Protein-Based Stable Isotope Probing (Protein-SIP): Applications for Studying Aromatic Hydrocarbon Degradation in Microbial Communities

2020 ◽  
pp. 277-284
Author(s):  
Nico Jehmlich ◽  
Martin von Bergen
Keyword(s):  
Stable Isotope ◽  
Aromatic Hydrocarbon ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
Hydrocarbon Degradation

scholarly journals Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

2016 ◽  
Vol 26 (1-3) ◽  
pp. 195-210 ◽  
Author(s):  
Carsten Vogt ◽  
Tillmann Lueders ◽  
Hans H. Richnow ◽  
Martin Krüger ◽  
Martin von Bergen ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Secondary Ion Mass Spectrometry ◽  
Stable Isotope Probing ◽  
Hydrocarbon Degradation ◽  
Common Mechanism ◽  
Detection And Identification ◽  
True Diversity ◽  
Phylogenetic Resolution ◽  
Hydrocarbon Degraders

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using <sup>13</sup>C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

scholarly journals Generation of 13C-Labeled MUC5AC Mucin Oligosaccharides for Stable Isotope Probing of Host-Associated Microbial Communities

2019 ◽  
Vol 5 (3) ◽  
pp. 385-393 ◽  
Author(s):  
Clayton Evert ◽  
Tina Loesekann ◽  
Ganapati Bhat ◽  
Asif Shajahan ◽  
Roberto Sonon ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing

Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing

2014 ◽  
Vol 9 (3) ◽  
pp. 453-464 ◽  
Author(s):  
Mary Beth Leigh ◽  
Wei-Min Wu ◽  
Erick Cardenas ◽  
Ondrej Uhlik ◽  
Sue Carroll ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
Contaminated Sediment

scholarly journals An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene

2014 ◽  
Vol 80 (10) ◽  
pp. 3233-3243 ◽  
Author(s):  
So-Jeong Kim ◽  
Soo-Je Park ◽  
Man-Young Jung ◽  
Jong-Geol Kim ◽  
Eugene L. Madsen ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Stable Isotope Probing ◽  
Hydrocarbon Degradation ◽  
Metabolic Reconstruction ◽  
Content Type ◽  
Degrading Bacterium ◽  
Gene Acquisition ◽  
Catabolic Genes

ABSTRACTStable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, aHerminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [13C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ∼3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate,p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the orderBurkholderialeswithin the classBetaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in theRhodocyclaceae(particularlyAromatoleum aromaticumEbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition byHerminiimonasvia horizontal gene transfer.

scholarly journals Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

2016 ◽  
Vol 7 ◽  
Author(s):  
Jeffrey J. Marlow ◽  
Connor T. Skennerton ◽  
Zhou Li ◽  
Karuna Chourey ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
Slow Growing

scholarly journals DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil

2020 ◽  
Vol 11 ◽  
Author(s):  
Julian Yu ◽  
Michael J. Pavia ◽  
Lauren M. Deem ◽  
Susan E. Crow ◽  
Jonathan L. Deenik ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Stable Isotope Probing ◽  
Shotgun Metagenomics ◽  
Biochar Amendment
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