Contamination of soil by copper affects the dynamics, diversity, and activity of soil bacterial communities involved in wheat decomposition and carbon storage

Soil microbial community are more sensitive to ecological regions than cropping systems in alpine annual grassland of the Qinghai-Tibet Plateau

Introduction

Modern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude.

Methods

To fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone.

Results

We found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p  < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m]  < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase.

Discussion

Our study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.

Nonlinear Effects Induced by Interactions among Functional Groups of Bacteria and Fungi Regulate the Priming Effect in Malagasy Soils

The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition abilities. Among those, stoichiometric decomposition results from FOM decomposition, which induces the decomposition of SOM by the release of exoenzymes by FOM-decomposers. Nutrient mining results from the co-metabolism of energy-rich FOM with nutrient-rich SOM by SOM-decomposers. While existing statistical approaches enable measurement of the effect of community composition (linear effect) on the PE, the effect of interactions among co-occurring populations (non-linear effect) is more difficult to grasp. We compare a non-linear, clustering approach with a strictly linear approach to separately and comprehensively capture all linear and non-linear effects induced by soil microbial populations on the PE and to identify the species involved. We used an already published data set, acquired from two climatic transects of Madagascar Highlands, in which the high-throughput sequencing of soil samples was applied parallel to the analysis of the potential capacity of microbial communities to generate PE following a ¹³C-labeled wheat straw input. The linear and clustering approaches highlight two different aspects of the effects of microbial biodiversity on SOM decomposition. The comparison of the results enabled identification of bacterial and fungal families, and combinations of families, inducing either a linear, a non-linear, or no effect on PE after incubation. Bacterial families mainly favoured a PE proportional to their relative abundances in soil (linear effect). Inversely, fungal families induced strong non-linear effects resulting from interactions among them and with bacteria. Our findings suggest that bacteria support stoichiometric decomposition in the first days of incubation, while fungi support mainly the nutrient mining of soil's organic matter several weeks after the beginning of incubation. Used together, the clustering and linear approaches therefore enable the estimation of the relative importance of linear effects related to microbial relative abundances, and non-linear effects related to interactions among microbial populations on soil properties. Both approaches also enable the identification of key microbial families that mainly regulate soil properties.

Response of soil enzyme activity and bacterial community to copper hydroxide nanofertilizer and its ionic analogue under single versus repeated applications

Nanosized agrochemicals like nanofertilizers are being applied to soils. Adverse impacts of nanofertilizers on soil microflora were reported in past studies, but only considering a single application. Repeated applications are however more likely to occur in agriculture. We investigated effects of single versus repeated applications of a copper hydroxide nanofertilizer formulation (NFF) on soil enzyme activity and bacterial community. One or three applications were performed within 21 days to achieve same final level of Cu in soil (48 mg(Cu)/kg: the recommended dose of NFF). Besides, the active ingredient (i.e., copper hydroxide nanotubes (NT)) and dispersing agent (DA) of NFF, and an ionic fertilizer (i.e., CuSO₄) were examined. Fluorescein diacetate hydrolase (FDAse), N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP), and urease (URE) showed negligible changes in the activities between the control and DA treatment. Bacterial community abundance, composition and diversity exhibited similar phenomena. Exposures to copper hydroxide NFF and NT or CuSO₄ enhanced the activities of FDAse and NAG, weakened the activity of URE, and showed negligible changes in the LAP activity irrespective of single and repeated applications. Concentrations of NO₃^--N and NH₄⁺-N in soil were also affected by the application mode of NFF. More importantly, responses of soil bacterial community to copper hydroxide NFF were highly dependent on its application mode, whereas similar responses were observed in the CuSO₄ treatment regardless of single or repeated applications. This study provided new insights into environmental risk of copper hydroxide NFF that were ignored in previous studies using a single exposure.

Bioleaching for environmental remediation of toxic metals and metalloids: A review on soils, sediments, and mine tailings

Owing to industrial evolution, a huge mass of toxic metals, including Co, Cu, Cr, Mn, Ni, Pb, and Zn, and metalloids, such as As and Sb, has inevitably been released into the natural environment and accumulated in soils or sediments. Along with modern industrialization, many mineral mines have been explored and exploited to provide materials for industries. Mining industries also generate a vast amount of waste, such as mine tailings, which contain a high concentration of toxic metals and metalloids. Due to the low economic status, a majority of mine tailings are simply disposed into the surrounding environments, without any treatment. The mobilization and migration of toxic metals and metalloids from soils, sediments, and mining wastes to water systems via natural weathering processes put both the ecological system and human health at high risk. Considering both economic and environmental aspects, bioleaching is a preferable option for removing the toxic metals and metalloids because of its low cost and environmental safety. This chapter reviews the recent approaches of bioleaching for removing toxic metals and metalloids from soils, sediments, and mining wastes. The comparison between bioleaching and chemical leaching of various waste sources is also discussed in terms of efficiency and environmental safety. Additionally, the advanced perspectives of bioleaching for environmental remediation with consideration of other influencing factors are reviewed for future studies and applications.

Prediction of copper ions adsorption by attapulgite adsorbent using tuned-artificial intelligence model

Copper (Cu) ion in wastewater is considered as one of the crucial hazardous elements to be quantified. This research is established to predict copper ions adsorption (Ad) by Attapulgite clay from aqueous solutions using computer-aided models. Three artificial intelligent (AI) models are developed for this purpose including Grid optimization-based random forest (Grid-RF), artificial neural network (ANN) and support vector machine (SVM). Principal component analysis (PCA) is used to select model inputs from different variables including the initial concentration of Cu (IC), the dosage of Attapulgite clay (Dose), contact time (CT), pH, and addition of NaNO₃ (SN). The ANN model is found to predict Ad with minimum root mean square error (RMSE = 0.9283) and maximum coefficient of determination (R² = 0.9974) when all the variables (i.e., IC, Dose, CT, pH, SN) were considered as input. The prediction accuracy of Grid-RF model is found similar to ANN model when a few numbers of predictors are used. According to prediction accuracy, the models can be arranged as ANN-M5> Grid-RF-M5> Grid-RF-M4> ANN-M4> SVM-M4> SVM-M5. Overall, the applied statistical analysis of the results indicates that ANN and Grid-RF models can be employed as a computer-aided model for monitoring and simulating the adsorption from aqueous solutions by Attapulgite clay.

Copper accumulation in agricultural soils: Risks for the food chain and soil microbial populations

The long-term use of Cu-based fungicides at doses of several kilograms per hectare stimulated a wide debate about the human health and environmental risks of the progressive accumulation of Cu in agricultural soils. Here, the health risks due to copper accumulation in agricultural soils were evaluated with a survey in intensive agricultural land of the Campania region (Italy), aiming to evaluate Cu accumulation in food crops. The health risk due to dietary exposure was estimated by using the Hazard Quotient (HQ), calculated as the ratio between the average daily dose and the reference dose of copper, suggesting that when HQ > 1 there is a potential risk for consumers. According to a survey of soils with a Cu content up to 217 mg kg^-1, no foodstuffs showed dietary risks. Nevertheless, the contribution of Cu contained in these foodstuffs to the overall intake of Cu by consumers could increase health risks since such risks must be evaluated on the basis of the whole standard diet by quantifying the Cu content not only in vegetables and fruits but also in other sources, such as cereals, not cultivated in the study area and thus not considered in this paper. The environmental risks due to copper accumulation in agricultural soils were then evaluated with a field experiment in a soil characterized by a very high Cu concentration (up to 1700 mg kg^-1), aiming to study the impacts of Cu on native soil microorganisms. The study of the microbiota highlighted that the presence of Cu in soil did not reduce the total richness and diversity of microorganisms, which were not related to increasing concentrations of Cu in the soil. Nevertheless, Cu contamination was found to exert significant selection pressure on the soil microbiota, as shown by beta diversity and correlation analysis between taxa and Cu content.

Effects of heavy metals on organic matter decomposition in inundated soils: Microcosm experiment and field examination

Microcosm and field investigation were conducted to examine the effects of heavy metals on the decomposition and accumulation of organic carbon in contaminated Mersey estuarine floodplain, northwest England. The results show that inhibition of microbially mediated decomposition of organic matter occurred in the water-inundated soils. However, individual heavy metals had differential effects on the inhibition of soil organic matter decomposition with arsenic and copper being much stronger, as compared to other investigated heavy metals. The weak inhibitory effects of chromium on organic matter decomposition was due to the conversion of highly toxic Cr(VI) to less toxic Cr(III) under reducing conditions. Lead also had a weaker capacity to inhibit organic matter decomposition due to its low solubility. It was surprising that the same phenomenon was not clearly observed during the field examination. The inhibitory effects of heavy metals on soil organic matter decomposition could be curtained under field conditions. pH, Eh and EC played more important roles, as compared to soil-borne heavy metals, in affecting the soil carbon dynamics in the contaminated Mersey estuarine floodplain.

Assessing the Impacts of Cu(OH)2 Nanopesticide and Ionic Copper on the Soil Enzyme Activity and Bacterial Community

Nanopesticides are being introduced in agriculture, and the associated environmental risks and benefits must be carefully assessed before their widespread agricultural applications. We investigated the impacts of a commercial Cu(OH)₂ nanopesticide formulation (NPF) at different agricultural application doses (e.g., 0.5, 5, and 50 mg of Cu kg^-1) on enzyme activities and bacterial communities of loamy soil (organic matter content of 3.61%) over 21 days. Results were compared to its ionic analogue (i.e., CuSO₄) and nano-Cu(OH)₂, including both the commercial unformulated active ingredient of NPF (AI-NPF) and synthesized Cu(OH)₂ nanorods (NR). There were negligible changes in the activity of acid phosphatase, regardless of exposure dose, whereas significant (p < 0.05) variations in activities of invertase, urease, and catalase were observed at a dose of 5 mg kg^-1 or higher. Invertase activity decreased with an increasing bioavailable Cu concentration in soil under various treatments. In comparison to CuSO₄, both Cu(OH)₂ nanopesticide (i.e., NPF) and nano-Cu(OH)₂ (i.e., AI-NPF and NR) caused a significant (p < 0.05) inhibition of urease activity, wherein a significant (p < 0.05) increase in the activity of catalase was observed, representing serious oxidative stress. Accordingly, NPF, AI-NPF, and NR differently affected soil bacterial abundance, diversity, and community compared to CuSO₄, which could have resulted from the changes in the bioavailable Cu concentration as a result of the distinct nature of copper spiked (i.e., nano form versus salt). Moreover, minor differences in the soil enzyme activity and bacterial community were observed between NPF and AI-NPF, reflecting that the impact of the Cu(OH)₂ nanopesticide was primarily attributed to the presence of nano-Cu(OH)₂. In total, the impacts of nano-Cu(OH)₂ on the soil bacterial community and enzyme activity tested in this study differed from CuSO₄, shedding light on the environmental risks of the Cu(OH)₂ nanopesticide in the long run.

Stability of in situ immobilization of trace metals with different amendments revealed by microbial 13C-labelled wheat root decomposition and efflux-mediated metal resistance of soil bacteria

The aim of the present study was to prove the long-term efficiency of the amendments zerovalent iron grit, zeolite, and Divergan® for trace metal remediation in heavily contaminated soils and to attain a recovery of microbial functionality and diversity by remediation. For immobilization of the trace metals the amendments zerovalent iron grit, natural zeolite, and Divergan® were used. Trace metal total and mobile contents were determined and bacterial communities were assessed after a SIP experiment with ¹³C-labelled wheat root by Ion-Torrent Sequencing targeting the bacterial 16S rRNA gene and two trace metal resistant genes for copper and cadmium (copA and czcA gene). The results show that the remediation effect of the three amendments is still stable after five years. The mobile trace metal contents were significantly (≤0.001) reduced in all treatments, except the Cu content in the zeolite treatment. A higher diversity in active metabolizing and growing soil bacteria was observed in remediated soils as compared to the non-remediated control, especially for the Divergan® treatment. The bacterial genera Kribbella, Glycomyces, Inquilinus, Nocardioides, and Lysobacter are the most significantly enriched genera in the ¹³C fractions of the treated samples. The occurrence of bacterial families, which could be identified carrying efflux-mediated metal resistance genes for Cd/Zn and Cu, were reduced in the remediated soils as compared to the non-remediated control. The most abundant bacterial family for the copA and the czcA gene is Xanthomonadaceae. The pH-value and the trace metal concentration could be identified as key drivers of bacterial community composition, and functions in trace metal contaminated soils and remediated soils.

Future Options for Sewage and Drainage Systems Three Scenarios for Transitions and Continuity

The challenge of sustainable development requires cities to aim for drastic improvements in the systems that support its vital functions. Innovating these systems can be extremely hard, and might take lots of time. A transparent and democratic strategy is important to guarantee support for change. Such a process should aim at developing consensus regarding a basic vision to guide the process of systems change. This paper sketches future options for the development of sanitation- and urban drainage systems in industrialized economies. It will provide an analysis of relevant trends for sewage system innovation. In history, sewage systems have emerged from urban sewage and precipitation removal systems, to urban sewage and precipitation removal and cleaning systems. The challenge for the future is recovering energy and resources from sewage systems while maintaining/improving its sanitary service and lowering its emissions.

Soil microbial diversity drives the priming effect along climate gradients: a case study in Madagascar

The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with ¹³C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.

High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils

To explore how heavy metal contamination in Chromite Ore Processing Residue (COPR) disposal sites determine the dissimilarities of indigenous microbial communities, 16S rRNA gene MiSeq sequencing and advanced statistical methods were applied. 13 soil samples were collected from three COPR disposal sites in Mouding of southwestern, Shangnan of northwestern and Yima of central China. The results of analyses of variance (ANOVA), similarities (ANOSIM), and non-metric multidimensional scaling (NMDS) showed that the structural diversity of the microbial communities in the samples with high total chromium (Cr) content (more than 300 mg kg^-1; High group) were significantly lesser than in the Low group (less than 90 mg kg^-1) regardless of their geographical distribution. But their diversity had virtually rehabilitated under the pressures of long-term metal contamination. Furthermore, the similarity percentage (SIMPER) analysis indicated that the major dissimilarity contributors Micrococcaceae, Delftia, and Streptophyta, possibly having Cr(VI)-resistant and/or Cr(VI)-reducing capability, were dominant in the High group, while Ramlibacter and Gemmatimonas with potential resistances to other heavy metals were prevalent in the Low group. In addition, the multivariate regression tree (MRT), aggregated boosted tree (ABT), and Mantel test revealed that total Cr content affiliated with Cr(VI) was the principal factor shaping the dissimilarities between the soil microbial communities in the COPR sites. Our findings provide a deep insight of the influence of these heavy metals on the microbial communities in the COPR disposal sites and will facilitate bioremediation on such site.

Intervals and Number of Applications of Acibenzolar-S-Methyl for the Control of Bacterial Spot on Processing Tomato

Acibenzolar-S-methyl (ASM) is a plant activator that triggers systemic acquired resistance that is labeled for use in Brazil for managing tomato bacterial spot. The aim of this study was to define the optimum relationship between interval and number of applications of ASM for the most efficacious control of bacterial spot on processing tomato. Four intervals between applications (4, 7, 10, and 14 days) and four application frequencies (4, 6, 8, and 10 applications) were evaluated in five trials performed between 2010 and 2011 in Brasília, Distrito Federal, and in Morrinhos, in the state of Goiás. Copper hydroxide (CH) was applied after ASM applications to complete 13 applications per growing season. Two check treatments were added: standard CH weekly applications and untreated. The following variables were evaluated: severity of bacterial spot, yield, percentage of ripe and rotten fruit, soluble solids content, and the benefit/cost ratio. Disease severity varied between treatments in three trials and yield varied in two trials. A greater number of applications resulted in a reduction of bacterial spot, and the ideal interval between applications was between 8 to 10 days. However, there was a reduction in yield with 10 ASM applications. The temporal effect of ASM applications on bacterial spot severity was evaluated under greenhouse conditions. Reduction in disease severity was observed up to 6 days following ASM application. Additionally, the weekly treatment of seven applications of ASM followed by six applications of CH was compared with a standard program of CH under commercial production conditions in Itaberaí, Goiás, where bacterial spot occurred naturally. The program with ASM and CH resulted in significantly less foliar disease severity than the standard program, which did not result in yield gains. In addition, no differences were detected between the two programs for soluble solids content, industrial yield, plant height, and percentage of ripe and rotten fruit.

Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil

The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.

Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (¹²C) or stable-isotope-labeled (¹³C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the ¹³C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes.

The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.

Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria

Bacteria responsible for cellulose hydrolysis in situ are poorly understood, largely because of the relatively recent development of cultivation-independent methods for their detection and characterization. This study combined DNA stable-isotope probing (DNA-SIP) and metagenomics for identifying active bacterial communities that assimilated carbon from glucose and cellulose in Arctic tundra microcosms. Following DNA-SIP, bacterial fingerprint analysis of gradient fractions confirmed isotopic enrichment. Sequenced fingerprint bands and clone library analysis of 16S rRNA genes identified active bacterial taxa associated with cellulose-associated labelled DNA, including Bacteroidetes (Sphingobacteriales), Betaproteobacteria (Burkholderiales), Alphaproteobacteria (Caulobacteraceae), and Chloroflexi (Anaerolineaceae). We also compared glycoside hydrolase metagenomic profiles from bulk soil and heavy DNA recovered from DNA-SIP incubations. Active populations consuming [(13)C]glucose and [(13)C]cellulose were distinct, based on ordinations of light and heavy DNA. Metagenomic analysis demonstrated a ∼3-fold increase in the relative abundance of glycoside hydrolases in DNA-SIP libraries over bulk-soil libraries. The data also indicate that multiple displacement amplification introduced bias into the resulting metagenomic analysis. This research identified DNA-SIP incubation conditions for glucose and cellulose that were suitable for Arctic tundra soil and confirmed that DNA-SIP enrichment can increase target gene frequencies in metagenomic libraries.

The combined effects of atrazine and lead (Pb): relative microbial activities and herbicide dissipation

The experiment was conducted to investigate the effects of single and combined pollution from different concentrations of atrazine (field rate, FR, 2.0 mg kg(-1) and 5 times FR, 10 mg kg(-1)) and lead (Pb) (300 mg kg(-1) and 600 mg kg(-1)) on enzyme activity, basal soil respiration (BSR), and net nitrogen (N) mineralization (NNM) in soil after exposure for 0, 7, 14, 21, and 28 days. In addition, residual atrazine was measured in the samples of combined contamination. Results showed that the notable effects of either or both contaminants on the microbial activity and biological processes. Enzyme activity data demonstrated that the order of sensitivity to contamination was urease>invertase>catalase. BSR was strongly stimulated by atrazine/Pb at the early exposure (0-7 days for single contaminant and 7-14 days for combined contaminants). The stimulation effects on BSR were higher at low concentrations of the contamination (FR and Pb300). The combined treatments of 5FR+Pb600 inhibit BSR and NNM. Overall, the parameters associated with N cycling (urease and NNM) were more sensitive than others. Both Pb concentrations (300 and 600 mg/kg) had little influence on the dissipation of high concentrations of atrazine (5FR) during the 28-day-incubation. This study has provided useful information on potential ecotoxicology effects of combined contamination of atrazine and Pb on relative microbial biological process.

Usefulness of pioneer vegetation for the phytomanagement of metal(loid)s enriched tailings: grasses vs. shrubs vs. trees

The goal of this work was to assess the selection of the most suitable combination of plant species for the phytomanagement of mine tailings, by comparing among different plant life-forms (grasses, shrubs and trees). A comparison on induced rhizosphere changes generated by four plant species (the grass Piptatherum miliaceum, the shrub Helichrysum decumbens, and the trees, Pinus halepensis and Tetraclinis articulata) and high density vegetation patches (fertility islands) at a mine tailing located at Southeast Spain and the description of their physiological status employing stable isotopes analyses were carried out. The edaphic niches for plant growth were determined by salinity, organic matter and total soil nitrogen while metal(loid)s concentrations played a minor role. Induced changes in plant rhizospheres had a significant impact in soil microbiology. While grasses and shrubs may play an important role in primary ecological succession, trees seem to be the key to the development of fertility islands. The low δ(15)N values (-8.00‰) in P. halepensis needles may reflect higher ectomycorrhizal dependence. Large differences in leaf δ(18)O among the plant species indicated contrasting and complementary water acquisition strategies. Leaf δ(13)C values (-27.6‰) suggested that T. articulata had higher water use efficiency than the rest of species (-29.9‰). The implement of a diverse set of plant species with contrasting life forms for revegetating tailings may result in a more efficient employment of water resources and a higher biodiversity not only in relation to flora but soil microbiology too.

Ecotoxicity of Cr, Cd, and Pb on two Mediterranean soils

Three potentially toxic elements [chromium (Cr), lead (Pb), and cadmium (Cd)] were tested to assess their effects on two soils of different properties and origin. The soils were a granitic soil (Haplic Arenosol), which meets the requirements of OECD ecotoxicity testing, and a calcareous soil (Calcaric Regosol) with properties often found in the Mediterranean areas. The metal concentrations used ranged from 0.001 to 5,000 mg kg(-1) soil. The effects on soil microbial activity and community composition (respirometry and polymerase chain reaction-denaturing gradient gel electrophoresis analysis), as well as the effects on plant germination and elongation (Lactuca sativa), were assessed. The toxicity of the soil water extracts was also evaluated by the growth inhibition of algal populations (Pseudokirschneriella subcapitata). Cr showed the highest level of toxicity to soil organisms in the assays performed because this element remains in soil as anionic form and is less retained by the soil solid matrix than Cd and Pb. The lowest observed-adverse effect level for Cr ranged from approximately 0.1 mg kg(-1) [substrate induced respiration (SIR) test for the granitic soil] to 10 mg kg(-1) (basal respiration and SIR tests for the calcareous soil). For Pb (SIR) and Cd (SIR and alga tests), these levels were approximately 100 mg kg(-1). Germination and algal tests showed higher sensitivity in Regosol soil than in Arenosol soil for Cr due to differences in the bioavailability between the soils. In the cases or areas where alkaline soils are abundant, these should also be considered in laboratory ecotoxicity testing to avoid underestimation of ecotoxicological risks.

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.

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a (13)C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of (12)CO(2) and (13)CO(2) were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum.

Soil microbial diversity: Methodological strategy, spatial overview and functional interest

Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.