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PubMed1999

Influence of microbes on the mobilization, toxicity and biomethylation of arsenic in soil.

To understand the effects of microbial activity on the mobilization and speciation of arsenic in soil, the cycling of arsenic was studied in microcosm experiments under laboratory conditions. Particular attention was paid to the biomethylation of arsenic and to the toxicity of inorganic and organic arsenic species for microbes. Microbes enhanced mobilization of arsenic from soil by 19-24% compared to formaldehyde inhibited controls. Formation of dissolved methylated arsenic species by microbes was low (< 0.1%) during the 5-day incubation. Even though methylation may function as a detoxification method, it was of minor importance in the soil tested.

Arsenic↗
PubMed2005

Experimental methods for assaying natural transformation and inferring horizontal gene transfer.

The observation of frequent lateral acquisitions of genes in sequenced bacterial genomes has spurred experimental investigations to elucidate the factors governing ongoing gene transfer processes in bacteria. The uptake of naked DNA by natural transformation is known to occur in a wide range of bacterial species and in some archaea. We describe a series of protocols designed to dissect the natural genetic transformability of individual bacterial strains under conditions that progress from standard in vitro conditions to purely in situ, or natural, conditions. One of the most important factors in ensuring the success of any transformation assay system is the use of a sensitive, effective, and distinguishable selection regimen. Detailed template protocols for assaying bacterial transformation in vitro are presented using the naturally competent bacterium Acinetobacter baylyi strain BD413 as a model. Factors increasing the complexity of the assay systems are included in the following section describing the incorporation of components of natural systems to the in vitro models, such as in soil and water microcosm experiments. We then present template protocols for the transformation of bacteria in modified natural systems, such as in the presence of host tissues and extracts or in the greenhouse. Clear and ecologically meaningful demonstrations of in situ natural transformation are most desirable but are also the most complex and challenging. Because of the highly variable nature of these experiments, we include a discussion of important factors that should be considered when designing such experiments. Some advantages and disadvantages of the experimental systems with regard to resolving the hypotheses tested are included in each section.

Acinetobacter↗
PubMed2003

Short-term environmental impact of clam dredging in coastal waters (south of Portugal): chemical disturbance and subsequent recovery of seabed.

The physical and chemical changes in sediment and near bottom water caused by clam dredging were examined during July and September 1999, at two locations Vilamoura (VL) and Armona (AR), south coast of Portugal. Sediment cores and near bottom water were collected simultaneously before dredging (control samples) and within short time intervals (min-h) after dredging. After dredging operations, microphytobenthos coming from the path were accumulated in the re-worked sediment (ridge). Chlorophyll a in superficial sediment increased from 1.2 microg x g(-1) before dredging to 1.7 microg x g(-1) after dredging and these higher values remained for a few hours. However, the expected increase of chlorophyll a in near bottom water due to re-suspension was not observed. After sediment disturbance an instantaneous sorption of phosphorus onto iron oxides occurred in the upper sediment layers (from 2 to 3 micromol x g(-1) before dredging to 4-5 micromol x g(-1) after dredging). A microcosm experiment showed that after sediment disturbance HPO(4)(2-) dissolved in pore water decreased from 40 to 10 microM being simultaneously sorbed onto iron oxides formed in the top layer of sediment. The ammonium, nitrates, organic nitrogen, phosphate and silicate dissolved in pore water decreased immediately after dredging activity and simultaneously an increase in near bottom water was sporadically observed. Generally, the re-establishment of seabed was reached within a short time (min-h), at both stations (VL and AR).

Animals↗
PubMed2000

Does historical exposure to hydrocarbon contamination alter the response of benthic communities to diesel contamination?

A microcosm experiment was used to compare the influence of diesel contamination on two benthic salt-marsh communities, one chronically exposed to petroleum hydrocarbons for decades (Louisiana [LA]) and the other relatively uncontaminated (Mississippi [MS]). Initial meiofaunal community composition of the two sites was similar. Higher organic content of MS sediments should have reduced bioavailability, and thus the toxicity of hydrocarbons relative to the LA site. Nevertheless, although responses to diesel contamination at the two sites were generally qualitatively similar, a species-specific and several community-response variables were influenced to a much greater degree in the MS community. In particular, the abundance of total nauplii, ostracods, and copepods were negatively impacted to a greater extent in MS than in LA, as was grazing by ostracods on benthic microalgae. Nematode:copepod ratios in contaminated sediments were much higher in MS than in LA sediments. Pseudostenhelia wellsi (a benthic copepod) nauplii suffered greater adverse effects of diesel in MS than in LA. We conclude that the MS community was more sensitive to diesel contamination than was the LA community. The differential sensitivity is presumably a manifestation of different tolerances to hydrocarbon contaminants, mediated by a higher proportion of more tolerant species and/or increased tolerance among individual species in LA. Although the MS site was more sensitive to diesel contamination, qualitative response of the LA and MS communities were similar, and comparable to previous studies of diesel contamination. The spatial and temporal consistency of diesel impacts on salt-marsh communities suggests that hydrocarbon contamination results in predictable community responses. Specifically, crustacean (e.g. copepods, ostracods, and nauplii) benthos are most sensitive to hydrocarbons. Reductions in abundance and grazing activity of crustaceans leads to enhanced algal biomass, reduced copepod diversity, and alters competitive interactions among meiofauna.

Animals↗
PubMed2003

Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences.

The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tm and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers.

Base Sequence↗
PubMed1997

Experimental effects of tributyltin (TBT) contaminated sediment on a range of meiobenthic communities.

Microcosm experiments have been carried out with whole natural meiobenthic communities to look at the effects of TBT sediment contamination on the community structure of the dominant nematode component of the meiobenthos. TBT has a high affinity for aquatic sediments, yet this is the first study of the effects of this contaminant in sediment on natural benthic communities. Three communities were studied from contrasting locations in south-west England: the intertidal of the Lynher estuary (muddy sediment) and the Exe estuary (sandy sediment) and the subtidal (50m depth) at Rame Head off Plymouth (muddy sand). Fresh sediment with natural meiobenthic communities was incubated for 2 months with TBT-contaminated sediment (three dose levels) in bottles. Nematodes were identified and enumerated and subjected to multivariate data analysis. The sandy Exe estuary fauna was significantly affected by TBT-contaminated sediment at all three doses (0.3, 0.6 and 0.9 microg g(-1) dry wt (as Sn) sediment), whereas the offshore fauna from Rame Head was significantly affected only at the highest dose. The muddy Lynher estuary meiofauna was affected (somewhat peculiarly) at the medium dose level only. Meiobenthic nematodes may not be as sensitive to TBT-contaminated sediment as other infaunal benthos but exhibited responses to levels of contamination still persisting in some UK estuaries and harbours. Comparing the effects of TBT with those of copper and zinc in the same laboratory experiments, our observations suggest that the relative impact of TBT on meiobenthic community structure is not as great as these contaminants in marine sediments. Although there are very few observations of TBT toxicity in sediment, it appears that TBT is toxic at much lower concentrations in seawater (ppb) than it is in sediment (ppm).

Journal Article↗
PubMed1997

Decomposer communities in contaminated soil: Is altered community regulation a proper tool in ecological risk assessment of toxicants?

Effects of patchy soil contamination on decomposer organisms, their community regulation and nutrient mineralization were studied in a microcosm experiment. Coniferous forest soil was patchily contaminated with three concentrations of sodiumpentachlorophenate PCP (0, 50 and 500 mg PCP kg(-1) of dry soil). Abundance of microbes, enchytraeids, nematodes, small oribatids and predatory mites were reduced by the PCP. Direct toxicity of PCP and lowered microbial biomass seemed to affect animal community composition in the most contaminated patches. Some large oribatids which seemed to be tolerant to PCP increased their numbers in the most contaminated patches. Although predatory mites suffered from PCP, no altered predator-prey interactions were observed. At the beginning of the experiment more nutrients were released in the patches with highest PCP concentration and the nutrients accumulated in the soil. Soil decomposer food webs seemed to be mainly bottom-up controlled: PCP strongly affects microbes and hence caused changes in the community structure of soil animals and nutrient cycling. Hence top-down orientated ecological models on community regulation and food web dynamics seem to be unsuitable when assessing effects of pesticides on soil communities.

Journal Article↗
PubMed2003

Biotransformation and accumulation of arsenic in soil amended with seaweed.

For many coastal regions of the world, it has been common practice to apply seaweed to the land as a soil improver and fertilizer. Seaweed is rich in arsenosugars and has a tissue concentration of arsenic up to 100 micro/g g(-1). These arsenic species are relatively nontoxic to humans; however, in the environment they may accumulate in the soil and decompose to more toxic arsenic species. The aim of this study was to determine the fate and biotransformation of these arsenosugars in soil using HPLC-ICP-MS analysis. Data from coastal soils currently manured with seaweeds were used to investigate if arsenic was accumulating in these soils. Long-term application of seaweed increased arsenic concentrations in these soils up to 10-fold (0.35 mg of As kg(-1) for nonagronomic peat, 4.3 mg of As kg(-1) for seaweed-amended peat). The biotransformation of arsenic was studied in microcosm experiments in which a sandy (machair) soil, traditionally manured with seaweed, was amended with Laminaria digitata and Fucus vesiculosus. In both seaweed species, the arsenic occurs in the form of arsenosugars (85%). The application of 50 g of seaweed to 1 kg of soil leads to an increase of arsenic in the soils, and the dominating species found in the soil pore water were dimethylarsinic acid (DMA(V)) and the inorganic species arsenate (As(V)) and arsenite (As(III)) after the initial appearance of arsenosugars. A proposed decomposition pathway of arsenosugars is discussed in which the arsenosugars are transformed to DMA(V) and further to inorganic arsenic without appreciable amounts of methylarsonic acid (MA(V)). Commercially available seaweed-based fertilizers contain arsenic concentration between 10 and 50 mg kg(-1). The arsenic species in these fertilizers depends on the manufacturing procedure. Some contain mainly arsenosugars while others contain mainly DMA(V) and inorganic arsenic. With the application rates suggested by the manufacturers, the application of these fertilizers is 2 orders of magnitude lower than the maximum permissible sewage sludge load for arsenic (varies from 0.025 kg ha(-1) yr(-1) in Styria, Austria, to 0.7 kg ha(-1) yr(-1) in the U.K.), while a direct seaweed application would exceed the maximum arsenic load by at least a factor of 2.

Arsenates↗
PubMed2003

Chlorine isotope fractionation during microbial reduction of perchlorate.

Perchlorate contamination of surface water and groundwater is an emerging public health problem that has adversely affected the drinking water supplies of millions of people in the western United States. Microbial reduction has shown promise as a cost-effective means for in situ bioremediation of perchlorate-contaminated water. Measurements of stable isotope ratios of light elements (H, C, N, O, S, Cl) can often be used to distinguish biodegradation of organic and inorganic molecules from abiotic loss mechanisms such as adsorption, dispersion, or volatilization because of the relatively large kinetic isotope effects accompanying biodegradation. We quantified chlorine isotope fractionation during perchlorate biodegradation by a common perchlorate-reducing bacterium, Dechlorosoma suillum, initially isolated from a perchlorate-contaminated groundwater source in southern California. The values of the chlorine isotopic fractionation factor alpha derived from two microcosm experiments were alpha = 0.9834 +/- 0.0001 (R2 = 0.9999) and alpha = 0.9871 +/- 0.0008 (R2 = 0.9832). These alpha values indicate that the rate of the 35ClO4 reduction is approximately 1.3-1.7% faster than that of the 37ClO4 reduction. This relatively large kinetic isotope effect indicates that chlorine isotope analysis provides a sensitive technique by which to document in situ bioremediation of perchlorate in groundwater.

Chlorine↗
PubMed2004

Hydrogen sulfide oxidation by a microbial consortium in a recirculation reactor system: sulfur formation under oxygen limitation and removal of phenols.

Wastewater from petroleum refining may contain a number of undesirable contaminants including sulfides, phenolic compounds, and ammonia. The concentrations of these compounds must be reduced to acceptable levels before discharge. Sulfur formation and the effect of selected phenolic compounds on the sulfide oxidation were studied in autotrophic aerobic cultures. A recirculation reactor system was implemented to improve the elemental sulfur recovery. The relation between oxygen and sulfide was determined calculating the O2/S2- loading rates (Q(O2)/Q(S)2- = Rmt), which adequately defined the operation conditions to control the sulfide oxidation. Sulfur-producing steady states were achieved at Rmt ranging from 0.5 to 1.5. The maximum sulfur formation occurred at Rmt of 0.5 where 85% of the total sulfur added to the reactor as sulfide was transformed to elemental sulfur and 90% of it was recovered from the bottom of the reactor. Sulfide was completely oxidized to sulfate (Rmt of 2) in a stirred tank reactor, even when a mixture of phenolic compounds was present in the medium. Microcosm experiments showed that carbon dioxide production increased in the presence of the phenols, suggesting that these compounds were oxidized and that they may have been used as carbon and energy source by heterotrophic microorganisms present in the consortium.

Air Pollutants↗
PubMed2005

Quantification of sequential chlorinated ethene degradation by use of a reactive transport model incorporating isotope fractionation.

Compound-specific isotope analysis (CSIA) enables quantification of biodegradation by use of the Rayleigh equation. The Rayleigh equation fails, however, to describe the sequential degradation of chlorinated aliphatic hydrocarbons (CAHs) involving various intermediates that are controlled by simultaneous degradation and production. This paper shows how isotope fractionation during sequential degradation can be simulated in a 1D reactive transport code (PHREEQC-2). 12C and 13C isotopes of each CAH were simulated as separate species, and the ratio of the rate constants of the heavy to light isotope equaled the kinetic isotope fractionation factor for each degradation step. The developed multistep isotope fractionation reactive transport model (IF-RTM) adequately simulated reductive dechlorination of tetrachloroethene (PCE) to ethene in a microcosm experiment. Transport scenarios were performed to evaluate the effect of sorption and of different degradation rate constant ratios among CAH species on the downgradient isotope evolution. The power of the model to quantify degradation is illustrated for situations where mixed sources degrade and for situations where daughter products are removed by oxidative processes. Finally, the model was used to interpret the occurrence of reductive dechlorination at a field site. The developed methodology can easily be incorporated in 3D solute transport models to enable quantification of sequential CAH degradation in the field by CSIA.

Biodegradation, Environmental↗
PubMed2004

Influence of total organic carbon and UV-B radiation on zinc toxicity and bioaccumulation in aquatic communities.

The effects of total organic carbon (TOC) and UV-B radiation on Zn toxicity and bioaccumulation in a Rocky Mountain stream community were assessed in a 10-d microcosm experiment. We predicted that TOC would mitigate Zn toxicity and that the combined effects of Zn and UV-B would be greater than Zn alone. However, TOC did not mitigate Zn toxicity in this study. In fact, treatments with TOC plus Zn had significantly lower community respiration as compared with the controls and Zn concentrations associated with the periphyton increased in the presence of TOC. UV-B had no additive effect on periphyton Zn accumulation or community respiration. Heptageniid mayflies (Ephemeroptera) were particularly sensitive to Zn, and reduced abundances were observed in all Zn treatments. UV-B did not additionally impact Heptageniid abundances; however UV-B did have a greater effect on macroinvertebrate drift than Zn alone. Ephemeroptera, Plecoptera, and Trichoptera (groups typically classified as sensitive to disturbance) were found in highest numbers in the drift of UV-B + Zn treatments. Measures of Zn accumulation in the caddisfly Arctopsyche grandis, periphyton biomass, and total macroinvertebrate abundance were not sufficiently sensitive to differentiate effects of TOC, UV-B, and Zn. These results indicate that UV-B and TOC affect Zn bioavailability and toxicity by impacting species abundance, behavior, and ecosystem processes.

Animals↗
PubMed2005

Thiol and metal contents in periphyton exposed to elevated copper and zinc concentrations: a field and microcosm study.

Phytochelatins are metal-binding polypeptides produced by algae under metal exposure. The aim of this study was to investigate the effects of metal concentration variations in natural systems on periphyton at the biochemical level by analyzing its intracellular thiol content, in particular phytochelatins. To that purpose, two field campaigns were conducted in a stream subject to an increase of dissolved metal concentrations (particularly Cu and Zn) during rain events, which results in an increase of their accumulation in periphyton. At background metal concentrations, several thiols were detectable in periphyton, namely, glutathione (GSH), gamma-glutamylcysteine (gammaGluCys), phytochelatins (PC2), and some unidentified thiols, U1 and U2. Glutathione and gammaGluCys contents were found to vary independently of the rain, as well as U1 and U2, whereas the phytochelatin content increased during the rain events. To investigate whether Cu or Zn may be responsible for this increase, microcosm experiments were carried out with natural water enriched with Cu, Zn, and Cd separately, and Cu and Zn in combination. In this study, GSH, PC2, and U1 were also detected, but not gammaGluCys. An increase in accumulated Cu content did not induce any changes in thiol content, whereas an increase of the Zn content induced a decrease in GSH content and an increase in phytochelatin content. Zinc rather than Cu may thus induce a phytochelatin content increase in periphyton in the field studies. Addition of Cu and Zn in combination also induced an increase in phytochelatin content. Cadmium was found to be the most effective inducer, with the production of larger phytochelatins (PC3-4). This study is the first one to report changes in thiol content in periphyton in response to an increase of the metal concentration in natural freshwaters.

Analysis of Variance↗
PubMed2005

Modeling the dynamics of fermentation and respiratory processes in a groundwater plume of phenolic contaminants interpreted from laboratory- to field-scale.

A biodegradation model with consecutive fermentation and respiration processes, developed from microcosm experiments and simulated mathematically with microbial growth kinetics, has been implemented into a field-scale reactive transport model of a groundwater plume of phenolic contaminants. Simulation of the anaerobic plume core with H2 and acetate as intermediate products of biodegradation allows the rates and parameter values forfermentation processes and individual respiratory terminal electron accepting processes (TEAPS) to be estimated using detailed, spatially discrete, hydrochemical field data. The modeling of field-scale plume development includes consideration of microbial acclimatization, substrate toxicity toward degradation, bioavailability of mineral oxides, and adsorption of biogenic Fe(ll) species in the aquifer, identified from complementary laboratory process studies. The results suggest that plume core processes, particularly fermentation and Fe(lll)-reduction, are more important for degradation than previously thought, possibly with a greater impact than plume fringe processes (aerobic respiration, denitrification, and SO4-reduction). The accumulation of acetate as a fermentation product within the plume contributes significantly to the mass balance for carbon. These results demonstrate the value of quantifying fermentation products within organic contaminant plumes and strongly suggest that the conceptual model selected for reactive processes plays a dominant role in the quantitative assessment of risk reduction by naturally occurring biodegradation processes.

Acetates↗
PubMed2006

Effect of organic co-contaminants on technetium and rhenium speciation and solubility under reducing conditions.

The chemical and biogeochemical reduction of pertechnetate (TcO4-) and perrhenate (ReO4-) have been compared alongside complexation of the reduced species by three anthropogenic ligands relevant to nuclear waste (ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), and isosaccharinic acid (ISA)). An HPLC size-exclusion column coupled to ICP-MS was used to separate the species and quantify Tc and Re. During method development, ReO4- showed recalcitrance to direct chemical reduction by Sn(ll) under conditions that readily reduced TcO4- and resulted in Tc(IV)-organic complexes. In microcosm experiments of a silty loam soil containing Tc04-, ReO4-, and ISA (3.0 mM), EDTA (0.17 mM), or NTA (2.4 mM), anoxia developed to iron-reducing conditions during the 42 day experimental period. The majority of the TcO4- was reduced to particle-reactive Tc(IV) and removed from solution during nitrate reduction, but there was no chromatographic evidence of Tc(IV)-organic complexes in the porewater. Overall, the excess organic complexants added did not cause a measurable difference in the solubility of Tc(IV) over the control experiments in this organic-rich (12% organic carbon) soil. ReO4- did not undergo reduction, as shown by the constant porewater concentration and the chromatographic data, and thus Re does notfunction as an analogue forTc under environmental nitrate- and iron-reducing conditions.

Chromatography, Gel↗
PubMed2003

Chemical contaminants and their effects in fish and wildlife from the industrial zone of Sumgayit, Republic of Azerbaijan.

Sediment from a wetland adjacent to an industrial wastewater treatment plant in Sumgayit contained concentrations of total PAHs, total PCBs, aldrin, biphenyl, chlordane, DDT, mercury, beta-endosulfan, heptachlor, alpha-hexacyclohexane (alpha-HCH), gamma-HCH, and several individual PAH congeners that were elevated relative to published sediment quality guidelines. Chemical analyses of tissues from European pond turtles (Emys orbicularis) had increased levels of many of the same chemicals including aldrin, chlordane, heptachlor, alpha-HCH, total PCBs, total PAHs, and mercury, compared to reference turtles. In addition, turtle tissues contained elevated levels of DDD, hexachlorobenzene (HCB), and pentachlorobenzene that were not elevated in the sediment sample. Some differences were observed in contaminant levels between European pond turtles and Caspian turtles (Mauremys caspica) taken from the ponds in Sumgayit. Salmonella/microsome mutagenicity assays on pond sediments were negative or weakly positive. Micronuclei in European pond turtles were statistically correlated with tissue levels of mercury, heptachlor, DDD, HCB, and trans-nonachlor. Microcosm experiments using Russian sturgeon (Acipenser gueldenstaedtii) showed a positive dose-response relationship between exposure to suspended contaminated pond sediment and acute toxicity. Chemical and biological assays used in this study show the industrial area of Sumgayit is heavily contaminated with a complex mixture of toxic pollutants. Exposure to contaminated sediments produced acute effects in Russian sturgeon, but genotoxic effects appear to be slight.

Animals↗
PubMed1998

Making mistakes when predicting shifts in species range in response to global warming.

Many attempts to predict the biotic responses to climate change rely on the 'climate envelope' approach, in which the current distribution of a species is mapped in climate-space and then, if the position of that climate-space changes, the distribution of the species is predicted to shift accordingly. The flaw in this approach is that distributions of species also reflect the influence of interactions with other species, so predictions based on climate envelopes may be very misleading if the interactions between species are altered by climate change. An additional problem is that current distributions may be the result of sources and sinks, in which species appear to thrive in places where they really persist only because individuals disperse into them from elsewhere. Here we use microcosm experiments on simple but realistic assemblages to show how misleading the climate envelope approach can be. We show that dispersal and interactions, which are important elements of population dynamics, must be included in predictions of biotic responses to climate change.

Animals↗
PubMed2002

Containment in industrial biotechnology within wastewater treatment plants.

Both physical and biological containment are considered to be essential parts in the risk analysis of industrial Good Industrial Large-Scale Practice (GILSP) processes using genetically modified organisms (GMOs). Biological containment of industrial microorganisms has become a more important issue since the introduction of recombinant DNA techniques. In the event of an accidental discharge in the production plant, a large amount of organisms could be released into the wastewater treatment (WWT) system. This WWT system should therefore be considered as a part of the containment. This study demonstrates both a hydrodynamic and a microbiological model for the containment aspects of industrial WWT plants. The models are verified by measurements using industrial hosts of GILSP GMOs at full scale. Both models describe the full-scale equipment accurately. The results are supplemented with microcosm studies on survival of GMOs in defined niches. It is shown that WWT plants can be considered as useful additional parts of the containment of microorganisms, in case of an accidental discharge. The effect of drainage of an enormous amount of microorganisms (several tons) through the WWT plant into the environment is shown to be comparable to the direct drainage of a small-scale fermenter. Microcosm experiments correlate well with the survival rates in the WWT and therefore can be of use to predict the behaviour of GMOs in this environment.

Biotechnology↗