Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp (Cyprinus carpio) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectatio...

Environmental conditions influence eDNA persistence in aquatic systems

Silicon (Si) is the second-most abundant element in the earth's crust. In the pedosphere, however, huge spans of Si contents occur mainly caused by Si redistribution in soil profiles and landscapes. Here, we summarize the current knowledge on the different pools and fluxes of Si in soils and terrestrial biogeosystems. Weathering and subsequent release of soluble Si may lead to (1) secondarily bound Si in newly formed Al silicates, (2) amorphous silica precipitation on surfaces of other minerals, (3) plant uptake, formation of phytogenic Si, and subsequent retranslocation to soils, (4) translocation within soil profiles and formation of new horizons, or (5) translocation out of soils (desilication). The research carried out hitherto focused on the participation of Si in weathering processes, especially in clay neoformation, buffering mechanisms for acids in soils or chemical denudation of landscapes. There are, however, only few investigations on the characteristics and controls of the low-crystalline, almost pure silica compounds formed during pedogenesis. Further, there is strong demand to improve the knowledge of (micro)biological and rhizosphere processes contributing to Si mobilization, plant uptake, and formation of phytogenic Si in plants, and release due to microbial decomposition. The contribution of the biogenic Si sources to Si redistribution within soil profiles and desilication remains unknown concerning the pools, rates, processes, and driving forces. Comprehensive studies considering soil hydrological, chemical, and biological processes as well as their interactions at the scale of pedons and landscapes are necessary to make up and model the Si balance and to couple terrestrial processes with Si cycle of limnic, fluvial, or marine biogeosystems.

http://wwwuser.gwdg.de/~kuzyakov/Sommer_JPNSS_2006_Si_Review.pdf

Silicon pools and fluxes in soils and landscapes—a review

In recent years, several protocols based on the extraction of nucleic acids directly from the soil matrix after lysis treatment have been developed for the detection of microorganisms in soil. Extraction efficiency has often been evaluated based on the recovery of a specific gene sequence from an organism inoculated into the soil. The aim of the present investigation was to improve the extraction, purification, and quantification of DNA derived from as large a portion of the soil microbial community as possible, with special emphasis placed on obtaining DNA from gram-positive bacteria, which form structures that are difficult to disrupt. Furthermore, we wanted to identify and minimize the biases related to each step in the procedure. Six soils, covering a range of pHs, clay contents, and organic matter contents, were studied. Lysis was carried out by soil grinding, sonication, thermal shocks, and chemical treatments. DNA was extracted from the indigenous microflora as well as from inoculated bacterial cells, spores, and hyphae, and the quality and quantity of the DNA were determined by gel electrophoresis and dot blot hybridization. Lysis efficiency was also estimated by microscopy and viable cell counts. Grinding increased the extracellular DNA yield compared with the yield obtained without any lysis treatment, but none of the subsequent treatments clearly increased the DNA yield. Phage λ DNA was inoculated into the soils to mimic the fate of extracellular DNA. No more than 6% of this DNA could be recovered from the different soils. The clay content strongly influenced the recovery of DNA. The adsorption of DNA to clay particles decreased when the soil was pretreated with RNA in order to saturate the adsorption sites. We also investigated different purification techniques and optimized the PCR methods in order to develop a protocol based on hybridization of the PCR products and quantification by phosphorimaging.

Quantification of bias related to the extraction of DNA directly from soils.

http://dspace.nitrkl.ac.in:8080/dspace/bitstream/2080/134/1/tksen5.pdf

Review on subsurface colloids and colloid-associated contaminant transport in saturated porous media.

The review discusses origin, state and function of extracellular DNA in soils and sediments Extracellular DNA can be released from prokaryotic and eukaryotic cells and can be protected against nuclease degradation by its adsorption on soil colloids and sand particles Laboratory experiments have shown that DNA adsorbed by colloids and sand particles can be taken up by prokaryotic competent cells and be involved in natural transformation Most of these experiments have been carried out under artificial conditions with pure DNA molecules and pure adsorbing matrices, but in soils and sediments, pure surface-reactive colloids are not present and DNA is present with other cellular components (wall debris, proteins, lipids, RNA, etc) especially if released after cell lysis The presence of inorganic compounds and organic molecules on both soil particles and DNA molecules can influence the DNA adsorption, degradation and transformation of competent cells Extracellular DNA can be used as C, N and P sources by heterotrophic microorganisms and plays a significant role in bacterial biofilm formation The nucleotides and nucleosides originated from the degradation of extracellular DNA can be re-assimilated by soil microorganisms Extracellular DNA in soil can be leached and moved by water through the soil profile by capillarity In this way, the extracellular DNA secreted by a cell can reach a competent bacterial cell far from the donor cell Finally, the characterisation of extracellular DNA can integrate information on the composition of the microbial community of soil and sediments obtained by analysing intracellular DNA

Extracellular DNA in soil and sediment: fate and ecological relevance.

Three different DNA fragments ranging size from 2.69 kbp (1.75 MDa) to 23 kbp (14.95 MDa) were used as tracers to study the adsorption of polydisperse solutions of calf thymus DNA to eight model soils. The adsorption of the three tracers to all soils was described by the Freundlich adsorption model, with adsorption coefficients (K) ranging from 1.1 for acid-washed sand to over 300 for one soil. An inverse relationship between tracer size and K was observed with six of the eight soils, indicating that smaller fragments are sorbed preferentially versus larger fragments in these soils. No significant correlation between K and the organic carbon contents, clay contents, pHs, or cation exchange capacities of the model soils was observed.

Effects of DNA polymer length on its adsorption to soils

Caustic nuclear wastes have leaked from tanks at the US Department of Energy’s Hanford site in Washington State (USA) causing hundreds of thousands of gallons of waste fluids to migrate into the underlying sediments. In this study, four simulant tank waste (STW) solutions, which are high in NaOH (1.4 and 2.8 mol/kg), NaNO3 (3.7 mol/kg) and NaAlO2 (0.125 and 0.25 mol/kg), were prepared and reacted with reference kaolinite KGa-1 and KGa-2 at 50 and 80°C for up to 2 months. The structure and morphology of the resulting products were characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. The products were also examined for cation exchange and Cs+ sorption as a function of ionic strength and types of cations in the background solutions. Cancrinite and sodalite were the only new minerals observed in all of the conditions tested in this experiment. Two major chemical processes were involved in the reactions: dissolution of kaolinite and precipitation of cancrinite and sodalite. Increasing NaOH concentration and temperature, and decreasing NaAlO2 concentration increased the transformation rate. Both cancrinite and sodalite appeared stable thermodynamically under the experimental conditions. The newly formed feldspathoids were vulnerable to acid attack and pronounced dissolution occurred at pH below 5.5. Cancrinite and sodalite can incorporate NaNO3 ion pairs in their cages or channels. Sodium in cancrinite and sodalite was readily exchangeable by K+, but less easily by Cs+ or Ca2+. The feldspathoid products sorb nearly an order of magnitude more Cs+ than the unaltered kaolinite. The Cs adsorption is reduced by competing cations in the background solutions. At low ionic strength (0.01 M NaNO3 or 0.005 M Ca(NO3)2), Ca2+ was more competitive than Na+. When the concentration of the background solution was increased 10 times, Na+ was more competitive than Ca2+.

Alteration of kaolinite to cancrinite and sodalite by simulated hanford tank waste and its impact on cesium retention

Mineral formation during simulated leaks of Hanford waste tanks

Noncrystalline aluminosilicates termed allophane and imogolite are common constituents of spodosols, soils derived from volcanic ash, and many inceptisols. The surface charge characteristics of their synthetic analogues may be used to better understand their ion retention properties. In this study, we determined the point of zero salt effect (PZSE) by potentiometric titration of allophanes with A1/Si ratios of 1.12, 1.52, and 2.04 and of imogolite with an A1/Si ratio of 2.02. We also used microelectro- phoresis to determine the point of zero charge (PZC) at the particle shear plane for the same materials in C1 solutions of Li, Na, Cs, and tetramethyl ammonium. The PZSE decreased with decreasing A1/Si ratio for the allophanes, but the imogolite PZSE was much lower than that of the allophane with 2.04 A1/Si. The PZC was always higher than the PZSE of the same material, especially for imogolite. The results are best explained if cations reside within the hollow tubes ofimogolite. This conclusion is supported by a fluorescence study that showed that only quenchers smaller than the inner diameter of the imogolite tube could fully quench Ce-imogolite.

Adsorption of cations on imogolite and their effect on surface charge characteristics

Biogeochemical processes in the rhizosphere can significantly alter interactions between contaminants and soil minerals. In this study, several strains of bacteria that exude aluminum (Al)-chelating compounds were isolated from the rhizosphere of crested wheatgrass (Agropyron desertorum) collected from the Idaho National Laboratory (INL). We examined the effects of exudates from bacteria in the genera Bacillus, Ralstonia, and Enterobacter on cesium (Cs) desorption from illite. Exudates from these strains of bacteria significantly enhanced Cs desorption from illite. In addition, Cs desorption increased with increasing Bacillus exudate concentrations. Cesium desorption from illite as a function of both exudate type and concentration was positively correlated with Al dissolution, suggesting that the Al-complexing ability of the exudates played an important role in enhancing Cs desorption. The density of frayed edge sites (FES) on illite increased as a result of treatment with bacterial exudates, while the Cs/K selectivity of FES decreased. These results suggestthat exudates from bacteria isolated from the rhizosphere can enhance Cs desorption from frayed edges of illite and, therefore, can alter Cs availability in micaceous soils.

Jeffrey S. Boyle

Papers

Effects of DNA polymer length on its adsorption to soils

Alteration of kaolinite to cancrinite and sodalite by simulated hanford tank waste and its impact on cesium retention

Mineral formation during simulated leaks of Hanford waste tanks

Adsorption of cations on imogolite and their effect on surface charge characteristics

Cesium desorption from illite as affected by exudates from rhizosphere bacteria.