Protein stable isotope probing with H
            2
            18
            O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in
            
              Escherichia coli
            
            K12

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.

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Prolonged cold stress response of Escherichia coli O157 and the role of rpoS

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2011.02.018 ◽

2011 ◽

Vol 146 (2) ◽

pp. 163-169 ◽

Cited By ~ 27

Author(s):

Sinisa Vidovic ◽

Anil K. Mangalappalli-Illathu ◽

Darren R. Korber

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Cold Stress ◽

Escherichia Coli O157

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The heterogeneous heat stress response of Escherichia coli K12

Procedia Food Science ◽

10.1016/j.profoo.2011.09.158 ◽

2011 ◽

Vol 1 ◽

pp. 1060-1066 ◽

Cited By ~ 1

Author(s):

Iris Cornet ◽

Eva Van Derlinden ◽

Astrid M. Cappuyns ◽

Wim Bruyninckx ◽

Agnes Kovacs ◽

...

Keyword(s):

Escherichia Coli ◽

Heat Stress ◽

Stress Response ◽

Heat Stress Response ◽

Escherichia Coli K12

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Optimal conditions for mutagenesis by ozone in Escherichia coli K12

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis ◽

10.1016/0027-5107(74)90175-4 ◽

1974 ◽

Vol 24 (3) ◽

pp. 271-279 ◽

Cited By ~ 37

Author(s):

C. Hamelin ◽

Y.S. Chung

Keyword(s):

Escherichia Coli ◽

Optimal Conditions ◽

Escherichia Coli K12

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Identification of Ciliate Grazers of Autotrophic Bacteria in Ammonia-Oxidizing Activated Sludge by RNA Stable Isotope Probing

Applied and Environmental Microbiology ◽

10.1128/aem.02777-09 ◽

2010 ◽

Vol 76 (7) ◽

pp. 2203-2211 ◽

Cited By ~ 29

Author(s):

Ana Maria Moreno ◽

Carsten Matz ◽

Staffan Kjelleberg ◽

Mike Manefield

Keyword(s):

Escherichia Coli ◽

Stable Isotope ◽

Nutrient Cycling ◽

Activated Sludge ◽

Functional Groups ◽

Clone Library ◽

Bacterial Biomass ◽

Stable Isotope Probing ◽

Autotrophic Bacteria

ABSTRACT It is well understood that protozoa play a major role in controlling bacterial biomass and regulating nutrient cycling in the environment. Little is known, however, about the movement of carbon from specific reduced substrates, through functional groups of bacteria, to particular clades of protozoa. In this study we first identified the active protozoan phylotypes present in activated sludge, via the construction of an rRNA-derived eukaryote clone library. Most of the sequences identified belonged to ciliates of the subclass Peritrichia and amoebae, confirming the dominance of surface-associated protozoa in the activated sludge environment. We then demonstrated that 13C-labeled protozoan RNA can be retrieved from activated sludge amended with 13C-labeled protozoa or 13C-labeled Escherichia coli cells by using an RNA stable isotope probing (RNA-SIP) approach. Finally, we used RNA-SIP to track carbon from bicarbonate and acetate into protozoa under ammonia-oxidizing and denitrifying conditions, respectively. RNA-SIP analysis revealed that the peritrich ciliate Epistylis galea dominated the acquisition of carbon from bacteria with access to CO2 under ammonia-oxidizing conditions, while there was no evidence of specific grazing on acetate consumers under denitrifying conditions.

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