Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure (original) (raw)
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FEMS Microbiology Ecology, 2016
Copper has been intensively used in industry and agriculture since mid-18 th century and is currently accumulating in soils. We investigated the diversity of potential active bacteria by 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal (∼15 mg kg −1), high (∼450 mg kg −1) or extremely high (∼4500 mg kg −1) copper levels. Results showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors (e.g. season and pH). As copper concentration increased, bacterial richness and evenness were negatively impacted, while distinct communities with an enhanced relative abundance of Nitrospira and Acidobacteria members and a lower representation of Verrucomicrobia, Proteobacteria and Actinobacteria were selected. Our analysis showed the presence of six functional response groups (FRGs), each consisting of bacterial taxa with similar tolerance response to copper. Furthermore, the use of FRGs revealed that specific taxa like the genus Nitrospira and several Acidobacteria groups could accurately predict the copper legacy burden in our system, suggesting a potential promising role as bioindicators of copper contamination in soils.
Environmental Toxicology and Chemistry, 2006
A systematic comparison of Cu toxicity thresholds was made between freshly spiked soils and soils in which elevated Cu concentrations have been present for various times. Three uncontaminated soils were spiked and experimentally leached or incubated outdoors for up to 18 months. Additionally, five field-contaminated soils with a 6- to 80-year-old Cu contamination were sampled, and corresponding uncontaminated soils were spiked to identical total concentrations. All soil samples were subjected to three microbial assays (nitrification potential, glucose-induced respiration, and maize residue C-mineralization). Experimental leaching or soil incubation after spiking reduced Cu toxicity (1.3- or 2.3-fold increase of dose, respectively, to inhibit process by 50% [ED50]). No significant effects of soil type, aging time (6, 12, or 18 months), or bioassay on the factor change of ED50 were found. Significant reductions of microbial activity in field-contaminated soils were only identified in 2 of the 15 series (three assays in five soils), whereas freshly spiking the corresponding control soils significantly affected these processes in 12 series. Soil solution Cu concentrations significantly decreased on leaching at corresponding total soil Cu, and smaller decreases were found during additional aging. Soil solution Cu concentrations largely explain changes in Cu toxicity on leaching and aging, although additional variation may be related to changes in the sensitivity of microbial populations. It is concluded that total Cu toxicity thresholds are lower in freshly spiked soils compared to soils in which Cu salts have equilibrated and leaching has removed excess soluble salts. The large variability of soil microbial processes creates a large uncertainty about the magnitude of the factor by which aging mitigates Cu toxicity.
FEMS Microbiology Ecology, 2006
The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO 4 , Ca(OH) 2 ] at the standard rate used in viticulture (B1 = 16 kg Cu kg À1 soil) and at a higher level of contamination (B3 = 48 kg Cu ha À1 soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using Band F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.
Research in Microbiology, 2008
The annual dynamics of soil bacterial community structure, including early, dose-dependent and transient modifications, was observed consecutively at different levels of copper contamination (high: 48 kg Cu ha À1 , low: 16 kg Cu ha À1) repeated yearly over a three-year field experiment. Repeated low-level Cu contamination led to an increase in community stability to metal stress without a long-term shift in the population structure, whereas repeated high-level Cu contamination induced a novel and stable bacterial community structure. Furthermore, field experimentation highlighted that episodic climatic stress can modulate copper impact by enhancing community stability.
European Journal of Soil Biology, 2001
The characteristics of copper (Cu)-resistant bacterial communities in a rhizosphere and a non-rhizosphere of the ditch reed, Phragmites, in a highly Cu-contaminated area near a copper mine were investigated. The total Cu concentration was 720 µg•g-1 in the rhizosphere soil and 5 680 µg•g-1 in the non-rhizosphere soil. In the rhizosphere, the multiplication of bacteria, particularly non-resistant bacteria, was promoted as compared with the non-rhizosphere. The properties of the bacterial community in the rhizosphere were quite different from those in the non-rhizosphere in terms of Cu sorption ability, growth rate and exopolymer production. Both the Cu-resistant bacteria and non-resistant bacteria in the rhizosphere grew more rapidly in media than those in the non-rhizosphere. For almost all the isolated Cu-resistant bacteria, exopolymer production was prompted by Cu stimuli especially for the isolates from the rhizosphere. The adverse effect of Cu on the growth rate was found to be small for the Cu-resistant bacteria producing exopolymers in a large quantity, suggesting the involvement of exopolymers in the detoxification of Cu. The role of Cu resistance in the bacterial chemotactic migration in the Cu-contaminated soils was not evident.
FEMS Microbiology Ecology, 2003
The impact of copper amendment on the bacterial community in agricultural soil was investigated by a 2-year field experiment complemented by short-term microcosm studies. In the field, the amendments led to total copper contents that were close to the safety limits laid down by European authorities. In parallel, bioavailable copper was determined with a copper-specific bioluminescent Pseudomonas reporter strain. The amounts of total Cu as well as of bioavailable Cu in the field declined throughout the experiment. Bacterial community structure was examined by terminal restriction fragment length polymorphism (T-RFLP) analysis of community DNA amplified with primers specific for 16S rDNA from the Bacteria domain, the Rhizobium-Agrobacterium group and the Cytophaga group. Similarity analysis of T-RFLP profiles from field samples demonstrated an impact of copper at the domain level and within the Rhizobium-Agrobacterium group. Comparable Cu effects were observed for microcosms, but in addition an impact on community structure within the Cytophaga group was observed.
Bioresource Technology, 2009
The metals contamination in surface soils and their accumulation in wild plants from the abandoned Burra and Kapunda copper mines located in South Australia were assessed, and the predominant bacterial diversity in the contaminated surface soils from these two abandoned copper mine sites were evaluated through polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. The results showed the average concentration of Cu in soils was 3821.59 mg/kg while wild plants accumulated up to 173.44 mg/kg. The concentration of Cu in shoots of spear grass (Stipa uitida) and berry saltbush (Afriplex semibaccata) was higher than that of roots. The concentration of total and extractable As, Cd, Cu and Pb in soils slightly correlated with of these elements in the corresponding wild plants. The toxicity of Cu in heavily contaminated soils impacted on the quantities of specific microbial populations and no significant change in the microbial diversity of highly contaminated soils.
Microbial Diversity and Resistance to Copper in Metal-Contaminated Lake Sediment
Microbial Ecology, 2003
Contamination of habitats with heavy metals has become a worldwide problem. We describe herein the analysis of lake sediment contaminated with high concentrations of copper as a consequence of mine milling disposal over a 100-year period. Copper concentrations in the sediment were found to vary with depth and ranged from 200 to 5500 ppm. Analysis of the microbial community with T-RFLP identified a minimum of 20 operational taxonomic units (OTU). T-RFLP analysis along a depth profile detected as many as nine shared OTUs across 15 centimeters, suggesting a conservation of community structure over this range. Only two genera, Arthrobacter and Ralstonia, were detected among 50 aerobic copper-resistant isolates cultivated on R2A, one of which (Ralstonia sp.) was characterized by the sequestration of copper, identified by electron diffraction scanning, in growing colonies. Scanning electron microscopy showed changes to the outer envelope of the cells when grown in the presence of copper. The copperresistant Ralstonia isolates were also resistant to Ni, Cd, and Zn, showing two patterns of phenotypic resistant to these three metals in which either resistance to Zn or Ni was expressed in an isolate but never both.