Impact of industrial waste water effluents on mycoflora of the shore sediments of the 3rd oxidation pond,with reference to biosorption of heavy metals

The third oxidation pond at 10th of Ramadan desert receives a number of industrial waste water effluents contaminated with the heavy metal ions Zn, Cd, Cu and Ni. The species diversity and fungal community structure of seven different sites at the onshore sediments and offshore were studied. Mycological analysis resulted in isolation of 3912 fungal colonies, 11.7% of this count were recovered from the onshore sediment sites (4 sites) whereas 88.3% were from the offshore sites (3 sites), in the desert. Fungal counts and species diversity at the onshore sites tend to increase with increasing distance far from the waste water input. A complete accordance was observed among the total fungal counts and species variabilities with organic matter content at each sampling site. This relationship was reversed in case of heavy metal contents with both counts and diversity. Seventeen fungal species belonging to seven genera were isolated from all sites under study. Aspergillus spp. constituted the majority of the isolates (51.7% of the total isolates), followed by Curvularia, Cephalosporium, and Humicola. Of nine isolated Aspergillus spp., A. humicola was the most dominant (37.4% of the total catch) and appeared at all polluted sites. Therefore, A. humicola was chosen to investigate its potential for heavy metals sorption from the contaminated waste water effluent. Four days old biomass pellets could sorb a large amount of heavy metals according to the following sequence: Zn>Cd>Cu>Ni ions. Agitation significantly increased Zn and Cd sorption, but not Cu and Ni. Heavy metals sorption took place at a wide pH range and particularly increased at alkaline pH (8-9).     

Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries

Developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures and to monitor their dynamics under in situ conditions. However, there has been a distinct lack of emphasis on monitoring the functional diversity in the environment. Genes encoding catechol 2,3-dioxygenases (C23O), as key enzymes of various aerobic aromatic degradation pathways, were used as functional targets to assess the catabolic gene diversity in differentially BTEX contaminated environments by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP). Site specific PCR-SSCP fingerprints were obtained, showing that gene diversity experienced shifts correlated to temporal changes and levels of contamination. PCR-SSCP enabled the recovery of predominant gene polymorphs, and results closely matched with the information retrieved from random sequencing of PCR-DNA clone libraries. A new method for isolating strains capable of growing on BTEX compounds was developed to diminish preselection or enrichment bias and to assess the function of predominant gene polymorphs. C23O abundance in isolates correlated with the levels of BTEX pollution in the soil samples analysed. Isolates harbouring C23O genes, identical to the gene polymorph predominant in all contaminated sites analysed, showed an unexpected benzene but not toluene mineralizing phenotype whereas isolates harbouring a C23O gene variant differing by a single point mutation and observed in highly polluted sites only, were capable, among some other isolates, to mineralize benzene and toluene, indicating a catabolically determined sharing of carbon sources on-site. The PCR-SSCP technique is thus a powerful tool for assessing the diversity of functional genes and the identification of predominant gene polymorphs in environmental samples as a prerequisite to understand the functioning of microbial communities.     

Arbuscular mycorrhizal fungi enhance root cadmium and copper accumulation in the roots of the salt marsh plant Aster tripolium L.

It is known that vegetation plays an important role in the retention of heavy metals in salt marshes by taking up and accumulating the metals. In this study, we investigated whether arbuscular mycorrhizal fungi (AMF) increase Cd and Cu uptake and accumulation in the root system of the salt marsh species Aster tripolium L., and whether indigenous AMF isolated from polluted salt marshes have higher capacity to resist and alleviate metal stress in A. tripolium than isolates of the same species originated from non-polluted sites. Plants inoculated with Glomus geosporum, either isolated from a polluted salt marsh site (PL isolate) or from a non-polluted site (NP isolate), and non-mycorrhizal (NM) plants were compared in a pot experiment at four different Cd and Cu concentrations. Cd had no effect in root colonization, whereas high concentrations of Cu decreased colonization level in plants inoculated with the NP isolate. AM colonization did not increase plant dry weight or P concentration but influenced root Cd and Cu concentrations. Inoculation with PL and NP isolates enhanced root Cd and Cu concentrations, especially at highest metal addition levels, as compared to NM plants, without increasing shoot Cd and Cu concentrations. There was no evidence of intraspecific variation in the effects between AMF isolated from polluted and non-polluted sites, since there were no differences between plants inoculated with PL or NP isolate in any of the tested plant variables. The results of this study showed that AMF enhance metal accumulation in the root system of A. tripolium, suggesting a contribution of AMF to the sink of metals within vegetation in the salt marshes.     

Trace metal biomonitoring in the soil and the leaves ofQuercus ilex in the urban area of Naples

The concentrations of Pb, Cu, Fe, and Mn were analyzed in surface deposit and tissue ofQuercus ilex leaves from several sites of the urban area of Naples, exposed to different degrees of air pollution. These included some major roads with heavy traffic loads, squares, and three urban parks. The soil from the trunk base area ofQ. ilex trees in the same sites was also analyzed for total and available metal contents. Pb, Cu, and Fe contents in the surface deposit and leaf tissue were significantly higher (p<0.01) in leaves from roadside sites than in leaves from parks; significant correlations were found between deposit- and tissue-contents of Pb, Cu, and Fe. Mn content in leaves from roadside sites and in leaves from parks were similar and Mn content in the leaf deposit was irrelevant. Significant differences (p<0.001) in both total and available Pb and Cu soil content were found between sampling sites. Also for available Fe and Mn soil content differences among sites were relevant, although the highest values were measured in soil from urban parks. A positive correlation between leaf and soil metal content was found only for Pb, thus suggesting that trace metal contents of leaves directly depend on atmospheric depositions. Seasonal variations of Pb, Cu, and Fe were pronounced at a polluted site, whereas no relevant seasonal variation was observed at a control site; moreover, metal accumulation was high at the polluted site. Mn content and seasonal dynamics were comparable at control and polluted sites.     

Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile

ABSTRACT: BACKGROUND: Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized. RESULTS: DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively. CONCLUSIONS: This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.     

Genetic Diversity and Mosaicism at the por Locus of Neisseria gonorrhoeae

The por genes of the predominant serovars of Neisseria gonorrhoeae circulating in a high-frequency transmitter core group located in Nairobi, Kenya, were examined for nucleotide sequence polymorphism. The level of por gene diversity did not differ significantly between core group-derived gonococcal strains and gonococcal strains originating elsewhere. However, por mosaicism appeared to be more frequent among core group-derived strains, suggesting that recombination of different por sequences may be a important strategy by which N. gonorrhoeae generates por gene diversity within core group populations. Despite extensive sequence variability, por expressed by gonococcal isolates of different geographic origin exhibited conserved patterns of nucleotide change, suggesting that diversity among por alleles may also be finite.     

Genetic variation and heavy metal tolerance in the ectomycorrhizal basidiomycete Suillus luteus

Twenty-one isolates of the ectomycorrhizal fungus Suillus luteus were screened for their tolerance to the heavy metals Zn, Cd, Cu and Ni, measured as inhibition of radial growth and biomass production. Two populations from even-aged pine stands were investigated: 10 isolates were obtained from an area polluted with high levels of Zn, Cd and Cu, and 11 isolates were obtained from a control population located in a nearby unpolluted area. RFLP patterns of the internal transcribed spacer region of the isolates confirmed the morphological identification of the carpophores. All isolates were maintained on basic medium without elevated metals to avoid phenotypically acquired metal tolerance. The in vitro Zn and Cd tolerance of the S. luteus isolates from the polluted habitat were significantly higher than the tolerances measured in the isolates from the nonpolluted site. This observation suggests that the elevated soil metal concentrations might be responsible for the evolution of adaptive Zn and Cd tolerance. Tolerance was maintained in an isolate not exposed to elevated metals for 3 yr. The two S. luteus populations did not differ in tolerance to Cu and Ni. The mechanisms for the adaptive Zn and Cd tolerance are not identical as there was no correlation between response to the two metals; the most Zn-tolerant isolate was the most sensitive for Cd in the metal-tolerant population. Zinc did not accumulate in basidiocarp tissue, whereas Cd levels in basidiocarps were significantly higher in the population on the polluted site. Inter-simple sequence-repeat fingerprints showed that 90% of the isolates were from different individuals. The genetic variation in the population from the unpolluted site was considerably larger than that observed at the polluted site.     

Environmental pollution affects genetic diversity in wild bird populations

Many common environmental pollutants, together with nuclear radiation, are recognized as genotoxic. There is, however, very little information on pollution-related genetic effects on free-living animal populations, especially in terrestrial ecosystems. We investigated whether genetic diversity in two small insectivorous passerines, the great tit (Parus major) and the pied flycatcher (Ficedula hypoleuca), was changed near point sources of heavy metals (two copper smelters) or radioactive isotopes (nuclear material reprocessing plant). We measured concentration of heavy metals and nucleotide diversity in mitochondrial DNA in feather samples taken from nestlings in multiple polluted areas and at control sites. In both species, heavy metal concentrations - especially of arsenic - were increased in feathers collected at smelter sites. The P. major population living near a smelter showed significantly higher nucleotide diversity than a control population in an unpolluted site, suggesting increased mutation rates in a polluted environment. On the contrary, F. hypoleuca showed reduced nucleotide diversity at both smelter sites but increased nucleotide diversity near the source of radioactivity. Our results show that heavy metal pollution and low level nuclear radiation affect the nucleotide diversity in two free-living insectivorous passerines. We suggest that the different response in these two species may be due to their different ability to handle toxic compounds in the body.     

Activity and heavy metal resistance of non-specific esterases in leaf beetle Chrysomela lapponica from polluted and unpolluted habitats

We compared the general activity and heavy metal resistance of non-specific esterases in two populations of the leaf beetle Chrysomela lapponica from habitats severely contaminated by heavy metals (mostly Ni and Cu) and two populations from unpolluted habitats. Concentrations of Ni and Cu in adult beetles from the most polluted site were 7.7 and 3.6 times higher that in beetles from unpolluted habitats. Larval esterases showed higher activity and lower susceptibility to heavy metals than esterases of adults. Larval esterase activity did not differ between populations from polluted and unpolluted sites, but adult beetles from polluted localities had lower esterase activity than beetles from unpolluted habitats. Both Cu and Ni sulfates in millimolar concentrations in vitro suppressed esterase activity of larvae from unpolluted habitats, but caused no negative effect on esterases of larvae from polluted sites. Similarly, inhibition of adult esterase activity by Ni was stronger in beetles from unpolluted localities than in beetles from polluted localities. This indicates that resistance of non-specific esterases to heavy metals is higher in leaf beetle populations from contaminated environment.     

Enhancing survival of <Emphasis Type="Italic">Escherichia coli</Emphasis> by increasing the periplasmic expression of Cu,Zn superoxide dismutase from <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

The gene for the Cu,Zn superoxide dismutase (Cu,ZnSOD) from Saccharomyces cerevisiae was cloned and expressed in Escherichia coli LMG194. The sod gene sequence obtained is 465 bp and encodes 154 amino acid residues. The sod gene sequence was cloned into the E. coli periplasmic expression vector pBAD/gIIIA, yielding pBAD-1. E. coli was transformed using the constructed plasmid pBAD-1 and induced by adding 0.02% l-arabinose to express Cu,ZnSOD protein. The results indicated that Cu,ZnSOD enzyme activity in the periplasmic space was about fivefold to sixfold higher in the recombinant E. coli strains bearing the sod gene than in the control strains. The yields of Cu,ZnSOD were about threefold higher at 48 h than at 24 h in the recombinant E. coli cells. Significantly higher survival of strains was obtained in cells bearing the sod gene than in the control cells when the cells were treated by heat shock and superoxide-generating agents, such as paraquat and menadione.     

Amplified functional DNA restriction analysis to determine catechol 2,3-dioxygenase gene diversity in soil bacteria

To determine phylogenetic diversity of a functional gene from strain collections or environmental DNA amplifications, new and fast methods are required. Catechol 2,3-dioxygenase (C23O) subfamily I.2.A genes, known to be of crucial importance for aromatic degradation, were used as a model to adapt the amplified ribosomal DNA restriction analysis to functional genes. Sequence data of C23O genes from 13 reference strains, representing the main branches of the C23O family I.2.A phylogeny, were used for simulation of theoretical restriction patterns. Among other restriction enzymes, Sau3A1 theoretically produce characteristic profiles from each subfamily I.2.A member and their similarities reassembled the main divergent branches of C23O gene phylogeny. This enzyme was used to perform an amplified functional DNA restriction analysis (AFDRA) on C23O genes of reference strains and 19 isolates. Cluster analyses of the restriction fragment profiles obtained from isolates showed patterns with distinct similarities to the reference strain profiles, allowing to distinguish four different groups. Sequences of PCR fragments from isolates were in close agreement with the phylogenetic correlations predicted with the AFDRA approach. AFDRA thus provided a quick assessment of C23O diversity in a strain collection and insights of its gene phylogeny affiliation among known family members. It cannot only be easily applied to a vast number of isolates but also to define the predominant polymorphism of a functional gene present in environmental DNA extracts. This approach may be useful to differentiate functional genes also for many other gene families.     

Bacterial Community Structure and Function along a Heavy Metal Gradient

The response of the planktonic, sediment, and epilithic bacterial communities to increasing concentrations of heavy metals was determined in a polluted river. None of the communities demonstrated a pollution-related effect on bacterial numbers (viable and total), heterotrophic activity, resistance to Pb or Cu, or species diversity as determined by either the Shannon-Wiener diversity index or rarefaction. The lack of correlation between concentrations of heavy metals and resistance in the sediment bacterial community was investigated and found to be due at least in part to the high pH of the river water and the resultant reduction in heavy metal toxicity. The three different communities demonstrated characteristic profiles based on the relative abundances of bacterial strains grouped according to functional similarities.     

Sequence analysis in the 23S rDNA region of Mycobacterium tuberculosis and related species

We sequenced a 516 base pair segment in the 23S rRNA gene of 54 Mycobacterium tuberculosis isolates, 52 of which were clinical isolates from Ethiopia. Sequence polymorphism was observed with 19 of the 54 strains; the polymorphic sites occurred in less than 2% (9/516) of the total sequence positions. The sequence variations represented base pair substitutions (14/23), insertions (9/23) or both (1/23). Insertions occurred at one site only, whereas substitutions were observed in various regions of the gene. There was no relation between mutational sites and drug susceptibility. However, using information from the GenBank database, comparison between the 23S rDNA sequences of M. tuberculosis and the corresponding sequences of other mycobacteria and of related non-mycobacterial species revealed considerable variation, suggesting that this region may provide a target for rapid detection and identification of mycobacteria both at the genus or species level.     

Localization of the insertion site and pathotype determination of the locus of enterocyte effacement of shiga toxin-producing Escherichia coli strains

Of 220 Shiga toxin-producing Escherichia coli (STEC) strains collected in central France from healthy cattle, food samples, and asymptomatic children, 12 possessed the eae gene included in the locus of enterocyte effacement (LEE) pathogenicity island. Based on gene typing, we observed 7 different eae espA espB tir pathotypes among the 12 STEC strains and described the new espAbetav variant. As previously observed, the O157 serogroup is associated with eaegamma, O26 is associated with eaebeta, and O103 is associated with eaeepsilon. However, the unexpected eaezeta allele was detected in 5 of the 12 isolates. PCR amplification and pulsed-field gel electrophoresis using the I-CeuI endonuclease followed by Southern hybridization indicated that the LEE was inserted in the vicinity of the selC (three isolates), pheU (two isolates), or pheV (six isolates) tRNA gene. Six isolates harbored two or three of these tRNA loci altered by the insertion of integrase genes (CP4-int and/or int-phe), suggesting the insertion of additional foreign DNA fragments at these sites. In spite of great genetic diversity of LEE pathotypes and LEE insertion sites, bovine strains harbor alleles of LEE genes that are frequently found in clinical STEC strains isolated from outbreaks and sporadic cases around the world, underscoring the potential risk of the bovine strains on human health.     

Genetic structure of Suillus luteus populations in heavy metal polluted and nonpolluted habitats

The genetic structure of populations of the ectomycorrhizal basidiomycete Suillus luteus in heavy metal polluted and nonpolluted areas was studied. Sporocarps were collected at nine different locations and genotyped at four microsatellite loci. Six of the sampling sites were severely contaminated with heavy metals and were dominated by heavy metal-tolerant individuals. Considerable genetic diversity was found within the geographical subpopulations, but no reduction of the genetic diversity, current or historic, was observed in subpopulations inhabiting polluted soils. The genetic differentiation between the geographical subpopulations was low, and no evidence for clustering of subpopulations from polluted soils vs. subpopulations from nonpolluted soils was found. These results indicate that heavy metal pollution has a limited effect on the genetic structure of S. luteus populations, and this may be due to the high frequency of sexual reproduction and extensive gene flow in S. luteus, which allows rapid evolution of the tolerance trait while maintaining high levels of genetic diversity.     

High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans

We investigated genetic polymorphism in the Caenorhabditis elegans srh and str chemoreceptor gene families, each of which consists of approximately 300 genes encoding seven-pass G-protein-coupled receptors. Almost one-third of the genes in each family are annotated as pseudogenes because of apparent functional defects in N2, the sequenced wild-type strain of C. elegans. More than half of these "pseudogenes" have only one apparent defect, usually a stop codon or deletion. We sequenced the defective region for 31 such genes in 22 wild isolates of C. elegans. For 10 of the 31 genes, we found an apparently functional allele in one or more wild isolates, suggesting that these are not pseudogenes but instead functional genes with a defective allele in N2. We suggest the term "flatliner" to describe genes whose functional vs. pseudogene status is unclear. Investigations of flatliner gene positions, d(N)/d(S) ratios, and phylogenetic trees indicate that they are not readily distinguished from functional genes in N2. We also report striking heterogeneity in the frequency of other polymorphisms among these genes. Finally, the large majority of polymorphism was found in just two strains from geographically isolated islands, Hawaii and Madeira. This suggests that our sampling of wild diversity in C. elegans is narrow and that identification of additional strains from similarly isolated regions will greatly expand the diversity available for study.     

Impact of wastewater discharge on the plant diversity,community structure and heavy metal pollution of range plants in eastern Saudi Arabia

The main objectives of this study were to determine the floristic composition of the vegetation cover and to find the effects of wastewater pollution on the plant community structure in eastern Saudi Arabia. 28 stands which were distributed among polluted and unpolluted sites, were chosen for this study. A total of 42 plant species were recorded (14 in the polluted and 28 in the unpolluted sites). The recorded plants comprised of 13 perennial plant species and 29 annual plant species. Seven vegetation communities were determined using TWINSPAN and DCA classification and ordination techniques. Three in the polluted sites, two in the unpolluted sites and the remaining two were mixed communities. The (Sarcopoterium spinosum – Pistacia len‐tiscus) community in the polluted sites, had the highest values of soil moisture, salinity, sulphate, calcium and potassium. On the other hand, Juniperus phoenicea – Olea europaea community in the unpolluted site, had the lowest value of organic matter, salinity and magnesium. In respect of genetic diversity, the community of Foeniculum vulgare - Nicotiana glauca in the unpolluted site, was the most diverse, while Ricinus communis - Chrysanthemum coronarium in the polluted sites was the least one. Both soil and wastewater heavy metal analysis indicated that Pb, Cd, Cr, Cu and Ni concentrations in the polluted sites were significantly higher than those in the unpolluted ones. The impact of wastewater discharge led to the appearance of new invasive plant species that may significantly affect plant diversity and community structure in eastern Saudi Arabia. Finally wastewater discharge in open rangelands could adversely affect the growth of plant species in the rangelands and thus adversely affect plant community structure and diversity.     

Effects of Cu,Cd and Zn on photosynthesis of freshwater benthic algae

One hundred and eighteen algal isolates comprising seven classes were obtained from a range of sites from polluted rivers running through Cu or Zn mining regions, and from unpolluted rivers. All the isolates were tested for photosynthetic activity when exposed to Cu, Cd or Zn. The tolerance levels of Bacillariophyceae, Charophyceae, Cyanophyceae and Chlorophyceae to Cu showed significant positive correlations with Cu concentrations in the field. However the distribution of metal sensitivities of the algae from the sites with the same metal concentration was broad. Both Bacillariophyceae and Charophyceae had a number of strains whose sensitivity to Cu differed more widely in relation to Cu levels in the environment than Cyanophyceae and Chlorophyceae. Cyanophyceae were sensitive to all three metals, whether or not isolates were obtained from polluted sites, whereas Chlorophyceae tended to have high tolerance even in isolates from unpolluted sites. For Cd and Zn the correlation between tolerance levels and concentrations in the field was not so clear as for Cu. The occurrence of Cu tolerance was shown in 4 diatom species and one Charophyceae, whereas metal resistance occurred in some Chlorophyceae. Cu-tolerant isolates tended also to be Zn-tolerant in Bacillariophyceae, and Cd-resistant isolates tended also to be Zn-resistant in Chlorophyceae.     

Assessment of ecological diversity of rhizobacterial communities in vermicompost and analysis of their potential to improve plant growth

Present study was designed to determine the microbial diversity from three distinctive sites (amended with vermicompost) of Gujarat, India. A set of 76 strains were screened from total of 438 strains that exhibit plant growthpromoting (PGP) and antagonistic potential isolated from sites PS1 (Mehsana district), BS2 (Dantiwada district) and VS3 (Gandhinagar district). Their diversity indices were studied for determining the species richness and evenness of screened isolates. Results revealed that site BS2 showed the most significant diversity indices in terms of Shannon (H′ 1.525) and Simpson (1/D 5.120) than other two samples. Principal component analysis showed that bacterial diversity (H′) was correlated with the soil characteristics. Chickpea and groundnut plants inoculated with MBCU1 and MBCU3 isolates showed an increase in the vegetative growth parameters that evaluate plant growth when compared to uninoculated controls. Strains MBCU1 and MBCU3 were identified as Pseudomonas stutzeri and Pseudomonas mosselii, respectively, according to sequence analysis of the 16S rRNA gene. These both isolates belong to site BS2 and they showed specific PGP traits suggesting that these isolates can promote plant growth by more than one mechanism with respect to their higher diversity index.