The Genome of
            <i>Polaromonas</i>
            sp. Strain JS666: Insights into the Evolution of a Hydrocarbon- and Xenobiotic-Degrading Bacterium, and Features of Relevance to Biotechnology

Mattes, Timothy E.; Alexander, Anne K.; Richardson, Paul M.; Munk, A. Christine; Han, Cliff; Stothard, Paul; Coleman, Nicholas V.

doi:10.1128/aem.00197-08

Cited by 131 publications

(110 citation statements)

References 52 publications

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“…It is therefore likely that this taxon is well adapted to life in the seasonal slush layer of the glacier, and thus proliferates rapidly within it, while other members of Polaromonas occupy a broader distribution within the snowpack. The appearance of a high ratio of local to global diversity in Polaromonas, as recently reported (Darcy et al, 2011), would provide opportunities for co-dispersed Polaromonas species to exploit distinct niches in space and time, utilizing their considerable metabolic versatility (Mattes et al, 2008;Yagi et al, 2009) to do so.…”

Section: Discussionmentioning

confidence: 99%

The dynamic bacterial communities of a melting High Arctic glacier snowpack

et al. 2013

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Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation.

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Section: Discussionmentioning

confidence: 99%

The dynamic bacterial communities of a melting High Arctic glacier snowpack

et al. 2013

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“…Genome annotation revealed widespread presence of CO dehydrogenase and absence of a complete CO 2 fixation pathway (Supplementary Table S6), consistently with the complete genome of Polaromonas JS666. This suggests that Polaromonas in cryoconite might use CO as energy source in presence of OC (mixotrophy) (Mattes et al, 2008).…”

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confidence: 99%

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces

et al. 2016

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Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers, providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules, which otherwise would be respired. Furthermore, data suggest that CO 2 could be produced also by microbiologically mediated oxidation of CO, which may be produced by photodegradation of organic matter. The ISME Journal Climate change is determining a global cryosphere shrinkage and mountain glacier environments are declining (IPPC, 2014). The consequent loss of biodiversity is yet to be fully assessed, particularly the loss of functional biodiversity in extreme environments (Stibal et al., 2012;Boetius et al., 2015). Cryoconite holes, that is, small depressions on glacier surfaces whose formation is because of windborne debris (cryoconite), are the most biologically active environments on glaciers (Boetius et al., 2015).We used whole-metagenomic sequencing to investigate the main functions of six cryoconite holes from Forni (Italian Alps) and six from Baltoro (Pakistani Karakoram) glaciers. We focused on carbon and energy metabolisms by comparing the total coverage of marker genes for photosynthesis, use of inorganic and organic compounds as energy source and autotrophy/heterotrophy. We also used metagenomic sequences for the taxonomic attribution of microorganisms carrying specific metabolic genes Table S4 reports the marker genes whose coverage (mean number per base of reads mapping the genes) was used to infer the abundance of each metabolism. Supplementary Table S5 and Figure 1 report their normalized coverages. Finally, we measured chemical/physical parameters of cryoconite holes and oxygen consumption rates on the days of sampling, both under light and dark conditions (Supplementary Table S3 and Supplementary Figure S2). The main hypothesis tested was whether oxygenic phototrophy and organotrophic respiration represent the only significant metabolisms affecting carbon balance on glacier surface, as currently conceived, or other microbial processes could contribute to it.On the basis of 16S rRNA gene sequencing, Cyanobacteria represented 22 and 3% of the microbial community on Forni and Baltoro, respectively (Supplementary Figure S3). High abundance of cyanobacteria has been already observed in polar and alpine cryoconite (Segawa et al....

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“…Scattered pca genes have also been detected in Pseudomonas putida KT2440, Polaromonas sp. JS666, and Pseudomonas stutzeri A1501 and are expected to correspond to regulatory mechanisms different from those of A. baylyi (14,25,26).…”

mentioning

confidence: 99%

Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

Jung

Madsen

Jeon

et al. 2011

Appl Environ Microbiol

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The comparative genomics of Acinetobacter oleivorans DR1 assayed with A. baylyi ADP1, A. calcoaceticus PHEA-2, and A. baumannii ATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator-and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of the nagI gene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution of Acinetobacter species.

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The Genome of Polaromonas sp. Strain JS666: Insights into the Evolution of a Hydrocarbon- and Xenobiotic-Degrading Bacterium, and Features of Relevance to Biotechnology

Cited by 131 publications

References 52 publications

The dynamic bacterial communities of a melting High Arctic glacier snowpack

The dynamic bacterial communities of a melting High Arctic glacier snowpack

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces

Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

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