ISPst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation

A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN 10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants (Journal)Funds were obtained from projects VEM2003-20565 and CTM2005-01783 from MEC, and project PRIB2004-10152 from CAIBPeer Reviewe

IS Pst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation

A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants

ISPst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation

A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN 10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants (Journal

Physiological role of NahW, the additional salicylate hydroxylase found in Pseudomonas stutzeri AN10

The physiological role of NahW, the second salicylate hydroxylase of Pseudomonas stutzeri AN10, has been analysed by gene mutation and further complementation. When grown on naphthalene as a unique carbon and energy source, the nahW mutant showed a strong decrease in salicylate hydroxylase activity when compared with the wild-type strain, exhibited lower specific growth rates and accumulated salicylate in culture supernatants. Similarly, lower specific growth rates and salicylate accumulation were observed for the nahW mutant when growth on naphthalene supplemented with succinate or pyruvate. When P. stutzeri AN10 was grown in Luria–Bertani medium in the presence of salicylate, or was cultivated on minimal medium supplemented with salicylate as a unique carbon and energy source, an increase in the lag phase and a decrease in the specific growth rate were observed on increasing the salicylate concentrations, suggesting a plausible toxic effect. This toxic effect of salicylate was much more evident for the nahW mutant than for the wild-type strain. Complementation of the nahW mutant restored all growth parameters. These results indicate that NahW may have two functions in P. stutzeri AN10: (1) to improve its capacity to degrade naphthalene and (2) effectively convert the salicylate produced during naphthalene degradation to tricarboxylic acid cycle intermediates, preventing its toxic effect

Physiological role of NahW, the additional salicylate hydroxylase found in Pseudomonas stutzeri AN10.

The physiological role of NahW, the second salicylate hydroxylase of Pseudomonas stutzeri AN10, has been analysed by gene mutation and further complementation. When grown on naphthalene as a unique carbon and energy source, the nahW mutant showed a strong decrease in salicylate hydroxylase activity when compared with the wild-type strain, exhibited lower specific growth rates and accumulated salicylate in culture supernatants. Similarly, lower specific growth rates and salicylate accumulation were observed for the nahW mutant when growth on naphthalene supplemented with succinate or pyruvate. When P. stutzeri AN10 was grown in Luria-Bertani medium in the presence of salicylate, or was cultivated on minimal medium supplemented with salicylate as a unique carbon and energy source, an increase in the lag phase and a decrease in the specific growth rate were observed on increasing the salicylate concentrations, suggesting a plausible toxic effect. This toxic effect of salicylate was much more evident for the nahW mutant than for the wild-type strain. Complementation of the nahW mutant restored all growth parameters. These results indicate that NahW may have two functions in P. stutzeri AN10: (1) to improve its capacity to degrade naphthalene and (2) effectively convert the salicylate produced during naphthalene degradation to tricarboxylic acid cycle intermediates, preventing its toxic effect. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.Funds were obtained from projects CTM2005-01783 and CTM2008-02574 from MEC, both with FEDER cofundingPeer Reviewe

Halophilic archaea in the human intestinal mucosa

The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd

Geographic locations of the study sites.

Ushuaia Bay is located on the South coast of Tierra del Fuego Island, Argentina, within the Beagle Channel, and Potter Cove is located on the Southwest coast of the 25 de Mayo (King George) Island, Antarctica. The top 5 cm of the subtidal sediments were sampled in triplicate, in two sites distanced approximately 500 m (bathymetry ranging between 9.5 and 23.45 m). At OR site, Ushuaia Bay, an intertidal sediment sample (0–3 cm) was also obtained, and used for the construction of a fosmid library, from which the dataset was generated by shotgun sequencing. Images: Ushuaia Bay (http://earthobservatory.nasa.gov/); Potter Cove (https://apps.sentinel-hub.com).</p

Phylogenetic analysis and genomic context of sequences assigned to the Bacteroidota phylum.

(A) Maximum-Likelihood phylogenetic tree of WS/DGAT homolog sequences assigned to Bacteroidota identified in the metagenomic dataset of intertidal sediments (OR07, in red) and sequences from public databases from genomes of members of the Bacteroidota phylum containing a putative SCP-2 domain at the C-term (in black; ID with numbers, IMG/M; numbers and letters, NCBI). Only unique sequences are included in the tree. IS: isolate; MAG: metagenome assembled genome; Red: sequences identified in this study. Bootstrap values higher than 50% based on 100 replicates are shown. (B) Genomic context and shared synteny of scaffolds containing the WS/DGAT homologs included in the rectangle in the phylogenetic tree. Gray/black regions correspond to the percentage identity at the nucleotide level shown on the right. (PDF)</p

Heatmap showing the 25 most abundant OPUs in the dataset (estimated values) including metagenomes from Subantarctic and Antarctic sediments.

The dataset contained 1,022 OPUs containing ≥ 10 sequences. Scale is arbitrary and goes from light (low relative abundance) to dark (high relative abundance). On the right, phylum or class of the representative sequence in the cluster is indicated. The symbol # next to the OPU number indicates clusters showing significantly differences between Antarctic and Subantarctic sediment metagenomes (Wilcoxon Rank Sum test corrected for multiple testing, as implemented in the R-script ANCOM). (PDF)</p

Phylogenetic analysis of sequences assigned to the Deltaproteobacteria class.

Maximum-Likelihood tree of WS/DGAT homolog sequences assigned to Deltaproteobacteria class, identified in the metagenomic dataset of intertidal sediments (OR07, in red) and related sequences from public databases (in black). GEN, sequence identified in a genome; MAG, sequence identified in a metagenome assembled genome. Bootstrap values higher than 50% based on 100 replicates are shown. (PDF)</p