Spotlight on a Researcher – Dr. Jose Lopez

Jose Lopez, PhD is a professor in the Halmos College of Arts and Sciences at NSU. His research focuses on application of the latest technologies for DNA sequence analysis of microorganisms and marine invertebrates. One of the primary objectives of his research is characterization and understanding of genetic diversity and how it contributes to the understanding of genetic and evolutionary relationships between various species. Dr. Lopez’s lab is also involved in projects aimed at understanding environmental issues such as harmful algae bloom and oil spill in marine environments, and supporting solutions for tackling them. We highlight here a few recent research projects that Dr. Lopez and his collaborators have been working on.

A team of researchers in Dr. Lopez’s lab at NSU conducted genetic characterization of bacterial symbionts of the pelagic tunicate, Pyrosoma atlanticum, a marine invertebrate that is known for its brilliant bioluminescence. Dr. Lopez and his team collected P. atlanticum from the Gulf of Mexico and implemented light and electron microscopy as well as molecular genetics to analyze the bacterial symbionts found in these tunicates. In the process of conducting this research and searching for lux genes of bioluminescence, his group generated a draft tunicate mitochondrial genome that can be used for identifying P.atlanticum.  The sequencing of mitochondrial DNA (mtDNA) of P. atlanticum obtained through this research provided furthers genetic information regarding their taxonomic identity. This study also produced a more detailed description of the symbiotic bacteria found in P. atlanticum than any previous work done on pyrosomes. The findings from this study were published in a peer-reviewed article in the journal Frontiers in Marine Science (https://www.frontiersin.org/articles/10.3389/fmars.2021.606818/full).

Symbionts are not only crucial for marine invertebrates, but they also perform an essential role in the biology of larger marine organisms. Dr. Lopez in collaboration with Dr. Mahmood Shivji at NSU studied the symbiotic microbiome of five species of sharks found in South Florida. They applied the latest high throughput DNA sequencing to study microbiome composition of nurse, lemon, sandbar, tiger, and Caribbean reef sharks. The results of this study that were published in the journal Frontiers in Microbiology in 2021 (https://www.frontiersin.org/articles/10.3389/fmicb.2021.605285/full) indicate that microbial diversity and composition differs depending on the anatomical location of the endosymbionts (teeth, gills, skin, cloaca) and also varies from species to species. The microbiome communities associated with these five species of sharks were also found to be distinct from those found in surrounding seawater. Studies like these offer better understanding of microbiomes associated with sharks and enable detection of potential human pathogens, especially in the teeth, that could be transferred from a shark bite which can aid in development of improved bite treatment protocols.

Another marine organism that is being studied by Dr. Lopez is a Bryozoan named Bugula Neritina. Bryozoans are colonial microscopic marine invertebrates that are commonly called “moss animals” due to their moss-like appearance. Researchers in Dr. Lopez’s lab implemented genome sequencing and transcriptomics to develop a draft assembly of B. neritina genome and published the findings of this genomic analysis in a peer-reviewed article in the journal Scientific Data (https://www.nature.com/articles/s41597-020-00684-y#Sec1) in 2020. Characterization of the B. neritina genome has significance for both ecology and biomedical science as Bryozoans such as B. neritina are known to produce bioactive compounds known as bryostatins that have multiple potential therapeutic applications in the treatment of cancer and Alzheimer’s disease. The draft genome of B. neritina was also contributed to two large scale genome projects, the Earth Biogenome Project and the Global Invertebrate Genomics Alliance (GIGA).

Research projects on genomic sequences of essential microbes being conducted by Dr. Lopez and colleagues at NSU also have environmental significance. One such study could possibly lead to a solution for harmful algae bloom, a major problem plaguing our state’s waterbodies and even affecting the livelihood of people. Together with research scientist Dr. Lauren Krausfeldt, Dr. Lopez has been applying metagenomics and metatranscriptomics to characterize microbial community composition and function in Lake Okeechobee and surrounding waterbodies. This project is partially funded by the DoD Army Corps of Engineers and involves experiments to assess biodiversity of these microorganisms and investigate environmental or anthropogenic triggers of harmful algae bloom. The findings from this research will help scientists understand the key factors resulting in these blooms and design better processes for preventing their repeated occurrence in Florida’s waterways. Another significant environmental project in which the Lopez lab has made important contributions is the DEEPEND (Deep Pelagic Nekton Dynamics of The Gulf of Mexico; http://restore.deependconsortium.org/) research consortium. Dr. Lopez contributed to this research consortium in collaboration with another NSU faculty member, Dr. Tracey Sutton who leads the consortium. The key goal of DEEPEND is to gain understanding of the full extent of the deleterious environmental effects of the British Petroleum Deepwater Horizon Oil Spill that occurred in 2010. NSU researchers conduct studies that use molecular genetics technologies to characterize microbial communities in the Gulf of Mexico and how they are influenced by this oil spill.

As mentioned previously, key objectives of the Lopez lab are contributing to global evolutionary genomics projects, and gaining better understanding of food webs and microbial distributions by studying genomic sequences of marine organisms and essential microbes. The findings from these genomic studies are used to develop robust phylogenetic trees that will offer the best possible estimate of the genetic and evolutionary relationships between various invertebrate species. Dr. Lopez also contributes to initiatives such as the Global Invertebrate Genomic Alliance (GIGA) and the Earth Biogenome Project. He was instrumental in founding GIGA (https://www.giga-cos.org/) in 2013 and currently serves as the President. The key objective of GIGA is to create a collaborative network of scientists to engage in resolving major challenges associated with genome/transcriptome sequencing across a large taxonomic spectrum and facilitate collaborations across the worldwide scientific community. GIGA is now part of the Earth BioGenome Project (EBP) , an even more ambitious project that aims to sequence, catalog, and characterize genomes of 1.5 million eukaryotic species in the next 10 years. Dr. Lopez is also part of the Aquatic Symbiosis Genomes (ASG) project underwritten by the Gordon and Betty Moore Foundation and the Sanger Institute in the UK (https://www.sanger.ac.uk/news_item/ambitious-genomics-project-seeks-to-understand-how-aquatic-species-thrive-together/). The ASG is an initiative involving hundreds of researchers that aims to gain better understanding of ecology and evolution of symbiosis by sequencing genetic codes of 1000 species involved in various symbiotic relationships.

Dr. Lopez’s contributions have been influential in creating the GIGA project, and his research contributes to other similar genomic initiatives. These projects facilitate a collaborative international scientific effort for establishing an open digital repository of genomic information for life on Earth. Understanding of the genomics of marine invertebrates not only offers valuable insight into our evolutionary tree, but also holds potential medical importance as many of these organisms are known to produce bioactive compounds. His lab at NSU has also made significant contributions toward finding solutions for major environmental hazards such as toxic algae bloom in Florida’s waterways and oil spill in the Gulf of Mexico. The research being conducted by Dr. Lopez in the Halmos College of Arts and Sciences highlights the importance of microscopic organisms in the environment and has far reaching potential benefits. Dr. Lopez’s work has had impact spanning a multitude of disciplines and continues to serve as an inspiration to the NSU community.