Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS
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Kirf, Mathias K.
Inglis, R. Fredrik
- Journal Article
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Rights / licenseCreative Commons Attribution 4.0 International
Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N_2 and CO_2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with ^15N2 and ^13CO_2 under in situ conditions with and without NH_4^+. Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation ^15N and ^13C stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N_2 in the absence of NH_4^+, but not in the presence of NH_4^+ as has previously been suggested. N_2 and CO_2 fixation were heterogeneous among cells and positively correlated indicating that N_2 and CO_2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature Show more
Journal / seriesFrontiers in Microbiology
Pages / Article No.
PublisherFontiers Research Foundation
SubjectFACS; Dinitrogen fixation; Lago di Cadagno; Green sulfur bacteria; Phenotypic noise; Diversity; Single-cell analysis
Organisational unit03746 - Van Bokhoven, Jeroen A. / Van Bokhoven, Jeroen A.
03328 - Wehrli, Bernhard / Wehrli, Bernhard
03743 - Ackermann, Martin / Ackermann, Martin
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