Preparing Diatom Samples: Part 1

After a career of almost 33 years in IT, I started volunteering at the Canadian Museum of Nature in January 2013. From my time as a youth, I had always had a keen interest in science and I was looking for something meaningful to keep me busy once a week. The Museum of Nature was a good fit.

In a weird coincidence, I was assigned to Paul Hamilton, who was in fact a former classmate from the 1970s at Laurentian High School in Ottawa. Paul is now a Senior Research Assistant in botany at the museum. He curates Canada’s Algae Collection and studies the biodiversity of microscopic life.

A man wearing protective gear stands in a laboratory.

Joe Holmes working at a fume hood in the lab. Image: Paul Hamilton © Canadian Museum of Nature

Working with Paul in the diatom lab, I have so far done a variety of jobs related to diatom preparation and observation. For a while I created slides from prepared samples, then did some work photographing microscopic specimens. Lately, I have been preparing samples from specimens taken from the field. The process of field collection, preparation, filing and study of diatom samples is quite involved and never ending, and not many are aware of the skill, complexity and intricacies of the process.

Phycology Collection and Diatoms

The Canadian Museum of Nature maintains an ever-growing algae (phycology) collection of over 110 000 samples. It contains everything from large seaweeds to small microscopic diatoms.

An array of diatoms.

Several diatom species, seen through an SEM microscope. Image: Paul Hamilton © Canadian Museum of Nature

Diatoms are a group of microscopic algae encased in a shell-like silica wall. There are over 15 000 documented species, most of which are 50 microns or less in length (a micron is one millionth of a metre).

In the environment, diatoms produce energy and free up oxygen in the process. Conservative estimates suggest that diatoms, in combination with other algae, can contribute up to 20% of global energy. These organisms are at the base of the food web, producing energy that is passed through their body to small life forms and progressing along the web to invertebrates, fish and ultimately, large mammals like whales.

Besides their importance to the environment and despite their small size, I have discovered through microscopes and photos in books that diatoms have very intricate, complex and beautiful structures, from round and oval to long, thin and even boat-like shapes. In my opinion, the beauty and wide variety of diatom shells has certainly contributed to the popularity of collecting and studying these organisms.

In the lab, we use diatoms as life indicators for researching climate change, climate history in the Arctic, water quality, evolution and single-cell DNA sequencing and analysis. In industry, they have even been used in products like mild abrasive in tooth paste and environmentally friendly insecticides for gardening (where the sharp silica shells can cut, and block insect movement).

A diatom.

A live diatom (Gyrosigma acuminate) under a light microscope at 1000x. Image: Paul Hamilton © Canadian Museum of Nature

The diatom specimens in the national collection come from across Canada and around the world. Samples are collected in the field by museum scientists or received as donations from other scientific institutions. Data on each sample, such as date, location found and photographs of diatoms within it are kept in the phycology collection database.

At the moment in the museum lab, Paul has had us process and study samples from Ungava in Northern Quebec, Haliburton Highlands in Ontario, Adirondack Park in New York State, U.S.A., Bolivia in South America, the Canadian Arctic Archipelago and Franz Josef Land in Arctic Russia. We have also photographed previously prepared slides from Lake Te Anau in New Zealand.

Obtaining Samples from the Field

Freshwater diatoms can be collected from all wet environments, like ponds, lakes, ditches and rivers. It is easy to collect diatom samples from bottom mud and sediments using a tool like a turkey baster, or from plain water. Samples can be dried in the field on filter paper or transferred wet into small bottles.

A note is made for each sample as to the exact location of where it was taken, latitude and longitude, along with who collected the sample and the date.

A bank of cabinets with a couple of open drawers.

Cabinet drawers with boxes containing sample bottles. Image: Joe Holmes © Canadian Museum of Nature

Upon returning to the lab, a reference number is assigned to each sample bottle based on available catalogue numbers. Corresponding sample data are registered in the museum’s phycology database, and additional data such as photographs are added later.

Bottles are sorted and placed within boxes of 100 for storage in the diatom collection cabinets awaiting the next processing step. Progress is recorded in a lab notebook to ensure proper procedure is followed and to carry on at a later date.

Samples can be in a variety of states:

  • Alive—raw samples from the field kept alive for a limited time to observe the organisms in their natural state and for DNA sequencing
  • Dry—as received from the field or after freeze drying.
  • Wet—preserved after cleaning and processing where all organic material has been removed, leaving only the silica diatom shells in a water solution
  • Slides—the final stage:
    • glass slides for light-microscope study
    • aluminum discs for SEM study.

Read my next blog article for more detail about preparing samples and making slides.

This entry was posted in Collections, Plants and Algae, Tools of the trade and tagged . Bookmark the permalink.

One Response to Preparing Diatom Samples: Part 1

  1. Pingback: Preparing Diatom Samples: Part 2 | Canadian Museum of Nature – Blog

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