Factors influencing the composition of bacterial communities found at abandoned copper-tailings dumps

Enlightening the Pathway of Phytoremediation: Ecophysiology and X-ray Fluorescence Visualization of Two Chilean Hardwoods Exposed to Excess Copper

In the present climate emergency due to global warming, we are urged to move away from fossil fuels and pursue a speedy conversion to renewable energy systems. Consequently, copper (Cu) will remain in high demand because it is a highly efficient conductor used in clean energy systems to generate power from solar, hydro, thermal and wind energy across the world. Chile is the global leader in copper production, but this position has resulted in Chile having several hundred tailing deposits. We grew two Chilean native hardwood species, quillay (Quillaja saponaria Molina) and espino (Vachellia caven (Molina) Seigler & Ebinger, under three increasing Cu levels (0, 50, and 100 µM) for 6 months in a greenhouse setting. We measured growth, photosynthetic performance and elemental contents of leaves and roots to further evaluate their potential for phytoremediation. Growth of quillay was unaffected by Cu treatment but growth of espino was enhanced, as was its photosynthetic performance, indicating that espino may have an unusually high requirement for copper. Excess Cu was mostly restricted to the roots of both species, where X-ray fluorescence (XRF) mapping indicated some tendency for Cu to accumulate in tissues outside the periderm. Calcium oxalate crystals were prominently visible in XRF images of both species. Nickel (but not Cu) showed a concurrent distribution pattern with these crystals.

The microbial community from the early-plant colonizer (Baccharis linearis) is required for plant establishment on copper mine tailings

Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.

Isolation and characterization of an acid and metal tolerant Enterobacter cloacae NZS strain from former mining lake in Selangor, Malaysia

Background

Metal polluted environments have been found to harbor acid and metal tolerant bacterial communities. Metal oxidizing bacteria in particular are industrially important microorganisms that can be utilized for potential applications in biomining and bioremediation. However, some well-characterized strains are not readily culturable as they are obligate and fastidious chemolithotrophs requiring special techniques for their cultivation. Hence, this study was aimed at isolating, identifying, and characterizing indigenous metal tolerant heterotroph(s) from abandoned mines that can potentially be used for biomining or bioremediation processes in the future.

Results

Seventeen bacteria from former mining lakes were isolated and identified using 16S rRNA. Minimal inhibition concentration (MIC) and growth study of isolated bacteria carried out in Luria-Bertani media containing three different metals ions, zinc (II), copper (II), and iron (II), showed that a particular isolate termed Enterobacter cloacae NZS was found to exhibit better growth and tolerance for copper (up to 90 mM), zinc (up to 200 mM), and iron (up to 170 mM). Growth of the strain was notably well in the presence of iron (II). Compared to all the isolates, only E. cloacae NZS was able to be enumerated at pH lower than 5 while other strains were culturable only at pH 7. Its capability in iron (II) oxidation was preliminary assessed based on the pH, cell count, glucose consumption, and amount of iron oxidized throughout incubation in 9K media. E. cloacae NZS strain was found to be capable of oxidizing iron (II) supplied in 9K media to iron (III).

Conclusion

As preliminary investigation showed that E. cloacae NZS was able to oxidize iron (II) in 9K media at pH2, further optimization on the strain, medium, and culture conditions in future may be able to provide a better insight on this strain to be possibly used as an iron oxidizer for various applications.

Integrated Management of Pig Residues and Copper Mine Tailings for Aided Phytostabilization

There is high demand for identifying socio-environmentally sound ways to dispose of large quantities of offensive odor-generating organic residues produced by intensive livestock farming. The use of these residues as amendments at large-scale mine tailings storage facilities for in situ plant-based reclamation may be a useful alternative. We performed a greenhouse assay to evaluate effectiveness of pig slurries and the solid organic fraction of aerobic-aerated pig slurries, both treated and not treated for odor emission, as amendments for copper tailings. Different doses of slurries or the solid organic fraction of the slurries, untreated and treated with either ozone or a commercial product used to manage strong odors (Just a Drop), were incorporated into tailings and stabilized (15 d) under greenhouse conditions. L. (ryegrass) was used as bioindicator for Cu and Zn toxicity. Plant performance (shoot and root dry biomass, Cu and Zn content in leaves) and general physicochemical characteristics of substrates were evaluated. Our results showed that odor management of pig residues was possible with commercial products, and their incorporation into tailings rapidly and effectively reduced odor emission. The solid organic fraction of the slurries neutralized acidic tailings, and both pig residues increased organic matter and nutrient content in tailings while reducing extractable Cu. As a result, ryegrass productivity was significantly improved by incorporation of either slurries or their solid organic fraction into tailings in a dose-dependent form. Foliar Cu content in ryegrass was not affected but foliar Zn content increased; however, Zn remained within acceptable ranges. Both the pig slurries and their soil organic fractions proved to be valuable residues for tailings reclamation.

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China

To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.

Soil physicochemical factors as environmental filters for spontaneous plant colonization of abandoned tailing dumps

Abandoned tailing dumps (ATDs) offer an opportunity to identify the main physicochemical filters that determine colonization of vegetation in solid mine wastes. The current study determined the soil physicochemical factors that explain the compositional variation of pioneer vegetal species on ATDs from surrounding areas in semiarid Mediterranean-climate type ecosystems of north-central Chile (Coquimbo Region). Geobotanical surveys-including physicochemical parameters of substrates (0-20 cm depth), plant richness, and coverage of plant species-were performed on 73 ATDs and surrounding areas. A total of 112 plant species were identified from which endemic/native species (67%) were more abundant than exotic species (33%) on ATDs. The distribution of sampling sites and plant species in canonical correspondence analysis (CCA) ordination diagrams indicated a gradual and progressive variation in species composition and abundance from surrounding areas to ATDs because of variations in total Cu concentration (1.3%) and the percentage of soil particles <2 μm (1.8%). According to the CCA, there were 10 plant species with greater abundance on sites with high total Cu concentrations and fine-textured substrates, which could be useful for developing plant-based stabilization programs of ATDs in semiarid Mediterranean-climate type ecosystems of north-central Chile.

Ecological restoration alters microbial communities in mine tailings profiles

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes.

Endophytic bacteria take the challenge to improve Cu phytoextraction by sunflower

Endophytic bacteria from roots and crude seed extracts of a Cu-tolerant population of Agrostis capillaris were inoculated to a sunflower metal-tolerant mutant line, and their influence on Cu tolerance and phytoextraction was assessed using a Cu-contaminated soil series. Ten endophytic bacterial strains isolated from surface-sterilized A. capillaris roots were mixed to prepare the root endophyte inoculant (RE). In parallel, surface-sterilized seeds of A. capillaris were crushed in MgSO4 to prepare a crude seed extract containing seed endophytes (SE). An aliquot of this seed extract was filtered at 0.2 μm to obtain a bacterial cell-free seed extract (SEF). After surface sterilization, germinated sunflower seeds were separately treated with one of five modalities: no treatment (C), immersion in MgSO4 (CMg) or SEF solutions and inoculation with RE or SE. All plants were cultivated on a Cu-contaminated soil series (13-1020 mg Cu kg(-1)). Cultivable RE strains were mostly members of the Pseudomonas genera, and one strain was closely related to Labrys sp. The cultivable SE strains belonged mainly to the Bacillus genera and some members of the Rhodococcus genera. The treatment effects depended on the soil Cu concentration. Both SE and SEF plants had a higher Cu tolerance in the 13-517 mg Cu kg(-1) soil range as reflected by increased shoot and root DW yields compared to control plants. This was accompanied by a slight decrease in shoot Cu concentration and increase in root Cu concentration. Shoot and root DW yields were more promoted by SE than SEF in the 13-114 mg Cu kg(-1) soil range, which could reflect the influence of seed-located bacterial endophytes. At intermediate soil Cu (416-818 mg Cu kg(-1) soil), the RE and CMg plants had lower shoot Cu concentrations than the control, SE and SEF plants. At high total soil Cu (617-1020 mg Cu kg(-1)), root DW yield of RE plants slightly increased and their root Cu concentration rose by up to 1.9-fold. In terms of phytoextraction efficiency, shoot Cu removal was increased for sunflower plants inoculated with crude and bacterial cell-free seed extracts by 1.3- to 2.2-fold in the 13-416 mg Cu kg(-1) soil range. Such increase was mainly driven by an enhanced shoot DW yield. The number and distribution of endophytic bacteria in the harvested sunflower tissues must be further examined.

Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

Efficacy of lime, biosolids, and mycorrhiza for the phytostabilization of sulfidic copper tailings in Chile: a greenhouse experiment

Inadequate abandonment of copper mine tailings under semiarid Mediterranean climate type conditions has posed important environmental risks in Chile due to wind and rain erosion. There are cost-effective technologies for tailings stabilization such as phytostabilization. However, this technology has not been used in Chile yet. This study evaluated in a greenhouse assay the efficacy of biosolids, lime, and a commercial mycorrhiza to improve adverse conditions of oxidized Cu mine tailings for adequate establishment and grow of Lolium perenne L. var nui. Chemical characterization of experimental substrates and pore water samples were performed; plant density, biomass production, chlorophyll content, and metal content in shoots was evaluated in rye grass plants after an eight-week growth period. Results showed that neutralization of tailings and superficial application of biosolids increased both aerial biomass production and chlorophyll content of rye grass. Increased Cu solubilization and translocation to shoots occurred after biosolids application (mixed), particularly on unlimed tailings, due to formation of soluble organometallic complexes with dissolved organic carbon (DOC) which can be readily absorbed by plant roots. Positive effects of mycorrhizal inoculation on rye grass growth were restricted to treatments with superficial application of biosolids, probably due to Cu toxicity effects on commercial mycorrhiza used (Glomulus intraradices).

Novel polymerase chain reaction primers for the specific detection of bacterial copper P-type ATPases gene sequences in environmental isolates and metagenomic DNA

AIMS

In the last decades, the worldwide increase in copper wastes release by industrial activities like mining has driven environmental metal contents to toxic levels. For this reason, the study of the biological copper-resistance mechanisms in natural environments is important. Therefore, an appropriate molecular tool for the detection and tracking of copper-resistance genes was developed.

METHODS AND RESULTS

In this work, we designed a PCR primer pair to specifically detect copper P-type ATPases gene sequences. These PCR primers were tested in bacterial isolates and metagenomic DNA from intertidal marine environments impacted by copper pollution. As well, T-RFLP fingerprinting of these gene sequences was used to compare the genetic composition of such genes in microbial communities, in normal and copper-polluted coastal environments. New copper P-type ATPases gene sequences were found, and a high degree of change in the genetic composition because of copper exposure was also determined.

CONCLUSIONS

This PCR based method is useful to track bacterial copper-resistance gene sequences in the environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first to report the design and use of a PCR primer pair as a molecular marker to track bacterial copper-resistance determinants, providing an excellent tool for long-term analysis of environmental communities exposed to metal pollution.

Culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings

A combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped Pb/Zn mine tailings that was undergoing intensive acid generation (pH 1.9). Culturable bacteria found in the extremely acidic mine tailings were Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermotolerans and Acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than that of the iron- and sulfur-oxidizing bacteria. Cloning and phylogenetic analysis revealed that, in contrast to the adjacent AMD, the mine tailings possessed a low microbial diversity with archaeal sequence types dominating the 16S rRNA gene library. Of the 141 clones examined, 132 were represented by two sequence types phylogenetically affiliated with the iron-oxidizing archaea Ferroplasma acidiphilum and three belonged to two tentative groups within the Thermoplasma lineage so far represented by only a few environmental sequences. Six clones in the library were represented by the only bacterial sequence type and were closely related to the well-described iron-oxidizer L. ferriphilum. The significant differences in the prokaryotic community structures of the extremely acidic mine tailings and the AMD associated with it highlights the importance of studying the microbial communities that are more directly involved in the iron and sulfur cycles of mine tailings.

Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site

Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8). Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples. The clones in the extremely acidic tailing sample were most closely related to acidophiles, none of which were detected in the OS control sample. The comparison generated by this study between the bacteria present in extremely acidic tailing and that in moderately acidic tailing communities with those in an OS control soil provides a reference point from which to evaluate the successful restoration of mine tailing disposal sites by phytostabilization.