Jose (Joe) Lopez, Ph.D.
Professor, Nova Southeastern University
Principle Investigator
I earned a BS at Georgia Tech, an MS at Florida State University, and my doctorate at George Mason University studying the evolution of mitochondrial DNA and its transpositions (Numt) in feline nuclear genomes under Stephen J. O’Brien. I then applied his training in postdoctoral appointments at the Smithsonian Tropical Research Institute with Nancy Knowlton characterizing the Orbicella annularis coral sibling species complex at the Smithsonian Tropical Research Institute in Panama, and sponge genetics at Harbor Branch Oceanographic Institute with Shirley Pomponi. The latter introduced me to investigate deepwater marine systems. Since 2007, our laboratory at Nova Southeastern University focuses on the genomic sequences from marine organisms and essential microbes in diverse projects. Our lab was a partner in the Porifera Tree of Life (PorToL) project to study the systematics of sponges. We are trying to better understand food webs and microbial distributions in the deep ocean through the DEEPEND project after the Deepwater Horizon oil spill. This includes characterizing “symbiotic” interactions (between host and beneficial microbes living together in sponges, corals, humans and fish (see bioluminescent symbionts of anglerfish. I also helped found the Global Invertebrate Genomics Alliance (GIGA) in 2013 which focuses on the genomes of diverse marine invertebrates comprising the Tree of Life. GIGA is now part of the Earth BioGenome Project (EBP) that aims to sequence most of the planet’s eukaryotic species. We are now focusing on inland Florida microbial communities which may be linked harmful algal blooms (HABs) that reach coral reefs and degrade water quality.
Postdoctoral Researchers
Lauren Krausfeldt, Ph.D.
I am a microbial ecologist who uses a suite of tools to study harmful algal blooms in aquatic ecosystems. My current project uses metagenomics and metatranscriptomics to characterize microbial community composition & function in Lake Okeechobee. Our goal is to identify specific triggers of cyanobacteria blooms in Lake Okeechobee and its surrounding tributaries. I received my B.Sc. in Biology from Elmhurst College and my Ph.D. in Microbiology from the University of Tennessee Knoxville.
Graduate Students
Rachel Bacaner
I earned my B.S. in Biology from Florida Atlantic University. While at FAU I was fortunate to participate in undergraduate research with Dr. Sarah Milton on the effects of temperature on cognitive behavior in Loggerhead Sea turtles. In addition, as an undergrad worked on the ongoing research of Dr. Xing-Hai Zhang, which focused on the detection and monitoring of the citrus green disease-causing bacterium using genetic analysis of plants. I am currently at NSU working towards my MS degree in Biological science (research concentration). My thesis research which will focus on exploring the molecular framework of cell culture and regeneration in soft corals using cnidarian model organisms. This research will aim to isolate cells, establish cell lines, and identify regeneration genes using comparative genomics. My project will also apply and contribute to the genomic data from the Aquatic Symbiosis Genome project. I am also working as a graduate research assistant on a project with the FL Dept of Environmental Protection with Dr. Lopez and PI Dr. Mark Butler from FIU. This project focuses on the role of sponge filtration in transforming coastal water quality in the Florida Keys. This project will involve assessing changes through molecular taxonomy analyses using 16S gene sequencing and more.
Alexis Berger
My project is focused on characterizing the bacterial symbionts in the pyrosome, specifically the pelagic tunicate, Pyrosoma atlanticum. These tunicatescan be found in tropical and temperate waters ranging from 45°N to 45°S. With rising sea temperatures, the pyrosome has been recorded outside its normal habitat range and with it its brilliant luminescence. This tunicate is well known for its bioluminescence and it has been observed since the 1840s. In this study, the bacterial symbionts believed to be responsible for the luminescence were observed using electron microscopy. We found that bacteria are in fact present within Pyrosoma atlanticum, both SEM and TEM confirmed the bacterial presence. The next stage of this project is to observe the light organs histologically and to identify the bacteria itself. We will be using either PCR or Sanger sequencing of the 16s rRNA gene to determine its identity and to develop probes for fluorescence in situ hybridization (FISH).
Paisley Samuel
I received my Bachelor’s degree in Marine Biology with minors in Marine Ecology and GIS at NSU. I’m currently finishing up the Master’s degree in Marine Science program here at NSU. I started out as a temporary research assistant in Dr. Lopez’s lab, helping out with a cyanobacterial harmful algal bloom (cyanoHABs) project funded by the Army Corps of Engineers. Now as a full-time research assistant in the lab, my current thesis project investigates how the microbial community changes in Lake Okeechobee due to the cyanoHABs that occur in the lake. We assess these changes through molecular taxonomy analyses using 16S gene sequencing. After assessing the microbial composition of the lake, we then look for any specific heterotrophic bacteria taxa that appear to change in accordance with the cyanoHABs as they occur.
Staff and Undergraduates
We are indebted to several individuals who have worked or volunteered in the laboratory as temporary, grant-funded staff or undergraduates looking to gain practical lab experience. Until we can get proper bios, there names are listed below.
Nina Pruzinsky
Catherine Bilodeau
Christian Rodriguez
Kristen Olenchak
Anna Volter
Celeste Banfill
Elena Grosu
Amanda Haussman
Bryce Parrish
Lopez Lab @ NSU 