Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria

Singleton, David R.; Hunt, Mark; Powell, Sabrina N.; Frontera-Suau, Roberto; Aitken, Michael D.

doi:10.1016/j.mimet.2006.12.019

Cited by 52 publications

(54 citation statements)

References 25 publications

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“…Besides, the microbial growth and metabolism might be also affected by the profile and bioavailability of the targeted PAHs compounds. The PAHs degraders in PAHscontaminated soils have the selectivity among similar polycyclic substrates, and they have simultaneous or sequential utilization of various targeting compounds under different conditions [28]. Our findings further proved that the PAHs degrading microorganisms in forest carbon-rich soils are similar to those of heavily contaminated soils, but their functions vary to a great extent.…”

Section: Discussionsupporting

confidence: 68%

“…There was no significant difference in PAHs removal between samples amended with 13 C-labeled and unlabeled PAHs [5,13,[26][27][28], and all the PAHs analysis in this study was then carried out for soil samples amended with unlabeled PAHs. More precisely, the soil samples (sterilize controls and unlabeled PAHs amended treatments) were sacrificed on day 3, 9 and 14 after the initiation of cultivation, according to previous instruction [26,27].…”

Section: Pahs Analysismentioning

confidence: 96%

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Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Song

Jiang

Zhang

et al. 2016

Journal of Hazardous Materials

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h i g h l i g h t s• Investigate PAHs degraders in forest carbon-rich soils via DNA-SIP.• Rhodanobacter is identified to metabolite anthracene for the first time.• The first fluoranthene degrader belongs to Acidobacteria.• Different functions of PAHs degraders in forest soils from contaminated soils. a r t i c l e i n f o a b s t r a c tInformation on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually 13 C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene-and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter-and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three-and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

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Section: Discussionsupporting

confidence: 68%

Section: Pahs Analysismentioning

confidence: 96%

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Song

Jiang

Zhang

et al. 2016

Journal of Hazardous Materials

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“…One group, designated 'Pyrene Group 2' or 'PG2', had no cultivated relatives and could only be classified to the class Gammaproteobacteria. Subsequent SIP experiments using pyrene, benz[a]anthracene or fluoranthene [2,3] further implicated bacteria belonging to PG2 in the degradation of high-molecularweight PAHs as well as the low-molecular-weight PAH phenanthrene [4] and potentially the low-molecular-weight PAH anthracene [5]. The 16S rRNA gene sequences comprising PG2 from these SIP projects possessed a relatively high (!96 %) intragroup 16S rRNA gene identity.…”

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confidence: 99%

“…Prior isolation attempts may have been hindered by the lack of required trace minerals or vitamins in the medium in addition to the slow growth of the organism. Subsequent tests of strain TR3.2 T grown in the liquid isolation medium excluding various components indicated that the following medium components were required for maximum growth: 'reactor buffer' (5 mM NaÀK phosphate buffer, 5 mM NH 4 ; containing 5 mg cyanocobalamin in 100 ml distilled water, filter sterilized and added after autoclaving), to a final pH of 7.0. Carbon was added before autoclaving as either 0.02 % (w/v) pyrene dissolved in acetone to the flask, allowing the solvent to evaporate prior to adding other components, or as 0.2 % (w/v) sodium pyruvate.…”

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confidence: 99%

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Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.

Corteselli

Aitken

Singleton

2017

International Journal of Systematic and Evolutionary Microbiology

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Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbondegrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.Elizabeth M. Corteselli, Michael D. Aitken and David R. Singleton* AbstractThe bacterial strain TR3.2 T was isolated from aerobic bioreactor-treated soil from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Salisbury, NC, USA. Strain TR3.2 T was identified as a member of 'Pyrene Group 2' or 'PG2', a previously uncultivated cluster of organisms associated with the degradation of high-molecular-weight PAHs by stable-isotope probing. Based on its 16S rRNA gene sequence, the strain was classified as a member of the class Gammaproteobacteria but possessed only 90.5 % gene identity to its closest described relative, Methylococcus capsulatus strain Bath. Strain TR3.2 T grew on the PAHs pyrene, phenanthrene, anthracene, benz[a]anthracene and fluorene, as well as the azaarene carbazole, and could additionally metabolize a limited number of organic acids. Optimal growth occurred aerobically under mesophilic temperature, neutral pH and low salinity conditions. Strain TR3.2 T was catalase and oxidase positive. Predominant fatty acids were C 17 : 0 cyclo and C 16 : 0 . Genomic G+C content of the single chromosome was 67.79 mol% as determined by complete genome sequencing. Due to the high sequence divergence from any cultivated species and its unique physiological properties compared to its closest relatives, strain TR3.2 T is proposed as a representative of a novel order, family, genus and species within the class Gammaproteobacteria, for which the name Immundisolibacter cernigliae gen. nov., sp. nov. is proposed. The associated order and family are therefore proposed as Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov. The type strain of the species is

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Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria

Baytshtok

Lü

Park

et al. 2008

Biotech & Bioengineering

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The goal of this study was to identify bacterial populations that assimilated methanol in a denitrifying sequencing batch reactor (SBR), using stable isotope probing (SIP) of (13)C labeled DNA and quantitatively track changes in these populations upon changing the electron donor from methanol to ethanol in the SBR feed. Based on SIP derived (13)C 16S rRNA gene clone libraries, dominant SBR methylotrophic bacteria were related to Methyloversatilis spp. and Hyphomicrobium spp. These methylotrophic populations were quantified via newly developed real-time PCR assays. Upon switching the electron donor from methanol to ethanol, Hyphomicrobium spp. concentrations decreased significantly in accordance with their obligately methylotrophic nutritional mode. In contrast, Methyloversatilis spp. concentrations were relatively unchanged, in accordance with their ability to assimilate both methanol and ethanol. Direct assimilation of ethanol by Methyloversatilis spp. but not Hyphomicrobium spp. was also confirmed via SIP. The reduction in methylotrophic bacterial concentration upon switching to ethanol was paralleled by a significant decrease in the methanol supported denitrification biokinetics of the SBR on nitrate. In sum, the results of this study demonstrate that the metabolic capabilities (methanol assimilation and metabolism) and substrate specificity (obligately or facultatively methylotrophic) of two distinct methylotrophic bacterial populations contributed to their survival or washout in denitrifying bioreactors.

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Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria

Cited by 52 publications

References 25 publications

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.

Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria

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