Whole-Cell MALDI-TOF Mass Spectrometry and Multilocus Sequence Analysis in the Discrimination of Pseudomonas stutzeri Populations: Three Novel Genomovars

Scotta, Claudia; Gomila, Margarita; Mulet, Magdalena; Lalucat, Jorge; Garcı́a-Valdés, Elena

doi:10.1007/s00248-013-0246-8

Cited by 16 publications

(21 citation statements)

References 44 publications

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“…Results obtained from proteomic analyses of strain AW-1 T were compared with biochemical data of key enzymes. However, later studies confirmed the existence of different phylogenetic classes in the P. stutzeri group (Scotta et al, 2013). Previously, P. chloritidismutans AW-1 T was proposed as the type strain of a novel species (Wolterink et al, 2002).…”

Section: Introductionmentioning

confidence: 98%

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor

Mehboob

Oosterkamp

Koehorst

et al. 2015

Environmental Microbiology

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Growth of Pseudomonas chloritidismutans AW-1 on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1 within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1 showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions.

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Section: Introductionmentioning

confidence: 98%

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor

Mehboob

Oosterkamp

Koehorst

et al. 2015

Environmental Microbiology

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“…All rpoD gene sequences were aligned, and phylogenetic analysis was performed as described previously (11). A similarity of Ն96% to a known Pseudomonas type strain allowed a sequence to be assigned to that species, as proposed previously (22,23). A similarity of Ͻ96% to any known Pseudomonas species type strain indicated that the sequence corresponded to a possible new species in the Pseudomonas genus.…”

Section: Methodsmentioning

confidence: 99%

rpoD Gene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River

Sanchez

Matthijs²,

Gomila

et al. 2014

Appl Environ Microbiol

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A water sample from a noncontaminated site at the source of the Woluwe River (Belgium) was analyzed by culture-dependent and -independent methods. Pseudomonas isolates were identified by sequencing and analysis of the rpoD gene. Cultureindependent methods consisted of cloning and pyrosequencing of a Pseudomonas rpoD amplicon from total DNA extracted from the same sample and amplified with selective rpoD gene primers. Among a total of 14,540 reads, 6,228 corresponded to Pseudomonas rpoD gene sequences by a BLAST analysis in the NCBI database. The selection criteria for the reads were sequences longer than 400 bp, an average Q 40 value greater than 25, and >85% identity with a Pseudomonas species. Of the 6,228 Pseudomonas rpoD sequences, 5,345 sequences met the established criteria for selection. Sequences were clustered by phylogenetic analysis and by use of the QIIME software package. Representative sequences of each cluster were assigned by BLAST analysis to a known Pseudomonas species when the identity with the type strain was greater than or equal to 96%. Twenty-six species distributed among 12 phylogenetic groups or subgroups within the genus were detected by pyrosequencing. Pseudomonas stutzeri, P. moraviensis, and P. simiae were the only cultured species not detected by pyrosequencing. The predominant phylogenetic group within the Pseudomonas genus was the P. fluorescens group, as determined by culture-dependent and -independent analyses. In all analyses, a high number of putative novel phylospecies was found: 10 were identified in the cultured strains and 246 were detected by pyrosequencing, indicating that the diversity of Pseudomonas species has not been fully described.

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“…; Scotta et al. , ), our results show that using of 16S rRNA gene sequences seemed to be applicable for the purpose due to the following reasons: (1) with the studies in microbial ecology of oil reservoirs, more 16S rRNA gene data of microbial community detected in oil reservoirs were reported, which provided a good resource for us to collected information worldwide. (2) 16S rRNA gene clone library, showing a clear picture of a microbial community of bacteria (Palys et al.…”

Section: Discussionmentioning

confidence: 79%

“…; Scotta et al. ). These reference strains were isolated mainly from marine, clinical, and soil environment and not a single strain was reported from the environment associated with oil reservoirs (Table S1).…”

Section: Methodsmentioning

confidence: 98%

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Genomovar assignment of Pseudomonas stutzeri populations inhabiting produced oil reservoirs

et al. 2014

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Oil reservoirs are specific habitats for the survival and growth of microorganisms in general. Pseudomonas stutzeri which is believed to be an exogenous organism inoculated into oil reservoirs during the process of oil production was detected frequently in samples from oil reservoirs. Very little is known, however, about the distribution and genetic structure of P. stutzeri in the special environment of oil reservoirs. In this study, we collected 59 P. stutzeri 16S rRNA gene sequences that were identified in 42 samples from 25 different oil reservoirs and we isolated 11 cultured strains from two representative oil reservoirs aiming to analyze the diversity and genomovar assignment of the species in oil reservoirs. High diversity of P. stutzeri was observed, which was exemplified in the detection of sequences assigned to four known genomovars 1, 2, 3, 20 and eight unknown genomic groups of P. stutzeri. The frequent detection and predominance of strains belonging to genomovar 1 in most of the oil reservoirs under study indicated an association of genomovars of P. stutzeri with the oil field environments.

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Whole-Cell MALDI-TOF Mass Spectrometry and Multilocus Sequence Analysis in the Discrimination of Pseudomonas stutzeri Populations: Three Novel Genomovars

Cited by 16 publications

References 44 publications

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor

rpoD Gene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River

Genomovar assignment of Pseudomonas stutzeri populations inhabiting produced oil reservoirs

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Whole-Cell MALDI-TOF Mass Spectrometry and Multilocus Sequence Analysis in the Discrimination of Pseudomonas stutzeri Populations: Three Novel Genomovars

Cited by 16 publications

References 44 publications

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1T that grows on n‐decane with chlorate or oxygen as electron acceptor

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1T that grows on n‐decane with chlorate or oxygen as electron acceptor

rpoD Gene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River

Genomovar assignment of Pseudomonas stutzeri populations inhabiting produced oil reservoirs

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Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor

Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1^T that grows on n‐decane with chlorate or oxygen as electron acceptor