Influence of soil zinc concentrations on zinc sensitivity and functional diversity of microbial communities

Remedial effect and operating status of a decommissioned uranium mill tailings (UMT) repository: A micro-ecological perspective based on bacterial community

From a radioecological perspective, increasing attention has been paid to the long-term stabilisation of decommissioned uranium mill tailings (UMT) repositories. However, little is known about the evaluation of decommissioning and remedial effects of UMT repositories from a microecological perspective based on bacterial communities. Here, we analysed the distribution and structure of soil community assemblies along different vertical soil profiles in a decommissioned UMT repository and explored the impact of soil properties, including physicochemical parameters, metal(loid)s, and radionuclides, on the bacterial assemblage. We found that the α diversity of the bacterial community was unaffected by variations in different soil profiles and taxa were classified at the phylum level with small significant differences. In contrast, the bacterial community structure in and around the UMT repository showed significant differences; however, this difference was significantly affected by soil metal(loid)s and physicochemical properties rather than soil radionuclides. In addition, seven bacterial genera with significant differences between the inner and surrounding regions of the repository could be used as potential indicators to further investigate the remedial effects on soil environmental quality. These findings provide novel insights into the construction of an assessment system and in situ biomonitoring of UMT repositories from a microecological perspective based on bacterial communities.

Influence of soil properties on the development of bacterial community tolerance to Cu, Ni, Pb and Zn

Pollution-Induced Community Tolerance (PICT) is a helpful and sensitive methodology to evaluate the effect of metal pollution in soils using microorganisms as indicators. PICT was used to determine the increase of bacterial community tolerance to Cu, Ni, Pb and Zn (Δlog IC₅₀), and to assess the influence of soil properties on the development of bacterial community tolerance to Cu, Ni, Pb, and Zn. Soil samples showed a wide range of properties, such as pH (3.96-7.47), texture (13.8-31.7% clay) or organic matter (9.7-30.7%). Bacterial growth measured by the [³H]-leucine incorporation method was used as the PICT endpoint. Bacterial communities generally developed tolerance in response to Cu, Ni and Zn additions to soils. However, bacterial communities showed no tolerance to Pb, probably due to high Pb sorption in studied soils. Soil properties influenced the development of bacterial community tolerance to Cu, Ni and Zn. Effective cation exchange and a soil sorption parameter (Freundlich's linearity index) were the selected variables to estimate Δlog IC₅₀ to Cu (R² = 0.65). Clay content and Ni-soluble are the main factors to estimate Δlog IC₅₀ to Ni (R² = 0.63). Organic matter content and a sorption parameter (maximum sorption capacity of the soil from Langmuir equation) are the soil properties to estimate Δlog IC₅₀ to Zn (R² = 0.45). Most of the variables exerted their effect in soil, i.e. PICT selection phase. However, clay content affected bacterial community tolerance determination (PICT detection phase), leading to overestimated measurements of bacterial community tolerance.

High Levels of Zinc Affect Nitrogen and Phosphorus Transformation in Rice Rhizosphere Soil by Modifying Microbial Communities

Due to global industrialization in recent decades, large areas have been threatened by heavy metal contamination. Research about the impact of excessive Zn on N and P transformation in farmland has received little attention, and its mechanism is still not completely known. In this study, we planted rice in soils with toxic levels of Zn, and analyzed the plant growth and nutrient uptake, the N and P transformation, enzyme activities and microbial communities in rhizosphere soil to reveal the underlying mechanism. Results showed high levels of Zn severely repressed the plant growth and uptake of N and P, but improved the N availability and promoted the conversion of organic P into inorganic forms in rice rhizosphere soil. Moreover, high levels of Zn significantly elevated the activities of hydrolases including urease, protease, acid phosphatase, sucrase and cellulose, and dehydrogenase, as well as the abundances of Flavisolibacter, Sphingomonas, Gemmatirosa, and subgroup_6, which contributed to the mineralization of organic matter in soil. Additionally, toxic level of Zn repressed the nitrifying process by decreasing the abundance of nitrosifying bacteria Ellin6067 and promoted denitrification by increasing the abundance of Noviherbaspirillum, which resulted in decreased NO₃⁻ concentration in rice rhizosphere soil under VHZn condition.

The Response of the Soil Microbiome to Contamination with Cadmium, Cobalt and Nickel in Soil Sown with Brassica napus

Soil fertility is determined by biological diversity at all levels of life, from genes to entire biocenoses. The aim of this study was to evaluate bacterial diversity in soil contaminated with Cd2+, Co2+ and Ni2+ and sown with Brassica napus. This is an important consideration because soil-dwelling microorganisms support phytoremediation and minimize the adverse effects of heavy metals on the environment. Microbial counts, the influence (IFHM) of Cd2+, Co2+ and Ni2+ on microorganisms, the colony development (CD) index, the ecophysiological diversity (EP) index and genetic diversity of bacteria were determined under controlled conditions. Soil contamination with Cd2+, Co2+ and Ni2+ significantly influenced microbial diversity and increased the values of CD and EP indices. The tested heavy metals decreased the genetic diversity of bacteria, in particular in the phyla Actinobacteria and Proteobacteria. Bacteria of the genera Arthrobacter, Devosia, Kaistobacter, Paenibacillus, Phycicoccus, Rhodoplanes and Thermomonas were identified in both contaminated and non-contaminated soil. These bacteria are highly resistant to soil contamination with Cd2+, Co2+ and Ni2+.

The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates

Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha^-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha^-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha^-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha^-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha^-1) and excess Zn (34.1 kg ha^-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.

Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient

The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.

Implication of zinc excess on soil health

This study was undertaken to evaluate zinc's influence on the resistance of organotrophic bacteria, actinomyces, fungi, dehydrogenases, catalase and urease. The experiment was conducted in a greenhouse of the University of Warmia and Mazury (UWM) in Olsztyn, Poland. Plastic pots were filled with 3 kg of sandy loam with pHKCl - 7.0 each. The experimental variables were: zinc applied to soil at six doses: 100, 300, 600, 1,200, 2,400 and 4,800 mg of Zn(2+) kg(-1) in the form of ZnCl2 (zinc chloride), and species of plant: oat (Avena sativa L.) cv. Chwat and white mustard (Sinapis alba) cv. Rota. Soil without the addition of zinc served as the control. During the growing season, soil samples were subjected to microbiological analyses on experimental days 25 and 50 to determine the abundance of organotrophic bacteria, actinomyces and fungi, and the activity of dehydrogenases, catalase and urease, which provided a basis for determining the soil resistance index (RS). The physicochemical properties of soil were determined after harvest. The results of this study indicate that excessive concentrations of zinc have an adverse impact on microbial growth and the activity of soil enzymes. The resistance of organotrophic bacteria, actinomyces, fungi, dehydrogenases, catalase and urease decreased with an increase in the degree of soil contamination with zinc. Dehydrogenases were most sensitive and urease was least sensitive to soil contamination with zinc. Zinc also exerted an adverse influence on the physicochemical properties of soil and plant development. The growth of oat and white mustard plants was almost completely inhibited in response to the highest zinc doses of 2,400 and 4,800 mg Zn(2+) kg(-1).

Mercury induced community tolerance in microbial biofilms is related to pollution gradients in a long-term polluted river

The net toxicity of different forms of mercury, in the long-term during their transformation processes, leads to the selection of resistant bacterial cells and this result in community tolerance which is pollution induced. Accordingly, based on profiles of a bacterial community structure, analysis of Hg resistant culturable bacteria and quantification of merA genes, we assessed development of pollution induced community tolerance in a mercury-polluted gradient in the Idrijca River. TTGE analysis did not show effects of mercury pollution to bacterial community diversity, while quantification of merA genes showed that merA genes can be correlated precisely (R(2)=0.83) with the total concentration of mercury in the biofilm microbial communities in the pollution gradient.

Metal immobilization and soil amendment efficiency at a contaminated sediment landfill site: a field study focusing on plants, springtails, and bacteria

Metal immobilization may contribute to the environmental management strategy of dredged sediment landfill sites contaminated by metals. In a field experiment, amendment effects and efficiency were investigated, focusing on plants, springtails and bacteria colonisation, metal extractability and sediment ecotoxicity. Conversely to hydroxylapatite (HA, 3% DW), the addition of Thomas Basic Slag (TBS, 5% DW) to a 5-yr deposited sediment contaminated with Zn, Cd, Cu, Pb and As resulted in a decrease in the 0.01 M Ca(NO(3))(2)-extractable concentrations of Cd and Zn. Shoot Cd and Zn concentration in Calamagrostis epigejos, the dominant plant species, also decreased in the presence of TBS. The addition of TBS and HA reduced sediment ecotoxicity and improved the growth of the total bacterial population. Hydroxylapatite improved plant species richness and diversity and decreased antioxidant enzymes in C. Epigejos and Urtica dïoica. Collembolan communities did not differ in abundance and diversity between the different treatments.

Heavy metal pollution exerts reduction/adaptation in the diversity and enzyme expression profile of heterotrophic bacteria in Cochin estuary, India

Over the past three decades heavy metal pollution has increased substantially in Cochin estuary, south west coast of India. Here we studied the distribution, diversity and enzyme expression profile of culturable microbial population along a pollution gradient. The distribution of resistance against 5 mM concentration of Zn, Co, Ni and Cu was observed among 90-100% of bacterial isolates retrieved from highly polluted Eloor, whereas it was less than 40% in Vypin and Munambam. Similarly, there was a difference in the distribution and diversity of bacterial phyla with predominance of Proteobacteria in Eloor and Firmicutes in Munambam and Vypin. We observed that 75-100% of the organisms retrieved from Eloor had low levels of expression for hydrolytic enzyme. In conclusion, the heavy metal pollution in Cochin estuary brought in reduction/adaptation in the distribution, diversity and enzyme expression profile of bacteria, which may impart adverse impacts on ecosystem functioning.

An enriched stable isotope technique to estimate the availability of soil zinc to Lumbricus terrestris (L.) across a salinization gradient

An enriched stable isotope approach was developed to evaluate Zn bioavailability to Lumbricus terrestris. The decrease in (68)Zn/(66) Zn in organ tissues was used to assess the relative magnitude of the bioavailable soil Zn pool. This tool was then used to specifically evaluate bioavailability as a function of soil cation distribution. Storm-water pond soils were modified using two treatment regimens whereby H(2)O-extractable Zn was varied either by different ZnCl(2) amendments or by constant ZnCl(2) amendment followed by varying the soil cation distribution through salt amendments (NaCl or CaCl(2)). Earthworms previously equilibrated in (68) Zn-spiked soil were introduced to experimental soils, and after 2 d, removed for analysis of isotopic ratios in specific tissues. Despite a wide range of H(2)O-extractable Zn values produced by the salt treatments (0.007-24.3 mg/kg), a significant relationship between Zn turnover rate in earthworm tissues and H(2)O-extractable Zn in the salt-treated soils was not observed. Rather, considering both treatment regimens, turnover rate better correlated with Zn present in broader pools, such as that extracted by 6M HNO(3). The bioavailability of trace metals to earthworms may be poorly characterized by loosely bound fractions such as the pore water. Additionally, the turnover rate of (68)Zn in anterior organ tissues may be an effective tool to evaluate the relative magnitude of the bioavailable soil Zn pool.

Field effects of pollutants at the community level--experimental challenges and significance of community shifts for ecosystem functioning

In the Stimulation Program System-oriented Ecotoxicological Research (SSEO) three sites in The Netherlands were investigated for field effects of the grey veil of pollutants. At each site several studies were performed in order to arrive at an adequate weight of evidence and to improve causal inference of pollutant effects. This paper contains a synthesis of results of the studies, performed at one of the sites, the Demmerikse polder. This site is characterized by an anthropogenic layer of soil (in old Dutch: 'toemaakdek') on top of the natural peat. Lead, copper and zinc concentrations were elevated, with lead concentrations above a Netherlands environmental quality criterion (Intervention Value) in 66% of the samples. Issues discussed in the paper are: the sampling strategy, selection of maximum gradient and suitable community end-points, both in space and in time. Specific emphasis was given to causal inference of ecological effects of pollutants, related to direct versus indirect effects, functioning of ecosystems, normal operation range and risk assessment. The plausibility of metal effects could be demonstrated on a number of occasions. In the Demmerikse polder changes in the bacterial and nematode communities could be related significantly to metal concentrations and separated from other environmental variables, such as organic matter content and pH.

Linking pollution induced community tolerance (PICT) and microbial community structure in chronically metal polluted estuarine sediments

We tested the ability of pollution induced community tolerance (PICT) to detect the effects of chronic metal pollution on estuarine sediment microbial communities, along a gradient spanning two orders of magnitude in metal concentrations. In tandem, we investigated the associated microbial community structure using terminal restriction fragment length polymorphism (T-RFLP). Tolerance of microbes to Cu, measured as IC50 (inhibitory concentration 50%), was strongly correlated with pore water Cu concentration (r(2)=0.842). No strong correlation existed for other metals tested, highlighting the ability of PICT to identify the pollutant causing a toxic effect. There was no correlation between microbial community structure and community tolerance to metals tested, but analysis of community structure did provide some information on reasons for observed PICT response. PICT methodology used here provided a greater strength and consistency of association with pollutant concentration compared to microbial community structure and can be recommended as a sensitive indicator of metal pollution on estuarine sediment microbial communities.