Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life?

Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria

Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsB^Ramp^R) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.

Horizontal gene transfer from genetically modified plants - Regulatory considerations

Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.

A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.

Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways

Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.

Silica-Carbonate of Ba(II) and Fe2+/Fe3+ Complex as Study Models to Understand Prebiotic Chemistry

The Precambrian era is called the first stage of the Earth history and is considered the longest stage in the geological time scale. Despite its duration, several of its environmental and chemical characteristics are still being studied. It is an era of special relevance not only for its duration but also because it is when a set of conditions gave rise to the first organism. This pioneer organism has been proposed to have been formed by a mineral and an organic part. A chemical element suggested to have been part of the structure of this cell is iron. However, what special characteristic does iron have with respect to other chemical elements to be proposed as part of this first cell? To answer this and other questions, it is indispensable to have a model that will allow extrapolating the first chemical structures of the pioneer organism formed in the Precambrian. In this context, for several decades, in vitro structures chemically formed by silica-carbonates have been synthetized, called biomorphs, because they could emulate living organisms and might resemble primitive organisms. It has been inferred that because biomorphs form structures with characteristic morphologies, they could resemble the microfossils found in the cherts of the Precambrian. Aiming at providing some insight on how iron contributed to the formation of the chemical structures of the primitive organism, we evaluated how iron contributes to the morphology and chemical-crystalline structure during the synthesis of these compounds under different conditions found in the primitive atmosphere. Experimentally, synthesis of biomorphs was performed at four different atmospheric conditions including UV light, nonionizing microwave radiation (NIR-mw), water steam (WS), and CO2 in the presence of Fe2+, Fe3+, and Fe2+/Fe3+, obtaining 48 different conditions. The produced biomorphs were observed under scanning electron microscopy (SEM). Afterward, their chemical composition and crystalline structure were analyzed through Raman and IR spectroscopy.

Metal cation saturation on montmorillonites facilitates the adsorption of DNA via cation bridging

Extracellular DNA (eDNA) is widely present in soil, with potential ecological impacts. Metal cations are naturally present on the surface of soil clay minerals, although the adsorption mechanism of eDNA on clay minerals saturated with metal cations is still not fully understood. The research investigated the adsorption of eDNA, using salmon sperm DNA as a representative, on metal cation (Na⁺, Ca²⁺, and Fe³⁺)-saturated montmorillonites (Mt). Metal cation-saturated Mt have higher adsorption capacities for DNA. Compared with Mt (3500 mg⋅kg^-1), the amounts of DNA adsorption on metal cation-saturated Mt (pH = 7.0) were increased by 0.74-5.38 times, and followed the descending order of Fe-Mt > Na-Mt > Ca-Mt > Mt. A temperature of 25 °C was found to be more suitable than 15 and 35 °C for DNA adsorption, while an increasing pH value (3.0-9.0) reduced DNA adsorption on Mt and metal cation-saturated Mt. Microscopic and spectroscopic analyses, together with a model computation technique, confirmed that metal cations saturated on the surface of Mt work like a "cation bridge" linking oxygen atoms in the phosphate groups of DNA and the negatively charged moieties of Mt, which were predominantly bound through electrostatic forces, thus, facilitating DNA adsorption at pH > 5. The results of this investigation provide valuable insight into eDNA adsorption on soil clay minerals and the transport and fate of eDNA in the natural soil environment.