2022-2023 BLOG POST

2022-2023 BLOG POST

Kate Davis, MS

Ph.D. Candidate, Zoology Vander Zanden Lab University of Florida

You are What you Drink: table isotopes and the fight against the illegal wildlife trade

The chemical elements that make up water, hydrogen (H) and oxygen (O), come in different varieties due to their molecular weight. These varieties, for example deuterium, the heavier variety of hydrogen, are known as isotopes. Isotopes are considered stable if they do not decay into other elements. The ratio of light to heavy stable isotopes in water follows predictable patterns in global precipitation. Rain that has just come in off the coast will have more heavy isotopes than a storm that has traveled inland. These patterns also exist across latitudes.

As organisms uptake the water in their ecosystems through drinking, respiration, and diet, isotopes are incorporated into their developing tissues, leaving a signature of where they’ve been. This principle has been used in human forensic analysis of remains of unknown origin by taking hair samples and looking at the isotope values along the length of the shaft. This can also be applied to items from the illegal wildlife trade, such as rhino horn and pangolin scales, when confiscated in a seizure, allowing conservationists and wildlife officers to get an idea of where these animals are being poached as well as provide insight into the networks responsible for transporting these items. By identifying at-risk areas, authorities can provide more resources for protecting those areas.

Additionally, stable isotope analysis can reveal if an animal has been taken from the wild or is being raised in captivity, away from its native habitat. This can illuminate situations of illegal captivity, as well as situations where a permit may indicate an animal was born legally in captivity, but was actually poached from the wild. The latter was shown for yellow-crested cockatoos at market in Hong-Kong, a species with fewer than 2,500 remaining in the wild in a study by Andersson et al in 2021 and highlights the importance of this tool for combating the illegal wildlife trade.

The advancements in stable isotope ecology applications are an exciting prospect in the fight against illegal wildlife activity. These applications also include understanding movement and migration patterns, analyzing ecological niche over time and between species, reconstructing paleoclimate and life histories of long-extinct animals. The field of stable isotope ecology continues to expand and become more refined as our understanding of isotopic patterns and biochemical pathways grows. This is a field that brings us back to the very building blocks of life to answer complex ecological questions and save species.


Andersson, A.A., Gibson, L., Baker, D.M., Cybulski, J.D., Wang, S., Leung, B., Chu, L.M. and Dingle, C. (2021), Stable isotope analysis as a tool to detect illegal trade in critically endangered cockatoos. Anim. Conserv., 24: 1021-1031. https://doi.org/10.1111/acv.12705

Abigail Uehling

Ph.D. Candidate Department of Biology

A Unique Reference Library

I still remember the amazement I felt when I first visited and then began volunteering at the Drexel Academy of Natural Sciences in Philadelphia, close to my hometown. I took a SEPTA train downtown on a gray winter day and after a few city blocks and an elevator ride I soon found myself in a library I didn’t even know existed. Before this I had been taught how to navigate many types of reference systems – public libraries, academic libraries, online databases and archives, but it had not occurred to me that biodiversity knowledge had its very own system. During my time volunteering here I was taught how specimens were pinned and prepared, integrated into the collection and sorted according to their changing classifications. I marveled at the sheer amount of biodiversity that was housed in a room of rolling shelves, and watched as specimens were used as a reference for a wide range of projects. I was given the task of trying to determine if some specimens needed updated names, and quickly learned that this library was far from static. Although I was just working with a single family of Lepidoptera at the time, I saw the care and meticulousness that went into ensuring these specimens were properly preserved and cataloged as accurately as possible. I also learned how important these collections are for preserving knowledge of biodiversity in our changing world.

Now as a third year graduate student in the Invertebrate Zoology Collection at the Florida Museum, I’ve begun using these special libraries for my own research. As I have begun piecing together my dissertation dataset, I have a great appreciation for the organization and quality of this immense library. During my year as a UFBI fellow, I will be working particularly closely with the asteroid collection (Asteroidea:Echinodermata). Commonly known as sea stars, this diverse group of echinoderms is found across all ocean depths and latitudes. My research focuses on how the distribution of sea stars is influenced by ecology and connectivity across large seascapes, therefore collections are an excellent source of knowledge for determining where different genera are found. Throughout the last few years I’ve collected occurrence coordinates, physical traits and genetic connectivity across an array of asteroid genera. I’ve learned how valuable it is to be able to walk into the asteroid section of the collection and physically examine a specimen for morphological features when I find an unexpected genetic result or need to compare different species. I’ve also learned that our knowledge of collection practices is also constantly evolving. As I’ve worked with asteroids collected from the early 1900s through the current day, I’ve seen firsthand that collection practices are always changing or being improved. Some fixation methods work great for preserving color but are poor for genetic use, while others are great for genetic use but decrease color quality. GPS quality has also certainly improved throughout the years, and some specimens are attached to more detailed locality information than others. Increased digitization of specimens has also allowed scientists to study many taxa fairly well without traveling to the collections.

I’ve also seen the many pipelines and people that are needed to keep the invertebrate collection running, and understand just how integral each step is. When specimens return from the field, they must be carefully taken care to ensure they are properly preserved for scientific use and that notes on habitat and locality are accurately recorded. After specimens arrive at the museum their care is far from over. On a given day in the collections, there are curators, collections managers, students and volunteers taking care of a variety of tasks – from rehousing specimens and getting them museum ready, to sending off specimen loans and making sure those that return get put away in the proper place. There is always more to do, and usually limited space to get it done.

In the upcoming weeks, the Invertebrate Zoology collection will make an exciting move to a brand-new spacious building. Although the old collection space has served many visitors and students in its day, there are great possibilities that come with moving the specimens to a space where there will be more room and resources for all involved in this extensive library system. As the collections make their way to new shelves and higher ceilings, they are being prepped for scientists to make many more discoveries of new species and visitors to learn about the amazing diversity of marine ecosystems.

Maria Beatriz de Souza Cortez

Ph.D. Candidate Department of Biology and Florida Museum of Natural History

Shifting Our Mindsets Towards Biocultural Diversity Conservation

In 2021, UFBI fellow Mahi Puri wrote a compelling and important blogpost about biodiversity loss and the ambitious targets set by the Convention on Biological Diversity (CBD) to protect it. In her article, Puri underscores how “none of the 20 targets that were set for biodiversity have been met”. Puri goes on to question the validity of setting even more ambitious targets towards biodiversity conservation for the decade of 2021-2030, especially when “bringing more public lands under protection” seems to be one of the main goals. It is very disappointing that in 10 years none of the CBD targets have been met and even more alarming that the creation of new targets seems to follow the same ambitious trajectory doomed to fail. As the blogpost suggests, creating additional protected areas is a “challenging proposition” and not as straightforward as it is made to be.

But what is so challenging about creating protected areas? Well, there are many challenges involved in this process, that range from conception to logistic. However, one of the most pressing challenges concerns the involvement of all levels of stakeholders, including local communities that rely on the land being conserved for their sustenance. Local communities are in the front lines of any type of conflict generated by and with the creation of protected areas. They are the ones that suffer with displacement, with negative direct contact with fauna, environmental disasters such as uncontrolled wildfires, etc. Yet, there are still conservation strategies and policies that insist on suggesting top-down approaches, in which local communities’ perspectives are not heard or are altogether disregarded. However, as Puri points out in her post, there are also alternative conservation strategies that propose “integrated approaches that contribute to the socio-economic development of people without displacing them”. Often, in the literature, such approaches are included in the realm of community-based conservation strategies and as suggested in the blogpost, they have shown positive results.

At this point, there is a chance that readers find themselves wondering why I started this blogpost talking about biodiversity when the title clearly states biocultural diversity. No, your eyes do not deceive you, you read it properly. This is a post about biocultural diversity conservation. Yet, it is impossible to talk about biocultural diversity conservation without considering how biodiversity conservation takes place in this world. There is no biocultural diversity conservation without biodiversity AND cultural conservation. The problem is that society tends to focus much of its efforts primarily on biodiversity conservation, by prioritizing, for instance, the creation of protected areas in which local communities are prohibited from using the land.

When thinking of conservation, generally our first thoughts (as demonstrated above) shift to the creation of protected areas as an easy solution. The idea of having areas around the globe where pristine nature thrives untouched by humans is very compelling. Yet, not realistic. First, the concept of pristine nature is debatable; how can we guarantee a certain stretch of forest, grassland or swamp has never been inhabited? According to recent research, humans have been shaping and reshaping the globe, including areas commonly believed to be untouched for over 12,000 years! This belief originates from the impacts of colonization. With the genocide of native indigenous populations, many of their cultivated lands were abandoned and further occupied by wilderness. As a consequence, after the first waves of colonization, settlers in the Americas were led to believe wilderness had always been pristine and its rich biodiversity was a result of the absence of humanity. For those of you more interested in the “myth of pristine wilderness,” I recommend the blogpost written by Claudia Geib for Sapiens; it is definitely an interesting read.

The second and perhaps more concerning issue related to the concept of thriving pristine nature is that currently many of the areas in line for being protected are the source of sustenance for local communities that live in or around them. It doesn’t seem fair, not to mention reasonable, to exclude these communities from the decision-making process and displace them from their land. Most of these communities hold extensive knowledge of their homelands (no surprise) and already employ solutions to properly care for or restore biodiversity. In the Gishwati forest, in Rwanda, a community-based conservation approach focused on the protection of the chimpanzee population has contributed to both lowering the levels of illegal cattle-grazing as well as increasing the number of chimpanzees. Across the Atlantic, communities in northwest Andean Ecuador have been actively planting trees to restore cloud forests. This effort has contributed to a more diverse forest when compared to secondary forests that are naturally regenerated. Moreover, as Puri mentioned in her blogpost, there are other types of human interference that produce much more harmful impacts, such as extensive monocultures and large-scale mining.

In Brazil, for example, the state of Minas Gerais has had to deal with the drastic consequences of two major disasters associated with large-scale mining endeavors. In 2015, a dam collapsed in the outskirts of Mariana, releasing 43.7 million cubic meters of toxic mud in the environment and killing 19 people. Fast forward to 2019 and the horror story repeats itself, now in the town of Brumadinho, but with a much more deadly outcome; 270 people were killed, and 12 million cubic meters of toxic mud were released into the environment. According to a report produced by Julia de Azevedo Oliveira while an undergraduate student at Universidade Federal Rural do Rio de Janeiro, the damages caused by the dams’ collapses were “significant, diversified and presented high magnitude”. Oliveira’s report shows a table detailing the impacts generated by the dams’ collapse on three different spheres, the physical, biological, and socioeconomic. The list is so extensive the table occupies nearly 5 pages. Among the impacts, we note deterioration of water quality, topographic alteration, worsening of species conservation (including WITHIN protected areas), probable extinction of endemic species, loss of agricultural lands, destabilization of local socioeconomic spheres, etc. And worst of all, loss of human lives and of biodiversity.

These examples demonstrate how conservation strategies focused solely on biodiversity protection, such as the creation of protected areas, are not only exclusionary but also minimally effective. They are exclusionary because they often ignore the human and cultural components necessary for biocultural diversity conservation. And they are minimally effective because they show restricted efficacy in mitigating the worst of human impact, such as the mining disasters detailed above. Moreover, community-based conservation strategies that represent a step in the direction of biocultural diversity conservation can show very positive results, as exemplified above. That is why I believe shifting our mentality towards prioritizing biocultural diversity conservation is necessary. I am not the first, nor will I be the last to advocate for this. In fact, this conversation is not even up for debate for some indigenous peoples who have always understood the connectivity between the human and more than human elements of this world. I hope we can continue to honor this knowledge as much as we value what is produced in academia so that we may have the chance to truly contemplate a future rich in diversity in all of its forms.


Chancellor, R. et al. 2020. Community‐based conservation and chimpanzee research in Gishwati forest, Rwanda. American Journal of Primatology. 2021;83:e23195.

Ellis, E. et al., 2021. People have shaped most of terrestrial nature for at least 12,000 years. PNAS Vol. 118 No. 17 e2023483118.

Fletcher, M.S., Hamilton, R., Dressler, W., Palmer, L., 2021. Indigenous knowledge and the shackles of wilderness. PNAS Vol. 118 No. 40 e2022218118.

Gavin, M.C. et al. 2015. Defining biocultural approaches to conservation. Trends in Ecology & Evolution 30: 140-145.

Geib, C. 2022. How “Wilderness” Was Invented Without Indigenous Peoples. (https://www.sapiens.org/culture/pristine-wilderness-conservation/)



Oliveira, J.A. 2019. Impactos Socioambientais Provocados Pelo Rompimento de Barragens de Contenção de Rejeitos de Mineração no Estado de Minas Gerais. Três Rios, Rio de Janeiro.

Puri, M. 2021. Is it enough to be ambitious to reverse biodiversity loss? (https://biodiversity.research.ufl.edu/is-it-enough-to-be-ambitious-to-reverse-biodiversity-loss/)

Wilson, S.J., Rhemtulla, J.M., 2016. Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest. Ecological Applications, 26: 203-218.

Brittany Cummings

Ph.D. Candidate, Invertebrate Zoology Department of Biology, Florida Museum of Natural History

It’s the Little Things…

Sometimes big things come in little animals. Amphipods are tiny crustaceans which comprise an abundant food source for fish. More akin to a kangaroo than a crustacean, amphipods do not have a thick carapace and use a brood pouch to protect offspring under their body (Figure 1). Species resemble shrimp with strange bodies and lifestyles. For example, neon sea fleas (Podocerus cristatus) purportedly mimic brightly colored sea slugs that are distasteful to fish; certain mast-building amphipods (Dulichia rhabdoplastis) assemble fecal rod nests off threatening sea urchin spines; skeleton shrimp (Caprellidae) adopt hyper-elongated bodies to blend into their branching habitat; and transparent floaters (Hyperiidae) ride out their entire lives on jelly hosts (Figure 2). However, these fanciful forms are difficult to find since amphipods are masters at avoiding their visual predators. As a biologist who studies amphipods, I must use both manual and molecular methods to locate and learn more about these elusive animals.

Figure 1. The general shrimp-like body form of an amphipod. Unlike other crustaceans, amphipods do not have a thick carapace and have a brood pouch to hold their offspring.

Figure 2. Examples of the extreme body diversity seen among amphipod species. Photos by Florida Museum of Natural History and Hakai Institute.

Why should we care?

Amphipod crustaceans are vital to aquatic ecosystems. There are over 10,000 amphipod species around the world which are found in all kinds of water environments: saltwater, freshwater, groundwater, and even moist land environments (Figure 3). Amphipods are decomposers that recycle nutrients and common prey items for fish consumers, including endangered Chinook salmon 1,2. As strong ecosystem interactors, amphipods are also powerful indicators of aquatic environment health 3–5. Patterns of amphipod species and distribution provide key insight into changes in marine environments.

Despite their importance to aquatic ecosystems, our knowledge of amphipod diversity and ecology remains limited. Many species live in cold and dark areas and escape detection by hiding under rocks or algae, building protective tubes, or blending into their environment. Most research has focused on the physical features of amphipod species, but body parts are fragile and vary by sex or life stage 6. Moreover, the accuracy of visual identification has been called into question by numerous discoveries of cryptic species over the past two decades 7–10. How do we improve our understanding of an animal that is hard to identify and even harder to locate?

Figure 3. The many different habitats and ecological roles of amphipods. Image from Harte Research Institute.

How do we find a pod?

Like many active children, I often played in the “ball pit” of my favorite fast-food restaurant play area. This pit contained thousands of colorful plastic balls through which I would pretend to swim. The ocean is like a massive “ball pit” containing all kinds of tiny swimming and sedentary organisms. Instead of different colors, the “balls” are different molecular compounds. Some are inorganic molecules, such as water, and others are organic molecules, such as DNA. This DNA originates from the organisms that regularly shed cellular material into their environment. If we want to identify amphipods in this ocean “ball pit”, we have two choices: (1) collect the amphipods, or (2) collect the amphipod DNA.

Most often, I collect amphipods by hand. Manual methods are the old-school way to find and identify animals. I take clumps of algae or habitat on which the amphipod lives and then shake them off in a lab. I also use homemade “traps” which consist of common household items, such as stiff horsehair brushes and scrubby dish sponges, secured to anchors made of metal bars. These traps are placed in different ocean habitats using SCUBA and collected after amphipods take residence in its various nooks and crannies.

As a modern alternative to hand collection, I am also using environmental DNA to locate and identify amphipods. Years of genetic research on amphipods and other animals has generated a large database of DNA sequences that serve as “barcodes” 11. To identify an organism, you sample its DNA and match it against these “barcode” sequences. The principle of environmental DNA (eDNA) is to sample DNA from the environment rather than from the animal itself. Since there are countless cells in the environment, molecular tools called primers are used to pick out DNA sequences that correspond to “barcodes” of your target animal group or species. These primers are bits of complementary DNA that bind to DNA from the water sample. Once the primer binds to the DNA, it acts as a guide for enzymes in Polymerase Chain Reaction (PCR) to produce enough copies of that bound DNA for sequencing. Thus, instead of manually collecting habitat to find amphipods, I can collect water around the habitat, sequence the amphipod DNA in that sample, and match the DNA sequences to known amphipod “barcodes” for identification (Figure 4). Thanks to the guidance of Hakai Institute and supplemental funding from the NSF INTERN program this summer, I am currently testing these molecular methods for amphipod detection in coastal habitat.

Figure 4. Environmental DNA (eDNA) sampling can be used as an alternative to manual sampling of animals to identify amphipod species in complex aquatic habitats. Special designed primers attach to target animal DNA from samples of water which contain shed animal cells. The bound DNA is sequenced and matched against known “barcode” DNA sequences to identify specific animal groups or species.


If I asked you to pick out all the red balls in a kid’s ball pit, you might think it was a hard task. But picking tiny animals or microscopic balls from an ocean? This task becomes impossibly more challenging! Both manual and molecular sampling can identify amphipod species in complex three-dimensional habitats, but both have their inherent drawbacks.

            Hand collection is the simplest method for finding amphipod species but is labor intensive and invasive. If the ecology and distribution of a species is known, one can reasonably find habitat that will yield specimens. However, amphipod ecology is usually poorly known, and individuals tend to be scattered across their aquatic landscape. In this case, manual collection requires more extensive sampling of habitats to locate and identify species. This is especially problematic since many amphipods are subtidal, and sampling requires exhausting SCUBA work with long hours of substrate picking. These methods also tend to be very disruptive to the ecosystem because I must remove the animals from their home. Even with all this work, there is no guarantee that all amphipods in an area will be identified.

Environmental DNA sampling is far less invasive and provides a more complete picture of an animal community, but the results are expensive and difficult to validate. Since there is minimal environmental impact from sampling water above habitat, molecular methods allow me to acquire as many samples as needed to characterize the amphipod species in an area. This method is also far less effort after sampling since water samples can be frozen until DNA processing. However, DNA sequencing is expensive and designing primers is a frustrating trial-and-error ordeal which must be completed before sampling can begin. Moreover, the results only provide genetic information about the amphipod community which is difficult to verify without direct observation (i.e., ground truthing) of the species that are present in the sampled area.

Finding pods in the future

It is vitally important to conservation that we combine traditional and modern methods to improve our understanding of small animals that support underwater ecosystems. Amphipod crustaceans are a particularly abundant food source whose ecology has largely been ignored because they are difficult to observe and collect. As a scientist who studies amphipods, I am often limited to manual collection which is labor intensive and inefficient at finding species. However, I am developing amphipod-specific molecular methods to improve search efficiency and locate species that evade manual detection. Sampling eDNA around a habitat will allow me to extensively identify its amphipod community with minimal effort and damage; then sampling habitat in careful moderation will help verify DNA results. In this way, the strengths of either method will complement the shortcomings of its counterpart. It’s no easy task finding a needle in a haystack, but I will continue developing tools to uncover these hidden crustaceans and learn more about their important ecosystem roles.


(1)     Orth, R. J.; van Montfrans, J. Epiphyte-Seagrass Relationships with an Emphasis on the Role of Micrograzing: A Review. Aquat Bot 1984, 18 (1–2), 43–69. https://doi.org/10.1016/0304-3770(84)90080-9.

(2)     Duffy, J. E.; Hay, M. E. Strong Impacts of Grazing Amphipods on the Organization of a Benthic Community. Ecol Monogr 2000, 70 (2), 237–263. https://doi.org/10.1890/0012-9615(2000)070[0237:SIOGAO]2.0.CO;2.

(3)     Thomas, J. D. Biological Monitoring and Tropical Biodiversity in Marine Environments: A Critique with Recommendations, and Comments on the Use of Amphipods as Bioindicators. J Nat Hist 1993, 27 (4), 795–806. https://doi.org/10.1080/00222939300770481.

(4)     Gesteira, J. L. G.; Dauvin, J. C. Amphipods Are Good Bioindicators of the Impact of Oil Spills on Soft-Bottom Macrobenthic Communities. Mar Pollut Bull 2000, 40 (11), 1017–1027. https://doi.org/10.1016/S0025-326X(00)00046-1.

(5)     Conradi, M.; López-González, P. J.; García-Gomez, C. The Amphipod Community as a Bioindicator in Algeciras Bay (Southern Iberian Peninsula) Based on a Spatio-Temporal Distribution. Marine Ecology 1997, 18 (2), 97–111. https://doi.org/10.1111/j.1439-0485.1997.tb00430.x.

(6)     Chapman, J. W. Amphipoda: Gammaridea. In The Light and Smith Manual: Intertidal Invertebrates from Central California to Oregon; Carlton, J. T., Ed.; University of California Press: Berkeley, CA, 2007; pp 545–611.

(7)     Seidel, R. A.; Lang, B. K.; Berg, D. J. Phylogeographic Analysis Reveals Multiple Cryptic Species of Amphipods (Crustacea: Amphipoda) in Chihuahuan Desert Springs. Biol Conserv 2009, 142 (10), 2303–2313. https://doi.org/10.1016/j.biocon.2009.05.003.

(8)     Havermans, C.; Nagy, Z. T.; Sonet, G.; de Broyer, C.; Martin, P. DNA Barcoding Reveals New Insights into the Diversity of Antarctic Species of Orchomene Sensu Lato (Crustacea: Amphipoda: Lysianassoidea). Deep Sea Res 2 Top Stud Oceanogr 2011, 58 (1–2), 230–241. https://doi.org/10.1016/j.dsr2.2010.09.028.

(9)     Beermann, J.; Westbury, M. v.; Hofreiter, M.; Hilgers, L.; Deister, F.; Neumann, H.; Raupach, M. J. Cryptic Species in a Well-Known Habitat: Applying Taxonomics to the Amphipod Genus Epimeria (Crustacea, Peracarida). Sci Rep 2018, 8 (1), 1–26. https://doi.org/10.1038/s41598-018-25225-x.

(10)   Westram, A. M.; Jokela, J.; Keller, I. Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species. PLoS One 2013, 8 (8), e69576. https://doi.org/10.1371/journal.pone.0069576.

(11)   National Center for Biotechnology Information (NCBI) Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/.

Adrian Barry Sosa

Ph.D. Candidate Department of Microbiology and Cell Science

Microbes: The Unseen Environmental Workforce

                Microbes…A collection of living organisms too tiny to be seen by the naked eye. But within those, we find the largest diversity of organisms, from Bacteria and Archaea to Fungi and algae. The collection of different genetics and metabolisms among them largely surpasses that of all organisms we can see. Sometimes, the mention of microbes induces the fear of diseases, and although some of them are our most terrible foes, they also include our most useful allies. In fact, life as we know it would have not been possible in this planet without the oxygen released by photosynthetic bacteria around 2 billion years ago. Besides, they provide direct benefits to us. For instance, an increasing body of research is strengthening the fact that gut microbiota is critical for our health. Good soil microbiomes are key to crop fertility. Microbes can also help us to produce foods as popular as cheese, bread or beer. Microorganisms are everywhere. A few decades ago, it was hard to believe that microbes could live in hot springs of nearly boiling water, in mines and caves several kilometers below the Earth’s surface and in lakes below the thick ice sheets of Antarctica. But so much of the scientific landscape has changed, that nowadays it would be surprising to find a natural environment that is completely sterile. Microbes are capable of surviving every possible challenge they face from high or low pressures, extreme temperatures, including above 100 C and below freezing, radiation, desiccation, extremely low nutrients… They were the first living beings on Earth and certainly they will be the last ones too.

                Among the myriad of places where microorganisms live, we find them in the Upper Floridan Aquifer, or UFA, which is the one area that I focus my current research on. The UFA is a large underwater reservoir, where water is stored within the pores of rocks, acting like a sponge. The UFA spans underneath the whole state of Florida, reaching some parts of southern Georgia, Alabama and South Carolina. The UFA is a critical water supply for all those areas, and it is responsible to feed many surface environments as well. The majority of the hundreds of springs scattered across north-central Florida are fed by this aquifer as well. The pristine waters of the aquifer, however, present a challenge to all microorganisms living there, owing to the fact that water here is isolated from the surface. In some places, it has been estimated that water remains underground for up to 40 years. This isolation prevents high loads of nutrients, organic matter or sunlight to fuel primary productivity from reaching deeper parts of the aquifer. In order to survive this scarcity of food, microorganisms living here need to develop strategies that help them to cope with such challenges. Although much research is still needed in this area, we are starting to have evidence that food webs in the UFA are able to provide organic matter of enough quality that it is enough to overcome their low quantities. Another strategy is reduced size. The smaller, the less amount of food you need to consume to stay alive, and that certainly apply to the microbes here too. In fact, some of the groups of microbes found here include the smallest group of living creatures known thus far.

                Natural microbial populations in the UFA are critical to maintain the health of the aquifer, and to make sure it can still provide water for future generations. Ensuring these populations maintain a good balance is critical for keeping a healthy environment. However, several human actions can severely impact this natural equilibrium, thus having negative consequences for the whole environment. Excessive and careless use of fertilizers releases nitrates that can make their way into the aquifer. These nitrates can fuel the activity of microbes that generate nitrous oxide, a powerful greenhouse gas. When waters contaminated with nitrates are discharged through the springs, not only this gas can be released into the atmosphere, but also excess nitrates can cause harmful algal blooms at the springs run. Wastewater seepage can drastically change the community´s composition to one where dangerous microbes, like enteric bacteria, start to be present and replace the good microorganisms. Finally, in coastal areas, water overdraft can cause saltwater intrusion that renders parts of the aquifer unsuitable for any human use.

In all, the natural microbial communities in the Floridan aquifer are doing a good job of keeping it healthy. Even if they seem tiny, the critical role of microbes in the environment cannot be neglected, as they help protecting the aquifer too. However, it is only now that we are starting to scratch the surface of this complex subterranean ecosystem, and more exciting discoveries are still awaiting us in the future.

Adrian Barry Sosa

Mitch Walters

Ph.D. Candidate Department of Biology and Florida Museum of Natural History

To app or not to app, that is the question

About two months ago I was at my family’s cabin along the tranquil Greenbrier River in West Virginia. My dad, also a fellow birdwatcher, was one of 3 million people in the spring/summer of 2022 to download the Cornell Lab of Ornithology’s breakthrough mobile app Merlin. Using machine learning the app is able to identify several hundred North American bird species using one’s own recording. One morning we decided to put it to the test with a bird calling in a sycamore right by the river. After clicking record, my dad pointed the iPhone’s mic toward the bird and within a couple of seconds, the app accurately identified the singing bird: Indigo Bunting. Like kids with a new toy on Christmas, we were amazed and successfully repeated the process with several other feathered friends. After our brief morning birding excursion, we tallied up 17 species and uploaded the whole list, including recordings, to another mobile app, eBird, so that any fellow eBird user could know exactly what was in our area at this time of year. It was only 7:45am, fog still clung to the Black Maples lining the shore, and I hadn’t even had my vanilla chai tea yet.


         Photo of how the Merlin app operates in real time                                     © Mitch Walters

This is just a snapshot of what today’s mobile-filled world is like for the average bird and nature enthusiast. It’s a far cry from my childhood birdwatching trips with dad in southern California, full of dusty field guides, some random book about birdwatching in our general region of interest, and printed out MapQuest directions (do you kids remember MapQuest??). It is nothing short of remarkable how far we’ve come, but is it… better?

In a lot of ways these applications are “better,” especially when it comes to scientific research. The mobile app eBird, launched in 2002, is used in almost every conceivable field of ornithology now, including spatial ecology1,2, breeding biology3,4, migration behavior5,6, population projection modeling7,8, and conservation/management9,10. Rather than only allowing researchers to collect publishable bird occurrence data, anyone with the eBird app and a passion for birds can contribute to science, one checklist upload at a time. This use of citizen science data (or “people power,” as coined in the latest issue of the Cornell Lab of Ornithology’s newsletter) is especially powerful when it comes to more inconspicuous taxa like insects. After talking to several grad students and faculty here about this particular blog post, several have claimed that the popular automated species identifier app iNaturalist has been nothing short of amazing for these smaller taxa, augmenting our knowledge of their world beyond anything we could’ve imagined.

But I believe there is a downside to the upside. As someone who is not a plant or insect person, I find myself using iNaturalist a lot these days. Yet despite experiencing the thrill of rapid field identification, I don’t find myself remembering much of anything. In a nutshell, I’m not learning my trees or my bugs.

Using iNaturalist or Merlin is kind of like using Google: we get the answer we want instantly, but an hour later we forget what we were even looking for, and we find ourselves searching for the answer again the next day! This observation troubles me, especially when it comes to teaching students. A 2017 study comparing the effectiveness of mobile identification apps versus traditional field guides found that students using traditional guides were significantly more likely to identify new species correctly than students using mobile apps11. Whether this was due to poor app design, students getting distracted with their phones, or other factors, it shows that mobile apps may not be the most effective tools for teaching field identification. It shows that there may still be room in our society for those dusty old field guides after all. Given the decline in field natural history teaching and taxonomy usage in undergraduate biology degree programs observed in several studies11,12,13, I think it’s therefore of utmost importance to continue teaching field identification the most effective and engaging way possible going forward.

That being said, I don’t think we need to abandon mobile apps entirely when it comes to teaching. In the same study cited previously, students were still optimistic about using mobile apps for learning, suggesting that these apps can still provide accessibility to relevant information outside class hours. Given the importance of citizen science data in today’s academic world, students should be encouraged to upload checklists to mobile apps like eBird so that they too can contribute to scientific research. In addition, there may also be more creative ways to use these apps that can still be beneficial to teaching, for example as shown through the iNaturalist teaching guide (https://www.inaturalist.org/pages/teacher%27s+guide). In the end, although I implore the use of traditional field identification methods when first learning one’s taxa of interest, I also agree that mobile apps can contribute greatly to science as a whole. In regards to the question asked in the title of this post: I think my answer is “to app,” but let’s just not get too carried away.


  1. Freeman BG, Strimas-Mackey M, Miller ET. 2022 Interspecific competition limits bird species’ ranges in tropical mountains. Science, 377(6604), 416-420 (DOI: 10.1126/science.abl72).
  2. Adde A, Casabona i Amat C, Mazerolle MJ, Darveau M, Cumming SG, O’Hara RB. 2021 Integrated modeling of waterfowl distribution in western Canada using aerial survey and citizen science (eBird) data. Ecosphere, 12(10) (https://doi.org/10.1002/ecs2.3790).
  3. Clark CJ. 2017 eBird records show substantial growth of the Allen’s Hummingbird (Selasphorus sasin sedentarius) population in urban Southern California. The Condor: Ornithological Applications, 119(1), 122-130 (https://doi.org/10.1650/CONDOR-16-153.1).
  4. Turella IZ, da Silva TL, Rumpel L, Marini MÂ. 2022 Breeding biology of swallow-tailed hummingbird (Eupetomena macroura) based on citizen science data. Ornithology Research, 1-9 (https://doi.org/10.1007/s43388-022-00098-x).
  5. Hedley RW. 2019 Long‐distance movements and evidence of post‐breeding elevational movements by Cassin’s Vireos. Journal of Field Ornithology, 90(4), 335-347 (https://doi.org/10.1111/jofo.12309).
  6. Haas EK, La Sorte FA, McCaslin HM, Belotti MC, Horton KG. 2022 The correlation between eBird community science and weather surveillance radar‐based estimates of migration phenology. Global Ecology and Biogeography (1-12) (https://doi.org/10.1111/geb.13567).
  7. Walker J, Taylor P. 2017 Using eBird data to model population change of migratory bird species. Avian Conservation and Ecology, 12(1) (https://doi.org/10.5751/ACE-00960-120104).
  8. Walker J, Taylor P. 2020 Evaluating the efficacy of eBird data for modeling historical population trajectories of North American birds and for monitoring populations of boreal and Arctic breeding species. Avian Conservation and Ecology, 15(2) (https://doi.org/10.5751/ACE-01671-150210).
  9. Callaghan CT, Gawlik DE. 2015 Efficacy of eBird data as an aid in conservation planning and monitoring. Journal of Field Ornithology, 86(4), 298-304 (https://doi.org/10.1111/jofo.12121).
  10. Stuber EF, Robinson OJ, Bjerre ER, Otto MC, Millsap BA, Zimmerman GS et al. 2022 The potential of semi-structured citizen science data as a supplement for conservation decision-making: Validating the performance of eBird against targeted avian monitoring efforts. Biological Conservation, 270 (https://doi.org/10.1016/j.biocon.2022.109556).
  11. Thomas RL, Fellowes MD. 2017 Effectiveness of mobile apps in teaching field-based identification skills. Journal of Biological Education, 51(2), 136-143 (https://doi.org/10.1080/00219266.2016.1177573).
  12. Smith D. 2004 Issues and trends in higher education biology fieldwork. Journal of Biological Education, 39(1), 6-10 (https://doi.org/10.1080/00219266.2004.9655946).
  13. Scott GW, Boyd M, Scott L, Colquhoun D. 2015 Barriers to biological fieldwork: What really prevents teaching out of doors? Journal of Biological Education, 49(2), 165-178 (https://doi.org/10.1080/00219266.2014.914556).
  14. Leather SR, Quicke DJL. 2009Where would Darwin have been without taxonomy? Journal of Biological Education, 43:2, 51-52 (https://doi.org/10.1080/00219266.2009.9656151).

Natalia Uribe-Castaneda

Research Assistant and Ph.D. Candidate School of Natural Resources and Environment

Socio-ecological theoretical frameworks to assess community engagement strategies in support of coral reef restoration


I am Natalia Uribe-Castañeda, a Colombian Fulbright Scholarship recipient with a background in marine management and experience working with communities. I began the SNRE Interdisciplinary Ecology Ph.D. program at the University of Florida in 2020. Through this program, I have strengthened my understanding of how other sciences such as Public Policy, Economics, Sociology and Communication can contribute to the success of restoration projects.

I am using socio-ecological theoretical frameworks to assess community engagement strategies in support of coral reef restoration.  The socio-ecological systems approach analyzes relationships between ecosystems and society, identifying humans as a part of the system instead of separate (Ostrom 2009). Comprehension of these complex interactions is necessary when creating conservation, restoration, and management strategies (Berrouet et al. 2018). 

My colleagues Alice Naewton and Martin Le Tissier (Uribe-Castañeda et al., 2018) are working in a conceptual framework to address both the socio-ecological system features of coral reefs with the implementation of restoration activity for degraded coral reefs. Such a framework can lead to better societal outcomes from restoration activities while restoring bio-physical, social and ecosystem service features of such systems. This framework can be used as a guide for managers, researchers, and decision makers to analyze the needs of coral reef restoration in a way that addresses both socio-economic and ecological objectives to analyze, design, implement and monitor reef restoration programs.



Berrouet, L.M., Machado, J., and Villegas-Palacio, C. 2018. Vulnerability of socio—Ecological systems: A conceptual Framework. Ecol. Indic. 84, 632-647.

Ostrom, E. 2009. A general framework for analyzing sustainability of social-ecological systems. Science. 325(5939), 419-422.

Uribe-Castañeda, N., Newton, A., and Le Tissier, M. 2018. Coral reef socio-ecological systems analysis & restoration. Sustainability. 10(12), 4490.  https://doi.org/10.3390/su10124490