Overview
Team Lichen began with a group of ecological researchers and college instructors (Drs. Danielle Garneau, Matthew Heard, and Mary Beth Kolozsvary) who have been working hard to deliver meaningful field and lab experiences to undergraduate students.
During this particularly challenging moment in time (COVID-19 era), it has become particularly difficult to navigate this task in our classrooms, but we believe that by working together and channeling support, creativity, complementary expertise, and experiences, all of us can deliver flexible research and teaching content to those eager to participate. As active board members of the Ecological Research as Education Network (EREN), we understand the need for collaboration to address important scientific questions and aim to engage our students and peers in this process.
Our approach in this EREN lichen flexible learning project is to offer a research experience which can be catered to student level, and accommodate time and course delivery constraints. We have developed 3 modules which can be administered in a 3 week model or as stand-alone modules delivered in 1 lab period.
- Module 1: Spatial Analysis of Biological and Environmental data
- Module 2: Lichens in YOUR Local Landscape
- Module 3: Data Analysis for NEON and Local Field Data
Aims include encouraging students to become active collaborators in research through a long-term citizen science project (EREN Lichen on the iNaturalist platform). We want students to see how their data will serve to fill in the gaps that exist and how they may complement long-term monitoring being performed at National Ecological Observatory Network (NEON) aquatic and terrestrial sites. These NEON sites are collecting observational, remotely sensed, and telemetered tower data across the country spanning 20 ecoregions. Student participation in this EREN Lichen project is an important component of testing hypotheses regarding lichen across latitudinal and environmental gradients and scale analyses up from the local field collection site to the national level.
Land-use change and human impacts to the environment can significantly affect ecosystem structure and function (Vitousek et al., 1997; Poschold et al., 2005; Newbold et al., 2015). In this module, we will use a combination of NEON data (NEON.DOC.014042) and student-led field data collection to examine how land-use change and other anthropogenic drivers of change (e.g., air pollution) affect the presence and abundance of lichens - an important group of bioindicator organisms. Lichens are a mutualistic symbiotic association between a fungus (called the mycobiont) and algae or cyanobacteria (called the photobiont) and are excellent examples of composite organisms (Hawksworth and Rose 1970).
Why Lichens?
- ubiquitous (easy student access)
- resilient (present any semester we teach)
- bioindicator species (inform us of environmental health)
- crustose: lichen adhere so tightly to their substrate that they would likely harm the underlying substrate if removed and are often considered to be “crusts”
- foliose: lichens have leaf-like lobes that protrude from substrate (leafy)
- fruticose: lichens are the most three dimensional of all types, and can stand erect or hang in strands (3D)
Lichens are also ubiquitous in both urban and rural areas, occurring on both natural (e.g., trees, rocks, soil) and artificial substrates (e.g., tombstones, buildings, abandoned equipment), and are sensitive to environmental change (Hawskworth and Rose 1970; Pescott et al., 2015; Outhwaite et al., 2020). Collectively, these traits make them well suited for designing field ecology laboratory modules and field research projects that involve students collecting data in a variety of settings (e.g., on campus, backyard, urban areas, Wagner et al., 2009).
Project-wide Learning Outcomes
- Learn about how NEON data can be used to examine relationships between key bioindicator organisms and ecological and land-use gradients.
- Explore how NEON data and locally collected field data can be linked with other geospatial datasets including the National Land Cover, air quality (EPA), and others hosted on the ESRI Living Atlas.
- Explore existing NEON data to generate hypotheses for testing with field collected or other available environmental datasets.
- Gain experience in species identification, morpho-species classification, and how to make biotic and abiotic measurements in field settings.
- Examine how bioindicator organisms can be used to assess land-use change, air pollution, and other environmental impacts.
- Explore how to use multi-site collaborative data to conduct regional and continental scale analyses to address ecological and macroecological questions.
Potential hypotheses, but you will explore more...
- Lichen presence and abundance will be negatively impacted by human caused land-use change,
- Increasing air pollution levels along an urbanization gradient will decrease lichen presence and abundance,
- Increasing light levels (or decreased canopy cover) will decrease lichen presence and abundance,
- Lichens persisting in different ecosystems will show similar responses to land-use change, urbanization, and air pollution.
Module 1: Spatial Analysis of Biological and Environmental Data
In this first module, students can explore data (iNaturalist and NEON) to examine relationships between plant presence and abundance (NEON.DP1.10058) to explore how lichen presence and abundance and environmental variables such as wet deposition chemical analysis (NEON DP1.00013.001)(pollutants) vary across field sites that span both ecological and land-use gradients.
Students will also explore relationships between lichen and other relevant geospatial datasets, including tree canopy cover (NLCD), particulate matter (2.5ppm)(ESRI), and AirNow air quality (EPA).
You are IMPORTANT, your participation (iNaturalist) lichen data collection helps tell a more complete story:
Based on their geospatial queries, students will generate hypotheses for testing with field collected or online data sources.
We have created 2 methods to approach these analyses and both are free geospatial software
- QGIS
- ArcGIS online (ESRI)
For the QGIS approach, follow the guidelines in this QGIS activity module:
For the ArcGIS online approach, follow the guidelines in the ArcGIS online activity module below:
Steps 1 & 2: Establishing accounts for ArcGIS online and creating a project
Step 3: Adding basemaps and orienting to the mapping interface
Step 7: Visualizing Living Atlas datasets
PLEASE NOTE: as of Sept 2020, this tree cover dataset was removed from the Living Atlas repository (maybe GlobalForestWatch is updating). DG- is working to try and find an alternative for us and will update when it is available. ALTERNATIVE DATASET 12/21/20 UPDATE: We recommend using INTACT HABITAT CORES as a dataset in place of this Tree Cover for the moment. When you interact with a location on the map, there are many useful attributes offered including forest percentage (NLCD-national land cover dataset) which is interchangeable with the above tree cover data.
Step 8: Visualizing land cover (NLCD dataset)
Step 9: Accessing, downloading, and importing iNaturalist observations (EREN Lichen or others)
Step 10: Adding and attributing NEON lichen datasets (putting it all together)
Step 11: Continued exploration and hypothesis generation with NEON wet deposition chemical analysis data and exemplar NEONcomplete datasets
Demonstration video to get you started on spatial analyses:
Module 2: Lichens in YOUR Local Landscape
This module provides an easy-to-implement field-based learning activity that introduces students and faculty to a new, collaborative iNaturalist project: EREN Lichen!
iNaturalist Project EREN Lichen!
- Students will be contributing to a new iNaturalist project “EREN Lichen.” iNaturalist is a web-based and smartphone app platform that is used to document observations of species in a particular date and time. It is used and supported by an online community of naturalists, citizen scientists, and biologists, who help in crowdsourcing and confirming species identifications.
- Submitted observations are accessible to all members of the iNaturalist community, so they provide an excellent resource for exploring, teaching, and citizen science research opportunities. It is a great, user-friendly way to learn more about natural history.
- The EREN Lichen project is new, so the number of observations in the iNaturalist project is limited. However, as classes from different locations adopt this module and contribute to the iNaturalist EREN Lichen project, these data can be used to explore hypotheses that address ecological questions across larger scales.
- The EREN Lichen project data can also be combined with other datasets (e.g., NEON, Living Atlas, NLCD) to broaden these types of analyses, and filling in gaps.
We are looking forward to working with participants in the EREN Lichen project to explore these possibilities as the project grows. So get into the ground-level with this project, and let's see where it takes us!
Download and join iNaturalist, and then join the EREN Lichen project!
And download the free app on your smartphone!
Module-specific Learning Goals
- Gain experience in species identification, morpho-species classification, and how to make abiotic and biotic measurements in field settings.
- Develop technical skills using modern technology (smartphone apps, spreadsheet programs, data analysis packages) and everyday materials (freezer baggie, sharpie permanent marker, string, measuring tape) to make scientific measurements and analyze data.
- Examine how bioindicator organisms can be used to assess land-use change, air pollution, and other environmental impacts.
- Explore how to use multi-site collaborative data can be used to conduct regional and continental scale analyses to address ecological and macroecological questions.
Easy (and Painless) to Implement!
- Instructor and Student Guide - takes you through, step-by-step
- Teacher Tips
- Flexible! - smartphones or not, dbh tape or strings and measuring tape, freezer baggies and permanent marker to make the sampling grid!
- Appendices (as separate files) - grid template and instructions, determining aspect in the field, and lichen field datasheet and sample of iNaturalist download
- Links to smartphone apps - (iNaturalist, Seek, Canopeo)
- Googlesheets template - for summarizing/analyzing data, if you don't use your smartphone in the field or have problems downloading your data
- Video demonstration - included in this SPARK (scroll down); demos the whole process for sampling a tree (11 minutes)
- Accommodates various sampling situations - on campus, if students get sent home (as long as the student has access to trees that are large enough, they can do the sampling)
How long will it take to sample a tree?
- This activity suggests that each student or group of students samples five trees.
- We suggest combining data from your entire class so that you will have a larger sample size.
- Students or groups of students develop and explore their own hypothesis with the class data.
- Field Lichen Demo narrated video (scroll down for the video; at the end of the field sampling protocol) took 11 minutes.
- Once the students sample one tree and get used to the procedures, it should go much faster.
Format for Learning Activity
- Pre-lab Reading - what are lichens, key habitat requirements, morpho-species types, bioindicators of air quality, iNaturalist project EREN Lichen, and learning goals
- Developing Hypotheses
- Equipment List
- Field Sampling Protocols
- Updating Observation Fields (and Adding New Observations) to EREN Lichen project
- Data Processing and Analysis
- References and Appendices
Pre-lab Reading sets up Developing Hypotheses
- Abiotic and biotic factors affect the distribution and abundance of species.
- Land-use modification and other anthropogenic drivers of environmental change affect landscape, local, & micro-site conditions.
- Lichens are ideal organisms to explore these relationships.
- Composite organisms; are mutualistic symbionts; both the fungus (mycobiont) and algae or cyanobacteria (photobiont) benefit.
- Fungus gains carbon compounds (sugars) that algae or cyanobacteria produce (from photosynthesis).
- Algae or cyanobacteria gain protection, nutrients, & moisture from fungus.
- A win-win situation!
Lichens are widespread and can be found in harsh climates, from hot deserts to cold alpine summits. However, within those ecosystems, they are found in specific habitats (natural environments in which they live). Key requirements for lichen habitat are:
- Water - absorb (and lose) water readily
- Air - absorb water, nutrients, and pollutants
- Nutrients - obtain (C, N, P) from water and air
- Light - produce own energy via photosynthesis
- Substrate Type - natural & artificial; can influence interactions with environment (e.g., substrate pH)
Lichens are Important Bioindicators
- Lichens are ubiquitous in urban and rural areas, and are also an important group of bioindicators - an organism whose presence, absence, and/or abundance in an area gives an indication of the degree of health of that ecosystem.
- Some organisms are very sensitive to pollution in the environment, so if pollutants are present, that organism may be absent, or may have different morphology or physiology, or may change its behavior.
- Other organisms are less sensitive to pollution in the environment.
- Documenting which bioindicators are present, absent, and/or abundant in an area can be valuable in assessing ecosystem health and determining whether an ecosystem may be impaired by pollution.
- Some lichen species are very sensitive to air pollution (e.g., nitrogen, sulfur, lead), whereas others are tolerant.
- Lichens can be grouped based on the structure of their thallus - vegetative (non-reproductive) parts.
- Degree of sensitivity of a lichen to air pollution varies roughly with their growth form.
- Three main types: crustose (thin, crust-like, very tightly attached to substrate); foliose (flat and leaf-like; 2-dimensional); and fruticose (upright, like tiny trees or shrubs, or hanging down like a miniature vine).
Lichen Air Quality Index Scoring
What will students be doing in this module?
- Complete a pre-lab reading.
- Develop potential hypotheses to test.
- Download iNaturalist smartphone app and join project: EREN lichen.
- Field sampling - flexible (e.g., street trees, backyards, campus, local natural areas).
- Use smartphones and simple equipment - determine lichen presence, abundance, and growth forms on tree surfaces.
- Measurements of abiotic and biotic variables - tree species, tree dbh, % canopy cover, bark pH (optional).
- Use lichen sampling grids - % lichen cover and score air quality using lichens.
- Optional: Gather bark sample to determine bark pH; requires access to deionized water and pH test strips.
- Summarize and test their hypothesis - analyze class data (or, possibly a larger dataset from the iNaturalist project EREN Lichen).
Developing Hypotheses (pre-field)
- Work individually, in pairs, or small groups
- Response (Dependent) Variable - lichen presence or abundance, air quality index
- Predictor (Independent) Variable - tree diameter, tree species, % canopy cover, aspect, bark pH
- What do you expect the relationship to be?
- Rationale
- Write Out Your Complete Hypothesis
- Share hypotheses and rationale with instructor and rest of the class
Larger Spatial Scale Analyses and Hypotheses to Test
Once the iNaturalist project EREN Lichen gets contributions from multiple sites, there is excellent potential to expand spatial scale of analyses and breadth of research questions to address. Data can be explored from multiple EREN Lichen sites. These data can also be combined with other datasets (e.g., NEON. Living Atlas, NLCD) to broaden these types of research questions and analyses.
Equipment List (required)
- Smartphone and apps - download apps: iNaturalist - and join EREN Lichen project!, Seek, Canopeo; if no smartphone, can use datasheet and upload into iNaturalist on the website
- Compass (handheld, compass app on phone, or orient with map - if possible)
- Measuring tape - to determine 1.37 m (4.5 ft) height above ground level
- DBH tape (cm) or string, thumbtack, and measuring tape
- Clear lichen sampling grid - easy to make with quart freezer baggie, Sharpie or permanent marker, grid template - provided
- Lichen air quality scoring index - provided
- Field datasheet - to write down data before entering into iNaturalist project EREN Lichen
Optional Equipment (for bark pH)
- Knife and sample container for bark
- Deoinized water
- Small container (e.g., beaker)
- pH meter or pH test strips
Field Sampling Protocols
Field Sampling Demonstration - sampling a tree in real time (11 min.)
NOTE: We revised the settings in iNaturalist project EREN Lichen after we filmed this video. Please note that as you enter data into fields for an observation, you will be required to submit something in each field. If you want to skip a data field for the EREN Lichen project, you need to enter something into the field. Just enter not applicable or NA if you want to skip a field.
Each student (pair or group of students) will collect data on five trees. Trees should be a minimum of approximately 30 cm (12 in) diameter. (It needs to have a large enough diameter to be able to take the four % lichen readings, without having any overlap). Be sure to bring a copy of the field data sheet (or notebook) to record measurements as you take them. At the end of sampling each tree, you will enter those data into the iNaturalist EREN Lichen project.
Step 1. Identify the tree species.
- Use field guides, identification keys, or smartphone app “Seek” to identify the tree to species level.
- Enter scientific name (preferred) or complete common name.
- Record tree species on your datasheet.
- If you cannot identify the tree to species level, then upload an observation to iNaturalist to crowdsource to identify the species.
- You can enter "NA", and then update the observation field later.
Step 2. Determine the north-facing aspect of the tree.
- Use a compass or compass app on your smartphone to identify North.
- Then, move to the tree.
- Standing with the compass in your hand, your back to the tree, and facing away from the tree - move around to determine which part of the trunk faces North.
Step 3. Measure percent canopy cover (if you do NOT have the Canopeo smartphone app, then skip this step).
- Stand at the base of the tree, at the north side of the tree.
- Open up the Canopeo app.
- With your back to the tree, hold the phone overhead (making sure it is parallel to the ground), and take the photo.
- Canopeo will give you percent canopy cover. (Be sure that you are getting % canopy cover and NOT % open!)
- Record the value on your datasheet.
Step 4. Measure tree diameter, in centimeters.
- Tree diameter (diameter at breast height; dbh) is measured at 1.37 m (4.5 ft) above ground level.
- Measure with a dbh (cm) tape, which will measure the diameter directly.
- If you do not have a dbh tape, you can use string, use a tack to fix it in place, then use the string to measure the circumference of the tree. Then you can calculate the tree diameter.
- Record the value on your datasheet.
Step 5. Record percent lichen at the north, east, south, and west faces of the tree.
- Take the clear lichen sampling grid, and place the top of the grid so that it aligns with where you took the dbh reading (1.37 m; 4.5 ft above the ground).
- The sampling grid has 10 rows of 10 circles. Count the number of circles that have lichens.
- Record the value on your datasheet.
Step 6. Take photos and upload to the iNaturalist EREN Lichen project.
IMPORTANT: Be sure that you take and upload photos in the specific order outlined below. That way it will be standardized and we will be able to match up the grid photos with the corresponding tree aspect.
Open up the iNaturalist app on your smartphone.
- Photo 1: Look around the tree and find the dominant lichen. Find a good example of the dominant lichen, take a photo, and upload it as your first image.
- Photo 2: Take an image of where you took the first lichen sampling grid reading, on the North face of the tree.
- Photo 3: Take an image of where you took the east-facing lichen grid sample.
- Photo 4: Take an image of where you took the south-facing lichen grid sample.
- Photo 5: Take an image of where you took the west-facing lichen grid sample.
- Photo 6: Take an image of the canopy, from the north end of the tree. (If you took a canopy cover image with CANOPEO, you will take the image in the same manner.)
- Photo 7 (or more): Take a photo (or photos) of the tree. Take whatever photo(s) that you think would be helpful in identifying the tree to species level.
Step 7. Add this observation record to the iNaturalist EREN Lichen project.
In iNaturalist, click on Add to Project, and select EREN Lichen.
REMEMBER: We revised the settings in iNaturalist project EREN Lichen after we filmed this video. Please note that as you enter data into fields for an observation, you will be required to submit something in each field. If you want to skip a data field for the EREN Lichen project, you need to enter something into the field. Just enter not applicable or NA if you want to skip a field.
Once you select the EREN Lichen project, there will be a number of fields to enter your data into:
- EREN Lichen tree species
- EREN Lichen percent canopy cover
- EREN LichenPercent NORTH
- EREN LichenPercent EAST
- EREN LichenPercent SOUTH
- EREN LichenPercent WEST
EREN Lichen air quality index score
- No lichens present = 1
- Crustose lichens only = 3
- Foliose lichens present, but no fruticose = 6
- Fruticose lichens present = 9
- Lobaria pulmonaria or Teloschistes exilis present; fruticose lichens, very sensitive to pollution = 10
Step 8. Collect bark sample for pH measurement (optional).
- If you will be measuring bark pH, select bark without lichen cover and with a smooth surface (>1 cm diameter needed for harvest).
- Use a flexible blade or chisel to remove 2 bark samples between 2-3 cm diameter from each tree.
- Air dry bark in labeled brown paper bags, leave overnight. Process the samples the next day (see instructions ).
NOTE: If you are planning to compare tree species with differing bark pH levels, consider sampling species in low, medium, and high categories and comparing them. This may depend on whether these species are available in your area.
Step 9. SAVE or SHARE the iNaturalist record.
- Don't forget to save the observation, then upload to iNaturalist when you have internet connection.
- Note: Exact wording may vary, depending on the type of phone or specific version of iNaturalist.
Processing the bark samples for pH (optional).
After the bark samples have air dried overnight (in labeled brown paper bags):
- The next day, soak bark samples in distilled water (neutral pH; can be purchased at a grocery store).
- Leave soaking overnight.
- The following day, use hand-held pH meter to measure pH of the liquid.
- Or, if using pH indicator strips, place strips in liquid, and compare to the color ramps provided with the indicator strips.
- Update the corresponding observation field in iNaturalist.
Updating and Accessing Your Data in iNaturalist Project EREN Lichen
Downloading iNaturalist EREN Lichen Data
Updating Fields for Uploaded Observations
Adding New Observation Records (not from Smartphone app)
Module 3: Data Analysis for NEON and Local Field Data
This module, which has three activities, provides an overview for instructors interested in teaching students how to collect and analyze data using protocols identified in the Lichens in Diverse Landscapes Project. This document focuses on helping instructors determine best practices for analyzing data and has multiple activities that could be employed in different levels of courses. It is meant to help instructors know answers/procedures ahead of time. Additionally, all activities are completed in Google Sheets, R, and other free online programs for ease of working with students. Each activity can also be tailored to specific courses and used or not used depending on the focus of the class.
Activity 1: Introduction to Google Sheets
The first activity in this module focuses on introducing students to the free program Google Sheets, which is part of the Google Drive Suite. https://www.google.com/sheets/about/
Activity 2: Making and Understanding Graphs and Introducing Statistical Analyses
The second activity helps students to figure out how to make graphs and use common statistical tools to analyze data. Topics covered in this portion of the module include making scatterplots, bar graphs, column graphs, and radar graphs. For the statistical analyses, we cover simple linear regression, t-tests, and ANOVA. Software programs used in this module are all free and include Google Sheets, R, R Studio, GraphPad, and VassarStats.
Activity 3: Analyzing NEON Data, Geospatial Data, and Local Field Data
The third activity helps students to analyze NEON and geospatial data and to think through hypothesis formation and how to analyze local field data collections. This activity uses Google Sheets and R to explore how to analyze large-scale datasets and to compare differences in lichen abundance and environmental conditions across field sites.
Acknowledgements
Many thanks to those who assisted in the development of this project including Dr. Mark Lesser, Eileen Allen, and Mark Baran (SUNY Plattsburgh), Erin Moseman (Onsemi- Industrial Lidar) for technical support and editing advice, and Dr. Janet Puhalla and Taylor Peet (class 2020) (SUNY Plattsburgh), and Dr. Jaclyn Schnurr (Wells College) for material review. Many thanks for the superb video production assistance from Christina Macfarlane (Schenectady High School, Siena College - class of 2016) to help demonstrate the EREN Lichen field sampling module.
This project was supported by the National Science Foundation under Grant No. DBI-2037827. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.