Research ProjectBiogeography of Microorganisms

  • Dr. Katrina Lohan with water sample from Punta Culebra, a site at the Pacific entrance to the Panama Canal.

    Dr. Katrina Lohan with water sample from Punta Culebra, a site at the Pacific entrance to the Panama Canal. Photo Credit Kristina Hill-Spanik

  • Kristina Hill-Spanik filtering a water sample in Mexico

    Kristina Hill-Spanik, being assisted by Dan Aguirre-Ayala (a graduate student at CINVESTAV) filtering a water sample in Mexico. Photo Credit Dr. Carmen Schlöder

  • Sediment sample from Fort Sherman, Panama

    Sediment sample collected at Fort Sherman, a site near the Caribbean entrance to the Panama Canal. Photo Credit Dr. Carmen Schlöder

  • Sampling microbial communities on the hulls of ships

    The aftermath of divers sampling microbial communities on the hulls of ships. Photo Credit Dr. Ian Davidson

Project Goal

We are examining patterns of diversity and distribution for different eukaryotic taxa*, primarily focusing on protistan taxa (or unicellular eukaryotes) over a latitudinal gradient from the Chesapeake Bay to Panama. We are looking at several micro-habitats including the water column, subtidal and intertidal sediments, and biofilms.


Protists* have many important roles in coastal waterways, including supporting the base of the food web, producing oxygen, and moving carbon and energy to higher trophic levels. Some protists also have detrimental impacts, for example those that cause harmful algal blooms, those that produce toxins that are harmful to marine animals and/or humans, and those that cause disease. Because these organisms are so small and have few obvious physical characteristics that can be used to tell them apart, relatively little is known about their taxonomy, diversity, and distribution (or biogeography*). Additionally, the current theories surrounding the dispersal of protists are based exclusively on the natural ways that they spread, ignoring the many ways that humans spread marine organisms around the world.

We are examining the diversity of many different protistan taxa in environmental samples from coastal waterways primarily using an amplicon-based* metabarcode approach. This approach takes full advantage of high throughput sequencing* technology. In an effort to assess as much diversity as possible, as well as to examine small spatial scale variation, we have sampled many micro-habitats including the water column, intertidal and subtidal sediments, and biofilms. To compare across different spatial scales, we have included environmental samples over a latitudinal gradient, from the Chesapeake Bay down to Panama, as well as collecting a number of samples within a single site. Additionally, we have extensively sampled around both sides of the Panama Canal, to determine the potential influence of the Canal in homogenizing the protistan communities on both coasts of Panama. Finally, we are examining the protistan communities associated with different surfaces on commercial shipping vessels in order to assess the role that commercial ships play in dispersing these organisms, thus changing their global distributions.

Feature Stories

What Parasites are Hitching a Ride to the Chesapeake Bay in Ballast Water? By Katrina Lohan. February 3, 2014


Lohan Pagenkopp, KM, RC Fleischer, KJ Carney, KK Holzer, & GM Ruiz (In Review) Molecular characterization of protistan species and communities in ships' ballast water across three U.S. coasts. Diversity and Distributions.

Lohan Pagenkopp, RC Fleischer, ME Torchin, & GM Ruiz (In Review) Biogeography of Marine Protists Across the Isthmus of Panama. Protist.

Lohan Pagenkopp, RC Fleischer, KJ Carney, KK Holzer, & GM Ruiz (2016) Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases. Microbial Ecology, 71(3): 530-542.


Dr. Katrina Lohan

Term Definition 
Eukaryotic taxa Any organism whose cells contain a nucleus and other organelles enclosed within membranes. The 'opposite' of prokaryotic cells, which are single-celled organism (such as bacteria) that lack a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle.
Protists Sometimes called the fifth Kingdom because they are not not animals, plants or fungi but members of an informal grouping of diverse eukaryotic organisms. They are unicellular or unicellular-colonial organisms which form no tissues. 
Biogeography The branch of biology that studies the geographical distribution of species, traits, and ecosystems
Amplicon-based sequencing A genomic method of sequencing an amplified or replicated piece of DNA or RNA 
High throughput sequencing technology Faster and less expensive methods of sequencing and analyzing large genomes.