styrene was polymerized in the presence of different proportions of organoclay ranging from 1 to 15% by weight. The results obtained confirm the intercalation of cetyltrimethylammonium bromide (CTA) surfactant in the clay layers, while the nanocomposites obtained showed morphologies in which the exfoliated forms were obtained. Nanocomposites showed a significant improvement in thermal stability compared to unmodified polystyrene. The highlighting of the modification was examined by mechanical tests (shock, traction). The Charpy impact test showed an increase in impact resilience, and this is mainly due to a better interfacial adhesion of the matrix. The tensile test showed an improvement in stiffness.

Graphic abstract

The preparation of polystyrene–clay nanocomposites containing various amounts of organoclays ranging from 1 to 15% using the mass polymerization technique has shown the positive effect of the introduction of a cetyltrimethylammonium bromide surfactant chain on the thermal stability of the nanocomposites. Exfoliated morphologies were obtained for the majority of the prepared nanocomposites. A structure, surface and thermal property relationship was established based on TGA, XRD and TEM/SEM analyses.

Introduction to virus origins and their role in biological evolution

Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.

Aggregation of Plate-like Colloids Induced by Charged Polymer Chains: Organization at the Nanometer Scale Tuned by Polymer Charge Density

We study the aggregation of charged plate-like colloids, Na-montmorillonite clays, in the presence of ionenes, oppositely charged polymer chains. The choice of the charged polymer allows tuning its linear charge density to match/mismatch the average charge separation on the clay surfaces. We assess the nanoscale structure of the aggregates formed by small-angle X-ray and neutron scattering. The nanoscale features of the formed clay aggregates are dominated by the presence of a stacking peak, giving clear evidence for the formation of clay tactoids, that is, a face-to-face aggregation geometry of the clay platelets. The chain charge density of ionenes influences not only the stacking repeat distance within the clay tactoids but also the extent of stacking and abundance of the tactoids. We may distinguish two regimes as a function of clay and ionene polymer charge densities (ρ_c and ρ_p, respectively). The first regime applies to ρ_p > ρ_c and ρ_p ≈ ρ_c, that is, for highly and "matching" charged chains. Under these conditions, the intercalated chains lie in a flat conformation within the tactoids, irrespective of the ionic strength (within the range studied, i.e., up to 0.05 M NaBr). For weakly charged chains, ρ_p < ρ_c, undulation of the ionene chains within the tactoid is seen. The degree of undulation increases with ionic strength due to the decreasing persistence length of the ionene chains. The extent of stacking (5-10 platelets per tactoid) is a general feature of all the systems, and its origin remains unknown. The system corresponding to the closest match in charge separations on the clay surface and on the polymer chain (ρ_p ≈ ρ_c) features the highest abundance of tactoids. This coincides with the highest macroscopic density as deduced from simple visual inspection of sediment volumes. This leads to the open question regarding the link between the density at the nanoscale and the macroscopic density and sedimentation behavior of the aggregate.

Reactivity of shape-controlled crystals and metadynamics simulations locate the weak spots of alumina in water

The kinetic stability of any material in water relies on the presence of surface weak spots responsible for chemical weathering by hydrolysis. Being able to identify the atomistic nature of these sites and the first steps of transformation is therefore critical to master the decomposition processes. This is the challenge that we tackle here: combining experimental and modeling studies we investigate the stability of alumina in water. Exploring the reactivity of shape-controlled crystals, we identify experimentally a specific facet as the location of the weak spots. Using biased ab initio molecular dynamics, we recognize this weak spot as a surface exposed tetra-coordinated Al atom and further provide a detailed mechanism of the first steps of hydrolysis. This understanding is of great importance to heterogeneous catalysis where alumina is a major support. Furthermore, it paves the way to atomistic understanding of interfacial reactions, at the crossroad of a variety of fields of research.

Gaining atomistic level understanding of alumina/water interfaces is key to unraveling alumina decomposition processes. Here the authors combine the experimental synthesis of shape-controlled γ-Al₂O₃ samples with metadynamics simulations to identify the surface weak spots responsible for alumina decomposition.

How do Nucleotides Adsorb Onto Clays?

Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which could have spanned a large range of settings. Adsorption being an interfacial phenomenon, experiments can be built around the minerals that probably exhibited the largest specific surface areas and were the most abundant, i.e., phyllosilicates. Our current work aims at understanding how nucleotides, the building blocks of RNA and DNA, might have interacted with phyllosilicates under various physico-chemical conditions. We carried out and refined batch adsorption studies to explore parameters such as temperature, pH, salinity, etc. We built a comprehensive, generalized model of the adsorption mechanisms of nucleotides onto phyllosilicate particles, mainly governed by phosphate reactivity. More recently, we used surface chemistry and geochemistry techniques, such as vibrational spectroscopy, low pressure gas adsorption, X-ray microscopy, and theoretical simulations, in order to acquire direct data on the adsorption configurations and localization of nucleotides on mineral surfaces. Although some of these techniques proved to be challenging, questioning our ability to easily detect biosignatures, they confirmed and complemented our pre-established model.

Extracellular DNA in natural environments: features, relevance and applications

Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.