title: Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state.
abstract: Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Gregor
authors.initials: G
authors.lastname: Schmid
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Zeitvogel
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Likai
authors.initials: L
authors.lastname: Hao
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Pablo
authors.initials: P
authors.lastname: Ingino
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Kuerner
authors.affiliation: 2 Canadian Light Source Inc., Saskatoon, Canada.
authors.forename: James J
authors.initials: JJ
authors.lastname: Dynes
authors.affiliation: 2 Canadian Light Source Inc., Saskatoon, Canada.
authors.forename: Chithra
authors.initials: C
authors.lastname: Karunakaran
authors.affiliation: 2 Canadian Light Source Inc., Saskatoon, Canada.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: 2 Canadian Light Source Inc., Saskatoon, Canada.
authors.forename: Yingshen
authors.initials: Y
authors.lastname: Lu
authors.affiliation: 3 Luxel Corp., Friday Harbor, USA.
authors.forename: Travis
authors.initials: T
authors.lastname: Ayers
authors.affiliation: 3 Luxel Corp., Friday Harbor, USA.
authors.forename: Chuck
authors.initials: C
authors.lastname: Schietinger
authors.affiliation: 4 McMaster University, Hamilton, Canada.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Hitchcock
authors.affiliation: 1 Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Obst
mesh_terms: D011232:Chemical Precipitation; D042621:Comamonadaceae / Q000737:chemistry* / Q000254:growth & development / Q000378:metabolism; D005296:Ferrous Compounds / Q000378:metabolism; D007091:Image Processing, Computer-Assisted; D008903:Minerals / Q000032:analysis*; D009566:Nitrates / Q000378:metabolism; D010084:Oxidation-Reduction; D019897:Periplasm / Q000737:chemistry; D055114:X-Ray Microtomography / Q000379:methods*
chemical_list: D005296:Ferrous Compounds; D008903:Minerals; D009566:Nitrates