<i>Pseudomonas</i>genomes: diverse and adaptable

Silby, Mark W.; Winstanley, Craig; Godfrey, Scott A. C.; Levy, Stuart B.; Jackson, Robert W.

doi:10.1111/j.1574-6976.2011.00269.x

Cited by 817 publications

(624 citation statements)

References 229 publications

(368 reference statements)

Supporting

Mentioning

586

Contrasting

Unclassified

Order By: Relevance

“…Several genera belonging to Acetobacteraceae have been linked with hydrocarbon degradation at moderately low pH levels (Hamamura et al, 2005;Rö ling et al, 2006). Sphingomonadaceae, Burkholderiaceae and Pseudomonadaceae are recognized for their extraordinary catabolic flexibility and are among the most common hydrocarbon degraders in a variety of soils (Leys et al, 2004;Stolz, 2009;Silby et al, 2011;Pérez-Pantoja et al, 2012); however, a thorough knowledge on pH optima of these groups is still lacking. Although these results provide clues about the pH preferences of these bacterial groups in the studied site, it remains to be shown whether they successfully degrade PAH or TPH compounds under these conditions.…”

Section: Discussionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

View full text Add to dashboard Cite

Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

show abstract

Section: Discussionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

View full text Add to dashboard Cite

show abstract

“…The objective of this study therefore was to employ PMA‐qPCR and pre‐rRNA analyses to assess the bacterial viability and VBNC state during antimicrobial treatment. We chose Pseudomonas aeruginosa as a model bacterium because the well‐recognized opportunistic pathogen can enter a VBNC state and be resuscitated later (Silby et al ., 2011; Zhang et al ., 2015). To the best of our knowledge, no previous study has evaluated PMA‐qPCR and pre‐rRNA analyses as a method to distinguish VBNC from dead cells inactivated by antibiotics.…”

Section: Introductionmentioning

confidence: 99%

Molecular viability testing of viable but non‐culturable bacteria induced by antibiotic exposure

Lee

Bae

2017

Microbial Biotechnology

View full text Add to dashboard Cite

SummaryNucleic acid amplification‐based methods are limited by their inability to discriminate between viable and dead cells. To overcome this drawback, propidium monoazide (PMA) combined with qPCR has been used to differentiate viable from nonviable cells in environmental samples. However, assessing bacterial physiology using PMA‐qPCR remains a challenge due to its incapability of detecting metabolic activities, leading to overestimation of the viable bacteria population under an inactivation condition (e.g. antibiotic treatments). A recent advanced technique to amplify ribosomal RNA precursors (pre‐rRNA) has been shown to detect viable cells because pre‐rRNAs are intermediates in rRNA synthesis. This study investigated the effect of different types of antibiotics on the bacterial viability or viable but non‐culturable (VBNC) state using both PMA‐qPCR and pre‐rRNA analyses with Pseudomonas aeruginosa. This study demonstrated that P. aeruginosa was more sensitive to colistin than it was to carbenicillin, gentamicin and levofloxacin. We could discriminate VBNC P. aeruginosa cells using PMA‐qPCR when antibiotic pressure induced the VBNC state. Also, pre‐rRNA was able to distinguish viable cells from colistin‐inactivated bacteria cells, and it could detect the presence of VBNC and persister cells. Our results showed that these two molecular methods could successfully eliminate false‐positive signals derived from antibiotics‐inactivated cells.

show abstract

“…For instance, Pseudomonas fluorescens, Pseudomonas putida and Pseudomonas chlororaphis have been described as antagonistic towards pathogens of crop plants (Chin-AWoeng et al, 2000;Espinosa-Urgel et al, 2002;Silby et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Fis regulates the competitiveness of Pseudomonas putida on barley roots by inducing biofilm formation

et al. 2012

View full text Add to dashboard Cite

An important link between the environment and the physiological state of bacteria is the regulation of the transcription of a large number of genes by global transcription factors. One of the global regulators, Fis (factor for inversion stimulation), is well studied in Escherichia coli, but the role of this protein in pseudomonads has only been examined briefly. According to studies in Enterobacteriaceae, Fis regulates positively the flagellar movement of bacteria. In pseudomonads, flagellar movement is an important trait for the colonization of plant roots. Therefore we were interested in the role of the Fis protein in Pseudomonas putida, especially the possible regulation of the colonization of plant roots. We observed that Fis reduced the migration of P. putida onto the apices of barley roots and thereby the competitiveness of bacteria on the roots. Moreover, we observed that overexpression of Fis drastically reduced swimming motility and facilitated P. putida biofilm formation, which could be the reason for the decreased migration of bacteria onto the root apices. It is possible that the elevated expression of Fis is important in the adaptation of P. putida during colonization of plant roots by promoting biofilm formation when the migration of bacteria is no longer favoured.

show abstract

Pseudomonasgenomes: diverse and adaptable

Cited by 817 publications

References 229 publications

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Molecular viability testing of viable but non‐culturable bacteria induced by antibiotic exposure

Fis regulates the competitiveness of Pseudomonas putida on barley roots by inducing biofilm formation

Contact Info

Product

Resources

About