First Week

In the first week, you will observe, separate, and identify oribatid mites and process them in the molecular lab to obtain DNA sequences for phylogenetic analyses.

Major Goals

Note

You will…

Gain foundational knowledge of oribatid mites’ ecology, evolution, and morphology.
Understand how their body plan relates to taxonomy and phylogeny.
Learn to distinguish oribatid mites from other mites and soil fauna.
Identify key morphological features for classifying oribatid mites into major groups.
Use identification keys to determine oribatid mites to genus, and possibly species level.
Collaboratively organize and manage collected specimens, including proper labeling and maintaining an updated inventory.
Learn the step-by-step process of DNA extraction and the properties of key chemical substances involved.
Be able to explain the PCR process and how to visualize its results.
Be able to differentiate between the various genes (markers) used for PCRs.
Understand the principles of Sanger sequencing and how to prepare samples for sequencing.

Monday

You already know how to collect soil animals (refer to How to Sample if you need a refresher). By the end of the day, you’ll have a collection of various mite species, roughly categorized into distinct morphological types (morphotypes).

In the morning, you’ll receive a general introduction to soil animal systematics and become familiar with common mesofauna representatives. Additionally, you’ll get an overview of the taxonomy and phylogeny of oribatid mites, learning about their distinctive body plans and lifestyles, which will help you differentiate them from other mites.

In the afternoon, you’ll observe soil fauna firsthand through a stereo microscope 🔬. While many of the soil animals in your samples will be deceased, the oribatid mites and other taxa will be alive. Oribatid mites exhibit remarkable diversity, ranging from agile runners to slow movers, and from tiny, transparent species to large, pitch-black ones. Some are smooth and glassy, while others are coated in dirt. Despite their differences, all oribatid mites share a common trait: an impressive array of defense strategies.

Tip

🔍 Take your time to observe oribatid mites and their characteristic movements and bodies. Write down three to five features (morphological and/or behavioural) of three living oribatid mites you observe. Remember, a character is everything you can observe. What type of defense strategy do the different oribatids display? Save your notes, we will use them later in this course. It may be helpful to make drawings or sketches of the observed species to more easily distinguish morphotypes based on certain character(s).

Note

By the end of the day, you will be able to identify the most relevant morphological characteristics to distinguish oribatid mites and classify them into separate major groups.

Differentiate oribatid mites from other mite species.
Classify oribatid mites into major groups.
Group oribatid mite species based on distinct morphotypes.

Tasks of the Day

Transfer all individuals belonging to the same morphotype into a Blockschälchen filled with EtOH.

Note

You can collect over 10 different morphotypes, but at least two are required.

Transfer two or more individuals per morphotype into a glass vial and add a small label.
The remaining morphotype individuals go into 2 ml tubes filled with EtOH, labelled in the same way as the samples in the glass vials.

Tuesday

Yesterday, you collected oribatid mites and left them in lactic acid overnight to clear their bodies for species determination under the stereo microscope🔬. Without this treatment, recognizing key morphological features is challenging.

Note

Today, you will…

Expand your knowledge on how to identify oribatid mites.
Learn to recognize additional morphological characters.
Be able to identify most of your specimens to species level.

For species-level identification (using the stereo microscope 🔬), take one or two individuals from the glass vials. The remaining specimens (in 2 ml reaction tubes filled with EtOH) will be used for molecular work.

Tasks of the Day

Enter the sample number, species name, morphotype number, and your name in the Taxa List. Click here.

Note

Everyone should have five different species identified by the end of the day.

Wednesday

In this course, we use a DNA extraction method based on spin columns with a silica membrane, provided as part of a DNA extraction kit. The kit includes carefully matched buffers, reaction tubes, and optimized incubation and centrifugation procedures, ensuring efficient processing and optimal DNA yield.

Note

You will…

Learn how to work safely and maintain cleanliness in a molecular lab.
Learn how to properly use a pipette.
Understand how to handle your samples without contaminating the workspace, your samples, or yourself.
Learn the names and roles of key chemical substances and conditions for each step of DNA extraction.
Gain skills in setting up a PCR efficiently.
Understand what a PCR mastermix is.
Learn how a PCR reaction works and the role of a thermocycler.

Tasks of the Day

Perform DNA extractions and PCR reactions with your samples in the lab.

Note

Maintain a clean and organized workspace in the lab 🧹🥼 and adhere to the lab rules ⚖️.

Thursday

Today, you will prepare an agarose gel and load a small amount of your PCR product to check whether the PCR was successful. Be sure to add loading dye to your samples before loading them onto the gel. After evaluating the gel, purify (i.e., wash) the PCR products that show bright and clear bands, in preparation for sequencing.

Tasks of the Day

Open the form and answer the questions? Click here. Do not forget to enter your name!

Friday

Friday will be a day off since your PCR products will be sent for sequencing, which takes some time. In the meantime, you’ll have some HOMEWORK to complete — please see the details below!

Homework

Make yourself familiar with Geneious Prime, watch the introductory videos about Sanger-sequencing, and answer the Questions of the day!

Watch A brief tour of Geneious Prime.
Check out the Geneious Prime User Manual.
If you are going to use your own PC on Monday next week, install the 30-days trial version of Geneious Prime.
Watch the tutorial about Geneious Prime here (courtesy of Dr. Ina Schäfer). It will explain the most important and common terms such as sequence assembly, sequence checking, ambiguous positions, consensus sequence, etc., and explains how to analyze your Sanger sequences.