Appl Microbiol Biotechnol (2010) 87:1271–1280 DOI 10.1007/s00253-010-2695-z

MINI-REVIEW

Metallomics: lessons for metalliferous soil remediation Götz Haferburg & Erika Kothe

Received: 19 May 2010 / Revised: 19 May 2010 / Accepted: 19 May 2010 / Published online: 8 June 2010 # Springer-Verlag 2010

Abstract The term metallomics has been established for the investigation of transcriptome, proteome, and metabolome changes induced by metals. The mechanisms allowing the organisms to cope with metals in the environment, metal resistance factors, will in turn change biogeochemical cycles of metals in soil, coupling the metal pool with the root system of plants. This makes microorganisms key players in introducing metals into food webs, as well as for bioremediation strategies. Research on physiological and metabolic responses of microorganisms on metal stress in soil is thus essential for the selection of optimized consortia applicable in bioremediation strategies such as bioaugmentation or microbially enhanced phytoextraction. The results of metallomics studies will help to develop applications including identification of biomarkers for ecotoxicological studies, bioleaching, in situ soil regeneration, and microbially assisted phytoremediation of contaminated land. This review will therefore focus on the molecular understanding of metal resistance in bacteria and fungi, as can be derived from metallomics studies. Keywords Metallomics . Proteomics . Heavy metal resistance . Bioremediation . Phytoextraction . Biostabilization . Bacteria . Fungi

G. Haferburg (*) : E. Kothe Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany e-mail: [email protected]

Introduction: metals in the environment The consequence of ore mining is pollution. With 1.4 billion tons, the output of the global metal production in 2008 was more than seven times higher than in 1950. The average per capita metal consumption has been rising from 77 kg in 1950 to 213 kg in 2008. While the benefits of metal production are clear, the negative outcome of mining operations is less obvious for most. Worldwide mining operations occupy an expanse of approximately 37,000 km2 which roughly equals the area of Belgium or 0.2% of the world’s land surface (Dudka and Adriano 1997). In addition, approximately 240,000 km2, equaling the size of UK, is influenced by metals released from waste dumps and open mines (Furrer et al. 2002). After the estimates of the European Environment Agency, 1.4 million contaminated sites are listed (Prasad et al. 2010). In contrast to organic pollution, it is impossible to reduce the extent of metal contamination by degradation. Thus, either they can be removed from arable land with subsequent safe depositing or the negative effects can be minimized by immobilization at the spot. Plant cover, carbon turnover, and regeneration are usually slow in soils contaminated with metals, leading to erosion, shift in soil composition, and ground and surface water contamination. Highly relevant for the ability to regenerate is the interference of metals with fundamental microbially driven cycles of matter including decomposition and formation of soil organic matter. Toxic concentrations of (heavy) metal reduce these essential processes (e.g., Nriagu 1996; Vivas et al. 2008). The relevant ecotoxicological risk depends on the metals present and their respective speciation or mineralization and can vary strongly between different indigenous consortia as has been shown in metabolic profiles for a

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number of bacterial mining isolates (Sprocati et al. 2006). Thus, resistant microbes can be used to restore microbial activity by bioaugmentation and to improve conditions in environmental protection and remediation. Lately, extensive discussion on how metal contamination could contribute to climate change has ensued. Inhibition of bacterial nitrous oxide reductase by metal toxicity leading to incomplete denitrification has been shown to increase accumulation of the potent greenhouse gas N2O known to interfere with the ozone layer (Dickinson and Cicerone 1986). This example shows but one potential link between local metal contamination and global climate change phenomena (Sobolev and Begonia 2008). Heavy metal contamination is enhanced by microbially accelerated pyrite (FeS2) weathering leading to acid mine drainage (AMD) or acid rock drainage, very prominent to be seen, e.g., in the Rio Tinto region of Spain (Grande et al. 2005). Since most active metal mines carry sulfidic ores, this process of producing sulfuric acid from low-grade ores in waste rock piles or tailings impoundments is gaining impact. The pH of effluents typically decreases to 2–3, leading to metal mobilization, and the mobile metals then are distributed horizontally and vertically by infiltration into the ground, as well as entering surface or ground waters. To prevent this process, oxygen supply for pyrite oxidation is reduced by technical measures like sealing and covering heaps, reducing at the same time oxygen and water entry, and thus formation of AMD. However, the reclamation of large areas already disturbed by AMD infiltration remains a challenge (Haferburg and Kothe 2007).

Metallomics The field of metallomics specifically investigates the interrelationships of metal-induced proteome and metabolome changes. Most of the work is still devoted to methodological aspects (Garcia et al. 2006; Lobinski et al. 2006; Mounicou et al. 2009; Muñoz et al. 2005; Szpunar 2004, 2005), but a couple of papers specifically addresses environmental issues (González-Fernández et al. 2009; López-Barea and Gómez-Ariza 2006). The currently increasing number of genomes sequenced, including bacterial as well as fungal strains, allows in silico searches for genes encoding metal-responsive proteins (Chance et al. 2004). The promoters of such genes could be interesting for specific metal response elements, which would be interesting targets for reporter gene fusions in biomarker establishing. The proteins encoded could be either involved in metal homeostasis—and thus being of interest for improving metal resistance of strains for bioremediation—or the enzymatic activity of the proteins might lead to new

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metabolites involved in metal binding, either as chelators/ siderophores or as specific detoxification products. Many promoters essential for the induction of several metal resistance determinants are well known now. The strong and tightly controlled mer promoter operates in bacterial mercury resistance (Silver and Phung 1996); from copperresistant strains of Pseudomonas syringae, the promoter (pcopA) was found (Mellano and Cooksey 1988). One example for the application of knowledge on metal resistance regulation is a reporter system developed for arsenic detection in environmental samples. This reporter system makes use of the sensory protein ArsR in Escherichia coli as molecular marker. The luciferin– luciferase-based luminescence bioassay could be deployed in natural waters containing arsenic to serve as an indicator for arsenic bioaccumulation (Diesel et al. 2009). Also, in silico search of metal binding proteins has been performed, using actinobacteria as subjects for a proof of principle (A. Schmidt and E. Kothe, unpublished). The proteins of 73 different actinobacteria were screened for potential metallothioneins or metallohistins, small proteins of less than 100 amino acids containing a high proportion of cysteine and/or histidine residues. In 49 genomes, altogether 99 putative metal sequestrating metallothioneins/metallohistins were identified (A. Schmidt and E. Kothe, unpublished). Thus, 0.1% of all proteins occurred in about two thirds of the strains investigated, which can be seen as clear indication that, first, metallothioneins in bacteria are more widely distributed than previously assumed (Robinson et al. 2001) and, second, metallothioneins are not part of the general genomic setup of bacteria but rather have been developed as a result of adaptation toward high metal loads in the environment. Phytochelatins have been identified first in Schizosaccharomyces pombe but were named after their isolation from plants (Goldsbrough and Cobbett 2002; Hirata et al. 2005). Likewise, metallothioneins can be found widely distributed within the eukaryotic domain (Bourdineaud et al. 2006). Metal resistance genes recently identified in corn indicate the impact of metal-containing soils on maize domestication (Vielle-Calzada et al. 2009). Other targets for genomics-oriented approaches are feasible, and the identification of metabolites only produced in streptomycetes grown with 0.2 mM nickel or cadmium in their growth media is indicating a huge potential for rescreening strains from culture collections for induction of metabolite biosynthesis gene clusters under metal stress (Haferburg et al. 2009; Tchize et al. 2009). Thus, the use of metals as inducers for new metabolites, including antibiotics, is another way of making metallomics (i.e., metallometabolomics; LópezBarea and Gómez-Ariza 2006) work for biotechnological reasons. All in all, the interdisciplinary field of metallomics keeps ready and provides at growing pace a great measure of information to be applied in biotechnology.

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Metal resistance mechanisms The bacteria and fungi in a typical soil have adapted to cope with metal stress where necessary. The mechanisms for (heavy) metal resistance include intracellular and extracellular mechanisms (Fig. 1; see also Bruins et al. 2000) which will be discussed in detail below. In bacteria, some general principles emerge, which are shared among Gram-positive and Gram-negative taxa (metal sorption and intra-/extracellular sequestration; see Silver 1996 and references therein), while other mechanisms seem to be dominating in only one group (see for metal cation efflux transporters below). Fungi, being the sister group of metazoa, may provide inside into mechanisms with analogies to toxicity in food chains, and they can be used as indicators for both ecotoxicity and also in biotechnology approaches in remediation. The uptake of metal ions cannot be avoided. Intracellular binding and detoxification are combined with protection from oxidative stress induced by Fenton reaction products. Superoxide dismutase, an enzyme detoxifying superoxide anions, could be shown to be protective against heavy metal stress in E. coli (Geslin et al. 2001). Enzyme overexpression in yeast leads to enhanced metal resistance (Culotta et al. 1995), and upregulation of genes coding for superoxide dismutase was seen in heavy metal-resistant streptomycetes (Schmidt et al. 2007, 2009). Detoxification of toxic metals in vacuoles is an example of particular detoxification principles dominating in fungi. As charge balancing anion, phosphorus has been found in many cases. Thus, detoxification is linked to phosphorus nutrition and phosphate mobilization and uptake (Shen et al. 2006). At the same time, a highly specific metal transporter is needed for transport across the vacuolar membrane. In Gram-negative bacteria, highly specific efflux transporter proteins have been identified as dominant resistance mechanisms (Nies 1999 and references therein), and in heavy metal-resistant Gram-positive Streptomyces acidiscabies, a sequence with similarity to highly specific nickel transporters has been found (Amoroso et al. 2000) which can be identified also in the genome of Streptomyces M2+ M-X

X

X

avermitilis, while in the genome of Streptomyces coelicolor, no sequence similarity is detected. The search in actinobacterial genomes has revealed several cases, where genes with similarities to heavy metal transporters contain either C-terminal or N-terminal cysteine- and histidine-rich additions. In other strains, homologous sequences are found as separate genes removed from the transporter. This has been taken as indication for development of metallothioneins from metal binding termini of transporters (A. Schmidt and E. Kothe, unpublished). Metallothioneins and metallohistins, as discussed before, are intracellular storage and detoxification molecules able to bind (heavy) metals (A. Schmidt and E. Kothe, unpublished). This shows that streptomycetes or actinobacteria in general with their versatile secondary metabolism may provide an excellent source of applicable mechanisms in biotechnological soil decontamination (see Haferburg and Kothe 2007). Another protection mechanism is the extracellular adsorption or binding of metals preventing excessive uptake. Cell wall adsorption has been shown for fungi including yeasts as well as bacteria (Albarracín et al. 2008; Congeevaram et al. 2007; Haferburg et al. 2007; Jiang et al. 2006; Siñeriz et al. 2009; Wang et al. 2007a), and this has been proposed and developed as bioremediation approach, specifically for water treatment. Especially isolates of the genera Bacillus and Streptomyces and yeasts possess the capacity of adsorbing high amounts of metals from solution (Vijayaraghavan and Yun 2008; Wang and Chen 2006). Extracellular excreted substances may contribute to metal binding, like the production of melanin which has been seen linked with metal sorption (Fomina and Gadd 2003). The correlation between production of melanin and metal resistance has been shown for the phytopathogenic Streptomyces scabies by assaying melanin-negative mutants (Beauséjour and Beaulieu 2004). The cell protection by melanin functions dually: Besides metal sequestration due to carboxylic groups of the molecule, melanin can reduce the concentration of reactive oxygen species. As melanin is seen both in many fungi and in streptomycetes, the same mechanisms of changing bioavailability may be present in both filamentous soil organism groups. Other factors changing bioavailability, including biomineralization, are discussed as metal resistance factors (Haferburg and Kothe 2007).

X-M cell wall sorption

Biomarkers for ecotoxicological studies

X M2+

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M2+

M-X intracellular sequestration precipitation/mineralization

Fig. 1 Microbial metal resistance mechanisms. M metal, X metal binding molecule

Concerning remediation of metal-contaminated soils, the famous quote of Paracelsus “dosis sola venenum facit!”— the dose makes the poison—could be shifted to the dose of the poisonous metal decides on the remediation route to be taken. The method of choice will depend on a number of

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factors including toxicity, mobility and concentration of the metal, soil type and hydrogeological setting, bioavailability and remobilization of the metal, and pedological and climatic requirements for plant growth. The bioavailable fraction can be considered the ecotoxicologically relevant part of metals in an environment. Generally, sequential extraction is used to determine the mobile and easily mobilized fractions of metals in soil considered to constitute the bioavailable pool (Zeien and Brümmer 1989; compare also Peters 1999). At the same time, use of solvents with higher capacity for metal mobilization allows the estimation of fractions bound to soil organics, manganese oxides, or amorphous and crystalline iron oxi(hydroxides). This applies well to normal soils. However, at former mining sites, the substrates are often hardly comparable to soil, with extremely low organic matter contents and high iron or manganese precipitations. Still, no alternative method has been developed that reproducibly could substitute the sequential extraction in use for the analysis of a wide range of materials, including tailings and other minederived wastes. What can metallomics provide for assessment of bioavailable fractions or ecotoxicological risk assessment? Promoters of ciliate and mouse metallothioneins are probably excellent tools in designing whole-cell biosensors to detect heavy metals in polluted ecosystems (Gutiérrez et al. 2009). However, promoter fusions to reporter genes in bacteria, as well as in fungi, might turn out to be easier systems to use. This approach was used by fusing bioluminescence reporter genes to metal-responsive promoters and inoculating the resulting E. coli cells in liquid systems (for review on bioluminescence-based metal detectors, see Virta et al. 1998). The same may be achieved for soil systems, where bioluminescence would have the advantage that microscopic or photometric assessment is possible in a complex, nontranslucent system (Alkorta et al. 2006). In addition, the identification of more and more metalresistant and metal-responsive genes will allow the production of microarrays to evaluate metal impact on fungi and bacteria inoculated in microcosm experiments into polluted soils. Such microarrays are feasible for soil organisms with sequenced genomes for homologous hybridization of RNA extracted from the microcosms, or even with heterologous hybridization, if a standardization to control for species- or strain-specific differential gene hybridization is achieved. Such a method would be preferable over the state-of-the-art ecotoxicity tests using Daphnia in liquid systems, plant germination, or plant performance tests, or even the use of Vibrio fischeri and Chromobacterium violaceum bioluminescence interference tests (Parvez et al. 2006; Poynton et al. 2007).

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The decreased microbial community and diversity in heavy metal-contaminated soils might also be addressed more specifically, as opposed to the generalizing soil respiration and colony-forming unit assessment currently used, if marker genes were identified. Potential candidates would be metal-specific transporters which should be found more widely distributed in populations living in metalliferous habitats. However, new groups of genes may arise from metallomics research, allowing high throughput for biomonitoring, e.g., in monitored natural and enhanced natural attenuation scenarios of bioremediation.

Biotechnology for changing biogeochemical cycles Soil bacteria and fungi influencing biogeochemical cycles can shorten the time needed for remobilization of metals (see Fig. 2; see also White et al. 1997). Thus, investigation of microbial properties in soil is needed. Aside from mechanisms for metal immobilization discussed above, mobilization needs to be investigated. Fungi specifically carry high potential for degradation of minerals (Gadd 2007; Sayer et al. 1997). This weathering capacity applies to many minerals, not only apatite for phosphorous acquisition, or hornblende as magnesium source, but also Corg-rich material (Wengel et al. 2006) and silicates (Adeyemi and Gadd 2005). A specifically interesting option is the use of mycorrhizal fungi, which can both change the availability of metals in soil and at the same time work as biofilters for delivery of nutrients and metals to plants (Schützendübel and Polle 2002). Establishing a functional mycorrhiza seems to be aided by mycorrhiza helper bacteria (for review, see FreyKlett et al. 2007), again showing the complexity of soil biology systems. Mycorrhization opens new options for phytostabilization and phytoextraction. Ectomycorrhiza, in which the fungus stays extracellularly in the root tissue, are distinguished from endomycorrhiza with fungal hyphae penetrating through the plant cell wall and entering the cell, albeit not disrupting the cellular membrane of the plant cell. The vesicular arbuscular mycorrhiza, as a typical endomyoxidation/reduction M M2+ + 2 eM2+

X

X

M-X siderophore export

M

efflux

organic acids

M-X X + M2+ degradation of chelators

M-X M2+ X leaching

Fig. 2 Alteration of biogeochemical metal cycles by microbial metal immobilization mechanisms which are working in addition to the metal resistance factors discussed before (see Fig. 1). M metal, X metal binding molecule

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corrhiza, has been mostly used since this type of mycorrhiza is formed between more than 90% of land plants and a specific group of fungi, the Glomerales (Smith and Read 1997). Indeed, many of the mechanisms discussed for fungi in general can be applied to mycorrhizal glomeromycetes (Hildebrandt et al. 2007). The resulting alteration in gene expression (Ouziad et al. 2005) can be seen as metallomics toward characterizing traits beneficial for plant symbiosis. The inoculation of plants with vesicular arbuscular mycorrhizal fungi could be shown to alter element uptake into the root as well as root–shoot transfer (Audet and Charest 2007; Göhre and Paszkowski 2006; Liang et al. 2009a; Wang et al. 2007b), most likely by changing metal speciation and providing counterions for symplastic transport across the endodermis of the root. For ectomycorrhizal fungi, specific associations of certain basidiomycete and ascomycete fungi with oaks in contaminated areas were observed (Iordache et al. 2009). While specifically melanized ascomycete associations were seen in contaminated and at lower numbers at undisturbed sites, the occurrence of contact type mycorrhiza was limited to uncontaminated forests, indicating a function of long exploration type mycorrhizal fungi in acquisition of nutrients from less contaminated areas at a distance, allowing access to lower contamination within the spatially heterogeneous contaminated site. Chelators, like EDTA, are often used in technical remediation approaches for the mobilization of metals. Chelate-based phytoextraction provides the advantage of solubilizing metals making them available to the plants. Alternatively, remediation could take advantage of rhizosphere bacteria producing chelators directly at the microbe– plant interface of the rhizosphere where root exudates stimulate bacterial growth. In this scenario, specific interactions can lead to enhancing specific bacterial communities, a field which has not yet received the attention deserved. Only a vivid bacterial community will be able to produce the amounts of chelators necessary to change metal mobility. Very potent chelators were found among both bacteria and fungi. Different soil inhabiting Trichoderma species were found to desorb three times more Zn from a charcoal matrix than a conventional desorption technique (Adams et al. 2007). Increased Cd uptake of sunflower, due to the release of hydroxamate siderophores by streptomycetes, could be shown as a potentially useful bioremediation process, and the application of microbial cells was clearly superior to the use of EDTA (Dimkpa et al. 2009). Utilization of microbial chelators, nonetheless, has not yet been introduced so far into phytoremediation. More than 500 microbial siderophores are known (Boukhalfa and Crumbliss 2002), and some of these could be shown to possess a high affinity for toxic heavy metals.

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One example is seen with soil born Streptomyces tendae F4 which produces three different hydroxamate siderophores reducing cadmium toxicity for plants, while at the same time increasing metal uptake (Dimkpa et al. 2009). A relation between the bioavailability of heavy metals and siderophore overproduction was also observed for the highly metalresistant Cupriavidus metallidurans CH34 (Diels et al. 2009). Besides Streptomyces and Cupriavidus, many genera of (soil) bacteria are known to produce siderophores, including the genera Azotobacter, Acinetobacter, Bacillus, Pseudomonas, and Staphylococcus. Siderophore synthesis, usually inhibited by iron, has been shown to be deregulated and thus ensue under high iron conditions in metal-resistant isolates (Dimkpa et al. 2008a, b), which is an essential trait, specifically in iron-rich AMD environments. Other metabolites with siderophore function, like citrate or oxalate, mobilize iron (as well as other metals) from minerals (Dimkpa et al. 2008b, 2009; Fomina et al. 2005; Gadd 1999; Magyarosy et al. 2002). In addition, metal demobilization can ensue since both substances have been found in biominerals (Gadd 2009; Pan et al. 2009; Peters 1999). This potential of stabilization of metals in soils reducing the risk of washout into ground or surface waters as well as limiting uptake into plants and the food chain could also provide a potential remediation strategy. Biominerals, also including nickel containing Nistruvite (Haferburg et al. 2008), have been shown to be formed only if actively growing bacterial isolates resistant to elevated metal contents were present. Biomineralization thus can be seen as resistance mechanism, at the same time removing metals from biogeochemical cycles. Thus, mobilization and immobilization, as well as acquisition of nutrients from contaminated soil, are controlled by microbial consortia present. This provides a so far untapped potential for incorporation into biotechnological applications.

Microbially assisted phytoremediation Plants, as well as bacteria and fungi, are relying on water for cation uptake. In plants, some transport through tissue in the cell wall material, the apoplastic transport, is possible, while uptake into the aboveground biomass is depending on active transport. The proteins in the cell membrane for cation influx thus play a decisive role in metal uptake. As monovalent and bivalent cations include essential elements, e.g., K, Ca, Mg, but also Zn, Ni, Cu, and others, transporters with low specificity can be found in all life forms. The uptake of cations into the cytosol in plants referred to as symplastic transport, determines root– shoot transfer, and since uptake by the essential and unspecific cation transporters also provides access of

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potentially toxic metal, other mechanisms are needed to protect the cell from these toxic effects of metal cations. For ecotoxicology, cations in solution are the most relevant speciation. If the bioavailable fraction of heavy metals is removed, this pool will be replenished over time. In a direct comparison, conventional treatment is faster, but more expensive, demands more manpower, and strongly influences the soil in structure and function. Often, conventional remediation is conducted off-site. Therefore, the soil has to be excavated and transported, and the soil horizons are completely disturbed. This interferes with the goal of soil protection in most countries. Bioremediation, on the other hand, can be seen as a technology of sustainability, restoring and improving soil fertility. Microbially enhanced phytoremediation by means of metallomics has shaped into an integral constituent of the zero waste concept that proclaims the importance of avoiding waste accumulation and instead improving cyclic processes. Phytoremediation, in this sense, can be seen as tool to channel and concentrate metals dispersed in the environment. Economically, $100/ton for in situ and $300–1,000 for ex situ technologies are opposed by costs as low as $0.05/m3 for bioremediation (Cunningham et al. 1997). The duration of a bioremediation approach is the main obstacle in introducing this technique. It depends on many factors, like soil layering, clay content, or humus thickness, influence metal binding and thus metal bioavailability and metal remobilization. Bioremediation, as low impact strategy, makes use of the unique metabolic capacities of microorganisms to establish and promote plant growth for metal uptake into harvestable biomass (Fig. 3), which then can be burned and safely deposited as ashes (Keller et al. 2005). The microorganisms for such bioaugmented phytoextraction need to possess resistance factors as discussed above, where, e.g., siderophore-producing bacteria could be applied for metal solubilization with a subsequent uptake into plant shoots improving phytoextraction strategies (Khan 2005, 2006; Lebeau et al. 2008). In addition, phosphate mobilization and nitrogen fixation are relevant to improve plant growth. Often, a big part of the phosphate pool in soils is not readily plant available. In general, soil phosphate concentration in the temperate climate is with 200 to 800 mg P kg−1 sufficient for agriculture, but most of the phosphate compounds have to be dissolved either by acidifying exudates of the plant root or by microorganisms of the rhizosphere (Schachtschabel et al. 1998). The microbial production of inorganic and organic acids, such as gluconate, oxalate, citrate, or lactate, leads to a decrease in pH, cation chelation, and exchange reactions, thereby attacking insoluble phosphates. The organically bound P of the soil matrix, which makes up to 85% (Ulrich and Benzler 1955) of the total P, can be liberated by the activity of microbial phosphatases.

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siderophores

apatite

N2

NH4+

phytohormones

PO4 mobilisation mycorrhizal helper bacteria

bacterial community immobilization

mobilization

bioavailable metal pool

Fig. 3 Effects of microbial communities on plant growth at metalliferous sites. The different processes are discussed in detail in the text

The identification of free living diazotrophs, able to fix nitrogen from the air, is relevant at contaminated sites which often are pour substrates. While fertilization seems the way to improve soil conditions in such places, fertilization itself tends to limit plant–microbe associations including mycorrhization (Smith and Read 1997). It therefore may be better to refrain from simple fertilization and instead use bioaugmentation with nitrogen fixing, phosphate mobilizing, and plant growth-promoting microbial consortia consisting of strains with heavy metal tolerance. However, plant–microbe interactions need to be understood in more detail, as soil bacteria (and fungi) often prefer specific host plants or even cultivars of plants (Behl et al. 2007; Narula et al. 2009). Plant growth promotion is seen through microbial production of phytohormones, specifically indole acetic acid, which can increase root formation and hence plant growth. The increased biomass then allows for higher extraction values, even if the plant is accumulating generally only medium metal concentrations in aboveground biomass. For different soil bacteria, production of phytohormones has been shown. Of special interest are investigations showing that the production of phytohormones can proceed even under heavy metal stress (Dimkpa et al. 2008a, b).

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Hyperaccumulator plants with higher enrichment factors for metals have been discussed for phytoextraction. However, the generally low biomass and the lack of agricultural methods for farming indicate the use of normal agricultural plants as being superior (Liang et al. 2009b). Especially plants which can be used for biofuel production seem to have great potential, as they do not pose the risk of introducing metals into the food chain via feeding stock or human consumption. Land use at contaminated sites would profit from production schemes alternating between periods of extraction for metal removal and periods of crop production for biofuels, during which times the replenishment of the bioavailable pool for a new round of phytoextraction is combined with bioaugmentation for phytostabilization and low input in aboveground biomass. An example for the latter strategy could be shown using metal-tolerant Lupinus luteus which decreases plant metal accumulation if inoculated with Bradyrhizobium (Dary et al. 2010). In both phytoextraction and phytostabilization, the plants reduce the risk of contaminating water bodies by improved evapotranspiration and improve pedogenesis through litter production. This is possible only if the microbe–plant associations for bioaugmentation are carefully chosen—with regard to extraction and stabilization schemes, with regard to the crop cultivated, and with regard to competitiveness and sustainability of the bioaugmented microbes in the substrate. Here, metallomics may provide access to potent strains which are then to be screened experimentally versus the current approach of testing strains isolated from the contaminated site at random with plants chosen artificially.

Conclusions: optimized consortia for bioremediation strategies While phytoextraction regarding plant physiology has been covered with many investigations, the essential effect of the soil microbial population on both metal removal and metal immobilization still remains underestimated. Research on metal resistance in bacteria, less well in fungi, is increasing but still leaves enough questions to be solved by making use of methods in metallomics for a proper understanding of the impact metals have in biogeochemical cycles on various soil functions. Today, the importance of metal research on microorganisms, plants, and animals is much more clearly emphasized than ever before. The increasing public awareness of contamination as environmental threat and the consequences for agriculture (and life quality in general) also lead to an advancement of modern (bio)remediation strategies.

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Bioaugmentation (strain insertion with a subsequent increase in soil activity) and biostimulation (modification of habitat characteristics for enhanced metabolic activity) can be seen as closely related measures for the introduction and establishment of microbial strains into a contaminated environment in order to support remediation. Both phytoextraction and phytostabilization combine stimulatory effects of rhizosphere microorganisms on plant growth with metal removal from the ground by keeping the soil structure intact. For sustainable consortia and active metabolism of inoculated strains, N2-fixing and PO4-mobilizing bacteria should be included since plant growth highly depends on a sufficient supply with the usually growth-limiting nutrients nitrogen and phosphorous. At the same time, the inoculated strains need to be metal-resistant themselves. The presence of siderophoreproducing organisms in the inocula will be preferable for a fast and continuous metal solubilization. Release of phytohormones leads to faster increase of biomass, and bioaugmentation can also protect against pathogens. Biomineralization seems a trait that is specifically beneficial for phytostabilization measures. The inoculum of choice should thus consist of metalresistant, N2-fixing, PO4-solubilizing, and auxin-producing bacteria with either siderophore production or biomineralization capacities adapted to the soil type they are applied to. Aside from plant growth-promoting effects, the inoculum may also contain mycorrhiza helper bacteria. The best possible remediation strategy should alternate between metal mobilization from the soil matrix by microbial metabolic activity associated with metal uptake into harvestable plant biomass, and phytostabilization by plant growth promoting bacteria for remobilization of metals combined with low metal accumulation in plant tissue. Such an alternation could help develop a continuous strategy of metal removal providing a constant control of ground water formation by a continuous plant cover. Metallomics has developed a set of tools for the identification of physiological and molecular traits of microorganisms, which by this means can be assayed for appropriate bioaugmentation consortia. These can then be tested for beneficial plant associations to allow microbial control of remediation operations. At the same time, metallomics provides targets for potential use as biomarkers useful in monitored natural attenuation. Thus, this new field of investigation potentially can provide solutions for reclamation of the vast areas of land that are influenced by heterogeneous and varying metal contamination. Acknowledgments The authors would like to thank the EU for the funding (UMBRELLA) and the DFG for the support through GRK1257 and GSC214.

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