Degradation of Aromatic Compounds in Pseudomonas: A Systems Biology View

Nogales, Juan; Garcı́a, José Luis; Dı́az, Eduardo

doi:10.1007/978-3-319-39782-5_32-1

Cited by 44 publications

(43 citation statements)

References 265 publications

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“…In the SMS community, we noted an association with a number of aromatic compound degradation pathways, including several for toluene degradation. This may be due to the enrichment in this community of the family Pseudomonadaceae (Figure 4), which includes several species with the capacity for degradation of these compounds (Zylstra et al, 1988; Otenio et al, 2005; Nogales et al, 2017). On the other hand, the water community was associated with several pathways for the degradation of lignin derivatives such as vanillin and gallates (Supplementary Figures S4, S5A and Supplementary Data S3; de Gonzalo et al, 2016; Kamimura et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

et al. 2019

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The microbiome of freshwater fish has important implications for both commercial and recreational fishing because it can have significant impacts on host heath, spoilage rates, and susceptibility to disease. The aqueous environment serves as a possible avenue for continuous introduction of microbes to an animal host, but little is known about how the surrounding microbiota contribute to piscine microbiomes. To better understand the composition of the fish microbiome exposed to the natural environment, we profiled the microbial composition of the gut and the skin mucosal surface (SMS) of northern pike (Esox lucius) and the surrounding river water. We collected fish samples from eight sites along a single river in southwestern Quebec, Canada and analyzed the microbial composition via 16S rRNA sequencing. Our results reveal robust taxonomic differences between the SMS and the gut, indicating a divergence between the microbiomes. The gut community was characterized by a lower alpha diversity compared to the SMS and a large proportion of Cetobacterium, a genus previously linked to carnivorous species. On the other hand, the SMS was more similar to the water than the gut at the family level but divergent at lower taxonomic levels, with fewer than 30% of amplicon sequence variants (ASVs) shared between the SMS and water. In total, our results suggest the establishment of distinct communities across the two fish sites, as well as a clear separation from the microbes in surrounding waters. These data indicate that despite continuous exposure to water, pike are able to establish and maintain unique microbial communities.

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Section: Discussionmentioning

confidence: 99%

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

et al. 2019

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“…Usually, these bacteria show no preferences in habitat colonisation and are generally found in different environments, ranging from soil to water and stone artwork [61], where multiple niches are available [60]. For example, Pseudomonas has broad ability to degrade complex molecules, including polycyclic aromatic compounds [62], which are very common in forest litter.…”

Section: Discussionmentioning

confidence: 99%

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment

et al. 2019

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Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition.

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“…In addition, shikimate degradation, which is connected with the protocatechuate branch, was also upregulated. For instance, quinate dehydrogenase (quiA) and 3-dehydroshikimate dehydratase (quiC) displayed 1.3-fold, 1.5-fold, and 2.0-fold up-regulation respectively, suggesting that there were multiple pathways involved in aromatic degradation [63].…”

Section: Resultsmentioning

confidence: 99%

Enhancement of Polyhydroxyalkanoate Production by Co-feeding Lignin Derivatives With Glycerol in Pseudomonas Putida KT2440

Chi

et al. 2020

Preprint

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Background: Efficient utilization of all available carbons from lignocellulosic biomass is critical for economic efficiency of a bioconversion process to produce renewable bioproducts. However, the metabolic responses that enable Pseudomonas putida to utilize mixed carbon sources to generate reducing power and Polyhydroxyalkanoate (PHA) remain unclear. Previous research has mainly focused on different fermentation strategies, including the sequential feeding of xylose as the growth stage substrate and octanoic acid as the PHA producing substrate, feeding glycerol as the sole carbon substrate, and co-feeding of lignin and glucose. This study developed a new strategy - co-feeding glycerol and lignin derivatives such as benzoate, vanillin, and vanillic acid in Pseudomonas putida KT2440 - for the first time, which simultaneously improved both cell biomass and PHA production. Results: Co-feeding lignin derivatives (i.e. benzoate, vanillin, and vanillic acid) and glycerol to P. putida KT2440 was shown for the first time to simultaneously increase cell dry weight (CDW) by 9.4 %-16.1 % and PHA content by 29.0 %-63.2 %, respectively, compared with feeding glycerol alone. GC-MS results revealed that the addition of lignin derivatives to glycerol decreased the distribution of long chain monomers (C10 and C12) by 0.4 %-4.4 % and increased the distribution of short chain monomers (C6 and C8) by 0.8 %-3.5 %. The 1H -13C HMBC, 1H-13C HSQC, and 1H-1H COSY NMR analysis confirmed that the PHA monomers (C6-C14) were produced when glycerol was fed to the bacteria alone or together with lignin derivatives. Moreover, investigation of the glycerol/benzoate/nitrogen ratios showed that benzoate acted as an independent factor in PHA synthesis. Furthermore, 1H, 13C and 31P NMR metabolite analysis and mass spectrometry-based quantitative proteomics measurements suggested that the addition of benzoate stimulated oxidative-stress responses enhanced glycerol consumption and altered the intracellular NAD(P)+/NAD(P)H ratios by up-regulating the proteins involved in energy generation and storage processes, including the Entner-Doudoroff (ED) pathway, the reductive TCA route, trehalose degradation, fatty-acid β-oxidation, and PHA biosynthesis.Conclusions: This work demonstrated an effective co-carbon feeding strategy to improve PHA yield and convert lignin derivatives into value-added products in P. putida KT2440. Co-feeding lignin derivativeswith other carbon sources, such as glycerol, has been demonstrated as an efficient way to utilize biomass to increase PHA production in P. putida KT2440. Moreover, the involvement of aromatic degradation favors further lignin utilization, and the combination of proteomics and metabolomics with NMR sheds light on the metabolic and regulatory mechanisms for cellular redox balance and potential genetic targets for a higher biomass carbon conversion efficiency.

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Degradation of Aromatic Compounds in Pseudomonas: A Systems Biology View

Cited by 44 publications

References 265 publications

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment

Enhancement of Polyhydroxyalkanoate Production by Co-feeding Lignin Derivatives With Glycerol in Pseudomonas Putida KT2440

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