Exploring diatom biodiversity in the Everglades and Caribbean wetlands
Water quality assessments frequently include biological indicators to evaluate aquatic ecosystem habitat type and health. Because diatoms are ubiquitous and are found in habitats where macroinvertebrates are not, they are often used in these assessments. Scientists also investigate the biodiversity at sample sites when making inferences about the stability and health of these aquatic systems. In this module, students will read and discuss a scientific article about biodiversity (instructor's choice and optional) and use this module to investigate diatom biodiversity in the Everglades and Caribbean karstic wetlands. As students explore these concepts, they will be introduced to and practice biostatistical skills needed to answer the over-arching question: Are these karstic wetland sites considered diverse, and are there dominant periphytic diatom species in karstic wetland communities?
This module is designed to guide students through statistical analyses and corresponding graphics with R statistical software. Students explore biodiversity concepts such as species richness, relative abundance, evenness, and diversity and similarity indices. Goals include comparing and interpreting results as well as generating and understanding rarefaction curves. This module can also be used in conjunction with the Exploring the relationship between periphyton and water quality in karstic wetlands module for multiple lab sessions.
- Demonstrate data management and analysis skills using R software (e.g. exporting and loading data, running scripts, generating graphs)
- Understand concepts in biodiversity (abundance, richness, evenness) and how they are used in environmental assessments
- Analyze and interpret biodiversity and similarity indices results and rarefaction curves
- Contextualize prior scientific findings (e.g., from a scientific paper) and interpret statistical information to answer the over-arching questions
Context for Use
- This module can be completed in 2-3 hours. This module can be used in conjunction with the Exploring the relationship between periphyton and water quality in karstic wetlands module for multiple lab classes
- Appropriate for advanced undergraduate students in a limnology or ecology course
- This module is designed for a class or lab size of up to 20 students. For larger class sizes, students can work in small groups.
- Students should be familiar with basic ecological concepts (species richness, diversity, abundance and evenness) and proficient in R.
- The length and concepts of this lab can be modified according to student skill level.
How Instructors Have Used This Module
Using Project EDDIE modules in Limnology
Ana Morales, University of Vermont and State Agricultural College
This module ran smoothly and tied into the curriculum well! Students commented that they enjoyed the module and had fun. The annotation of the R code was excellent, clear, and easy to use. Using this module to explore biodiversity indices after teaching phytoplankton or zooplankton community ecology is a nice follow-up.
Description and Teaching Materials
Teaching materials files are provided below. For a step-by-step description for carrying out this module, please refer to the Instructor's R script and PowerPoint. RStudio output and PDF of graphs to check student progress are also provided.
Quick overview of the activities in this module
- Activity A: As a class, students will generate a bar graph of diatom species relative abundance for the Caribbean using the LTER data set. Then, individually, students will select another wetland in this data set to investigate diatom species richness. With both graphs and the scientific article (optional), students will answer the questions in the PowerPoint before moving to the next activity.
- Activity B - Part 1: As a class, students will evaluate the Shannon-Wiener biodiversity index and evenness (Pilou's J) for the Caribbean. Then, comparing communities in the Caribbean and Belize, students will calculate the similarity coefficient (Sorensen-Dice) to answer the questions in the PowerPoint before moving to the next activity.
- Activity B - Part 2: As a class, students will generate a rarefaction curve for the Caribbean and answer questions in the PowerPoint before moving to the next activity.
- Activity C: Individually, students will generate a curve for the site of their choice. With both curves (this one and the curve from Activity B - Part 2) and the information in activities A-C, students will apply techniques to answer the PowerPoint and over-arching questions before moving to the post-lab questions.
Workflow of this module:
- Assign pre-lab questions (students should come to class having already read the scientific article, if assigned).
- Start the PowerPoint presentation as a refresher for basic biodiversity concepts pausing to conduct activities after going over each basic concept (see PPT).
- Instructor guides students through the module activities using RStudio (if available, an assistant is recommended to walk around and aid students). Module activities are broken down into parts conducted as class and worked on individually. After initial RStudio work, students will continue the module independently.
- After all activities are completed, the instructor assigns post-lab questions and homework (optional, if students were unable to complete activities A-C).
- Instructor's PowerPoint (PowerPoint 2007 (.pptx) 5.8MB Aug3 22)
- Student handout (Microsoft Word 2007 (.docx) 237kB Aug3 22)
- Student R script (R script 18kB Jul27 22)
- Zipped RStudio project ready to go with the data files and student R script (Zip Archive 20kB Jul27 22)
- Data files:
- Caribbean (Comma Separated Values 18kB Jul27 22)
- Everglades (Comma Separated Values 73kB Jul27 22)
Teaching Notes and Tips
Use Instructor's PowerPoint to introduce concepts, stopping along the way to carry out activities. The Instructor's key R output provides all possible calculations and plots. The student R script provides commented guidance to generate calculations and plots.
- Cover concrete examples of how biodiversity is different than abundance, richness, and evenness, and how each concept plays a role in the math behind the index calculations.
- We recommend using the student R script when walking students through the exercises. The student R script allows students to choose from different sites, and the instructor's R script combines all sites to generate all graphs and answers to the module exercises.
- We recommend using this module before and in conjunction with the Exploring the relationship between periphyton and water quality in karstic wetlands module for multiple class sessions.
Assessment for this module is both formative and summative. Student success can be measured by the completion of steps throughout the lab and the quality of answers/inferences made at the end (i.e., their interpretation of results and how they connect them to the overarching question). Student success can also be measured by comparing answers to the pre-module and post-module questions. By the end of this module, students should:
- Activity A: demonstrate understanding of the difference between species richness, abundance, and evenness by answering questions in the PowerPoint or posed by the instructor during class discussion or written work. Students should also show basic graphing abilities in RStudio by generating a bar graph.
- Activity B - Part 1: show an understanding of how species richness, abundance, and evenness are incorporated in biodiversity indices and similarity coefficients by calculating them for karstic wetland sites. Students should be able to make these calculations in RStudio and interpret/compare results about these sites/regions.
- Activity B - Part 2: exhibit the ability to use rarefaction curves as a different technique for interpreting species richness by generating a graphic in RStudio and answering PowerPoint/instructor's questions during class discussion or written work.
- Activity C: demonstrate individual skill level at applying techniques and concepts learned in activity A-B to answer the overarching questions ('are these karstic wetland sites considered diverse and are there dominant periphytic diatom species in karstic wetland communities?').
References and Resources
- Pre-reading (optional):
- Article of instructor's choice. Recommended article:
- La Hée, J. M., & Gaiser, E. E. 2012. Benthic diatom assemblages as indicators of water quality in the Everglades and three tropical karstic wetlands. Freshwater Science, 31(1), 205-221.
- Article of instructor's choice. Recommended article:
- Biodiversity concepts: Kricher, J.. 2011. Tropical ecology. Princeton University Press.
- Data sets:
- Gaiser, E. 2012. Diatom Species Abundance Data from LTER Caribbean Karstic Region (CKR) study (FCE) in Yucatan, Belize and Jamaica during 2006, 2007, 2008. Environmental Data Initiative. https://doi.org/10.6073/pasta/84241f5358c01c8dacd832b42d3fc736. Dataset accessed 2022-03-29.
- Gaiser, E. 2021. Relative Abundance Diatom Data from Periphyton Samples Collected from the Greater Everglades, Florida USA from September 2005 to November 2014. Environmental Data Initiative. https://doi.org/10.6073/pasta/a9dca89331d33221c59a6aa0ae96278a. Dataset accessed 2022-03-29.
- Diatom Image Database from the Florida Coastal Everglades LTER
- Conjunction module: Exploring the relationship between periphyton and water quality in karstic wetlands (this module is pending publication - likely out Fall 2022)
- Additional optional resources:
- Gaiser, et al. 2015. New perspectives on an iconic landscape from comparative international long‐term ecological research. Ecosphere, 6(10), pp.1-18.
- Ambrose, H. W., & Ambrose, K. P. 1987. A handbook of biological investigation. Winston-Salem, N.C., Hunter Textbooks.
- Online resources about diatom species: