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Juan M Gonzalez

Publications and source records attributed to Juan M Gonzalez.

17 recordsLinked to original sources
PubMed2006

Nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale.

Biogenic production of sulfide in wastewater treatment plants involves odors, toxicity and corrosion problems. The production of sulfide is a consequence of bacterial activity, mainly sulfate-reducing bacteria (SRB). To prevent this production, the efficiency of nitrate addition to wastewater was tested at plant-scale by dosing concentrated calcium nitrate (Nutriox) in the works inlet. Nutriox dosing resulted in a sharp decrease of sulfide, both in the air and in the bulk water, reaching maximum decreases of 98.7% and 94.7%, respectively. Quantitative molecular microbiology techniques indicated that the involved mechanism is the development of the nitrate-reducing, sulfide-oxidizing bacterium Thiomicrospira denitrificans instead of the direct inhibition of the SRB community. Denitrification rate in primary sedimentation tanks was enhanced by nitrate, being this almost completely consumed. No significant increase of inorganic nitrogen was found in the discharged effluent, thus reducing potential environmental hazards to receiving waters. This study demonstrates the effectiveness of nitrate addition in controlling sulfide generation at plant-scale, provides the mechanism and supports the environmental adequacy of this strategy.

Calcium Compounds↗
PubMed2006

Epilithic biofilms in Saint Callixtus Catacombs (Rome) harbour a broad spectrum of Acidobacteria.

The phylum Acidobacteria is broadly represented in a variety of environments as reported during microbial molecular surveys. This study represents the first attempt to analyze the diversity of Acidobacteria in Roman Catacombs (Rome, Italy). Both 16S and 23S rRNA gene sequences were used to confirm the affiliation within different acidobacterial subgroups. The results showed Acidobacteria belonging to subgroups 3, 4, 6, 9, and 10 in the analyzed samples. The presence of acidobacterial sequences in biodeteriorating biofilms in Roman Catacombs suggest they could participate in this negative process, most likely in cooperation with other microbial groups.

Bacteria↗
PubMed2006

Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs.

Three xylan-degrading actinobacterial strains were isolated from different sampling sites in the Roman catacombs of Domitilla and San Callisto. The organisms showed morphological and chemotaxonomic properties such as peptidoglycan type A4alpha, L-lys-L-thr-D-Glu; whole-cell sugars (glucose, mannose and galactose); octa-, hexa- and tetrahydrogenated menaquinones with nine isoprene units; phosphatidylglycerol and diphosphatidylglycerol as the major phospholipids; anteiso-C(15 : 0), iso-C(15 : 0) and iso-C(16 : 0) as the predominant fatty acids; and a DNA G+C content of 72 mol%. These features are consistent with affiliation of these isolates to the genus Myceligenerans. The three isolates shared a 16S rRNA gene similarity of 99.9 % and were most closely related to Myceligenerans xiligouense DSM 15700T (97.9 % sequence similarity). The low level of DNA-DNA relatedness (about 14 %) and the differences in phenotypic characteristics between the novel strains and M. xiligouense DSM 15700T justify the proposal of a novel species of the genus Myceligenerans, Myceligenerans crystallogenes sp. nov., with CD12E2-27T (= HKI 0369T = DSM 17134T = NCIMB 14061T = VTT E-032285T) as the type strain.

Actinobacteria↗
PubMed2006

Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave.

A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family 'Aurantimonadaceae' (showing 96% sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16:0 and C18:1omega7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T).

Alphaproteobacteria↗
PubMed2005

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Base Sequence↗
PubMed2005

Metabolically active Crenarchaeota in Altamira Cave.

Altamira Cave contains valuable paleolithic paintings dating back to 15,000 years. The conservation of these unique paintings is attracting increasing interest, and so, understanding microbial proliferation in Altamira Cave represents a prioritary objective. Here, we show for the first time that members of the Crenarchaeota were metabolically active components of developing microbial communities. RNA was extracted directly from the studied environment, and a number of 16S rRNA gene sequences belonging to the low-temperature Crenarchaeota were detected. Although low-temperature Crenarchaeota detected in a variety of ecosystems by using molecular techniques remain uncultured, this RNA-based study confirms an active participation of the Crenarchaeota in cave biogeochemical cycles.

Base Sequence↗
PubMed2005

Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA-DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

Actinomycetales↗
PubMed2005

Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs.

A polyphasic study was carried out to clarify the taxonomic positions of three Gram-positive isolates from the Catacombs of Domitilla, Rome (Italy). 16S rRNA gene sequence comparisons placed these strains within the genus Agromyces. The morphological and chemotaxonomic characteristics of these isolates were consistent with the description of the genus Agromyces. The three isolates could be readily distinguished from one another and from representatives of all Agromyces species with validly published names by a broad range of phenotypic characteristics and DNA-DNA relatedness studies. Therefore, these isolates are proposed to represent three novel species of the genus Agromyces, Agromyces italicus sp. nov. (type strain CD1(T)=HKI 0325(T)=DSM 16388(T)=NCIMB 14011(T)), Agromyces humatus sp. nov. (type strain CD5(T)=HKI 0327(T)=DSM 16389(T)=NCIMB 14012(T)) and Agromyces lapidis sp. nov. (type strain CD55(T)=HKI 0324(T)=DSM 16390(T)=NCIMB 14013(T)).

Actinomycetales↗
PubMed2005

Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla.

In order to clarify the taxonomic position of an actinobacterium from the Roman catacomb of Domitilla, a combination of phenotypic characterization, phylogenetic analysis based on the 16S rRNA gene sequence and DNA-DNA relatedness studies was used. The results from the polyphasic taxonomic study of this organism showed that strain HKI 0342(T) (=DSM 16849(T)=NCIMB 14033(T)) should be considered as the type strain of a novel species of the genus Isoptericola, for which the name Isoptericola hypogeus sp. nov. is proposed.

Actinomycetales↗
PubMed2005

Agromyces subbeticus sp. nov., isolated from a cave in southern Spain.

An actinomycete, strain Z33(T), was isolated from a cyanobacterial biofilm in the Cave of Bats, near Zuheros (Cordoba, southern Spain). 16S rRNA gene sequence analysis showed that strain Z33(T) formed a distinct phyletic line within the genus Agromyces. This isolate could be readily distinguished from representatives of all recognized Agromyces species on the basis of a broad range of phenotypic characteristics and DNA-DNA relatedness data. Genotypic and phenotypic properties indicate that strain Z33(T) represents a novel species, for which the name Agromyces subbeticus sp. nov. is proposed. The type strain is Z33(T) (=HKI 0340(T)=DSM 16689(T)=NCIMB 14025(T)).

Actinomycetales↗
PubMed2005

Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments.

Microbial assessment of natural biodiversity is usually achieved through polymerase chain reaction (PCR) amplification. Deoxyribonucleic acid (DNA) sequences from natural samples are often difficult to amplify because of the presence of PCR inhibitors or to the low number of copies of specific sequences. In this study, we propose a non-specific preamplification procedure to overcome the presence of inhibitors and to increase the number of copies prior to carrying out standard amplification by PCR. The pre-PCR step is carried out through a multiple displacement amplification (MDA) technique using random hexamers as priming oligonucleotides and phi 29 DNA polymerase in an isothermal, whole-genome amplification reaction. Polymerase chain reaction amplification using specific priming oligonucleotides allows the selection of the sequences of interest after a preamplification reaction from complex environmental samples. The procedure (MDA-PCR) has been tested on a natural microbial community from a hypogean environment and laboratory assemblages of known bacterial species, in both cases targeting the small subunit ribosomal RNA gene sequences. Results from the natural community showed successful amplifications using the two steps protocol proposed in this study while standard, direct PCR amplification resulted in no amplification product. Amplifications from a laboratory assemblage by the two-step proposed protocol were successful at bacterial concentrations >or= 10-fold lower than standard PCR. Amplifications carried out in the presence of different concentrations of fulvic acids (a soil humic fraction) by the MDA-PCR protocol generated PCR products at concentrations of fulvic acids over 10-fold higher than standard PCR amplifications. The proposed procedure (MDA-PCR) opens the possibility of detecting sequences represented at very low copy numbers, to work with minute samples, as well as to reduce the negative effects on PCR amplifications of some inhibitory substances commonly found in environmental samples.

Bacillus Phages↗
PubMed2004

A truncated-dose regimen of daclizumab for prevention of acute rejection in kidney transplant recipients: a single-center experience.

Daclizumab can decrease the incidence of acute rejection (AR) in renal transplant (RTx) recipients. In this prospective study, 52 RTx patients were divided into two groups according to the dose of daclizumab: 1 mg/kg on day 0 and every 14 days for five doses (group 1, n = 30) or a truncated regimen of 2 mg/kg on day 0 and on the day of discharge (group 2, n = 22). The following variables were recorded: demographics; delayed graft function; AR at 3, 6, and 12 months; time to AR; chronic allograft nephropathy (CAN); and serum creatinine. The overall incidences of AR were 23% and 27% (P = 0.76) in groups 1 and 2, respectively, whereas at 6 months they were 21% and 18% (P = 1.0). Median time to AR was 10 days in group 1 and 94 days in group 2 (P = 0.09). The incidence of CAN was 6.6% in group 1 and 13% in group 2 (P = 0.63). These data suggest that the truncated dose of daclizumab is as effective as the standard regimen for AR prophylaxis.

Antibodies, Monoclonal↗
PubMed2004

A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures.

Determination of whole-genome DNA-DNA similarity is today a standard technique for species delineation in microbial taxonomy. However, these studies demand hard-to-perform and time-consuming experiments. Herein, we present an easy and rapid fluorimetric method to estimate DNA-DNA relatedness between microbial strains from differences of the thermal denaturation temperatures of hybrid and homologous genomic DNA. Double-stranded DNA was specifically stained with SYBR Green I, and its thermal denaturalization was followed by measuring a decrease in fluorescence. A quantitative, real-time PCR thermocycler was used to perform the experiment and obtain fluorescence determinations at increasing temperatures. The proposed method was validated by comparing species of the hyperthermophilic genera Pyrococcus and Thermococcus. The method proves to be an easy, rapid, and inexpensive alternative to estimate DNA-DNA relatedness between closely related species.

Benzothiazoles↗
PubMed2004

Evaluating putative chimeric sequences from PCR-amplified products.

MOTIVATION: PCR amplification of highly homologous genes from complex DNA mixtures is known to generate a significant proportion of chimeric sequences. Ribosomal RNA genes are used for microbial species detection and identification in natural environments, and current assessments of microbial diversity are based on these sequences. Thus, chimeric sequences could lead to the discovery of non-existent microbial species and false diversity estimates. METHODS: In essence, our only source of information to decide if a sequence is chimeric or not is to compare it with known, non-chimeric sequences. Putative chimeric sequences were analyzed from sequence fragments of selected length (referred to as words) by comparing nucleotides at corresponding positions. Distances for each word between reference sequences (closely related to the tested sequence) were compared to the differences introduced by the tested sequence. The proposed strategy considers the actual variability existing in different regions throughout the analyzed sequences. The result is an efficient strategy for the evaluation of putative chimeric sequences. AVAILABILITY: A program computing the above procedure, Chimera and Cross-Over Detection and Evaluation (Ccode), is available at http://www.irnase.csic.es/users/jmgrau/index.html and http://www.rtphc.csic.es/download.html.

Algorithms↗
PubMed2004

Microbial diversity in biodeteriorated monuments as studied by denaturing gradient gel electrophoresis.

Studies of the microorganisms living on cultural assets and their potential damaging effects begin with an understanding of the microbial diversity present in such samples. Recently, molecular techniques have started to attract considerable interest since they do not require the culture of microorganisms in order to detect their presence. The basic protocol followed during microbial diversity analysis on cultural heritage assets utilizes electrophoretic techniques for separating highly homologous sequences. At present, Denaturing Gradient Gel Electrophoresis (DGGE) is the most frequently reported technique for separating DNA fragments during microbial diversity studies of art objects. In this report, we describe DGGE profiling techniques, show the most common applications, and present some examples of their use in microbial diversity studies on cultural heritage.

Art↗
PubMed2004

Pectinatus portalensis nov. sp., a relatively fast-growing, coccoidal, novel Pectinatus species isolated from a wastewater treatment plant.

The genus Pectinatus is currently composed by two species, Pectinatus cerevisiiphilus and Pectinatus frisingensis , both asociated with beer spoilage. This study describes a novel isolate (strain B6) retrieved from a wastewater treatment plant collecting residues from a large number of wineries. Based on similarity analysis of 16S rRNA gene sequences, strain B6 belongs to the genus Pectinatus . Strain B6 is a strict anaerobe like other Pectinatus species and it presents non-motile, coccoid cells showing a slight oval shape. Strain B6 shows marked physiological differences with other Pectinatus species both in fatty acid composition and carbon source utilization. The most abundant fatty acids found in strain B6 were 18:1 (42.8%) and 16:0 (18.3%) representing a total of over 61% of fatty acids in this microorganism while these fatty acids represented 41.3% in P. cerevisiiphilusT and 2.4% in P. frisingensisT of their total. Fatty acid 15:0 was not significant in strain B6 and represented 28.6% and 13.3% for P. cerevisiiphilusT and P. frisingensisT, respectively. Strain B6 showed a faster growth rate and higher optimum temperature than its relatives P. cerevisiiphilus and P. frisingensis . Strain B6, P. cerevisiiphilus and P. frisingensis could be clearly differentiated by acid production tests from substrates such as esculine and gluconate, and the lack of acid production from rhamnose and fucose among others. G+C mol% content in strain B6 is 36.5%. Based on genotypic and phenotypic differences, strain B6 is proposed as a novel Pectinatus species, P. portalensis nov. sp. Both strain B6 and the two described species of Pectinatus grow on beers and wines. These results provide insights about the origin and reservoirs of Pectinatus species and spoiling alcoholic beverages.

Base Sequence↗