RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines

Functional & Integrative Genomics - Adenosine to inosine (A-to-I) editing in RNA is involved in various biological processes like gene expression, alternative splicing, and mRNA degradation...     

PCR–DGGE‐based methodologies to assess diversity and dynamics of Aeromonas communities

Aims: Aeromonas is ubiquitous in aquatic environments and may cause infectious diseases in fish and humans. However, reliable and specific methods to evaluate the diversity and dynamics of Aeromonas populations are currently unavailable. This study aimed to develop PCR–DGGE methodologies for culture‐independent analysis of Aeromonas populations in water systems. Methods and Results: Three primer sets were designed to amplify selected sections of genes gyrB, rpoD and sodB from Aeromonas. Their specificity was confirmed by in silico analysis and by PCR on DNA from pure cultures. Estuarine water samples were analyzed by PCR–DGGE using those primers. DGGE patterns clearly clustered according to seasonal factors, and Aeromonas communities were surprisingly stable along a salinity gradient. Sequences of cloned amplicons affiliated to sequences belonging to seven Aeromonas species previously isolated from the same environment. Conclusions: The three systems used showed to be useful to describe the diversity of Aeromonas communities. However, the combined use of more than one primer set is advisable. Significance and Impact of the Study: The methods presented here can be applied to understand the natural pool of Aeromonas and also to monitor and control these bacteria in aquatic reservoirs.     

Resistance to beta-lactam antibiotics in Aeromonas hydrophila isolated from rainbow trout (Oncorhynchus mykiss).

Bacterial infections caused by members of the genus Aeromonas, with a relatively high antibiotic resistance, are among the most common and troublesome diseases of fish raised in ponds with recirculation systems. In this study, carried out at an experimental aquaculture station in northern Portugal, 51 strains identified as belonging to the genus Aeromonas were isolated from 20 rainbow trout (Oncorhynchus mykiss) skin and kidney samples, as well as from raceway water samples. Macro- and microscopic examination of the fish tissues revealed lesions or cellular alterations in skin and kidney that seemed to correlate with the presence of those isolates. The sensitivity of all isolated strains to different groups of beta-lactam antibiotics (penicillins, cephalosporins, monobactams and carbapenems) was evaluated using the disc diffusion method. The highest rates of resistance were to amoxicillin, carbenicillin and ticarcillin. Unexpected resistance to imipenem, an antibiotic of clinical usage, was also detected, which suggests that resistance may have been transferred to the Aeromonas population from the environment.     

Molecular assessment of microbiota structure and dynamics along mixed olive oil and winery wastewaters biotreatment

The major parcel of the degradation occurring along wastewater biotreatments is performed either by the native microbiota or by added microbial inocula. The main aim of this study was to apply two fingerprinting methods, temperature gradient gel electrophoresis (TGGE) and length heterogeneity-PCR (LH-PCR) analysis of 16S rRNA gene fragments, in order to assess the microbiota structure and dynamics during mixed olive oil and winery wastewaters aerobic biotreatment performed in a jet-loop reactor (JLR). Sequence homology analysis showed the presence of bacterial genera Gluconacetobacter, Klebsiella, Lactobacillus, Novosphingobium, Pseudomonas, Prevotella, Ralstonia, Sphingobium and Sphingomonas affiliated with five main phylogenetic groups: alpha-, beta- and gamma-Proteobacteria, Firmicutes and Bacteroidetes. LH-PCR analysis distinguished eight predominant DNA fragments correlated with the samples showing highest performance (COD removal rates of 67 up to 75%). Cluster analysis of both TGGE and LH-PCR fingerprinting profiles established five main clusters, with similarity coefficients higher than 79% (TGGE) and 62% (LH-PCR), and related with hydraulic retention time, indicating that this was the main factor responsible for the shifts in the microbiota structure. Canonical correspondence analysis revealed that changes observed on temperature and O₂ level were also responsible for shifts in microbiota composition. Community level metabolic profile analysis was used to test metabolic activities in samples. Integrated data revealed that the microbiota structure corresponds to bacterial groups with high degradative potential and good suitability for this type of effluents biotreatments.     

Resistance to broad-spectrum antibiotics in aquatic systems: anthropogenic activities modulate the dissemination of bla(CTX-M)-like genes

We compared the resistomes within polluted and unpolluted rivers, focusing on extended-spectrum beta-lactamase (ESBL) genes, in particular bla(CTX-M). Twelve rivers from a Portuguese hydrographic basin were sampled. Physicochemical and microbiological parameters of water quality were determined, and the results showed that 9 rivers were classified as unpolluted (UP) and that 3 were classified as polluted (P). Of the 225 cefotaxime-resistant strains isolated, 39 were identified as ESBL-producing strains, with 18 carrying a bla(CTX-M) gene (15 from P and 3 from UP rivers). Analysis of CTX-M nucleotide sequences showed that 17 isolates produced CTX-M from group 1 (CTX-M-1, -3, -15, and -32) and 1 CTX-M that belonged to group 9 (CTX-M-14). A genetic environment study revealed the presence of different genetic elements previously described for clinical strains. ISEcp1 was found in the upstream regions of all isolates examined. Culture-independent bla(CTX-M)-like libraries were comprised of 16 CTX-M gene variants, with 14 types in the P library and 4 types in UP library, varying from 68% to 99% similarity between them. Besides the much lower level of diversity among CTX-M-like genes from UP sites, the majority were similar to chromosomal ESBLs such as bla(RAHN-1). The results demonstrate that the occurrence and diversity of bla(CTX-M) genes are clearly different between polluted and unpolluted lotic ecosystems; these findings favor the hypothesis that natural environments are reservoirs of resistant bacteria and resistance genes, where anthropogenic-driven selective pressures may be contributing to the persistence and dissemination of genes usually relevant in clinical environments.     

Evaluation of 16S rDNA- and gyrB-DGGE for typing members of the genus Aeromonas

The DNA sequence of the gyrB gene is a suitable phylogenetic marker for bacterial systematics. In this study, the diversity of Aeromonas spp. present in environmental samples was assessed by a PCR combined with DGGE approach. PCR primers targeting the gyrB gene of aeromonads were designed and the resulting amplicons were analyzed by DGGE. The gyrB-DGGE analysis was evaluated with Aeromonas isolates and reference strains allowing discrimination of the majority of strains. The gyrB-DGGE analysis is a powerful tool to monitor the presence and evaluate the diversity of aeromonads in complex samples, as is the case of water from a wastewater treatment plant.     

Characterization of bacterial diversity in two aerated lagoons of a wastewater treatment plant using PCR-DGGE analysis

Aerated lagoons are commonly used for domestic and industrial wastewater treatment due to their low cost and minimal need of operational requirements. However, little information is known regarding microbial communities that inhabit these ecosystems. In this study, a 16S-DGGE approach was used to estimate bacterial diversity and to monitor community changes in two aerated lagoons from a wastewater treatment plant receiving urban and industrial effluents. Pronounced shifts between bacterial communities collected in winter–spring and summer–autumn months were detected. Temperature, dissolved oxygen (DO) and pH were the variables that most influenced the bacterial communities. Phylogenetic affiliation of predominant members was assessed by the determination of the 16S rDNA sequence of correspondent bands. Affiliations to Cytophaga–Flexibacter–Bacteroides (CFB) group, Firmicutes, and β- and ε-proteobacteria were found.     

BOX-PCR is an Adequate Tool for Typing <Emphasis Type="Italic">Aeromonas</Emphasis> spp.

PCR-based methods of fingerprinting take advantage of the presence of repetitive sequences that are interspersed throughout the genome of diverse bacterial species. They include the repetitive extragenic palindromic (REP) sequence, the enterobacterial repetitive intergenic consensus sequence (ERIC) and the 154-bp BOX element. The combination of the three methods is used for fine discrimination of strains and is designated as rep-polymerase chain reaction (PCR). REP-PCR and ERIC-PCR have been shown to be useful for typing Aeromonas strains. To our knowledge, rep-PCR fingerprinting method using the BOXA1R primer has never been tested on aeromonads. In this study, the BOX-PCR fingerprinting technique was evaluated for the discrimination of strains of some Aeromonas species. All strains were typeable and the majority showed unique banding patterns. Four strains from culture collections were used to investigate the reproducibility of the method. According to our results, BOX-PCR fingerprinting is applicable for typing of Aeromonas strains and can be considered as a useful complementary tool for epidemiological studies of members of this genus.