Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants

Iyer, Rupa; Iken, Brian; Damania, Ashish

doi:10.1016/j.gdata.2017.07.011

Cited by 9 publications

(8 citation statements)

References 9 publications

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“…Pseudomonas spp. (phylum Proteobacteria) can perform denitrification as well as POM degradation, including degradation of lignin (166) and aromatic compounds (167). Like SRB, some denitrifying bacteria are also syntrophs within AOM consortia (168).…”

Section: Overview Of the H 2 Biogeochemical Cyclementioning

confidence: 99%

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

Piché-Choquette

Constant

2019

Appl Environ Microbiol

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The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2as a driver of biogeochemical processes.

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Section: Overview Of the H 2 Biogeochemical Cyclementioning

confidence: 99%

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

Piché-Choquette

Constant

2019

Appl Environ Microbiol

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“…On the other hand, Pseudomonas nitroreducens has been reported for its presence in contaminated sites, and its capacity of degrading complex molecules, mainly xenobiotic aromatic substances [15] . However, this species does not have records where its capacity to interact with heavy metals has been described.…”

Section: Discussionmentioning

confidence: 99%

Bioremediation potential of Pseudomonas genus isolates from residual water, capable of tolerating lead through mechanisms of exopolysaccharide production and biosorption

Vélez

Martínez

Ospina

et al. 2021

Biotechnology Reports

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“…Carbon selective media was prepared as previously described in Iyer et al., 2016 [2]. A total of 5 mL of carbon selective media was used for initial sample inoculation.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Genome data of Stenotrophomonas maltophilia DF07 collected from polluted river sediment reveals an opportunistic pathogen and a potential antibiotic reservoir

2019

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Stenotrophomonas maltophilia DF07 is a gram negative bacterium isolated from polluted San Jacinto River sediment near Moncrief Park in Channelview, Texas. The genome of strain DF07 (chromosome and plasmid) was compiled at the scaffold level and can be accessed through the National Center for Biotechnology Information database under accession NZ_NJGC00000000. The DF07 genome consists of a total of 4,801,842 bp encoding for approximately 4,351 functional proteins. Approximately 86 proteins are associated with broad-spectrum antibiotic resistance, 11 are associated with bacteriocin production, and a total of 17 proteins encode for an assortment of Mycobacterium -like virulence and invasion operons. S. maltophilia DF07 is genetically similar to the nosocomial S. maltophilia strain AU12-09, but also harbors an unusually large plasmid that encodes for over 150 proteins of unknown function. Taken together, this strain is potentially an important antibiotic reservoir and its origin within a recreational park merits further study of the area.

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Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants

Cited by 9 publications

References 9 publications

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

Bioremediation potential of Pseudomonas genus isolates from residual water, capable of tolerating lead through mechanisms of exopolysaccharide production and biosorption

Genome data of Stenotrophomonas maltophilia DF07 collected from polluted river sediment reveals an opportunistic pathogen and a potential antibiotic reservoir

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