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Rhodococcus folensis sp. nov., an orange-red-pigmented bacterium from mining soil.

Mining-impacted environments represent chemically complex ecosystems that may harbor metabolically versatile and pigment-producing microorganisms. During a survey of pigment-producing bacteria from abandoned mining soil in Trabzon, Türkiye, a red-pigmented strain, designated FMA22T, was isolated and characterized using a polyphasic taxonomic approach. 16 S rRNA gene sequence analysis placed the strain within the genus Rhodococcus, showing the highest similarity to R. corynebacterioides DSM 20,151T (99.57%), R. kroppenstedtii DSM 44908ᵀ (99.06%) and R. trifolii T8T (98.96%). The strain was Gram-stain-positive, aerobic and non-motile, and grew at 4-40 °C. Polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylcholine, five unidentified glycolipids, four unidentified lipids, one unidentified phospholipid and one unidentified phosphoglycolipid; MK-8(H2) was the major respiratory quinone. Major fatty acids were C18:1 ω9c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and C16:0. ANI and dDDH values with the closest relatives were below 76.8% and 20.5%, respectively. The draft genome (4.23 Mb; 67.2 mol% G + C; 4,106 CDSs) harbors a terpene-associated carotenoid cluster containing crtB, crtI and crtY. The orange-red pigment (λmax = 475 nm) showed antioxidant activity (DPPH SC₅₀ = 5.38 mg mL⁻¹; FRAP = 4.34 µmol TE g⁻¹) and weak but measurable HIV-1 reverse transcriptase inhibition (IC₅₀ = 22 mg mL⁻¹). These data support the proposal of Rhodococcus folensis sp. nov., with FMA22ᵀ (= LMG 34144ᵀ = DSM 120048ᵀ) as the type strain.

Soil Microbiology↗

Lability of Cd, Cu, and Zn in polluted soils treated with lime, beringite, and red mud and identification of a non-labile colloidal fraction of metals using istopic techniques.

The use of soil amendments has been proposed as a low input alternative for the remediation of metal polluted soils. However, little information is available concerning the stability, and therefore the longevity, of the remediation treatments when important soil parameters change. In this paper we investigate the effect of pH changes on the lability of heavy metals in soils treated with lime, beringite, and red mud using a modified isotopic dilution technique in combination with a stepwise acidification procedure. Significant amounts of nonlabile (fixed) Cu and Zn were found to be associated with colloids <0.2 microm in the solution phase. The results obtained indicated that the mobility of fixed colloidal metals is significant and increases with soil pH. This must be considered because most of the soil amendments are alkaline and increase soil pH. All the soil amendments significantly decreased the lability of Cd, Zn, and Cu in the soils as a whole. However, when the soils were re-acidified, the labile pool of metals increased sharply and in the case of lime and beringite, the lability of the metals was similar, at equal pH, to the untreated soil. In contrast the lability of metals in the red mud treated soils was always smaller than that in the untreated soils across the range of pH values tested. These results suggest that the mechanism of action of lime and beringite is similar and probably related to increased metal adsorption and precipitation of metal hydroxides and carbonates at high pH. In the case of red mud, a combination of pH dependent and independent mechanisms (possibly solid-phase diffusion or migration into micropores) may be responsible for the metal fixation observed.

Adsorption↗

Toxicologic studies with lambs fed sugar beets grown on municipal sludge-amended soil: lowered relative hemoglobin in red blood cells and mutagens in blood and excreta.

Sugar beets grown on municipal sludge-amended soil were fed to growing lambs for 66 days. The relative hemoglobin content was significantly lower (P less than 0.05) in the lambs fed the sludge-grown sugar beets. The concentration of direct-acting mutagens was significantly higher (P less than 0.05) than controls in blood and urine of the lambs fed the sludge-grown beets. Cadmium concentration was higher, but not significantly (P greater than 0.05) in the livers and kidneys of the lambs fed the sludge-grown beets as compared with controls. Significant differences between treatment groups were not observed in active or passive K+ influxes in RBC; in the activity of hepatic microsomal aniline hydroxylase in p-nitroanisole-O-demethylase, aminopyrene-N-demethylase, or arylhydrocarbon hydroxylase; in tissue ultrastructure of kidney, liver, or muscle as examined by electron microscopy; or in carcass weight, dressing percentage, quality, or yield grade.

Animal Feed↗

Toxic effect caused on microflora of soil by pesticide picloram application.

The toxic effect of the herbicide picloram on the microbial population of a typical Brazilian red Latosol soil was studied in a series of microcalorimetric experiments. The activity of the soil was stimulated by the addition of 6.0 mg of glucose and 6.0 mg of ammonium sulfate, under 34.8% controlled moisture, to a 1.50 mg soil sample, at 298.15 +/- 0.02 K. The net thermal effect due to the addition of the picloram to the soil was determined by interpreting the power-time curves, which were recorded on the microcalorimeter. The total thermal effect evolved by the microorganisms was affected by the increasing doses of herbicide, and varied from 0 to 10.00 micrograms g-1. An increase in picloram exposure caused a decrease of the original thermal effect, reaching a null value above 20.89 micrograms of herbicide per gram of soil. The decreases of the thermal effect evolved by microorganisms and the increase of the lag phase period are associated with the death of the microbial population. The effects caused by picloram application in this typical Brazilian soil resulted in a strong effect on the soil microbial communities.

Calorimetry↗

The effect of the herbicide diuron on soil microbial activity.

The inhibitory effect of the herbicide diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] on microbial activity in red Latosol soil was followed using microcalorimetry. The activity of the micro-organisms in 1.50 g of soil sample was stimulated by addition of 6.0 mg of glucose and 6.0 mg of ammonium sulfate under 35% controlled humidity at 298.15 (+/- 0.02) K. This activity was determined by power-time curves that were recorded for increasing amounts of diuron, varying from zero to 333.33 micrograms g-1 soil. An increase in the amount of diuron in soil caused a decrease of the original thermal effect, to reach a null value above 333.33 micrograms g-1 of herbicide. The power-time curve showed that the lag-phase period and peak time increased with added herbicide. The decrease of the thermal effect evolved by micro-organisms and the increase of the lag-phase period are associated with the death of microbial populations caused by diuron, which strongly affects soil microbial communities.

Ammonium Sulfate↗

Soil-water distribution coefficients and plant transfer factors for (134)Cs, (85)Sr and (65)Zn under field conditions in tropical Australia.

Measurements of soil-to-plant transfer of (134)Cs, (85)Sr and (65)Zn from two tropical red earth soils ('Blain' and 'Tippera') to sorghum and mung crops have been undertaken in the north of Australia. The aim of the study was to identify factors that control bioaccumulation of these radionuclides in tropical regions, for which few previous data are available. Batch sorption experiments were conducted to determine the distribution coefficient (K(d)) of the selected radionuclides at pH values similar to natural pH values, which ranged from about 5.5 to 6.7. In addition, K(d) values were obtained at one pH unit above and below the soil-water equilibrium pH values to determine the effect of pH. The adsorption of Cs showed no pH dependence, but the K(d) values for the Tippera soils (2300-4100 ml/g) exceeded those for the Blain soils (800-1200 ml/g) at equilibrium pH. This was related to the greater clay content of the Tippera soil. Both Sr and Zn were more strongly adsorbed at higher pH values, but the K(d) values showed less dependence on the soil type. Strontium K(d)s were 30-60 ml/g whilst Zn ranged from 160 to 1630 ml/g for the two soils at equilibrium pH. With the possible exception of Sr, there was no evidence for downward movement of radionuclides through the soils during the course of the growing season. There was some evidence of surface movement of labelled soil particles. Soil-to-plant transfer factors varied slightly between the soils. The average results for sorghum were 0.1-0.3 g/g for Cs, 0.4-0.8 g/g for Sr and 18-26 g/g for Zn (dry weight) with the initial values relating to Blain and the following values to Tippera. Similar values were observed for the mung bean samples. The transfer factors for Cs and Sr were not substantially different from the typical values observed in temperate studies. However, Zn transfer factors for plants grown on both these tropical soils were greater than for soils in temperate climates (by more than an order of magnitude). This may be related to trace nutrient deficiency and/or the growth of fungal populations in these soils. The results indicate that transfer factors depend on climatic region together with soil type and chemistry and underline the value of specific bioaccumulation data for radionuclides in tropical soils.

Australia↗

Accumulation and phytoavailability of benzo[a]pyrene in an acid sandy soil.

Effects of benzo[a]pyrene (B[a]P) on ryegrass (Lolium perenne L.) growth, plant accumulation and dissipiation of B[a]P in a red sandy soil (Hapli-Udic Argosol) were studied in a pot experiment. The plants were grown for 61 days in soil spiked with B[a]P at 0, 12.5, 25 and 50 mg kg(-1). Control pots without plants were also set up. Soil extractable B[a]P, plant shoot and root biomass, and concentrations of B[a]P in plant shoots and roots were determined. Ryegrass biomass was increased by addition of B[a]P and root B[a]P concentrations were significantly correlated with B[a]P application rate, but no such correlation was found for shoot B[a]P concentrations. This indicates that B[a]P enhanced the growth of the ryegrass. The extractable B[a]P concentration in the planted soil was significantly lower than that in the unplanted control soil at the rate of 50 mg B[a]P kg(-1). This indicates that ryegrass may help to dissipate B[a]P in soil at concentrations over 50 mg kg(-1) soil although the mechanism for this is not understood.

Acids↗

The possible role of soil particles in the aetiology of non-filarial (endemic) elephantiasis: a macrophage cytotoxicity assay.

A link between the incidence of non-filarial elephantiasis and tropical red clay soil has been suggested after epidemiological surveys in Ethiopia and other African countries, although the mode of action of these soils in disease induction is unknown. We have thus investigated the physical composition of soils from both endemic and non-endemic areas of Ethiopia and their effect on the viability of macrophages using in vitro systems. Endemic and non-endemic soils were avidly phagocytosed by the macrophages. Cell shape was seen to change over a 144-hour period, the cells changing from approximately circular to spindle or stellate shape. Both groups of soils were cytotoxic towards the macrophages. Greatest cell death occurred during the first 48-hour period although some cells were viable after 96 hours. The soil groups could be divided by assessing their contents of silicon and aluminium, as well as observing the number of sub-2 micron particles they contained. The present study gives support to the epidemiological studies implicating soils as the cause of non-filarial elephantiasis.

Aluminum↗

A kinetic study of trace element leachability from abandoned-mine-polluted soil treated with SS-MSW compost and red mud. Comparison with results from sequential extraction.

The effect of adding treated red mud, a by-product of alumina production, to soil polluted by an abandoned mine and characterised by high concentrations of heavy metals, relatively low reaction grade, and low organic carbon content, was investigated. Also studied was addition of both red mud and compost (produced from source-separated municipal solid waste)--the synergistic action of red mud and compost could be exploited to achieve both metal trapping and an increase in organic carbon content. Leaching batch tests were performed on four different systems: soil, soil and treated red mud, soil and compost, soil and compost plus treated red mud. Dilute sulfuric acid and EDTA solution (liquid/solid ratio 10:1) were used in the tests--sulfuric acid to "mimic" acid rain and EDTA in accordance with general methods for estimating "plant-available" metals. Sequential extraction was also applied to the same samples. The use of relatively non-specific extractant reagents in the leaching tests led to a kinetic approach (already proposed in literature), because measurements of trace elements extracted at equilibrium cannot be related to their speciation. Comparison of information obtainable by the kinetic approach to evaluation of data from leaching tests with results from sequential extraction enabled evaluation whether the "kinetic fractionation method", a relatively rapid and simple procedure, furnishes adequate information about the mobility and bioavailability of trace elements. Especially interesting results were obtained for Mn, Zn, and Ni, present in large amounts in the soil studied--their leachability was significantly reduced by addition of red mud and compost, suggesting interesting perspectives in soil-remediation activity.

Journal Article↗

The association of endemic elephantiasis of the lower legs in East Africa with soil derived from volcanic rocks.

Endemic elephantiasis of the lower legs in Ethiopia, which reaches a maximum of 86-7 per 1,000 adults in affected areas, is related to the distribution of red clay soil derived from volcanic rocks, particularly basalt. Prevalence falls rapidly on leaving these areas. This observation has been tested in regions of non-filarial elephantiasis reported in Kanya and north-western Tanzania and further investigated in volcanic areas of Rwanda where the disease had not previously been reported. The same relationship is found to occur in these areas. The limitation to the lower legs of the barefooted section of the farming community suggests that the aetiological factor or factors enter by the feet. The occurrence at high altitude (over 1,200 metres) is noted and the predominance of basalt or basalt-like lava in each case is considered significant. The altitude governs rainfall and temperature and thus governs the type of soil produced. The soil produced from these rocks is rich in colloidal iron oxide, alumina and silica, to which a number of metallic ions are adsorbed. This soil is a reddish-brown clay which, when wet, is strongly adherent to the skin. The derived ions are known to be toxic to human tissue and absorption through intact human skin has been shown to occur experimentally. It is suggested that absorption of these irritants through the bare feet is responsible for the irreversible damage to the lymphatic channels. The present studies support the hypothesis that "high-altitude" elephantiasis of the lower legs in East Africa is a geochemical disease.

Elephantiasis↗

Toxicity of three halogenated flame retardants to nitrifying bacteria, red clover (Trifolium pratense), and a soil invertebrate (Enchytraeus crypticus).

Halogenated flame retardants have a high sorption affinity to particles, making soils and sediments important sinks. Here, three of the most commonly used flame retardants have been tested for sub-lethal toxicity towards soil nitrifying bacteria, a terrestrial plant (seed emergence and growth of the red clover, Trifolium pratense), and a soil invertebrate (survival and reproduction of Enchytraeus crypticus). Tetrabromobisphenol A (TBBPA) was quite toxic to enchytraeids, with significant effects on reproduction detected already at the 10 mgkg(-1) exposure level (EC(10)=2.7 mgkg(-1)). In contrast, decabromodiphenyl ether (DeBDE) was not toxic at all, and short-chain chloroparaffins (CP(10-13)) only affected soil nitrifying bacteria at the highest test concentration (EC(10)=570 mgkg(-1)). Exposure concentrations were verified by chemical analysis for TBBPA and DeBDE, but not for CP(10-13), as a reliable method was not available. Based on the generated data, a PNEC for soil organisms can be estimated at 0.3 mgkg(-1) for TBBPA and 57 mgkg(-1) for short-chain chloroparaffins. No PNEC could be estimated for DeBDE. Measurements of TBBPA in soil are not available, but measured concentrations in Swedish sludge are all lower than the estimated threshold value for biological effects in soil.

Animals↗

Effects of water management and herbicide treatments on red rice control.

Two field experiments were conducted in 1999 and 2000 at Zeme (Pavia, Italy) to determine the effects of water managements and herbicide treatments on red rice control. In the first experiment, all plots were flooded 10-13 cm deep from April 1 to May 17 in 1999 and from April 3 to May 6 in 2000. At the same time, in the second experiment, the plots were alternately drained-flooded. At the end of water management, all plots of both experiments were drained and sprayed with herbicides to control the emerged red rice plants. In both years were applied: Propaquizafop 78 g a.i.ha-1, Cycloxydim at 300 and 400 g a.i. ha-1; Dalapon at 15.300 Kg a.i. ha-1; Quizalofop-ethyl at 100 g a.i. ha-1. Six days after the chemical treatments, all field plots were flooded 10 cm deep and three days later, an early variety of rice (Loto) was sown at 150 Kg ha-1. Seedling emergence was reduced by lack of oxygen (especially from seeds covered with soil in flooded condition). In alternately drained-flooded soil, the red rice emerged and developed from seeds located in the top 4-5 cm. In flooded condition, no red rice plants emerged from seeds at more than 1 cm depth. In both experiments, the density of red rice plants increased during the season in the untreated check and in the plots where treatments were ineffective or performed poorly. The best red rice control, both in submerged and in alternately drained-flooded soil, was obtained with Quizalofop-ethyl (100 g a.i./ha), Cycloxydim (300 and 400 g a.i.ha-1) and Propaquizafop (78 g a.i.ha-1). These herbicides controlled 90-99% of red rice. Partial control of red rice resulted with the other chemical treatments. The shattered grains of red rice were reduced in both experiments by the herbicide treatments. Grain yield reflected the level of red rice control. In fact, the highest commercial grain yields were obtained with Quizalofop-ethyl, Propaquizafop, and Cycloxydim (400 g a.i.ha-1), in both years and experiments. The red rice percentages of the total yields resulted about 3.6-5.7% with all chemical treatments except Dalapon, which was not much effective.

Cyclohexanes↗

Podoconiosis: a tropical model for gene-environment interactions?

Podoconiosis (endemic non-filarial elephantiasis) is a geochemical disease occurring in individuals exposed to red clay soil derived from alkalic volcanic rock. It is a chronic, debilitating disorder and a considerable public health problem in at least 10 countries in tropical Africa, Central America and northern India. Only a small proportion of individuals exposed to red clay develop disease and familial clustering of cases occurs, so we tested the hypothesis that disease occurs in genetically susceptible individuals on exposure to an environmental element in soil. Using multiple statistical genetic techniques we estimated sibling recurrence risk ratio (lambda(s)) and heritability for podoconiosis, and conducted segregation analysis on 59 multigenerational affected families from Wolaitta Zone, southern Ethiopia. We estimated the lambda(s) to be 5.07. The heritability of podoconiosis was estimated to be 0.629 (SE 0.069, P=1x10(-7)). Segregation analysis showed that the most parsimonious model was that of an autosomal co-dominant major gene. Age and use of footwear were significant covariates in the final model. Host genetic factors are important determinants of susceptibility to podoconiosis. Identification of the gene(s) involved will lead to better understanding of the gene-environment interactions involved in the pathogenesis of podoconiosis and other complex multifactorial conditions.

Age of Onset↗

Degradation of monocrotophos in soils.

The degradation of a widely used organophosphorus insecticide, monocrotophos (dimethyl (E)-1-methyl-2-methylcarbamoyl vinyl phosphate) in two Indian agricultural soils at two concentration levels, 10 and 100 microg g(-1) soil under aerobic conditions at 60% water-holding capacity at 28+/-4 degrees C was studied in a laboratory. The degradation of monocrotophos at both concentrations in black vertisol and red alfinsol soils was rapid accounting for 96-98% of the applied quantity and followed the first-order kinetics with rate constants (k) of 0.0753 and 0.0606 day(-1) and half-lives (t1/2) of 9.2 and 11.4 days, respectively. Degradation of monocrotophos in soils proceeded by hydrolysis with formation of N-methylacetoacetamide. Even three additions of monocrotophos at 10 microg g(-1) soil did not result in its enhanced degradation. However, there was cumulative accumulation of N-methylacetoacetamide in soils pretreated with monocrotophos to the tune of 7-15 microg g(-1) soil. Both biotic and abiotic factors were involved in degradation of monocrotophos in soils.

Agriculture↗

Transfer of antibiotic resistance genes from soil to rice in paddy field.

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Oryza↗

Seasonal changes of redox potential and microbial activity in two agricultural soils of tropical Australia: some implications for soil-to-plant transfer of radionuclides.

Very little is known of the factors controlling soil-to-plant transfer of radionuclides in tropical environments. As part of an IAEA/FAO coordinated research project (CRP) designed to elucidate some of those factors, near-surface samples of two agricultural red-earth soils (Blain and Tippera) were collected from a study site in the Northern Territory. The climate is tropical monsoonal with crops being grown over the wet season from December to March/April. It is important to understand soil variables that may be related to this dramatic seasonality. In this investigation, soil redox state and microbial populations were assessed before and after the growing season with a view to generating hypotheses for future evaluation. The X-ray absorption near edge structure (XANES) technique was used to determine overall changes in the solid-state redox speciation of Fe and Mn in soils across the growing period. Fe speciation did not change but approximately 10% of the total Mn was oxidised from Mn(II) to Mn(III) and Mn(IV) in both soils between October 1999 and April 2000. An apparent disconnect between Fe and Mn was not unexpected given the >10 times higher concentration of Fe in the soils compared with Mn. These results have implications for the bioavailability of redox sensitive radionuclides such as Tc and Pu. Similarly, microbial population estimates were derived before and after the growing period. Total bacterial populations did not vary from 10(6) to 10(7) colonies per gram. Fungal populations increased over the growing season from 3-6 x 10(5) to 1-4 x 10(6) colonies per gram of soil. Fungi have the potential to decrease soil pH and hence increase the bioavailability of radionuclides such as Cs. In addition, fungi act to facilitate plant nutrition. This could lead to enhanced accumulation of nutrient analogues (e.g. Sr and Ra for Ca; Tc for Mn), but this effect may be masked by improved biomass production.

Agriculture↗

Influence of different factors on the adsorption of carbofuran (2, 3-dihydro-2,2-dimethyl-7-benzofuranyl-N-methyl carbamate) on soils.

The effects of exchangeable cations (H+ and Na+), autoclaving, organic matter, cationic and anionic surfactants, and temperature on the adsorption of carbofuran on two different types of soils were studied. The adsorption isotherms for all effects/treatments were in close agreement with the Freundlich equation and yielded S-shaped isotherms. The amount of carbofuran adsorbed in all cases was higher in Jhansi red loam soil than in Pilibhit sandy loam soil and was related to organic matter content, clay content, CaCO3 content, surface area, and cation-exchange capacity of the soils. The adsorption on soils from both sites follows the order H soil-->Na soil-->natural soil at 25 degrees C-->autoclaved soil-->soil from which organic matter had been removed-->cationic surfactant-->anionic surfactant-->natural soil at 50 degrees C and was in accordance with Freundlich constant K values and distribution coefficient Kd values. The adsorptive capacity of carbofuran for organic matter and clay content for both the Jhansi and the Pilibhit soils was also evaluated by calculating Kom and Kc values, and it was found that the carbofuran adsorption was better correlated with clay content than with organic matter content of soils. On the basis of adsorption isotherms, various thermodynamic parameters such as the thermodynamic equilibrium constant Ko, standard free energy (delta G zero) changes standard ethalpy (delta H zero) changes, and standard entropy (delta S zero) changes have been calculated in order to predict the nature of isotherms.

Adsorption↗

Determination of sarin, soman and their hydrolysis products in soil by packed capillary liquid chromatography-electrospray mass spectrometry.

An analytical method based on aqueous ultrasonic extraction and packed capillary liquid chromatography-electrospray mass spectrometry (LC-ESI-MS) analysis was developed and compared to an existing gas chromatography(GC)-MS based method for the determination of sarin, soman and their hydrolysis products in contaminated soil. Three soils, a red clay, a tan sandy clay and a brown sandy clay loam, were spiked with sarin and soman and their initial hydrolysis products, isopropyl methylphosphonic acid and pinacolyl methylphosphonic acid, at the 10 microg/g level to assess recovery efficiency. Recovery of sarin and soman from the aqueous soil extracts was comparable to the existing analytical method, with a significant improvement in recovery being demonstrated for the chemical warfare agent hydrolysis products. Sarin and soman were recovered in the 20-90% range from the three soil types with aqueous extraction, while the hydrolysis products of these chemical warfare agents were extracted with recoveries in excess of 80%. The developed soil extraction and analysis method appears to be an attractive alternative to the GC-MS based method, since aqueous extracts containing chemical warfare agent hydrolysis products may be analysed directly, eliminating the need for additional sample handling and derivatization steps.

Chemical Warfare Agents↗