Trace metal exposure of soil bacteria depends on their position in the soil matrix

Effects of Mercury Contamination on Microbial Diversity of Different Kinds of Soil

Soil microorganisms promote the recovery of contaminated soil by influencing the cyclic transformation of various substances. In this study, we investigated the impact of mercury pollution on the structure, composition, and main populations of soil microbial communities using a high-throughput sequencing method and observed that mercury pollution significantly influenced the diversity, structure, and distribution pattern of microbial communities. Furthermore, during mercury pollution, the Shannon and Chao indices decreased for the bacterial communities and increased for the fungal communities. Mercury pollution mainly reduced the relative abundances of Proteobacteria (16.2−30.6%), Actinomycetes (24.7−40.8%), and other dominant bacterial phyla. The relative abundance of Ascomycota decreased by 17.4% and 16.7% in alkaline and neutral soils, respectively, whereas the relative abundance of unclassified_k_Fungi increased by 26.1% and 28.6%, respectively. In acidic soil, Ascomycota increased by 106.3% and unclassified_k_Fungi decreased by 71.2%. The results of redundancy and correlation analyses suggested that soil microbial diversity was significantly correlated with soil properties such as pH, cation exchange capacity, soil organic carbon, and total nitrogen (p < 0.05) under different treatments. Our findings highlight the impact of Hg pollution on soil microbial communities, thereby providing a theoretical foundation for the bioremediation of soil Hg pollution.

Microbial Metal Resistance within Structured Environments is Inversely Related to Environmental Pore Size

The physical environments in which microorganisms naturally reside rarely have homogeneous structure, and changes in their porous architecture can have a profound effect on microbial activities - effects that are not typically captured in conventional laboratory studies. Here, to investigate the influence of environmental structure on microbial responses to stress, we constructed structured environments with different pore properties (determined by X-ray Computed Tomography). First, using glass beads in different arrangements and inoculated with the soil yeast Saitozyma podzolica, increases in the average equivalent spherical diameters (ESD) of a structure's porous architecture led to decreased survival of the yeast under a toxic metal challenge. This relationship was reproduced when yeasts were introduced into additively-manufactured lattice structures, comprising regular arrays with ESDs comparable to those of the bead structures. The pore ESD-dependency of metal resistance was not attributable to differences in cell density in micro-environments delimited by different pore sizes, supporting the inference that pore size specifically is the important parameter here in determining microbial survival of stress. These findings highlight the importance of the physical architecture of an organism's immediate environment for its response to environmental perturbation, while offering new tools for investigating these interactions in the laboratory. IMPORTANCE Interactions between cells and their structured environments are poorly understood but have significant implications for organismal success in both natural and non-natural settings. This work uses a multidisciplinary approach to develop laboratory models with which the influence of a key parameter of environmental structure - pore size - on cell activities can be dissected. Using these new methods in tandem with additive manufacturing, we demonstrate that resistance of yeast soil-isolates to stress (from a common metal pollutant) is inversely related to pore size of their environment. This has important ramifications for understanding how microorganisms respond to stress in different environments. The findings also establish new pathways for resolving the effects of physical environment on microbial activity, enabling important understanding that is not readily attainable with traditional bulk-sampling and analysis approaches.

Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?

Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.

Adaptive Evolution of Escherichia coli to Ciprofloxacin in Controlled Stress Environments: Contrasting Patterns of Resistance in Spatially Varying versus Uniformly Mixed Concentration Conditions

A microfluidic gradient chamber (MGC) and a homogeneous batch culturing system were used to evaluate whether spatial concentration gradients of the antibiotic ciprofloxacin allow development of greater antibiotic resistance in Escherichia coli strain 307 (E. coli 307) compared to exclusively temporal concentration gradients, as indicated in an earlier study. A linear spatial gradient of ciprofloxacin and Luria-Bertani broth (LB) medium was established and maintained by diffusion over 5 days across a well array in the MGC, with relative concentrations along the gradient of 1.7-7.7× the original minimum inhibitory concentration (MIC_original). The E. coli biomass increased in wells with lower ciprofloxacin concentrations, and only a low level of resistance to ciprofloxacin was detected in the recovered cells (∼2× MIC_original). Homogeneous batch culture experiments were performed with the same temporal exposure history to ciprofloxacin concentration, the same and higher initial cell densities, and the same and higher nutrient (i.e., LB) concentrations as in the MGC. In all batch experiments, E. coli 307 developed higher ciprofloxacin resistance after exposure, ranging from 4 to 24× MIC_original in all replicates. Hence, these results suggest that the presence of spatial gradients appears to reduce the driving force for E. coli 307 adaptation to ciprofloxacin, which suggests that results from batch experiments may over predict the development of antibiotic resistance in natural environments.

Differential effects of nickel dosages on in vitro and in vivo seed germination and expression of a high affinity nickel-transport family protein (AT2G16800) in trembling aspen (Populus tremuloides)

It has been demonstrated that a number of metals including mercury (Hg), zinc (Zn), cadmium (Cd), cobalt (Co), lead (Pb), copper (Cu), and nickel (Ni) decrease seed germination rates and plant growth. The threshold levels of metal toxicity on seed germination, plant development, and gene regulation have not been studied in detail. The main objective of this study was to assess in vitro and in vivo the effects of different doses of nickel on Trembling aspen (Populus tremuloides) seed germination and regulation of the high affinity nickel transporter family protein (AT2G16800) gene. The in vitro assays showed that Nickel completely inhibited seed germination even at the lowest concentration of 0.401 mg Ni per mL (in media) tested. However, when the same concentration of nickel (150 mg Ni per 1 kg of dry soil) was added to soil samples, during the vivo assays, almost all of the seeds germinated. Significant inhibition of seed germination was observed when soil samples were treated with at least 400 mg/kg of Ni. No damages were observed on growing seedlings treated with 150, 400, and 800 mg/kg of Ni. Only the highest dose of 1, 600 mg/kg resulted in visible leaf and stem damages and reduced growth on 75% of seedlings. A significant repression of the AT2G16800 gene was observed for the 400, 800, and 1600 mg/kg of nickel treatments compared to the water control with the lowest level of expression observed in samples treated with 800 mg/kg of Ni. Results of this study suggest that P. tremuloides populations will likely be sustainable for long term in sites that are highly contaminated with Ni including mining regions since the bioavailable amount of this metal is usually below 400 mg/kg in Canada.

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.

Comparison of aerobic and anaerobic [3H]leucine incorporation assays for determining pollution-induced bacterial community tolerance in copper-polluted, irrigated soils

Pollution-induced community tolerance (PICT) constitutes a sensitive and ecologically relevant impact parameter in ecotoxicology. We report the development and application of a novel anaerobic [(3) H]leucine incorporation assay and its comparison with the conventional aerobic [(3) H]leucine incorporation assay for PICT detection in soil bacterial communities. Selection of bacterial communities was performed over 42 d in bulk soil microcosms (no plants) and in rice (Oryza sativa) rhizosphere soil mesocosms. The following experimental treatments were imposed using a full factorial design: two soil types, two soil water regimes, and four Cu application rates (0, 30, 120, or 280 µg g(-1)). Bacterial communities in bulk soil microcosms exhibited similar Cu tolerance patterns when assessed by aerobic and anaerobic PICT assays, whereas aerobic microorganisms tended to be more strongly selected for Cu tolerance than anaerobic microorganisms in rhizosphere soil. Despite similar levels of water-extractable Cu, bacterial Cu tolerance was significantly higher in acid sulfate soil than in alluvial soil. Copper amendment selected for significant PICT development in soils subjected to alternate wetting and drying, but not in continuously flooded soils. Our results demonstrate that soil bacterial communities subjected to alternate wetting and drying may be more affected by Cu than bacterial communities subjected to continuous flooding. We conclude that the parallel use of anaerobic and aerobic [(3) H]leucine PICT assays constitutes a valuable improvement over existing procedures for PICT detection in irrigated soils and other redox gradient environments such as sediments and wetlands.

Organic matter control of mercury and lead toxicity in mor layers

This study evaluated the effect of organic matter composition on Hg and Pb toxicity for heterotrophic respiration in mor layers in long-term in vitro dose-response experiments. Pb proved to be a more potent toxin than Hg at comparable metal additions. The degree of litter decomposition and fragmentation and background Hg concentration levels were key factors determining metal toxicity. Higher sensitivity to metal additions in the fermentation layer than in litter and humification layers was corroborated. The role of organic matter composition was further examined in litter after structural disintegration by milling, which significantly increased the sensitivity of heterotrophic respiration to metal additions. A threshold value causing 5% reduction in heterotrophic respiration was estimated at 800 microg Hg kg(-1). In boreal forests in the northern hemisphere, the mean regional Hg concentrations in mor layers amount to approximately half this threshold value.

Survival and spread of Shiga toxin-producing Escherichia coli in alpine pasture grasslands

AIMS

To determine the fate of Shiga toxin-producing Escherichia coli (STEC) strains defecated onto alpine grassland soils.

METHODS AND RESULTS

During the summers of 2005 and 2006, the field survival of STEC was monitored in cowpats and underlying soils in four different alpine pasture units. A most probable number (MPN)-PCR stx assay was used to enumerate STEC populations. STEC levels ranged between 3.9 and 5.4 log(10) CFU g(-1) in fresh cowpats and slowly decreased until their complete decay (inactivation rates k < 0.04 day(-1)). PFGE typing of STEC strains isolated from faecal and soil samples assessed the persistence of various clonal types for at least 2 months in cowpats and their vertical dispersal down through the soil at a depth up to at least 20 cm. STEC cells counts in soil were always below 2 log(10) CFU g(-1), regardless of the pasture unit investigated. The soil became rapidly free of detectable STEC once the cowpat had decomposed. The eight STEC strains isolated during this study belonged to six distinct serotypes and tested positive for the gene(s) stx2, including the stx2g and stx2 NV206 variants.

CONCLUSIONS

STEC were able to persist in cowpats and disseminate down through the soil but were unable to establish.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides useful information concerning the ecology of STEC in alpine pasture grasslands and may have implications for land and cattle management.

Increased pollution-induced bacterial community tolerance to sulfadiazine in soil hotspots amended with artificial root exudates

Sulfadiazine (SDZ) residues constitute an important pollutant in soils that may increase environmental reservoirs of antibiotic resistance. Our primary aim was to compare the development of pollution-induced community tolerance (PICT) to SDZ concentration levels in bulk soil and nutrient amended soil hotspots. Agricultural soil microcosms were amended with different concentrations of SDZ with or without weekly additions of artificial root exudates corresponding to realistic rhizodeposition rates. Bacterial community tolerance to SDZ residues, as determined by the [3H]leucine incorporation technique, increased progressively with elevated SDZ exposure, and was significantly increased in soil hotspots (LOEC of 1microg kg(-1)). An alternative PICT approach based on single-cell esterase probing by flow cytometry failed to demonstrate SDZ impacts. Bacterial growth rates ([3H]leucine incorporation) were significantly reduced in both bulk soil and hotspots 24 h after amendment with environmentally relevant concentrations of SDZ, while soil respiration remained unaffected even at 100 microg SDZ g(-1). Our study for the first time demonstrates a drastically increased PICT response of a soil bacterial community due to increased carbon substrate amendment per se. Hence, hotspot soil environments such as rhizosphere and manure-soil interfaces may comprise key sites for proliferation of bacteria that are resistant or tolerant to antibiotics.

Linking rhizoplane pH and bacterial density at the microhabitat scale

Ion-selective microelectrodes and a novel micro-sampling technique were used to investigate the relationship in field soil between Brassica napus rhizoplane pH and bacterial density at a spatial scale approximating a microhabitat. Bacterial densities were observed to increase with decreasing pH, rhizoplane pH measurements varied by up to 1 pH unit over a distance of 1 mm and the mean pH of the rhizoplane at the root base varied by more than 1 pH unit between plants. These findings highlight the appropriateness of investigating the interactions between bacterial communities and their environment at the micro-spatial scale and the utility of the micro-sampling method.

Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2(-) and O2 concentrations

The oxygen control of denitrification and its emission of NO/N2O/N2 was investigated by incubation of Nycodenz-extracted soil bacteria in an incubation robot which monitors O2, NO, N2O and N2 concentrations (in He+O2 atmosphere). Two consecutive incubations were undertaken to determine (1) the regulation of denitrification by O2 and NO2(-) during respiratory O2 depletion and (2) the effects of re-exposure to O2 of cultures with fully expressed denitrification proteome. Early denitrification was only detected (as NO and N2O) at <or=80 microM O2 in treatments with NO2(-), and the rates were three orders of magnitude lower than the rates observed after oxygen depletion (with N2 as the primary product). When re-exposed to O2, the cultures continued to denitrify (8-55% of the rates during the foregoing anoxic phase), but its main product was N2O. The N2O reductase activity recovered as oxygen was being depleted. The results suggest that expression of the denitrifying proteome may result in significant subsequent aerobic denitrification, and this has profound implications for the understanding and modelling of denitrification and N2O emission. Short anoxic spells caused by transient flooding during rainfall, could lead to subsequent unbalanced aerobic denitrification, in which N2O is a major end product.

Establishment and early succession of a multispecies biofilm composed of soil bacteria

Most soil bacteria are likely to be organized in biofilms on roots, litter, or soil particles. Studies of such biofilms are complicated by the many nonculturable species present in soil, as well as the interspecific bacterial interactions affecting biofilm biology. We in this study describe the development of a biofilm flow model and use this system to establish an early (days 1-7) flow biofilm of soil bacteria from agricultural soil. It was possible to follow the succession in the early flow biofilm by denaturing gradient gel electrophoresis (DGGE) analysis, and it was demonstrated that the majority of strains present in the biofilm were culturable. We isolated and identified nine strains, all associated with unique DGGE profiles, and related their intrinsic phenotypes regarding monospecies biofilm formation in microtiter plates and planktonic growth characteristics to the appearance of the strains in the flow biofilm. The ability of the strains to attach to and establish biofilm in microtiter plates was reflected in their flow biofilm appearance, whereas no such reflection of the planktonic growth characteristics in the flow biofilm appearance was observed. One strain-specific synergistic interaction, strongly promoting biofilm formation of two strains when cultured together in a dual-species biofilm, was observed, indicating that some strains promote biofilm formation of others. Thus, the biofilm flow model proved useful for investigations of how intrinsic phenotypic traits of individual species affect the succession in an early soil biofilm consortium.

Experimental evaluation and mathematical modeling of microbially enhanced tetrachloroethene (PCE) dissolution

Experiments to assess metabolic reductive dechlorination (chlororespiration) at high concentration levels consistent with the presence of free-phase tetrachloroethene (PCE) were performed using three PCE-to-cis-1,2-dichloroethene (cis-DCE) dechlorinating pure cultures (Sulfurospirillum multivorans, Desulfuromonas michiganensis strain BB1, and Geobacter lovleyi strain SZ) and Desulfitobacterium sp. strain Viet1, a PCE-to-trichloroethene (TCE) dechlorinating isolate. Despite recent evidence suggesting bacterial PCE-to-cis-DCE dechlorination occurs at or near PCE saturation (0.9-1.2 mM), all cultures tested ceased dechlorinating at approximately 0.54 mM PCE. In the presence of PCE dense nonaqueous phase liquid (DNAPL), strains BB1 and SZ initially dechlorinated, but TCE and cis-DCE production ceased when aqueous PCE concentrations reached inhibitory levels. For S. multivorans, dechlorination proceeded at a rate sufficient to maintain PCE concentrations below inhibitory levels, resulting in continuous cis-DCE production and complete dissolution of the PCE DNAPL. A novel mathematical model, which accounts for loss of dechlorinating activity at inhibitory PCE concentrations, was developed to simultaneously describe PCE-DNAPL dissolution and reductive dechlorination kinetics. The model predicted that conditions corresponding to a bioavailability number (Bn) less than 1.25 x 10(-2) will lead to dissolution enhancement with the tested cultures, while conditions corresponding to a Bn greater than this threshold value can result in accumulation of PCE to inhibitory dissolved-phase levels, limiting PCE transformation and dissolution enhancement. These results suggest that microorganisms incapable of dechlorinating at high PCE concentrations can enhance the dissolution and transformation of PCE from free-phase DNAPL.

Decreased abundance and diversity of culturable Pseudomonas spp. populations with increasing copper exposure in the sugar beet rhizosphere

Recent studies have indicated that culturable bacteria constitute highly sensitive bioindicators of metal-induced stress in soil. We report the impact of different copper exposure levels characteristic of contaminated agricultural soils on culturable Pseudomonas spp. in the rhizosphere of sugar beet. We observed that the abundance of Pseudomonas spp. was much more severely affected than that of the general population of culturable heterotrophic bacteria by copper. For diversity assessment, Pseudomonas isolates were divided into operational taxonomic units based on amplified ribosomal DNA restriction analysis and genomic PCR fingerprinting by universally primed PCR. Copper significantly decreased the diversity of Pseudomonas spp. in the rhizosphere and significantly increased the frequency of copper-resistant isolates. Concomitant chemical and biological analysis of copper in the rhizosphere and in bulk soil extracts indicated no rhizosphere effect and a relatively low copper bioavailability in the studied soil, suggesting that the observed effects of copper may occur at lower total concentrations in other soils. We conclude that culturable Pseudomonas sensu stricto constitutes a highly sensitive and relevant bioindicator group for the impact of copper in the rhizosphere habitat, and suggest that continued application of copper to agricultural soils poses a significant risk to successful rhizosphere colonization by Pseudomonas spp.