The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation.     

The exposition of a calcareous Mediterranean soil to toxic concentrations of Cr, Cd and Pb produces changes in the microbiota mainly related to differential metal bioavailability

The involvement of the bacterial community of an agricultural Mediterranean calcareous soil in relation to several heavy metals has been studied in microcosms under controlled laboratory conditions. Soil samples were artificially polluted with Cr(VI), Cd(II) and Pb(II) at concentrations ranging from 0.1 to 5000 mg kg⁻¹ and incubated along 28 d. The lowest concentrations with significant effects in soil respirometry were 10 mg kg⁻¹ Cr and 1000 mg kg⁻¹ Cd and Pb. However, only treatments showing more than 40% inhibition of respirometric activity led to significant changes in bacterial composition, as indicated by PCR-DGGE analyses. Presumable Cr- and Cd-resistant bacteria were detected in polluted microcosms, but development of the microbiota was severely impaired at the highest amendments of both metals. Results also showed that bioavailability is an important factor determining the impact of the heavy metals assayed, and even an inverted potential toxicity ranking could be achieved if their soluble fraction is considered instead of the total concentration. Moreover, multiresistant bacteria were isolated from Cr-polluted soil microcosms, some of them showing the capacity to reduce Cr(VI) concentrations between 26% and 84% of the initial value. Potentially useful strains for bioremediation were related to Arthrobacter crystallopoietes, Stenotrophomonas maltophilia and several species of Bacillus.     

PCB accumulation and tissue distribution in cave salamander (Proteus anguinus anguinus, Amphibia, Urodela) in the polluted karstic hinterland of the Krupa River, Slovenia

For over two decades, a manufacturer of electrical capacitors disposed of its waste within the karstic hinterland of the Krupa River (Slovenia) resulting in the surroundings becomming heavily polluted with PCB. Albeit the extent of the contamination has been known since 1983 and the Krupa River has become one of the most PCB polluted river in Europe, the effects on the cave fauna of the region remain unknown. The most famous cave dweller of the Krupa hinterland is the endemic cave salamander Proteus anguinus anguinus. In this study we determine the levels of PCB in the tissues of the Proteus and in river sediments. The total concentration of PCB in individual tissue samples from specimens of the Krupa spring was between 165.59 μg g⁻¹ and 1560.20 μg g⁻¹ dry wt, which is at least 28-times higher than those from an unpolluted site. The kidneys contained the lowest concentration, while the highest concentration was in subcutaneous fat and tissues with high lipid contents like visceral fat and liver. Total PCB concentrations in sediment samples from the Krupa River were between 5.47 and 59.20 μg g⁻¹ dry wt showing that a high burden of PCB still remains in the region. The most abundant PCB congeners in all analyzed samples were di-ortho substituted (PCB #101, #118, #138 and #158), but higher proportion of mono-ortho PCB was present in sediments. The ability of Proteus to survive a high PCB loading in its environment and especially in its tissues is remarkable. Its partial elimination of low chlorinated and mono-ortho substituted congeners is also reported.     

Mercury in San Francisco Bay forage fish

In the San Francisco Estuary, management actions including tidal marsh restoration could change fish mercury (Hg) concentrations. From 2005 to 2007, small forage fish were collected and analyzed to identify spatial and interannual variation in biotic methylmercury (MeHg) exposure. The average whole body total Hg concentration was 0.052 μg g⁻¹ (wet-weight) for 457 composite samples representing 13 fish species. MeHg constituted 94% of total Hg. At a given length, Hg concentrations were higher in nearshore mudflat and wetland species (Clevelandia ios, Menidia audens, and Ilypnus gilberti), compared to species that move offshore (e.g., Atherinops affinis and Lepidogobius lepidus). Gut content analysis indicated similar diets between Atherinops affinis and Menidia audens, when sampled at the same locations. Hg concentrations were higher in sites closest to the Guadalupe River, which drains a watershed impacted by historic Hg mining. Results demonstrate that despite differences among years and fish species, nearshore forage fish exhibit consistent Hg spatial gradients.     

The presence of Bacillus thuringiensis (Bt) protein in earthworms Eisenia fetida has no deleterious effects on their growth and reproduction

Earthworms Eisenia fetida, bred in substances with stover of two genetically-engineered Bacillus thuringiensis (Bt) corns (5422Bt1 (Event Bt11) and 5422CBCL (MON810)) expressing Cry1Ab and their near-isogenic non-Bt corn (5422), were used to investigate the non-target effects of Bt corn on soil-dwelling organisms. Cry1Ab concentrations in substances, casts and guts of E. fetida were also investigated by Enzyme-linked immunosorbent assay (ELISA). More than 90% individuals of E. fetida survived over a period of 30 d, irrespective of whether they received Bt corn or non-Bt corn. Compared to 5422 treatments, significantly higher relative growth rate and more number of new offspring and cocoons of E. fetida were found in 5422Bt1 and 5422CBCL treatments. These results were unlikely to be directly caused by Cry1Ab released from Bt corns but rather by differences in other factors of plants such as plant components (soluble sugar, total organic carbon, total protein and available phosphorus of Bt corns were more than 5422). ELISA results indicated immunoreactive Cry1Ab was detectable in substances, and the casts, guts of E. fetida from Bt corns treatments, of which the highest levels were detected in substances under the corresponding experimental conditions. With the increase of treated time, a strong decline was observed in Cry1Ab from substances and casts of E. fetida, whereas Cry1Ab in guts of E. fetida from 5422Bt1 treatments gradually increased and that from 5422CBCL treatments increased between 14 and 30 d. Therefore, the presence of Cry1Ab in E. fetida had no deleterious effects on their growth and reproduction.     

Processing of antifouling paint particles by Mytilus edulis

Particles of spent antifouling paint collected from a marine boatyard were ground and subsequently administered to the filter-feeding bivalve, Mytilus edulis, maintained in static aquaria. Concentrations of Cu and Zn were measured in seawater throughout a 16 h feeding phase and a 24 h depuration phase, in rejected and egested particles collected during the respective phases, and in the organisms themselves at the end of the experiments. Concentrations and distributions of Cu and Zn in processed particles indicated that M. edulis was able to ingest paint particles, regardless of whether nutritionally viable silt was present, and no mechanism of particle discrimination was evident. Enrichment of Cu and Zn in the visceral mass of individuals and in the aqueous phase during depuration supported these assertions, although elevated concentrations in other compartments of the organism (e.g. shell, gill) suggested that biotic and abiotic uptake of aqueous metal was also important.     

Degrader density determines spatial variability of 2,6-dichlorobenzamide mineralisation in soil

The metabolite 2,6-dichlorobenzamide (BAM) is a frequent groundwater pollutant produced during degradation of the herbicide 2,6-dichlorobenzonitrile (dichlobenile). Spatial variability of BAM mineralisation is uncharacterized in surface soil, however, and factors controlling the heterogeneity remain unknown. We addressed these issues by sample-to-sample comparisons of BAM mineralisation rates and a range of soil characteristics at spatial scales ranging from meters to centimetres. For mineralisation assays nano-molar concentrations of labelled BAM were added to determine mineralisation rates under realistic conditions. We found a significant variability of BAM mineralisation which increased with decreasing spatial scale. BAM mineralisation rates were correlated to the density of BAM-degrading bacteria but not to water content, TOC, NH₄⁺, NO₃⁻, or pH. The genus Aminobacter, which contains the only BAM degraders known, was detected in MPN samples of BAM degraders by a specific PCR assay targeting the 16S rRNA gene, confirming a role of Aminobacter in BAM mineralisation.     

Long-term Hg pollution induced Hg tolerance in the terrestrial isopod Porcellio scaber (Isopoda, Crustacea)

The aim of our work was to assess the pollution-induced community tolerance (PICT) of isopod gut microbiota and pollution-induced isopod population tolerance (PIPT). Animals collected from a chronically Hg polluted and an unpolluted location were exposed for 14 days to 10microg Hg/g dry food under laboratory conditions. The lysosomal membrane stability, hepatopancreas epithelium thickness, feeding activity and animal bacterial gut microbiota composition were determined. The results confirm the hypothesis that the response to short-term Hg exposure differs for animals from the Hg polluted and the unpolluted field locations. The animals and their gut microbiota from the Hg polluted location were less affected by Hg in a short-term feeding experiment than those from the unpolluted environment. We discuss the pollution-induced population tolerance of isopods and their gut microbiota as a measure of effects of long-term environmental pollution. The ecological consequences of such phenomena are also discussed.     

Comparative bioremediation potential of four rhizospheric microbial species against lindane

Four microbial species (Kocuria rhizophila, Microbacterium resistens, Staphylococcus equorum and Staphylococcus cohnii subspecies urealyticus) were isolated from the rhizospheric zone of selected plants growing in a lindane contaminated environment and acclimatized in lindane spiked media (5-100 μg mL⁻¹). The isolated species were inoculated with soil containing 5, 50 and 100 mg kg⁻¹ of lindane and incubated at room temperature. Soil samples were collected periodically to evaluate the microbial dissipation kinetics, dissipation rate, residual lindane concentration and microbial biomass carbon (MBC). There was a marked difference (p < 0.05) in the MBC content and lindane dissipation rate of microbial isolates cultured in three different lindane concentrations. Further, the dissipation rate tended to decrease with increasing lindane concentrations. After 45 d, the residual lindane concentrations in three different spiked soils were reduced to 0%, 41% and 33%, respectively. Among the four species, S. cohnii subspecies urealyticus exhibited maximum dissipation (41.65 mg kg⁻¹) and can be exploited for the in situ remediation of low to medium level lindane contaminated soils.     

Bioaccumulation in Porcellio scaber (Crustacea, Isopoda) as a measure of the EDTA remediation efficiency of metal-polluted soil

Leaching using EDTA applied to a Pb, Zn and Cd polluted soil significantly reduced soil metal concentrations and the pool of metals in labile soil fractions. Metal mobility (Toxicity Characteristic Leaching Procedure), phytoavailability (diethylenetriaminepentaacetic acid extraction) and human oral-bioavailability (Physiologically Based Extraction Test) were reduced by 85-92%, 68-91% and 88-95%, respectively. The metal accumulation capacity of the terrestrial isopod Porcellio scaber (Crustacea) was used as in vivo assay of metal bioavailability, before and after soil remediation. After feeding on metal contaminated soil for two weeks, P. scaber accumulated Pb, Zn and Cd in a concentration dependent manner. The amounts of accumulated metals were, however, higher than expected on the basis of extraction (in vitro) tests. The combined results of chemical extractions and the in vivo test with P. scaber provide a more relevant picture of the availability stripping of metals after soil remediation.     

Hexavalent chromium reduction and plant growth promotion by Staphylococcusarlettae strain Cr11

Cr(VI), a mutagenic and carcinogenic pollutant in industrial effluents, was effectively reduced by an indigenous tannery effluent isolate Staphylococcus arlettae strain Cr11 under aerobic conditions. The isolate could tolerate Cr(VI) up to 2000 and 5000 mg L⁻¹ in liquid and solid media respectively. S. arlettae Cr11 effectively reduced 98% of 100 mg L⁻¹ Cr(VI) in 24 h. Reduction for initial Cr(VI) concentrations of 500 and 1000 mg L⁻¹ was 98% and 75%, respectively in 120 h. The isolate was also positive for siderophore, indole acetic acid, ammonia and catalase production, phosphate solubilization and biofilm formation in the presence and absence of Cr(VI). The isolate showed halotolerance (10% NaCl) and cross tolerance to other toxic heavy metals such as Hg²⁺, Ni²⁺, Cd²⁺ and Pb²⁺. Bacterial inoculation of Triticum aestivum in controlled petri dish and soil environment showed significant increase in percent germination, root and shoot length as well as dry and wet weight in Cr(VI) treated and untreated samples. This is the first report of simultaneous Cr(VI) reduction and plant growth promotion for a S. arlettae strain.     

Slow growth of Empetrum nigrum in industrial barrens: combined effect of pollution and age of extant plants

We studied the impact of industrial pollution on population demography (age structure), growth and reproduction of crowberry, Empetrum nigrum L. Crowberry growing in severely polluted sites near non-ferrous smelters (at Harjavalta, Monchegorsk and Nikel) was on average twice as old as in unpolluted habitats, as indicated by the number of annual rings at root collar. Shoot length decreased both with plant ageing and due to pollution impact, while neither the proportion of generative plants nor berry production was affected by pollution or plant age. Our results suggest that death of the extant individuals of E. nigrum near the non-ferrous smelters is to a large extent explained by age-related damage of the main stem accelerated by pollution. Since vegetative propagation, seed germination and seedling establishment are hampered by soil toxicity, E. nigrum populations near the smelters continue to decline with ageing in spite of the gradual decline of emissions.     

Evaluation of effectiveness of EDTA and sodium thiosulfate in removing metal toxicity toward sea urchin embryo-larval applying the TIE

Since the development of the TIE (Toxicity Identification and Evaluation) in 1988 it has been assumed that the capacity of EDTA and sodium thiosulfate to complex some metals, and thus remove their toxicity, can be applied to both freshwater and seawater ecotoxicological tests and the results subsequently interpreted. However, it is now known that there is a wide variability in the extent of this complexation. In this context, the removal of toxicity caused by the presence of Hg²⁺, Cd²⁺, Cu²⁺, Cr⁶⁺, Zn²⁺, Ni²⁺, Pb²⁺, Ag¹⁺ and Se²⁺, through metal complexation by EDTA and sodium thiosulfate, in relation to the performance of embryo-larval tests with the sea urchin Arbacia lixula was investigated. It was observed that EDTA was capable of removing the toxicity of Pb²⁺, Zn²⁺ and Cu²⁺ while sodium thiosulfate only reduced the toxicity of Ag¹⁺. Compared to the complexation observed in freshwater ecotoxicological tests, the complexing agents used in this study (EDTA and sodium thiosulfate) have a lower capacity to complex metals in the marine ecotoxicological test with A. lixula.     

Nano-TiO2 enhances the toxicity of copper in natural water to Daphnia magna

The acute toxicity of engineered nanoparticles (NPs) in aquatic environments at high concentrations has been well-established. This study demonstrates that, at a concentration generally considered to be safe in the environment, nano-TiO₂ remarkably enhanced the toxicity of copper to Daphnia magna by increasing the copper bioaccumulation. Specifically, at 2 mg L⁻¹ nano-TiO₂, the (LC₅₀) of Cu²⁺ concentration observed to kill half the population, decreased from 111 μg L⁻¹ to 42 μg L⁻¹. Correspondingly, the level of metallothionein decreased from 135 μg g⁻¹ wet weight to 99 μg g⁻¹ wet weight at a Cu²⁺ level of 100 μg L⁻¹. The copper was found to be adsorbed onto the nano-TiO₂, and ingested and accumulated in the animals, thereby causing toxic injury. The nano-TiO₂ may compete for free copper ions with sulfhydryl groups, causing the inhibition of the detoxification by metallothioneins.     

Isolation and characterization of lead-tolerant Ochrobactrum intermedium and its role in enhancing lead accumulation by Eucalyptus camaldulensis

In this study, the potential of rhizospheric bacteria in promoting the growth and Pb accumulation by the woody plant Eucalyptus camaldulensis under hydroponic conditions was investigated for the first time. Three Pb-tolerant bacteria were isolated from the rhizosphere of E. camaldulensis grown in Pb-contaminated soils in the Bo Ngam Pb mine, Thailand. Based on analysis of partial 16S rRNA gene sequence, the three isolates were identified as Microbacterium paraoxydans BN-2, Ochrobactrum intermedium BN-3, and Bacillus fusiformis BN-4. Among these strains, O. intermedium BN-3 showed the highest tolerance to not only Pb but also Cd and Zn. After growth in the presence of Pb, the membranes of O. intermedium BN-3 cells exhibited an increase in unsaturated fatty acid levels but a decrease in fluidity. In hydroponic studies, inoculation of O. intermedium BN-3 significantly increased the biomass and Pb accumulation by E. camaldulensis compared to the uninoculated control. The results suggested the role of the natural rhizospheric bacteria localized to the root surface of E. camaldulensis in promoting Pb accumulation and plant growth. Our results indicate that O. intermedium BN-3 and other indigenous rhizospheric bacteria have the potential to improve the efficiency of phytoremediation of Pb-contaminated sites.     

Characterization of mercury species in brown and white rice (Oryza sativa L.) grown in water-saving paddies

In China, total Hg (Hg_T) and methylmercury (MeHg) were quantified in rice grain grown in three sites using water-saving rice cultivation methods, and in one Hg-contaminated site, where rice was grown under flooded conditions. Polished white rice concentrations of Hg_T (water-saving: 3.3 ± 1.6 ng/g; flooded: 110 ± 9.2 ng/g) and MeHg (water-saving 1.3 ± 0.56 ng/g; flooded: 12 ± 2.4 ng/g) were positively correlated with root-soil Hg_T and MeHg contents (Hg_T: r² = 0.97, MeHg: r² = 0.87, p < 0.05 for both), which suggested a portion of Hg species in rice grain was derived from the soil, and translocation of Hg species from soil to rice grain was independent of irrigation practices and Hg levels, although other factors may be important. Concentrations of Hg_T and other trace elements were significantly higher in unmilled brown rice (p < 0.05), while MeHg content was similar (p > 0.20), indicating MeHg infiltrated the endosperm (i.e., white rice) more efficiently than inorganic Hg(II).     

The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation

To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg⁻¹. Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg⁻¹ MCP and TCP, and above 100 mg kg⁻¹ PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them.The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5 d of incubation in laboratory assays (initial pollutant concentration of 50 mg L⁻¹). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.     

Phytoextraction of heavy metal polluted soils using Sedum plumbizincicola inoculated with metal mobilizing Phyllobacterium myrsinacearum RC6b

The aim of this study was to investigate the effects of metal mobilizing plant-growth beneficial bacterium Phyllobacterium myrsinacearum RC6b on plant growth and Cd, Zn and Pb uptake by Sedum plumbizincicola under laboratory conditions. Among a collection of metal-resistant bacteria, P. myrsinacearum RC6b was specifically chosen as a most favorable metal mobilizer based on its capability of mobilizing high concentrations of Cd, Zn and Pb in soils. P. myrsinacearum RC6b exhibited a high degree of resistance to Cd (350 mg L⁻¹), Zn (1000 mg L⁻¹) and Pb (1200 mg L⁻¹). Furthermore, P. myrsinacearum RC6b showed multiple plant growth beneficial features including the production of 1-aminocyclopropane-1-carboxylic acid deaminase, indole-3-acetic acid, siderophore and solubilization of insoluble phosphate. Inoculation of P. myrsinacearum RC6b significantly increased S. plumbizincicola growth and organ metal concentrations except Pb, which concentration was lower in root and stem of inoculated plants. The results suggest that the metal mobilizing P. myrsinacearum RC6b could be used as an effective inoculant for the improvement of phytoremediation in multi-metal polluted soils.     

Characterization of bacterial communities at heavy-metal-contaminated sites

The microbial community in soil samples from two long-term contaminated sites was characterized by using culture-dependent and culture-independent methods. The two sites investigated contained high amounts of heavy metals and were located in the upper Silesia Industrial Region in southern Poland. The evaluation of the aerobic soil microbial population clearly demonstrated the presence of considerable numbers of viable, culturable bacteria at both sites. A high fraction of the bacterial population was able to grow in the presence of high amounts of metals, i.e. up to 10 mM Zn²⁺, 3 mM Pb²⁺ or 1 mM Cu²⁺. Site 1 contained significantly (P < 0.05) lower bacterial numbers growing in the presence of 10 mM Zn²⁺ than site 2, while the opposite was observed for bacteria tolerating 1 mM Cu²⁺. This coincided with the contents of these two metals at the two sites. Ecophysiological (EP) indices for copiotrophs (r-strategists) and oligotrophs (K-strategists) pointed to high bacterial diversity at both sites. Fluorescence in situ hybridization (FISH) analysis indicated that Actinobacteria and Proteobacteria represent the physiologically active fraction of bacteria at the two sites. Shannon diversity (H′) indices for FISH-detected bacterial phylogenetic groups were not significantly different at the two sites.     

Lethal effects of abamectin on the aquatic organisms Daphnia similis, Chironomus xanthus and Danio rerio

Abamectin is used as an acaricide and insecticide for fruits, vegetables and ornamental plants, as well as a parasiticide for animals. One of the major problems of applying pesticides to crops is the likelihood of contaminating aquatic ecosystems by drift or runoff. Therefore, toxicity tests in the laboratory are important tools to predict the effects of chemical substances in aquatic ecosystems. The aim of this study was to assess the potential hazards of abamectin to the freshwater biota and consequently the possible losses of ecological services in contaminated water bodies. For this purpose, we identified the toxicity of abamectin on daphnids, insects and fish. Abamectin was highly toxic, with an EC₅₀ 48 h for Daphnia similis of 5.1 ng L⁻¹, LC₅₀ 96 h for Chironomus xanthus of 2.67 μg L⁻¹ and LC₅₀ 48 h for Danio rerio of 33 μg L⁻¹.