Current Lab Members

Jose (Joe) Lopez

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. Lopez 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. The latter allowed me to apply submersible technology to investigate marine systems. Since 2007, our laboratory at NSU 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.

Postdoctoral Researchers

Lauren Krausfeldt
My project is focused on characterizing the cyanobacterial of harmful algal blooms plaguing South Florida.

Graduate Students

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).

Deepesh Tourani
I am studying the microbial ecology of Gulf of Mexico (GoM), as part of the DEEPEND Consortium. To study the functional composition of microbial communities (or microbiome), I am using the PICRUSt approach which infers function using 16S rRNA gene sequences and reference databases. Microbial communities constitute a significant portion of the biomass in the oceans, and drive the nutrient-chemical cycles, such as carbon, nitrogen and phosphorus, essential for sustenance of life. They act as primary producers and decomposers, in turn also responding to physico-chemical changes throughout the water column.
Studying these communities thus helps in understanding the direct effects of physical processes in the ocean and human activities on a marine ecosystem such as the GoM. Using statistical analyses, my project aims to study the functional structure and dynamics of microbial communities, and establish a baseline across the northern GoM, which will help in assessing and tracking ecological changes in the region.

Elizaveta Shmakova
I am originally from Russia. I am currently completing my master’s degree in biological sciences at Nova Southeastern University. I completed my bachelor’s degree in biology at NSU as well. My thesis project focuses on the analysis of 28 sponge associated whole bacterial genomes. The project can reveal novel genomes of sponge associated microbes providing insight into microbial speciation and Cinachyrellasponge microbiome. The goals of my research are to 1) bioinformatically characterize novel bacterial symbiont genomes now completed sequenced with state of the art methods 2) determine the differences between the genomes in side by side comparisons of the sequences to find the functional roles in the microbial-sponge symbiosis. The most abundant and dominant bacterial genomes will be annotated, which will increase our knowledge about major sponge symbionts. Moreover, these data will increase the data available for sponge-microbiome interactions will be studied and provide more microbial genomes which will contribute substantially to future sequence databases. It will help to provide the necessary information about the involved genes and their functional roles within the host.

Colleen Mcmaken
I graduated from Nova Southeastern University with Bachelors in Marine Biology and Biology and will be starting in the Master’s program for Marine Biology for the Fall 2019 semester. I have been a volunteer in the lab since my junior year at NSU helping with DNA extractions from water, soil, and sponge samples and other various tasks that graduate students have needed assistance with. I am currently assisting with a microbiome study on the endangered flowering plant Deeringothamnus rugelii (commonly known as Rugel’s pawpaw or yellow squirrel banana) from multiple locations found at Bok Tower Gardens. My research interests include microbiome studies to help with the conservation of marine species. I am hoping to pursue my research interests through a thesis project on the impacts of microbial transfer from the sand to the eggs of sea turtles in South Florida.

Victoria Pecci
I am originally from Chicago and I’m currently pursuing my master’s degree in biological sciences at NSU.  I have my bachelor’s in marine biology that I also obtained from NSU where I participated for the NCAA division II women’s soccer, cross country, and track teams.  I am in the molecular biology and genetics lab working on sponge DNA.  I am working to find sponge specific genes as well as homologs to other invertebrates from a sponge in the genus Cinachyrella. I will also be identifying it down to the species level, as the common species found in South Florida are visually difficult to distinguish from one another.

Yvain Desplat
My thesis project focuses on linking the effect of oil and dispersant effect on the gene expression of a Florida reef sponge from the Cinachyrella species. The sponges were exposed to three different treatment: oil (WAF), dispersant (Corexit CE9500A), and oil+dispersant (CE-WAF). Using cDNA libraries preparations, Next Generation Sequencing, and the Bluebee bioinformatics pipeline the expression (up-regulation, down-regulation, or no change) of different genes in that organism will be identified based of the control sponges (not exposed to chemicals). Along the genetic expression profiling, the cinachyrella transcriptome will be constructed and annotated using Bridger, Trinity, Oases, and the completeness of will be checked using BUSCO, all of these being command line based.
This project preceded the DEEPEND project, a project started after the Deep Water Horizon oil spill in the Gulf of Mexico in 2010. As well, this project will aim to establish sponges from the Cinachyrella species as bioindicators for water quality on South Florida reefs.

Eric Fortman
My thesis research focuses on the influence of runoff on the microbiome of Northern and Central Biscayne Bay. I am using high-throughput genetic sequencing to identify the bacterial communities present in the bay. Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. While there are good timeseries data on water quality, the bacterioplankton community is not as well described. The study examines the bacterial community at 14 stations throughout Biscayne Bay, focusing on the mouths of canals. One liter, surface water grab samples were collected monthly for one year. The filtered samples were then be sequenced for 16s rRNA, to identify bacterial community composition. Erroneous sequences will be filtered out using DADA2 in QIIME 2. Statistical analysis will be done using Phyloseq and VEGAN in R-Studio.

Shelby Cain
My research interests include genetics, bioinformatics analysis, marine sponge microbial community, filtration rates, and computational biology. I am studying the sulfur cycle within various sea sponges in the Ft. Lauderdale area. This includes collecting various species of sponges and determine the filtration rate of hydrogen sulfite using microsensors. My project also consists of characterizing how the microbial community within sponges changes after being exposed to hydrogen sulfide. Much recent data has focused on the microbial community, but not their direct functions. My project’s goal is to determine which microbes contribute to the sulfur cycle, thus understand the microbial community’s function.


Lab Alumni