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R Amils

Publications and source records attributed to R Amils.

At least 19 recordsLinked to original sources
PubMed2006

Microbiological and structural aspects of granular sludge from autotrophic denitrifying reactors.

Denitrification is applied in the tertiary treatment of wastewater to reduce N-pollutants. Fluorescence in situ hybridisation (FISH), CARD (catalyzed reporter deposition)-FISH, cloning, and scanning electron microscopy (SEM) were applied to follow the evolution of the microbial composition and structure of granular sludge in autotrophic denitrifying bioreactors fed with nitrate and thiosulfate. With this goal, FISH oligonucleotide probes for the autotrophic denitrifiers, Thiobacillus denitrificans and Thiomicrospira denitrificans, were designed and their utility tested. CARD-FISH and cloning data showed that bacterial diversity changed with bioreactor operation time. After 110 days of operation, the abundance of Thiobacillus denitrificans cells increased considerably: from 1 to 35% of total DAPI-stained cells and from no isolated clones to 30% of the total positives clones. This fact strongly suggests that this microorganism played a dominant role in the autotrophic denitrification. The Archaeal diversity remained almost unchanged and it was mainly represented by Methanosaeta soehngenii. Scanning electron microscopy results indicated a considerable loss in the integrity of the sludge granules during the operation, with risk of sludge buoyancy.

Base Sequence↗
PubMed2005

Internal iron biomineralization in Imperata cylindrica, a perennial grass: chemical composition, speciation and plant localization.

* The analysis of metal distribution in Imperata cylindrica, a perennial grass isolated from the banks of Tinto River (Iberian Pyritic Belt), an extreme acidic environment with high content in metals, has shown a remarkable accumulation of iron. This property has been used to study iron speciation and its distribution among different tissues and structures of the plant. * Mossbauer (MS) and X-ray diffraction (XRD) were used to determine the iron species, scanning electron microscopy (SEM) to locate iron biominerals among plant tissue structures, and energy-dispersive X-ray microanalysis (EDAX), X-ray fluorescence (TXRF) and inductively coupled plasma emission spectroscopy (ICP-MS) to confirm their elemental composition. * The MS spectral analysis indicated that iron accumulated in this plant mainly as jarosite and ferritin. The presence of jarosite was confirmed by XRD and the distribution of both minerals in structures of different tissues was ascertained by SEM-EDAX analysis. * The convergent results obtained by complementary techniques suggest a complex iron management system in I. cylindrica, probably as a consequence of the environmental conditions of its habitat.

Biological Transport, Active↗
PubMed2004

Ecological study of the fungal populations of the acidic Tinto River in southwestern Spain.

The characterization of the microbial ecology of the Tinto River, an extreme habitat with an extremely low pH and a high concentration of heavy metals, revealed an unexpected level of microbial richness. A variety of microbial eukaryotes was isolated, among them several fungal strains that were identified and their physiological characteristics studied. Ninety strains of yeast were isolated from the Tinto River. Fifty-two percent of them were capable of growth in vitro using medium amended with river water. They belong to 6 genera of basidiomycetes (Rhodotorula, Cryptococcus, Tremella, Holtermannia, Leucosporidium, and Mrakia) and 2 of ascomycetes (Candida and Williopsis). In addition, 349 strains of hyphomycetes belonging to 17 genera (most of them ascomycetes) were isolated and studied. Forty-four percent of the isolated filamentous fungi (154 strains) were capable of growing in vitro using medium amended with Tinto River water. Of this percentage, 19% (29 strains) belonged to the genus Penicillium (16 species) and 66% (102 strains) were included in the genera Scytalidium, Bahusakala, Phoma, and Heteroconium or showed dark sterile mycelia, which probably are of dematiaceous hyphomycetes. In addition, we characterized strains of the ascomycete genera Lecythophora and Acremonium and of the zygomycete genus Mortierella, all of them capable of growing in medium amended with river water. Statistical correlation of biological and physicochemical variables suggested a positive relationship between the dematiaceous hyphomycetes and the most extreme physicochemical conditions found in the Tinto River. Principal components analysis confirmed this relationship and also showed that the Acremonium and Lecythophora groups had environmental preferences similar to those of dematiaceous fungi. The spatial positions of the sampling sites were grouped in 2 main clusters: (i) sampling sites in the mine zone in which most of the dematiaceous, Acremonium, and Lecythophora strains were isolated and (ii) sites that were not in the mine zone and sampling station 5 from which were isolated mainly strains of fungi that were not capable of growing in the medium amended with river water and species of the Penicillium genus.

Culture Media↗
PubMed2003

Microbial ecology of an extreme acidic environment, the Tinto River.

The Tinto River (Huelva, southwestern Spain) is an extreme environment with a rather constant acidic pH along the entire river and a high concentration of heavy metals. The extreme conditions of the Tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the Iberian Pyrite Belt. Molecular ecology techniques were used to analyze the diversity of this microbial community. The community's composition was studied by denaturing gradient gel electrophoresis (DGGE) using 16S rRNA and by 16S rRNA gene amplification. A good correlation between the two approaches was found. Comparative sequence analysis of DGGE bands showed the presence of organisms related to Leptospirillum spp., Acidithiobacillus ferrooxidans, Acidiphilium spp., "Ferrimicrobium acidiphilum," Ferroplasma acidiphilum, and Thermoplasma acidophilum. The different phylogenetic groups were quantified by fluorescent in situ hybridization with a set of rRNA-targeted oligonucleotide probes. More than 80% of the cells were affiliated with the domain Bacteria, with only a minor fraction corresponding to Archaea. Members of Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, and Acidiphilium spp., all related to the iron cycle, accounted for most of the prokaryotic microorganisms detected. Different isolates of these microorganisms were obtained from the Tinto ecosystem, and their physiological properties were determined. Given the physicochemical characteristics of the habitat and the physiological properties and relative concentrations of the different prokaryotes found in the river, a model for the Tinto ecosystem based on the iron cycle is suggested.

DNA Fingerprinting↗
PubMed2003

Molecular ecology of anaerobic granular sludge grown at different conditions.

Qualitative and quantitative diversity of microorganisms present in anaerobic granular sludges fed with different substrates, as well as the structure of these granules have been studied using fluorescent 16S rRNA-targeted in situ hybridization and electron microscopy. The granules showed a multi-layered structure, in which both densely packed and loose micro-colonies, channels and holes could be observed. Only bacteria were found in the outer shell of the granules, while both archaea and bacteria were detected in the inner core. Although high cell density was found in the granules (more than 10(11) cells/gram, determined by DAPI-stain) only a low percentage of cells was able to hybridize with the rRNA-targeted probes. Significant quantitative and qualitative differences were observed in the composition of granules fed with different substrates (formate, acetate at high and low concentrations, propionate, sucrose, starch and peptone). Bacterial cells were mostly gram-positives. Active proteobacteria were scarce in the granules exposed to VFA. Syntrophobacteria became dominant in the propionate-grown biomass. Concerning methanogenic archaea, Methanosaeta was the predominant species using complex substrates or low acetate concentration fed granules, while Methanosarcina and members of Methanobacteriales were predominant in the granules grown at high concentration of acetate or formate, respectively. Other Methanomicrobiales and Methanococcales, have been detected in the anaerobic granular sludge in the conditions used in this work.

Bacteria, Anaerobic↗
PubMed2001

Association between intimin (eae) and EspB gene subtypes in attaching and effacing Escherichia coli strains isolated from diarrhoeic lambs and goat kids.

Attaching and effacing Escherichia coli (AEEC) strains isolated from diarrhoeic lambs and goat kids were characterized for intimin (eae) and EspB (espB) gene subtypes by PCR and sequencing, and for genetic relatedness by PFGE. Fifty (23 ovine and 27 caprine) AEEC strains of 398 (246 ovine and 152 caprine) analysed were detected by colony blot hybridization. These strains were epidemiologically unrelated since they were isolated from different outbreaks of neonatal diarrhoea over a long period. Ovine AEEC strains belonged to serogroups O2, O4, O26, O80, O91 or were untypable, and caprine strains belonged to serogroups O3, O153 and O163. Two intimin subtypes were detected among the ovine and caprine strains studied. Most of the strains (43/50) had the beta type intimin gene, but seven ovine strains possessed a variant gamma type intimin gene (gamma(V)). Analysis of deduced amino acid sequences of the eae gene revealed that the sequences of beta intimin of ovine and caprine strains were virtually identical to those of beta intimin of rabbit EPEC, human EPEC clone 2 and swine AEEC, whereas the gamma(V) intimin present in seven ovine strains had 75-76% identity with gamma intimin of human EHEC clone 1 strains, and 96% of identity with intimin of the human EHEC strain 95NR1 of serotype O111:H-. A PCR test was developed to identify the three different espB gene subtypes, espB of human EPEC clone 1 (espBalpha), espB of human EHEC clone 1 (espBgamma) and espB of rabbit EPEC and human EPEC clone 2 (espBbeta). There was close correlation between the intimin beta type and the espBbeta gene subtype in the ovine and caprine AEEC strains. The seven ovine strains possessing the gamma(V) intimin gene possessed the espBalpha gene subtype. None of the strains studied possessed the espBgamma gene found in human O157:H7 EHEC strains. PFGE analysis of genomic DNA of selected strains showed a great diversity among strains. Cluster analysis of PFGE patterns showed greater divergence between strains with the gamma(V) intimin gene than between strains with the beta intimin gene. This study showed that most of the AEEC strains isolated from diarrhoeic lambs and goat kids possessed beta intimin and espB genes identical to those of rabbit EPEC, and they may be associated with enteric disease in small ruminants.

Adhesins, Bacterial↗
PubMed2001

Biodegradation of 1,1,1,2-tetrachloroethane under methanogenic conditions.

Chlorinated aliphatic hydrocarbons are widely used as solvents and as intermediates in chemical synthesis, so they can be found in industrial wastewaters and released to the environment where they became a serious health risk due to their toxic properties and high chemical stability. Most of these compounds are xenobiotic and recalcitrant to biodegradation. In this article we report the effect of different co-substrates in the 1,1,1,2-tetrachloroethane (1,1,1,2-TeCA) degradation by anaerobic granular sludge, and its degradative pathway. Our results show that this compound is easy and rapidly biodegradable under methanogenic conditions, even in the absence of external electron donors. 1,1,1,2-TeCA is equimolecularly degraded to 1,1-dichloroethene (1,1-DCE) by reductive dichloroelimination. 1,1-DCE is only completely biodegraded in the presence of lactic acid as co-substrate. Although 1,1,1,2-TeCA can be apparently removed by autoclaved granular sludge, the compound is not transformed but retained inside the granules. The primary biodegradation of 1,1,1,2-TeCE to 1,1-DCE is a biotic process mediated by anaerobic bacteria.

Bacteria, Anaerobic↗
PubMed2000

Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA.

23S rRNA gene from the halophilic archaeon Haloferax mediterranei (strain ATCC 33500) was cloned and sequenced. Proceeding from the 2,912 nucleotides long sequence, the secondary structure of Haloferax genus large subunit rRNA was proposed. Haloferax mediterranei intergenic spacers 16S/23S and 23S/5S were also sequenced, and found to be 382 and 116 nucleotides long respectively. The 16S/23S spacer showed an Ala-tRNA intervening sequence, which is a common feature in Euryarchaeota. Sequence analysis of 23S rRNA and 16S rRNA was performed for the six organisms from the family Halobacteriaceae with both available gene sequences. Phylogenetic trees with completely different topology were obtained using both molecules.

Base Sequence↗
PubMed2000

Puromycin-rRNA interaction sites at the peptidyl transferase center.

The binding site of puromycin was probed chemically in the peptidyl-transferase center of ribosomes from Escherichia coli and of puromycin-hypersensitive ribosomes from the archaeon Haloferax gibbonsii. Several nucleotides of the 23S rRNAs showed altered chemical reactivities in the presence of puromycin. They include A2439, G2505, and G2553 for E. coli, and G2058, A2503, G2505, and G2553 for Hf. gibbonsii (using the E. coli numbering system). Reproducible enhanced reactivities were also observed at A508 and A1579 within domains I and III, respectively, of E. coli 23S rRNA. In further experiments, puromycin was shown to produce a major reduction in the UV-induced crosslinking of deacylated-(2N3A76)tRNA to U2506 within the P' site of E. coli ribosomes. Moreover, it strongly stimulated the putative UV-induced crosslink between a streptogramin B drug and m2A2503/psi2504 at an adjacent site in E. coli 23S rRNA. These data strongly support the concept that puromycin, along with other peptidyl-transferase antibiotics, in particular the streptogramin B drugs, bind to an RNA structural motif that contains several conserved and accessible base moieties of the peptidyl transferase loop region. This streptogramin motif is also likely to provide binding sites for the 3' termini of the acceptor and donor tRNAs. In contrast, the effects at A508 and A1579, which are located at the exit site of the peptide channel, are likely to be caused by a structural effect transmitted along the peptide channel.

Base Sequence↗
PubMed1999

A Comparative Ecological Study of Two Acidic Rivers in Southwestern Spain.

> Abstract We have analyzed select physicochemical and biological characteristics of two acidic rivers, the Tinto and the Odiel, located in the Pyritic Belt of Southwestern Spain. Despite a common geography and geochemistry, they exhibit important differences. Most of the measured physicochemical parameters, especially pH and those related to conductivity (heavy metal concentrations), showed more extreme values in the Tinto than in the Odiel. However, it was at the microbiological level (fungal and bacterial populations) where both rivers showed the most important differences according to the statistical analysis of principal components. Lithoautotrophic bacteria were more abundant in the more acidic Tinto River and fungal diversity varied significantly from one river to the other.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p146.html

Journal Article↗
PubMed1999

Bioremoval of organic and inorganic sulphur from coal samples

The microbial ecology of different Spanish coal samples has been studied. Several bacteria have been isolated from enrichment cultures and characterised and their biodesulphurization abilities evaluated. Using morphological and physiological properties, different isolates have been related to species of the Xanthomonas, Pseudomonas, Chryseomonas and Moraxella genera. Some of the isolates, B(30)15 and T(30)10, gave important levels of organic desulphurization, close to 70%. Other isolates, B(30)7 and B(30)8, were able to remove inorganic sulphur with high efficiencies, over 67%. One of the isolates, B(30)10, metabolically related to Xanthomonas maltophila, was able to remove both organic and inorganic sulphur at neutral pH, with efficiencies of 69% and 68% respectively. The results obtained underline the potential use of some of these strains for industrial coal desulphurization processes.

Journal Article↗
PubMed1999

Characterization of nonenterotoxigenic Escherichia coli strains producing F17 fimbriae isolated from diarrheic lambs and goat kids.

Forty-five ovine and caprine nonenterotoxigenic Escherichia coli strains producing F17-related fimbriae were characterized with respect to the fimbrial structural subunit and adhesin subtypes produced. In addition, several characteristics related to the virulence of strains producing F17 fimbriae were studied. Most of the strains (73%) possessed the f17cA structural subunit gene, whereas the f17aA and f17dA genes were detected only on three (6%) and two (4%) strains, respectively. The f17bA gene was not detected. All but one of these strains possessed the f17G genes of the adhesin subfamily II. The only strain having the f17G gene of subfamily I possessed the structural subunit gene f17dA. Sequencing of the f17A and f17G genes of four selected strains confirmed the association of f17cA and f17dA structural subunit genes with the f17G genes of the adhesin subfamily II. These results indicated that adhesins of the subfamily II are prominent among ovine and caprine isolates and that they are indistinctly associated with the F17 structural subunit subtypes on these field strains. CS31A- and CNF2-related genes were not detected. Most of the strains adhered in vitro to ovine intestinal brush borders (36 of 45) and agglutinated the erythrocytes of different species in the presence of D-mannose (39 of 45). F17-positive strains produced colicin V (57%) and were resistant to the bactericidal effect of serum (91%) in significantly higher percentages than F17-negative strains (34% produced colicin V, and 66% were serum resistant). Thus, most of the studied ovine and caprine strains showed phenotypic characteristics of septicemic strains.

Amino Acid Sequence↗
PubMed1998

Genomic organization analysis of acidophilic chemolithotrophic bacteria using pulsed field gel electrophoretic techniques.

The genomic organization of acidophilic chemolithotrophic bacteria belonging to the genus Thiobacillus, Thiomonas and Leptospirillum was studied using pulsed field gel electrophoresis techniques (PFGE). The electrophoretic analysis of intact DNA prepared from different strains showed that all have a circular chromosome, with sizes ranging from 1.9 Mb for Leptospirillum ferrooxidans ATCC 49879, the smallest genome for an acidophilic strict chemolithoautotrophic microorganism, to 3.8 Mb for Thiomonas cuprina DSM 5495, the largest in this study. The number of extrachromosomal elements present varied from none, as observed in several isolates of Leptospirillum ferrooxidan, to five in Thiobacillus thiooxidans ATCC 8085. The mixotroph Thiomonas cuprina DSM 5495 was found to have a linear 50 kb megaplasmid which was inducible when the bacteria was grown in chemolithotrophic conditions. Low-frequency restriction fragment analysis (LFRFA) of different acidophilic chemolithotrophs and related species was carried out by PFGE to determine macrorestriction patterns for rare cutters (SpeI, XbaI, SwaI, PmeI), which were then used for taxonomic identification (karyotyping), genome size determination, and generation of physical and genetic maps.

Chromosome Mapping↗
PubMed1998

Functional phylogeny: the use of the sensitivity of ribosomes to protein synthesis inhibitors as a tool to study the evolution of organisms.

In order to study the functional phylogeny of organisms, forty different protein synthesis inhibitors with diverse domain and functional specificities have been used to analyze forty archaeal, bacterial and eukaryotic translational systems. The inhibition curves generated with the different ribosome-antibiotic pairs have shown very interesting similarities among organisms belonging to the same phylogenetic group, confirming the feasibility of using such information in the development of evolutionary studies. A new method to extract most of the information contained in the inhibition curves is presented. Using a statistical treatment based on the principal components analysis of the data, we have defined coordinates for the organisms which have allowed us to perform a functional clustering of them. The phenograms obtained are very similar to those generated by 16/18S rRNA sequence comparison. These results prove the phylogenetic value of our functional analysis and suggest an interesting intersection between genotypic and phenotypic (functional) information.

Animals↗
PubMed1998

The evolution of function: a new method to assess the phylogenetic value of ribosomal sensitivity to antibiotics.

Thirty-five archaeal, bacterial and eukaryotic translational systems have been proved against forty different protein synthesis inhibitors with diverse domain and functional specificities. The inhibition curves generated in every ribosome-antibiotic combination had previously shown interesting similarities among organisms belonging to the same phylogenetic group. This opened the possibility of using such functional information for developing evolutionary studies. A new mathematical method based on the main data components analysis has been developed to extract most of the information contained in the inhibition curves. The phenograms obtained closely resemble those generated by the small ribosomal subunit rRNA sequence comparison and such functional clustering is also congruent when a particular subset of organisms and/or antibiotics is used. These results prove the phylogenetic value of our functional analysis and suggest that the ribosome represents an interesting intersection between genotypic and phenotypic (functional) information stored in organisms.

Animals↗
PubMed1997

Genomic organization of the metal-mobilizing bacterium Thiobacillus cuprinus.

The genomic organization of Thiobacillus cuprinus, a facultative chemolithotrophic bacterium that preferentially solubilizes copper from complex ores, has been studied by Pulsed Field Gel Electrophoresis (PFGE). It has been determined that T. cuprinus has a circular chromosome of about 3.8 Mb in size as concluded by analysis of gamma-irradiated total DNA and restriction analysis. Macrorestriction patterns for several restriction enzymes have been generated. Restriction enzymes AseI, DraI, SpeI, SwaI and XbaI give a number of fragments that can be adequately resolved by PFGE and then be used for electrophoretic karyotyping and for the construction of physical maps of the chromosome. Such a map has been constructed for the endonucleases SpeI and SwaI. The localization of several heterologous and homologous genes on the physical map, including those for rRNA, has paved the way for the construction of a genetic map.

Chromosomes↗
PubMed1997

Phylogeny of Thiobacillus cuprinus and other mixotrophic thiobacilli: proposal for Thiomonas gen. nov.

The complete 5S and 16S ribosomal DNA (rDNA) sequences of the facultatively chemolithotrophic bacterium Thiobacillus cuprinus and results of a comparison of these sequences with homologous sequences from several proteobacterial species supported affiliation of T. cuprinus with the beta 1 subgroup of the Proteobacteria. T. cuprinus, Thiobacillus intermedius, Thiobacillus perometabolis, and Thiobacillus thermosulfatus form a phylogenetic cluster that comprises some of the thiobacilli capable of mixotrophic growth. This cluster is related to some pseudomonads and Alcaligenes species belonging to the beta subclass. In addition, a low-frequency restriction fragment analysis (LFRFA) of some mixotrophic thiobacilli and some related species was carried out by using pulsed-field gel electrophoresis (PFGE) to determine the SpeI and XbaI macrorestriction patterns and genome sizes of these organisms. The correlation of the LFRFA results and the 16S rDNA analysis results and the usefulness of the two analyses are discussed. The PFGE fingerprints suggested that Thiobacillus sp. strain ATCC 27793 is related to T. intermedius rather than to T. perometabolis, as described previously. The distinctive characteristics of the mixotrophic species analyzed in this work, their phylogenetic relatedness, and their physiological differences from other groups belonging to the Proteobacteria, including other thiobacilli, suggest that these organisms should be transferred to a new genus, the genus Thiomonas gen. nov.

DNA, Bacterial↗