focused ion beam (fib) equipped scanning electron microscope (sem-fib helios g5 dualbeam)  (Thermo Fisher)

Journal: Microbiome

Article Title: Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level

doi: 10.1186/s40168-024-01837-6

Figure Lengend Snippet: The pipeline developed in this study. For the target-specific cell sorting and mini-metagenomics, different numbers of magnetotactic bacteria (MTB) cells were sorted with a micromanipulation system (Step 1), which were then lysed and used as the template of whole genome amplification (Step 2). After sequencing, assembly, and binning, the draft genome of the MTB population was obtained (Step 3). Genome annotation and subsequent analysis (including phylogeny analysis, metabolism analysis) were then performed (Step 4). For the NanoSIMS-based isotopic analysis, the stable-isotope incubated MTB cells were first magnetically enriched (Step 1), then characterized by fluorescence in situ hybridization (FISH) (Step 2) and focused ion beam scanning electron microscope (FIB-SEM) (Step 3), and finally analyzed by NanoSIMS at the single-cell level (Step 4)

Article Snippet: The silicon wafer with enriched MTB cells was placed in a scanning electron microscope (SEM) equipped with a focused ion beam (FIB) system (Zeiss Auriga Compact FIB-SEM, Germany).

Techniques: FACS, Bacteria, Micromanipulation, Whole Genome Amplification, Sequencing, Incubation, Fluorescence, In Situ Hybridization, Microscopy

Journal: Microbiome

Article Title: Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level

doi: 10.1186/s40168-024-01837-6

Figure Lengend Snippet: A combination of FISH, FIB-SEM, and NanoSIMS analyses. a–c LHC-1 cells were mixed with E. coli cells and incubated with NaH 13 CO 3 for 1 h and then fixed and dried on a silicon wafer. Thereafter, the FISH experiment was conducted using a universal bacterial probe EUB338 ( a ) and an LHC-1-specific probe BTC19 ( b ), and the bacteria were imaged with an Olympus Optical BX51 fluorescence microscope. c A merged image of a and b . The white arrowheads point to E. coli cells in a – c . d SEM image of the same region of interest (ROI) of a to c , which was acquired at an accelerating voltage of 5 kV with a 6-mm working distance. The LHC-1 cells can be easily distinguished from E. coli due to their disparity in sizes, and the correspondence with the LHC-1-specific probe BTC19 in b . e Pt deposition (yellow arrowheads) on the ROI with FIB-SEM as markers for NanoSIMS imaging. The ROI analyzed using NanoSIMS is outlined as white rectangular. f NanoSIMS image of 12 C − of the same ROI

Article Snippet: The silicon wafer with enriched MTB cells was placed in a scanning electron microscope (SEM) equipped with a focused ion beam (FIB) system (Zeiss Auriga Compact FIB-SEM, Germany).

Techniques: Incubation, Bacteria, Fluorescence, Microscopy, Imaging