JCU Aquatic Resources : Diatom slides from core sample

This week in lab we extruded sediment from the core we collected at Beach City on October 10^thand learned how to prepare and examine diatom slides. The process of preparing diatom slides from a sediment core occurs in five steps: extruding the core from the collection tube, cleaning the sediment in nitric acid, rinsing and centrifuging the sediment, drying cleaned sample onto coverslips, and fixing dried material onto microscope slides.

Step 1: Extruding the core

extruding a core

For the sake of time, we only collected 4 samples from our core, but ordinarily an entire sediment core would be extruded and collected in 1-cm or 1/2-cm intervals. To extrude the core, the sediment must be pushed from the bottom up through the top of the collection tube. To prevent loss of sample, a plastic “stage” is attached to the top of the collection tube (fig. 1). This stage also allows for the sediment to be scraped into Whirl-Paks at desired intervals. Each Whirl-Pak was labeled with its corresponding measurement in the core (i.e. the top centimeter of sediment is labeled “0-1”).

Step 2: ‘Cleaning’ the sediment

plastic "stage" attached to collection tube

Approximately 0.5 grams of each sediment sample was mixed with 20 mL of DI water and 10 mL of nitric acid in a beaker and boiled on a hot plate until the solution reached a volume of ~10 mL. This step is necessary to remove organic matter from the sample. Because the inorganic sediment and diatoms cannot be separated in core samples, removing organic material makes diatom identification and count data easier to collect. At the end of this step, we are left with inorganic material (sediment + diatoms) and nitric acid.

samples boiled in nitric acid

Step 3: Rinsing the sediment

We did not complete this step in class, but the samples must be rinsed with DI water in order to remove the nitric acid. To do this, the sample is transferred to a Falcon tube and centrifuged at 2000 rpm for 10 minutes. The supernatant nitric acid is decanted and the tube is refilled with DI water. Next, the tube must be shaken to resuspend the sediment pellet. This process is repeated 6 times to completely remove the acid.

Steps 4 and 5: Preparing permanent mount slides

A solution of ~0.1 mL of cleaned sample + ~0.9 mL DI water was pipetted onto a coverslip and allowed to dry for 24 hours. Three dilutions of each sample were made and prepared slides were examined for concentration of diatoms. Dry coverslips were fixed to microscope slides using Naphrax permanent mountant. For the remainder of class, we looked at previously made permanent mount diatom slides and identified different genera based on morphology.

Some of the common genera found were also known indicator organisms. Acidophiles: Eunotia, Frustulia, and Actinella, as well as Pleurosira, an indicator of elevated conductivity. Below are examples of each morphological group of diatoms: Centrics, with radial symmetry (most often seen in valve view); Araphids, without a raphe and often found in chains or star-shaped colonies; Eunotioids, acidophiles with an abbreviated (short) raphe along the valve mantle; Monoraphids (not pictured), with a raphe on only one of the two valve faces, Biraphids, with raphes on both valve faces (pictured: a "Naviculoid" biraphid with symmetry to both the apical and transapical axes); Gomphocymbelloids, with asymmetry to one or both axes (or symmetrical to both!), Epithemioid, with its raphe in a canal, Nitzschoid, with its raphe in a keel along one side of the valve, and Surirelloid, with a single raphe in a keel around the entire periphery of the valve face.