Fungi in fabricated soils

Fabricated soil (FS) is usually used for landscape rehabilitation, and is an excellent example of environmental remediation. These soils were used to revitalise damaged and eroded soils caused by acid mine drainage, a common site in Western Pennsylvania. The ratio of bacterial and fungal microbiota contributes to the health, fertility and sustainability of the soil. The structure and function of the soils foodweb have been suggested for numerous times as a prime indicator of ecosystem health (Bongers, 1990; Coleman et al., 1992; Kalevitch et al., 2003). The measurement of disrupted soil processes, decreased bacterial or fungal activity or decreased fungal or bacterial biomass can indicate a problem long before the natural vegetation is lost (Bongers, 1990). After the exposure of FS to the natural habitat, we evaluated the bacterial and fungal activity in soil as this is an important indicator of soil health. Details on bacterial presence and specifics in application of FS are described in previous publications (Kalevitch et al., 2003, 2004a, 2004b). In this paper, we will concentrate on the role of fungal biomass in FS.     

Copper activity in soil solutions of calcareous soils

Copper partitioning was studied in seven calcareous soils at moisture content corresponding to 1.2 times the field moisture content (soil water potential 7.84 J kg(-1)). Copper retention was accompanied by the release in soil solution of Ca(2+), Mg(2+), Na(+), and H(+), and the total amount of these cations released was 0.8 to 1.09 times the amount of Cu sorbed (mol(c):mol(c)). The relationships between Cu activity and pH, and the balance of cations in soils correspond with the surface precipitation of CuCO(3) as the main mechanism of Cu retention. The values of ion activity product of surface precipitate were close for all studied soils with the average log(IAP(CuCO(3)))=-15.51. The relationship between copper activity in soil solutions and soil properties is well fit by a regression relating pCu (-log copper ion activity) with soil pH, total Cu, and carbonate content.     

Laccase activity in soils: considerations for the measurement of enzyme activity

Laccases (benzenediol: oxygen oxidoreductases, EC 1.10.3.2) are copper-containing enzymes that catalyze the oxidative conversion of a variety of chemicals, such as mono-, oligo-, and polyphenols and aromatic amines. Laccases have been proposed to participate in the transformation of organic matter and xenobiotics as well as microbial interactions. Several laccase assays have been proposed and used in soils. Here, we show that the optimal pH conditions for the laccase substrates 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS, pH 3-5), 2,6-dimethoxyphenol (4-5.5), L-3,4-dihydroxyphenylalanine (DOPA; 4-6), guaiacol (3.5-5), 4-methylcatechol (3.5-5), and syringaldazine (5.5-7.0) are similar between purified laccases from Trametes versicolor and Pyricularia sp. and soil extracts; the substrate affinities of purified enzymes (K(M)) and soil extracts were also similar. The laccase assays showed specificity overlap with tyrosinase and ligninolytic peroxidases when hydrogen peroxide is present. The ABTS oxidation assay is able to reliably detect the presence of 13.5 pg mL(-1) or 0.199×10(-12) mol mL(-1) of T. versicolor laccase, which is three times more sensitive than the 2,6-dimethoxyphenol-based assay and more than 40 times more sensitive than any of the other assays. The low molecular mass soil-derived compounds and the isolated fulvic and humic acids influence the laccase assays and should be removed from the soil extracts before measurements of the enzyme activity are performed.     

Intrinsic and induced isoproturon catabolic activity in dissimilar soils and soils under dissimilar land use

The catabolic activity with respect to the systemic herbicide isoproturon was determined in soil samples by (14)C-radiorespirometry. The first experiment assessed levels of intrinsic catabolic activity in soil samples that represented three dissimilar soil series under arable cultivation. Results showed average extents of isoproturon mineralisation (after 240 h assay time) in the three soil series to be low. A second experiment assessed the impact of addition of isoproturon (0.05 microg kg(-1)) into these soils on the levels of catabolic activity following 28 days of incubation. Increased catabolic activity was observed in all three soils. A third experiment assessed levels of intrinsic catabolic activity in soil samples representing a single soil series managed under either conventional agricultural practice (including the use of isoproturon) or organic farming practice (with no use of isoproturon). Results showed higher (and more consistent) levels of isoproturon mineralisation in the soil samples collected from conventional land use. The final experiment assessed the impact of isoproturon addition on the levels of inducible catabolic activity in these soils. The results showed no significant difference in the case of the conventional farm soil samples while the induction of catabolic activity in the organic farm soil samples was significant.     

A comparative analysis of endophytic bacterial communities associated with hyperaccumulators growing in mine soils

Interactions between endophytic bacterial communities and hyperaccumulators in heavy metal-polluted sites are not fully understood. In this study, the diversity of stem-associated endophytic bacterial communities of two hyperaccumulators (Solanum nigrum L. and Phytolacca acinosa Roxb.) growing in mine soils was investigated using molecular-based methods. The denaturing gradient gel electrophoresis (DGGE) analysis showed that the endophytic bacterial community structures were affected by both the level of heavy metal pollution and the plant species. Heavy metal in contaminated soil determined, to a large extent, the composition of the different endophytic bacterial communities in S. nigrum growing across soil series (five sampling spots, and the concentration of Cd is from 0.2 to 35.5 mg/kg). Detailed analysis of endophytic bacterial populations by cloning of 16S rRNA genes amplified from the stems of the two plants at the same site revealed a different composition. A total of 51 taxa at the genus level that included α-, β-, and γ-Proteobacteria (68.8% of the two libraries clones), Bacteroidetes (9.0% of the two libraries clones), Firmicutes (2.0% of the two libraries clones), Actinobacteria (16.4% of the two libraries clones), and unclassified bacteria (3.8% of the two libraries clones) were found in the two clone libraries. The most abundant genus in S. nigrum was Sphingomonas (23.35%), while Pseudomonas prevailed in P. acinosa (21.40%). These results suggest that both heavy metal pollution and plant species contribute to the shaping of the dynamic endophytic bacterial communities associated with stems of hyperaccumulators.     

Aging activity of DDE in dissimilar rice soils in a greenhouse experiment

A green-house study was conducted in late 2005 to investigate the aging behavior of p,p'-DDE in two types of soil, Hydragric Anthrosols (An) and Hydragric Acrisols (Ac), according to the World Reference Base (WRB) [FAO/ISRIC/ISSS. 1998. World reference base for soil resources. World soil resources reports, Rome. p. 87]. Paddy rice and dry rice were grown in submerged paddy soils and non-submerged upland soils, respectively. The concentration of extractable p,p'-DDE in fresh DDE-spiked soils was 746.2ngg(-1). During the first few weeks of the experiment, the extractability of p,p'-DDE became increasingly low as the aging period prolonged. However, certain amount of p,p'-DDE that had been captured by soil minerals and organic matter (OM) could be released and became extractable in the later period. The extractability of p,p'-DDE in submerged soils was significantly lower than that in non-submerged soil, because flooding could increase the binding of pollutants to soil particles. The plantation of both dry rice and paddy rice slowed down the aging process of p,p'-DDE. After one month's growth of rice, p,p'-DDE bound to soil particles was released and became extractable. The OM and silt content of An are higher than that of Ac, resulting in more bound residues and relative lower extractability of p,p'-DDE in An. In addition, the extractability of p,p'-DDE could be reduced by the addition of rice straw to soils.     

Impact of the novel neonicotinoid insecticide Paichongding on bacterial communities in yellow loam and Huangshi soils

Insecticides are widely sprayed in modern agriculture for ensuring the crop yield, which could also lead to contamination and insecticide residue in soils. Paichongding (IPP) is a novel neonicotinoid insecticide and was developed recently in China. Soil bacterial community, diversity, and community composition vary widely depending on environmental factors. As for now, little is known about bacterial species thriving, bacterial community diversity, and structure in IPP-spraying soils. In present study, IPP degradation in yellow loam and Huangshi soils was investigated, and bacterial communities and diversity were examined in soil without IPP spray and with IPP spray through pyrosequencing of 16S ribosomal RNA (rRNA) gene amplicons. The degradation ratio of IPP at 60 days after treatment (DAT) reached 51.22 and 34.01 % in yellow loam and Huangshi soil, respectively. A higher richness of operational taxonomic units (OTUs) was found in yellow loam soil (867 OTUs) and Huangshi soil (762 OTUs) without IPP spray while OUTs were relatively low in IPP-spraying soils. The community composition also differed both in phyla and genus level between these two environmental conditions. Proteobacteria, Firmicutes, Planctomycetes, Chloroflexi, Armatimonadetes, and Chlorobi were stimulated to increase after IPP application, while IPP inhibited the phyla of Bacteroidetes, Actinobacteria, and Acidobacteria.     

Assessment of heavy metal bioavailability in contaminated sediments and soils using green fluorescent protein-based bacterial biosensors

A green fluorescent protein (GFP)-based bacterial biosensor Escherichia coli DH5alpha (pVLCD1) was developed based on the expression of gfp under the control of the cad promoter and the cadC gene of Staphylococcus aureus plasmid pI258. DH5alpha (pVLCD1) mainly responded to Cd(II), Pb(II), and Sb(III), the lowest detectable concentrations being 0.1 nmol L(-1), 10 nmol L(-1), and 0.1 nmol L(-1), respectively, with 2h exposure. The biosensor was field-tested to measure the relative bioavailability of the heavy metals in contaminated sediments and soil samples. The results showed that the majority of heavy metals remained adsorbed to soil particles: Cd(II)/Pb(II) was only partially available to the biosensor in soil-water extracts. Our results demonstrate that the GFP-based bacterial biosensor is useful and applicable in determining the bioavailability of heavy metals with high sensitivity in contaminated sediment and soil samples and suggests a potential for its inexpensive application in environmentally relevant sample tests.     

Organic carbon effects on aerobic polychlorinated biphenyl removal and bacterial community composition in soils and sediments

Certain organic compounds, including biphenyl and salicylic acid, stimulate polychlorinated biphenyl (PCB) degradation by microorganisms in some environments. However, the usefulness of these amendments for improving PCB removal by microorganisms from diverse habitats has not been extensively explored. This study evaluated the effects of biphenyl, salicylic acid, and glucose on changes in aerobic PCB removal and bacterial communities from an agricultural soil, a wetland peat soil, a river sediment, and a mixture of these samples. PCB removal patterns were significantly different between soils and sediments amended with carbon compounds: (i) terrestrial soil microorganisms removed more PCBs than river sediment microorganisms, particularly with regard to PCBs with >4 chlorine substituents, (ii) glucose-supplemented, agricultural soil microorganisms removed more hexachlorobiphenyl than unsupplemented samples, (iii) biphenyl-supplemented, river sediment microorganisms removed more di- and tri-chlorobiphenyls than unamended samples. Carbon amendments also caused unique shifts in soil and sediment bacterial communities, as determined by specific changes in bacterial 16S rRNA denaturing gradient gel electrophoresis banding patterns. These results indicate that organic carbon amendments had site-specific effects on bacterial populations and PCB removal. Further work is needed to more accurately characterize PCB degrading communities and functional gene expression in diverse types of environments to better understand how they respond to bioremediation treatments.     

Effect of glyphosate on the microbial activity of two Brazilian soils

Glyphosate [N-(phosphonomethyl)-glycine] is a broad-spectrum, non-selective, post-emergence herbicide that is widely used in agricultural. We studied, in vitro, changes in the microbial activity of typical Hapludult and Hapludox Brazilian soils, with and without applied glyphosate. Glyphosate was applied at a rate of 2.16 mg glyphosate kg(-1) of soil and microbial activity was measured by soil respiration (evolution of CO(2)) and fluorescein diacetate (FDA) hydrolysis over a period of 32 days. We found an increase of 10-15% in the CO(2) evolved and a 9-19% increase in FDA hydrolyses in the presence of glyphosate compared with the same type of soil which had never received glyphosate. Soil which had been exposed to glyphosate for several years had the strongest response in microbial activity. Most probable number (MPN) counts showed that after 32 days incubation the number of actinomycetes and fungi had increased while the number of bacteria showed a slight reduction. After the incubation period, high pressure liquid chromatography (HPLC) detected the glyphosate metabolite aminomethyl phosphonic acid (AMPA), indicating glyphosate degradation by soil microorganisms.     

Ion activity and distribution of heavy metals in acid mine drainage polluted subtropical soils

The oxidative dissolution of mine wastes gives rise to acidic, metal-enriched mine drainage (AMD) and has typically posed an additional risk to the environment. The poly-metallic mine Dabaoshan in South China is an excellent test site to understand the processes affecting the surrounding polluted agricultural fields. Our objectives were firstly to investigate metal ion activity in soil solution, distribution in solid constituents, and spatial distribution in samples, secondly to determine dominant environment factors controlling metal activity in the long-term AMD-polluted subtropical soils. Soil Column Donnan Membrane Technology (SC-DMT) combined with sequential extraction shows that unusually large proportion of the metal ions are present as free ion in the soil solutions. The narrow range of low pH values prevents any pH effects during the binding onto oxides or organic matter. The differences in speciation of the soil solutions may explain the different soil degradation observed between paddy and non-paddy soils.     

New bacterial strain of the genus Ochrobactrum with glyphosate-degrading activity

Thirty bacterial strains with various abilities to utilize glyphosate as the sole phosphorus source were isolated from farm soils using the glyphosate enrichment cultivation technique. Among them, a strain showing a remarkable glyphosate-degrading activity was identified by biochemical features and 16S rRNA sequence analysis as Ochrobactrum sp. (GDOS). Herbicide (3 mM) degradation was induced by phosphate starvation, and was completed within 60 h. Aminomethylphosphonic acid was detected in the exhausted medium, suggesting glyphosate oxidoreductase as the enzyme responsible for herbicide breakdown. As it grew even in the presence of glyphosate concentrations as high as 200 mM, Ochrobactrum sp. could be used for bioremediation purposes and treatment of heavily contaminated soils.     

Recombinant luminescent bacterial sensors for the measurement of bioavailability of cadmium and lead in soils polluted by metal smelters

Environmental hazard of heavy metals in soils depends to a large extent on their bioavailability. The approach used in this study enables the determination of bioavailable metals in solid-phase samples. Two recombinant bacterial sensors, one responding specifically to cadmium and the other to lead and cadmium by increase of luminescence (firefly luciferase was used as a reporter) were used to determine the bioavailability of these metals in soil-water suspensions (a contact assay) and respective particle-free extracts. Fifty agricultural soils sampled near zinc and lead smelters in the Northern France containing up to (mg/kg) 20.1 of Cd, 1050 of Pb and 1390 of Zn were analysed. As the soil matrix interferes with the assay, recombinant luminescent control bacteria lacking the metal recognizing protein and corresponding promoter (thus, being not metal-inducible) but otherwise comparable to the sensor bacteria (the same host bacterium and plasmid encoding luciferase) were used in parallel to take into account the possible quenching and/or stimulating effects of the sample on the luminescence of the sensor bacteria. Both, chemical and sensor analysis showed that only microg/l levels of metals were extracted from the soil into the water phase (0.1% of the total Cd, 0.07% of Pb and 0.5% of Zn). However, 115-fold more Cd and 40-fold more Pb proved bioavailable if the sensor bacteria were incubated in soil suspensions (i.e., in the contact assay). The bioavailability of metals in different soils varied (depending probably on soil type) ranging from 0.5% to 56% for cadmium and from 0.2% to 8.6% for lead.     

Function of bacterial cells and their exuded extracellular polymeric substances (EPS) in virus removal by red soils

The potential influence of autochthonous microorganisms on virus fate in soil is usually determined through extreme conditions of sterilization vs. nonsterilization; however, the relative importance of microbial cells and their exudates remains unclear. In this study, bacterial cells (cell) were harvested, and their exuded extracellular polymeric substances (EPS) were extracted from three strains of bacteria, namely, Gram-negative bacteria Pseudomonas putida and Pseudomonas aeruginosa as well as Gram-positive bacterium Bacillus subtilis. This study aimed to evaluate virus removal in solutions in the presence of cell, EPS, and their combination (cell/EPS), as well as to investigate how their presence affects virus removal efficiencies by four red soils based on batch experiments. Results showed that virus removal percentage in solutions ranged from 11 to 23 in the presence of cells only and from 12 to 15 in the presence of EPS only. The removal percentage in the combined cell/EPS treatment can be estimated by summing the results achieved by the cell and EPS treatments, separately. Meanwhile, cell presence had a negligible effect on virus removal by red soils. EPS and combined cell/EPS significantly reduced virus removal by 20 to 69 % and 16 to 50 %, respectively, which indicated that EPS served a dominant function in reducing virus removal. This study clearly demonstrated that the prediction of virus removal by red soils must consider the effect of bacteria, especially those producing large quantities of EPS, which can be responsible for the underestimation of viral load in certain studies.     

Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments

The effectiveness of two amendments for the in situ remediation of a Cd- and Ni-contaminated soil in the Louis Fargue long-term field experiment was assessed. In April 1995, one replicate plot (S1) was amended with 5% w/w of beringite (B), a coal fly ash (treatment S1+B), and a second plot with 1% w/w zerovalent-Fe iron grit (SS) (treatment S1+SS), with the aim of increasing metal sorption and attenuating metal impacts. Long-term responses of daily respiration rates, microbial biomass, bacterial species richness and the activities of key soil enzymes (acid and alkaline phosphatase, arylsulfatase, beta-glucosidase, urease and protease activities) were studied in relation to soil metal extractability. Seven years after initial amendments, the labile fractions of Cd and Ni in both the S1+B and S1+SS soils were reduced to various extents depending on the metal and fractions considered. The soil microbial biomass and respiration rate were not affected by metal contamination and amendments in the S1+B and S1+SS soils, whereas the activity of different soil enzymes was restored. The SS treatment was more effective in reducing labile pools of Cd and Ni and led to a greater recovery of soil enzyme activities than the B treatment. Bacterial species richness in the S1 soil did not alter with either treatment. It was concluded that monitoring of the composition and activity of the soil microbial community is important in evaluating the effectiveness of soil remediation practices.     

Diversity and characterization of culturable bacterial endophytes from Zea mays and their potential as plant growth-promoting agents in metal-degraded soils

In this study, we evaluated the phylogenetic diversity of culturable bacterial endophytes of Zea mays plants growing in an agricultural soil contaminated with Zn and Cd. Endophytic bacterial counts were determined in roots and shoots, and isolates were grouped by random amplified polymorphic DNA and identified by 16S ribosomal RNA (rRNA) gene sequencing. Endophytes were further characterized for the production of plant growth-promoting (PGP) substances, such as NH₃, siderophores, indol-3-acetic acid (IAA), hydrogen cyanide and extracellular enzymes, and for the capacity to solubilize phosphate. The endophytes producing higher amounts of IAA were screened for their tolerance to Zn and Cd and used as bioinoculants for maize seedlings grown in the Zn/Cd-contaminated soil. The counts of endophytes varied between plant tissues, being higher in roots (6.48 log₁₀ g^?1 fresh weight) when compared to shoots (5.77 log₁₀ g^?1 fresh weight). Phylogenetic analysis showed that endophytes belong to three major groups: α-Proteobacteria (31 %), γ-Proteobacteria (26 %) and Actinobacteria (26 %). Pseudomonas, Agrobacterium, Variovorax and Curtobacterium were among the most represented genera. Endophytes were well-adapted to high Zn/Cd concentrations (up to 300 mg Cd l^?1 and 1,000 mg Zn l^?1) and showed ability to produce several PGP traits. Strains Ochrobactrum haematophilum ZR 3-5, Acidovorax oryzae ZS 1-7, Frigoribacterium faeni ZS 3-5 and Pantoea allii ZS 3-6 increased root elongation and biomass of maize seedlings grown in soil contaminated with Cd and Zn. The endophytes isolated in this study have potential to be used in bioremediation/phytoremediation strategies.     

Assessment of bacterial communities and characterization of lead-resistant bacteria in the rhizosphere soils of metal-tolerant Chenopodium ambrosioides grown on lead-zinc mine tailings

Bacterial communities in the rhizosphere soils of metal tolerant and accumulating Chenopodium ambrosioides grown in highly and moderately lead-zinc mine tailings contaminated-soils as well as the adjacent soils with low metal contamination were characterized by using cultivation-independent and cultivation techniques. A total of 69, 73, and 83 bacterial operational taxonomic units (OTUs) having 84.8-100% similarity with the closest match in the database were detected among high, moderate, and low-contamination soil clone libraries, respectively. These OTUs had a Shannon diversity index value in the range of 4.06-4.30. There were 9, 10, and 14 bacterial genera specific to high, moderate, and low metal-contaminated soil clone libraries, respectively. Phylogenetic analysis showed that the Pb-resistant isolates belonged to 8 genera. Pseudomonas and Arthrobacter were predominant among the isolates. Most of the isolates (82-86%) produced indole acetic acid and siderophores. More strains from the highly metal-contaminated soil produced 1-aminocyclopropane-1-carboxylate deaminase than the strains from the moderately and lowly metal-contaminated soils. In experiments involving canola grown in quartz sand containing 200 mg kg⁻¹ of Pb, inoculation with the isolated Paenibacillusjamilae HTb8 and Pseudomonas sp. GTa5 was found to significantly increase the above-ground tissues dry weight (ranging from 19% to 36%) and Pb uptake (ranging from 30% to 40%) compared to the uninoculated control. These results show that C. ambrosioides harbor different metal-resistant bacterial communities in their rhizosphere soils and the isolates expressing plant growth promoting traits may be exploited for improving the phytoextraction efficiency of Pb-polluted environment.     

Seasonal phosphatase activity in three characteristic soils of the English uplands polluted by long-term atmospheric nitrogen deposition

Phosphomonoesterase activities were determined monthly during a seasonal cycle in three characteristic soil types of the English uplands that have been subject to long-term atmospheric nitrogen deposition. Activities (micromol para-nitrophenol g(-1) soil dry wt. h(-1)) ranged between 83.9 and 307 in a blanket peat (total carbon 318 mg g(-1). pH 3.9), 45.2-86.4 in an acid organic grassland soil (total carbon 354 mg g(-1), pH 3.7) and 10.4-21.1 in a calcareous grassland soil (total carbon 140 mg g(-1) pH 7.3). These are amongst the highest reported soil phosphomonoesterase activities and confirm the strong biological phosphorus limitation in this environment.     

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.     

表面活性剂在北京碱性土壤中的吸附行为研究

通过静态吸附实验,研究了北京碱性土壤对阴离子表面活性剂SDS、阳离子表面活性剂CTAB和非离子表面活性剂Tween80的吸附行为,考察了温度对表面活性剂吸附的影响.结果表明:7种不同土样对SDS、CTAB和Tween80的吸附等温线均较好地符合Langmuir吸附模式,其吸附能力的大小顺序为2号轻壤土》轻粘土》中壤土》砂壤土》5号轻壤土》重壤土》紧砂土,这主要是由于7种土样的pH、有机质含量和机械组成不同的缘故;同一土壤中,CTAB的吸附量》Tween80的吸附量》SDS的吸附量;温度的升高,不利于SDS和CTAB在土壤中的吸附,而有利于Tween80的吸附.