Amplification of plasmid DNA bound on soil colloidal particles and clay minerals by the polymerase chain reaction

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

A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.

Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface

DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10^-3 to 3.55 × 10^-1 min^-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 10³ and 9.48 × 10² mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.

Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep

BACKGROUND

Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study.

METHODOLOGY/PRINCIPAL FINDINGS

We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat ( approximately 400 cm and approximately 10 cm from the mat's edge) contrasted with sharply diminished activity at approximately 50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12-20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity.

CONCLUSIONS/SIGNIFICANCE

The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12-20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes.

Plasmid DNA is released from nanosized acicular material surface by low molecular weight oligonucleotides: exogenous plasmid acquisition mechanism for penetration intermediates based on the Yoshida effect

When a colloidal solution consisting of nanosized acicular material and bacterial cells is stimulated with sliding friction at the interface between the hydrogel and interface-forming material where the frictional coefficient increases rapidly, the nanosized acicular material accompanying the bacterial cells forms a penetration intermediate. This effect is known as the Yoshida effect in honor of its discoverer. Through the Yoshida effect, a novel property in which penetration intermediates incorporate exogenous plasmid DNA has been identified. This report proposes a possible mechanism for exogenous plasmid acquisition by penetration intermediates in the Yoshida effect. Escherichia coli cells, pUC18, and chrysotile were used as recipient cells, plasmid DNA, and nanosized acicular material, respectively. Even when repeatedly washing the mixture consisting of pUC18 and chrysotile, transformation efficiency by pUC18 was stable. Accordingly, pUC18 adsorbed onto chrysotile was introduced into recipient E. coli cells. At saturation, the amount of pUC18 adsorbed onto chrysotile was 0.8-1.2 microg/mg. To investigate whether pUC18 adsorbed on chrysotile is replicated by polymerase, polymerase chain reaction (PCR) was carried out with the chrysotile. Amplification of the beta-lactamase gene coded in pUC18, which was adsorbed onto chrysotile, was strongly inhibited. This suggests that DNA adsorbed onto chrysotile is not replicated in vivo. When we searched for substances to release pUC18 adsorbed onto chrysotile, we found that a 300-bp single- or double-stranded segment of DNA releases pUC18 from chrysotile. Competitive adsorption onto chrysotile between double-stranded DNA and pUC18 was then examined through the Yoshida effect. The 310- and 603-bp double-stranded nucleotides caused 50% competitive inhibition at the same molar ratio with pUC18. Hence, the adsorbed region of pUC18 is about 300 bp in length. As the culture period for recipient cells increases, transformation efficiency decreases while the expression levels of small RNA of 300-600 bp also decrease. These results suggest that pUC18 adsorbed onto chrysotile can be released by 300-bp small RNA, replicated by DNA polymerase, and transferred to daughter cells.