Viewing Microorganisms Under a Microscope

A drop of pond water can hold dozens of kinds of living things: green algae, gliding diatoms, ciliates spinning through the water, and rotifers pulling food in with their crowns of cilia. With a basic compound microscope you can see most of them. Bacteria are harder, and viruses are out of reach for any light microscope. Knowing which is which saves a lot of frustration.

What counts as a microorganism, and how big are they?

“Microorganism” is a loose term for anything living that is too small to see clearly without magnification. It includes bacteria, archaea, protozoa, microscopic algae and fungi, and is often stretched to cover tiny animals such as rotifers and tardigrades. Viruses are usually discussed alongside them, although most biologists don’t consider viruses to be organisms in the usual sense.

Sizes vary hugely, and size determines what you need to see them:

What microscope do you need?

A compound light microscope with 4x, 10x and 40x objectives (40x, 100x and 400x total with a 10x eyepiece) handles most pond life. To see bacterial shapes clearly, you’ll want a 100x oil-immersion objective (1000x total) and a proper condenser with an iris diaphragm. An Abbe condenser is the usual type.

A stereo microscope at 10x to 40x is very useful for scanning a dish of pond water and spotting the larger creatures. You then pick them out with a pipette for closer viewing.

What type of microscope is used in microbiology?

Microbiology labs mainly use brightfield compound microscopes, very often with oil-immersion objectives, to examine stained smears. Labs also use:

• Phase contrast microscopes to view living, unstained cells, which are otherwise nearly transparent.
• Darkfield microscopes, which make small, faint objects (including some thin bacteria) glow against a black background.
• Fluorescence microscopes, together with dyes or antibodies that tag specific organisms.
• Electron microscopes, for viruses and fine internal structure.

Many hobbyists add a cheap darkfield stop under the condenser, a small opaque disc that blocks the central light, and get striking views of protozoa and algae.

What you can see at each magnification

• 40x–100x: rotifers, small worms (nematodes), water fleas, larger ciliates, algae filaments and colonies such as Volvox, diatoms as small golden shapes. This is the best range for scanning.
• 400x: most protozoa in useful detail: Paramecium, Euglena, Vorticella and amoebae, plus diatom shell patterns, yeast cells, and chloroplasts in algae. Bacteria appear as tiny moving specks.
• 1000x with oil: bacterial shapes (rods, spheres, spirals) and their arrangements (chains, clusters), especially in stained smears.

Can bacteria be seen with a microscope?

Yes, with limits. At 400x, bacteria in a wet mount look like tiny dots and dashes, some of them moving. You can tell they’re there, but not much else. At 1000x with oil immersion and a stain, you can usually make out basic shapes and arrangements: cocci (spheres), bacilli (rods) and spirilla (spirals).

What you can’t do with a microscope alone is tell most species apart. Many very different bacteria look alike under the microscope.

A good, reliable first look at bacteria is plain unflavoured yoghurt (with live cultures) smeared thinly and stained. Plaque gently scraped from your own teeth also works. Both show rods and cocci at 1000x.

Where to find microorganisms

• Ponds, ditches and slow streams. Sample the edges, squeeze water out of submerged plants, and scrape the brown film off stones and stems. Sediment from the bottom often holds the most.
• Old flower vase water, birdbaths and rain barrels.
• Gutters and wet moss. Soaked moss releases rotifers, nematodes and tardigrades. See how to find tardigrades in moss and lichen.
• Your own culture. A hay infusion grows a changing population of bacteria and protozoa over a couple of weeks.

Let collected water stand for a day or so in an open jar out of direct sun. The organisms tend to gather at the surface, on the sides or near the bottom.

Preparing and viewing live samples

1. Make a wet mount. Put a small drop on a clean slide and lower a coverslip at an angle. Our guide to wet mounts without air bubbles covers the details.
2. Use a depression (well) slide for larger, fast-moving organisms, so they aren’t crushed.
3. Slow them down. Fast ciliates are hard to follow. A thickening agent sold for this purpose, usually methyl cellulose, mixed into the drop slows them. Shreds of cotton wool or lens tissue in the drop work as a crude alternative, trapping organisms in a mesh.
4. Lower the light and add contrast. Unstained protozoa are nearly transparent. Close the condenser diaphragm partway and turn down the lamp. If you have darkfield or phase contrast, try them.
5. Scan systematically. Move the slide in rows at low power, then switch up when you find something.
6. Watch the edges and debris. Many organisms gather near bits of plant matter and around the edges of the coverslip.

As the water evaporates, the drop becomes crowded and organisms die or burst, so make a fresh mount every 10–20 minutes. Ringing the coverslip with a little petroleum jelly slows drying.

Staining for bacteria and cell detail

Staining kills cells but greatly improves contrast. For bacteria, a simple approach is:

1. Spread a very thin smear on a slide and let it air dry.
2. Fix it, traditionally by passing the slide briefly through a flame, or with a few drops of alcohol.
3. Cover with a basic stain such as methylene blue for a minute or so, then rinse gently and blot dry.
4. View under oil immersion.

Methylene blue is a good general stain for both bacteria and nuclei in protozoa. Our methylene blue staining guide explains concentrations and technique. The Gram stain, which sorts bacteria into two broad groups, needs more reagents and practice.

Odd shapes that move with the slide, crystals of stain, and bubbles can all mimic microbes. Our guide to microscopy artifacts helps you tell them apart.

What bacteria can be seen without a microscope?

Individual bacteria are almost always too small to see with the naked eye. A few rare exceptions exist: Thiomargarita species, sulfur bacteria from marine sediments, can reach a size visible to the eye. You won’t meet them in an ordinary home sample.

What you can see is bacteria in huge numbers: colonies on agar plates, slimy biofilms on surfaces, cloudy water, and coloured mats in hot springs or ponds. Cyanobacteria (sometimes called blue-green algae) can form visible green scums and filaments.

How bacteria are detected beyond the microscope

Labs identify bacteria with a combination of methods, including:

• Culturing on selective growth media and examining the colonies.
• Staining (such as the Gram stain) and microscopy to see shape and staining group.
• Biochemical tests that check which nutrients a bacterium can use or which enzymes it produces.
• Molecular methods such as PCR and DNA sequencing.
• Antigen and antibody tests, including many rapid tests.

For a hobbyist, the microscope tells you a lot about the shape and behaviour of microbes, but not usually which species you have.

Safety notes

• Natural water can contain organisms that cause illness. Wash your hands after handling samples, don’t pipette by mouth, and keep samples away from food.
• If you grow bacteria on agar plates, for example from household swabs, assume the growth may include harmful organisms. Tape the lids shut, view them through the lid, and don’t open plates once colonies have grown. Soak used plates in household bleach before throwing them away.
• Clean slides that have held body fluids, such as saliva or plaque, with disinfectant before reusing them.

For more ideas on what to look at next, see our overview of what everyday things look like under a microscope.