Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter

Selvakumaran, Suguna; Kapley, Atya; Kashyap, Sanjay M.; Daginawala, Hatim F.; Kalia, Vipin Chandra; Purohit, Hemant J.

doi:10.1016/j.biortech.2011.01.011

Cited by 22 publications

(7 citation statements)

References 29 publications

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“…Microbial communities potentially harbor a wide array of organisms with distinct ARD and that can shift quickly in response to PAH inputs (Wang et al, 2008a;Kimura and Kamagata, 2009;Selvakumaran et al, 2011). After the oxygenation step, the dihydrodiol intermediate ring structure is cleaved by intradiol-or extradiol oxygenases in between the hydroxyl groups (meta-cleavage) or before the hydroxyl groups (ortho-cleavage) yielding protocatechuate and catechol intermediates that can be further converted to tricarboxylic acid cycle (TCA) intermediates (Jiménez et al, 2004;Seo et al, 2009;Nzila, 2013).…”

Section: Pathways Of Pah Degradation In Marine Environmentsmentioning

confidence: 99%

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe–pollutant interactions in a remote environment

Louvado

Gomes

Simões

et al. 2015

Science of The Total Environment

100

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Section: Pathways Of Pah Degradation In Marine Environmentsmentioning

confidence: 99%

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe–pollutant interactions in a remote environment

Louvado

Gomes

Simões

et al. 2015

Science of The Total Environment

100

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“…For example, some members of the Enterobacteriales are widely used as indicators of fecal contamination [71], and the presence of E. coli and other gastrointestinal associated bacteria in the urban site in Buenos Aires (Figure S2a in supplementary materials) was likely related to sewage flow in that area [34]. In addition to being common residents of the human intestinal tract, Enterobacter and Citrobacter are capable of degrading various types of hydrocarbons [72,73]. The increase of these genera in suburban and urban sites (Figure S2a in supplementary materials) may be attributed to heavy boat traffic and industrialization.…”

Section: Discussionmentioning

confidence: 99%

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina

et al. 2019

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Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and rural setting were located near Buenos Aires, Argentina, and Washington D.C., USA. We sampled soil associated with two pairs of functionally similar plant species, and used Illumina sequencing of the 16S rRNA gene to examine changes in prokaryotic communities. Urban stressors included raw sewage inputs, nutrient pollution, and polycyclic aromatic hydrocarbons. Prokaryotic communities changed along the gradient (nested PerMANOVA, Buenos Aires: p = 0.005; Washington D.C.: p = 0.001), but did not differ between plant species within sites. Indicator taxa included Methanobacteria in rural sites, and nitrifying bacteria in urban sites, and we observed a decrease in methanogens and an increase in ammonia-oxidizers from rural to urban sites. Functional profiles in the Buenos Aires communities showed higher abundance of pathways related to nitrification and xenobiotic degradation in the urban site. These results suggest that changes in prokaryotic taxa across the gradient were due to surrounding stressors, and communities in urban and rural wetlands are likely carrying out different functions.

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“…And perhaps the best part of this study is its potential to be extended to any gene and organism of interest. A few studies have in fact been conducted, where RE digestion patterns of functional genes have been used as markers [8,10,[13][14][15][16][17].…”

Section: Discussionmentioning

confidence: 99%

Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains

et al. 2015

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Microbial classification is based largely on the 16S rRNA (rrs) gene sequence, which is conserved throughout the prokaryotic domain. The Ribosomal Database Project (RDP) has become a reference point for almost all practical purposes. The use of this gene is limited by the fact that it can be used to identify only to the extent to what has been known and is available in the RDP. In order to identify an organism whose rrs is not present in the RDP database, we need to generate novel markers to place the unknown on the evolutionary map. Here, sequenced genomes of 27 Clostridium strains belonging to 9 species have been used to identify two sets of genes: (1) common to most of the species, and (2) unique to a species. Combinations of genes (recN, dnaJ, secA, mutS, and/or grpE) and their unique restriction endonuclease digestion (AluI, BfaI and/or Tru9I) patterns have been established to rapidly identify Clostridium species. This strategy for identifying novel markers can be extended to all other organisms and diagnostic applications.

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Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter

Cited by 22 publications

References 29 publications

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe–pollutant interactions in a remote environment

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe–pollutant interactions in a remote environment

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina

Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains

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