Microbiological Analysis

With particular expertise in polar microbiology, phycology and photophysiology, we house a dedicated microbiology laboratory (MicroLab), fully equipped to support the needs of microbiological and molecular research. Our equipment and techniques include:

1. Microbial Culturing

  • LMS Incubators; including a suite of temperature controlled cabinets of various sizes for microbial culturing with programmable temperature cycling (-10oC to +50oC) and integrated shelf lighting.
  • PSI Multi-Cultivator Photobioreactors (MC 1000-OD-MULTI); x3 units for small-scale culturing of autotrophic and heterotrophic microorganisms in suspension (batch & turbidostatic modes), with customisable thermoregulation, illumination (spectral quality & quantity), and aeration.  
  • Air flow hoods; details to follow
  • LOWTEX; access to a dedicated Low Temperature Experimental Facility allowing the culturing of psychrophilic microbial communities for a range of purposes.

2. Microbial Imaging and Enumeration

  • Epi-fluoroescence Microscopy (Olympus BX41 with CoolLED pE300 white illumination system & Micropublisher 6 MegaPixel Color CCD Camera); for microscopy of all biological specimens, fixed or alive. Frequently used for determination of microbial abundance, to image specific microbial features, selective recognition of particular components of complex biomolecular structures, and a wide array of further biological applications. It also serves as an important tool to generate high-resolution, good-quality images for publications.
  • Flow Cytometery (BD ACCURI C6); for rapid identification and quantification of cells from a range of (heterogeneous) samples.
  • Inverted microscope & mechanical stage (Leica DMi1); for general microscopy and determination of community composition and abundance, including ‘industry standard’ quantitative assessments of cell ID using e.g. the Utermohl settling method.

3. Autotroph Photophysiology and Bio-Optical Properties

We specialise in measurements of variable chlorophyll fluorescence for determination of autotroph health, productivity and photophysiology, complemented by assessments of autotroph pigmentation and bio-optical properties. Our current suite of instruments includes:

  • Walz Water-PAM fluorometer; for highly-customisable measurements of variable chlorophyll fluorescence in both aquatic (cuvette-system) and benthic/terrestrial (fiber-optic system) samples.
  • Walz PHYTO-PAM fluorometer; for multi-wavelength and fast-kinetic (O-J-I-P) measurements of variable chlorophyll fluorescence in aquatic (community) samples.
  • PSI Handy Fluor-Cam (FC 1000-H with TOMI-2 High Resolution Camera); for time-resolved imagery (i.e. pixel-by-pixel measurements) of variable chlorophyll fluorescence on a range of samples, including leaves, small plants, algal colonies, agar plates and microphytobenthic biofilms.
  • Trilogy Laboratory Fluorometer; for rapid measurements of extracted or in-vivo chlorophyll a fluorescence allowing real-time monitoring of autotroph abundance and biomass.
  • UV-VIS Spectrophotometers (details); for measurements of a host of solvent and water extractable pigments and wave-scan determination of in-vivo absorbance/transmission spectra.
  • High Performance Liquid Chromatography (Agilent 110 HPLC equip with a Diode-Array-Detector); optimised for the separation, identification and quantification of autotroph pigments at trace concentrations.

4. Molecular Biology

In support of our diverse microbiological investigations, we host strong capabilities across a range of molecular biology applications, including phylogenetics, DNA and RNA barcoding, metagenomics, transciptomics and whole genome sequencing. Current instrumentation to support these applications include:

  • Oxford Nanopore Technologies MinION sequencer; for real-time DNA and RNA sequencing in the lab and in the field.
  • Oxford Nanopore Technologies VOLTRAX library preparation; for automation of processes associated with nanopore sequencing ranging from sample extraction to library preparation.
  • PCR machines; details to follow
  • Gel electrophoresis and Plate Reader; details to follow
  • Dedicated flow-hood; details to follow.
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