The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm

A quantitative endonuclease assay, which relies on the introduction of single and double strand breaks into supercoiled plasmid DNA, was used to study the activity of the extracellular nuclease of Serratia marcescens SM6 in buffer and in groundwater. The parallel enzyme concentration-dependent production of relaxed and linear plasmid molecules suggests that the nuclease produces single and double strand breaks in duplex DNA. Bovine serum albumin stimulated the nuclease activity towards DNA and RNA and increased the stability of the enzyme against thermal inactivation. The DNase activity at 4 °C and 50 °C was almost half of that at the optimum temperature (37 °C). The nuclease was active in groundwater, although the specific activity was lower than in buffer. In a groundwater aquifer microcosm, mineral-adsorbed transforming DNA was substantially less accessible to the nuclease than was dissolved DNA. The data suggest that the extracellular nuclease of Serratia marcescens may contribute to DNA turnover in the environment and that adsorption of DNA to minerals provides protection against the nuclease.Abbreviations GW groundwater GWA groundwater aquifer     

Biomass structure and dry matter dynamics of subtropical alluvial and exotic Ligustrum forests at the Río de la Plata,Argentina

Biomass, litterfall, litter standing crop, and decomposition was studied in a native subtropical alluvial forest locally known as Selva Marginal (SM) and an exotic Ligustrum lucidum forest (LF) at the Reserva Integral de Punta Lara, Buenos Aires Province, 34°47S and 58°1W. The alluvial forest site was at the southern limit of distribution of subtropical forests in South America. The Ligustrum forest was invading disturbed areas. Total biomass was 147.7 Mg/ha (86% aboveground and 14% belowground) in the SM, and 71.4 Mg/ha (93% and 7%, respectively) in the LF. Litterfall was 10.3 Mg/ha·yr and 13.8 Mg/ha·yr respectively. Annual leaf decomposition rate was greater for Ligustrum (k=4.07) than for SM species (k=1.48). The mean residence time of aboveground biomass was 12 yr for the SM and 5 yr for the LF. The k₁ values (litterfall/standing crop) were 1.9 and 2.0 for SM and LF respectively. The influence of coastal road and wall in the hydroperiod, native forested wetland ecosystem survival and exotic forest invasion is discussed.     

Are the characeae able to indicate the origin of groundwater in former river channels?

The macroscopic algae Characeae are usually assumed to occur in waterbodies supplied by groundwater with low phosphate content, but the indicative value of the species is seldom defined in bibliography. Former braided channels of the Rhône river are supplied with groundwater originating from the main channel (seepage) or from hillslope aquifer. The aim of the present paper was to determine if it possible to use the Characeae as indicators of physicochemical characteristies of water in order to assess the origin of groundwater supplying former river channels. Four former braided channels of the Rhône River colonized by Characeae were investigated, and the physico-chemical characteristics of i) the channels, ii) the groundwater and iii) the river were measured over a period of several months. Species are arranged along a gradient of conductivity, alkalinity, ammonium and phosphate content of the water. Charophyte species can indicate the origin of groundwater, either seepage or hillslope nutrient-poor aquifer, and integrate both the average value of the chemical parameter, and their variations. C. hispida occurs in a nutrient-poor channel mainly supplied by highly calcareous groundwater coming from hillslope aquifer. Chara major has requirements close to those of C. hispida, but is more tolerant to periodic inputs of nutrients. C. vulgaris and N. syncarpa both tolerate mesotrophic waters originating from both hillslope aquifer and seepage, and C. globularis is associated to a channel mainly supplied by mesotrophic to eutrophic river seepage.     

Understanding of Aquifer Microbiology is Tightly Linked to Sampling Approaches

Primary samples of groundwater or core are collected and analyzed to characterize the microbiology of aquifers and to predict biogeochemical transformations. Alternative sampling devices have been developed that are incubated for some length of time in the aquifer to accrue biomass for analysis. Considering data generated from different types of aquifer samples, it appears that the type of sample collected and analyzed may strongly influence the resulting view of aquifer microbiology. Borehole artifacts need to be rigorously considered when incubated substrata are used. The indigenous attached populations in deeper, fractured rock aquifers remain understudied and await new sampling approaches.     

Inhibition of Real-Time PCR in DNA Extracts from Aquifer Sediment

Variation in inhibition of real-time PCR was investigated with DNA extracts from 50 aquifer sediment core samples of 5 cm length collected through a 2.5 meter vertical profile across a landfill leachate plume. The inhibition was quantified using an internal control of the green fluorescent protein ( gfp ) gene, which was spiked into the real-time PCR reactions. The inhibition was investigated at two gfp gene concentrations: at 1.7 · 10 ⁷ gfp gene copies/g sediment (5.1 · 10 ⁴ gfp gene copies/PCR reaction) and at 1.7 · 10 ⁵ gfp gene copies/g sediment (5.1 · 10 ² gfp gene copies/PCR reaction). Despite the low TOC content of the sediment (average 0.4 mg C/g dw) the average real-time PCR response was partially inhibited, compared to a reference (pure water), at both high and low gfp concentrations. The relative amplification (reference = 1) was 0.85 ± 0.20 (high) and 0.66 ± 0.23 (low), showing significantly (P < 0.05) stronger inhibition at the lower target gene concentration. The inhibition of the real-time PCR did not show a systematic variation in the vertical profile related to plume position but variations were significant on a small scale of 5–15 cm depth intervals. One of the 50 samples failed to produce a signal with either concentration of the gfp internal control and three other samples inhibited real-time PCR at both high and low gfp concentration. These 4 samples, which were the samples with the highest inhibition, were the only DNA extracts with a visible brown colouration, indicating contents of humic-like substances. Elevated absorbance at 400 nm of these samples also indicated that humic-like substances were responsible for inhibition. However, other factors not associated with either absorbance or TOC may have contributed to the inhibition in less inhibited samples since the variation in real-time PCR response could not be sufficiently explained by absorbance or TOC. The results of this study suggest that an internal control is needed in real-time PCR reactions with DNA from environmental samples due to variation in inhibition to correctly quantify the number of target genes, especially at low target gene concentrations, when dilution of DNA extracts is not practical.     

Influence of Arsenate on Lipid Peroxidation Levels and Antioxidant Enzyme Activities in Bacillus cereus Strain XZM002 Isolated from High Arsenic Aquifer Sediments

Bacillus cereus strain XZM002 isolated from high arsenic aquifer sediments of Datong Basin was applied to examine the effects of arsenate stress on antioxidant enzyme activities, lipid peroxidation levels and cell growth inhibition rate. After 2 d exposure, the cell growth inhibition rate enhanced with an increase of As(V) concentrations (0, 800, 1600 μg/l). Reactive oxygen species and glutathione contents, lipid peroxidation levels, and antioxidant enzymes (glutathione peroxidase, and other three) activities of the treated cells were significantly higher than those of the controls during 3 d exposure (p < 0.05). Besides, the levels of nine parameters reached maximum after 2 d exposure and increased significantly with increasing arsenate stress (p < 0.05). However, they returned to levels similar to those of the control on the fourth day of exposure. The results suggested that the antioxidant defense system in B. cereus strain XZM002 could protect the cells from oxidative damage induced by arsenate.     

Chemical speciation and competitive cationic partitioning on a sandy aquifer material

Abstract

Coupled geochemical speciation/transport models are being developed to assess potential transport of metal contaminants in the subsurface environment. In a test of the geochemical speciation portion of the effort, MINTEQA2 model predictions are compared with laboratory data concerning the pH dependent partitioning behavior of eight cationic contaminants (Ba, Be, Cd, Cu, Ni, Pb, Tl and Zn) on a sandy aquifer material in an oxidized environment. MINTEQA2 contains provisions for describing potential attenuation due to both mineral phase precipitation processes and adsorption processes resulting from amorphous iron oxides in aquifer materials (MIT Diffuse Layer Model). In the comparison, several trends were discerned. (1) Adsorptive processes tend to better describe the pH-dependent partitioning behavior of transition metals (especially Pb, Zn and Ni). (2) Cd behavior is better described by precipitation as a cadmium carbonate phase. (3) Cu behavior is not reasonably described by the model. (4) Ba and Be comparisons are poor (although presumably their partitioning behavior results from adsorptive and/or pH sensitive solid solution processes). (5) unlike the other elements, the behavior of Tl is relatively insensitive to pH.     

Fluvial response to late Quaternary climate change in NE Queensland, Australia

Samples of alluvial and colluvial deposits from the coastal plain and coastal valleys north and south of Cairns (17°S) have been dated using optically stimulated luminescence (OSL) protocols, with additional thermoluminescence (TL) and Radiocarbon assays. Coarse fanglomerates from elevated coastal terraces date back to 81 ka, but most are clustered in oxygen isotope stage three (OIS3, 64-28 ka), indicating high-energy conditions during this period. Extensive fans and terraces of finer calibre sediments are widely represented grading from coarse gravels and cobbles in proximal zones fine sand and silt in distal areas. Dates show that vertical accumulation of 10-15 m of sediment occurred between ∼ 28 and 14 ka (OIS2), after which the fans were dissected and Holocene deposits become fragmentary. A number of deposits indicating hillslope instability were successfully dated and these fall mainly into OIS3 and post 12 ka. These results are interpreted as catchment responses to Late Pleistocene climate and vegetation changes, documented elsewhere from local pollen and ocean drilling sites. Correlation with these records and with evidence for regional climate change from the Austral-Asian region is good and indicates that these changes were sufficient to transform fluvial activity and slope processes.