SelectedWorks - Jose V. Lopez

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Selected Works of Jose V. Lopez

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Main interests lie in molecular evolution, biodiversity, microbial symbiosis and genomics. Characterization of gene sequences from rare and relatively overlooked marine invertebrates and microorganisms have enabled the PI to contribute to increasingly valuable genetic biodiversity research and data during the current period of accelerated worldwide habitat destruction. With a background in molecular evolutionary biology and macromolecular sequence analysis, the PI has been conducting research within this framework and through multidisciplinary laboratory collaborations.

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About Jose V. Lopez

Main interests lie in molecular evolution, biodiversity, microbial symbiosis and genomics. Characterization of gene sequences from rare and relatively overlooked marine invertebrates and microorganisms have enabled the PI to contribute to increasingly valuable genetic biodiversity research and data during the current period of accelerated worldwide habitat destruction. With a background in molecular evolutionary biology and macromolecular sequence analysis, the PI has been conducting research within this framework and through multidisciplinary laboratory collaborations.

Articles (104)

Journal articles written or co-written by Dr. Jose V. Lopez

Potential Impacts of Environmental Bacteria on the Microbiota of Loggerhead (Caretta caretta) and Green (Chelonia mydas) Sea Turtle Eggs and Their Hatching Success (Colleen McMaken, Derek Burkholder, Rosanna J Milligan, et al.) Microbiologyopen (2023)

Sea turtle hatching success can be affected by many variables, including pathogenic microbes, but it is unclear which microbes are most impactful and how they are transmitted into the eggs. This study characterized and compared ...

Morphological and Transcriptional Effects of Crude Oil and Dispersant Exposure on the Marine Sponge Cinachyrella Alloclada (Yvain Desplat, Jacob F. Warner, Emily J. Blake, et al.) Science of The Total Environment (2023)

Marine sponges play important roles in benthic ecosystems. More than providing shelter and food to other species, they help maintain water quality by regulating nitrogen and ammonium levels in the water, and bioaccumulate heavy metals. ...

Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs (Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, et al.) PeerJ (2023)

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port ...

Nitrosomonas supralitoralis sp. nov., an ammonia-oxidizing bacterium from beach sand in a supralittoral zone (Hidetoshi Urakawa, Gabrianna A. Andrews, Jose V. Lopez, et al.) Archives of Microbiology (2022)

A betaproteobacterial chemolithotrophic ammonia-oxidizing bacterium designated APG5T was isolated from supralittoral sand of the Edmonds City Beach, WA, USA. Growth was observed at 10–35 °C (optimum, 30 °C), pH 5–9 (optimum, pH 8) and ammonia ...

Three complete mitochondrial genomes of shortfin mako sharks, Isurus oxyrinchus, from the Atlantic and Pacific Oceans (Marissa Mehlrose, Andrea Bernard, Kimberly A Finnegan, et al.) Mitochondrial DNA Part B (2022)

We present complete mitogenome sequences of three shortfin mako sharks (Isurus oxyrinchus) sampled from the western Pacific, and eastern and western Atlantic oceans. Mitogenome sequence lengths ranged between 16,699 bp and 16,702 bp, and all ...

Standards recommendations for the Earth BioGenome Project (Mara K. Lawniczak, Richard Durbin, Paul Flicek, et al.) Proceeding of the National Academy of Sciences of the United States of America (2022)

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP ...

The Earth BioGenome Project 2020: Starting the clock (Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, et al.) Proceedings of the National Academy of Sciences of the United States of America (2022)

Why sequence all eukaryotes? (Mark Blaxter, John M Archibald, Anna K. Childers, et al.) Proceedings of the National Academy of Sciences (2022)

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations ...

Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada (Yvain Desplat, Jacob F. Warner and Jose V. Lopez) Journal of Heredity (2021)

Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only two sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species ...

The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life (Victoria McKenna, John M Archibald, Roxanne Beinart, et al.) Wellcome Open Research (2021)

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of ...

ddPCR Reveals SARS-CoV-2 Variants in Florida Wastewater (Eben Gering, Jacob Colbert, Sarah Schmedes, et al.) medRxiv (2021)

Wastewater was screened for the presence of functionally significant mutations in SARS-CoV-2 associated with emerging variants of concern (VOC) by ddPCR, and results accorded with sequencing of clinical samples from the same region. We propose ...

Editorial: Deep Pelagic Ecosystem Dynamics in a Highly Impacted Water Column: The Gulf of Mexico After Deepwater Horizon (Tracey Sutton, Kevin M Boswell, Heather Bracken-Grissom, et al.) Frontiers in Marine Science (2021)

The intermediate-sized midwater fauna (fishes, shrimps, and cephalopods; “micronekton” collectively) are dominant components of the pelagic ocean, which is by far the largest ecosystem type on Earth by several metrics (volume, organismal numbers, biomass, and ...

Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species (Rachael Storo, Cole Easson, Mahmood S Shivji, et al.) Frontiers in Microbiology (2021)

Profiles of symbiotic microbial communities (“microbiomes”) can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in ...

Microscopic and Genetic Characterization of Bacterial Symbionts With Bioluminescent Potential in Pyrosoma atlanticum (Alexis Berger, Patricia L. Blackwelder, Tamara Frank, et al.) Frontiers in Marine Science (2021)

The pelagic tunicate pyrosome, Pyrosoma atlanticum, is known for its brilliant bioluminescence, but the mechanism causing this bioluminescence has not been fully characterized. This study identifies the bacterial bioluminescent symbionts of P. atlanticum collected in ...

A Multidisciplinary Approach to Investigate Deep-Pelagic Ecosystem Dynamics in the Gulf of Mexico Following Deepwater Horizon (April Cook, Andrea Bernard, Kevin M. Boswell, et al.) Frontiers in Marine Science (2020)

The pelagic Gulf of Mexico (GoM) is a complex system of dynamic physical oceanography (western boundary current, mesoscale eddies), high biological diversity, and community integration via diel vertical migration and lateral advection. Humans also heavily ...

Draft Genome of Bugula neritina, a Colonial Animal Packing Powerful Symbionts and Potential Medicines (Mikhail Rayko, Aleksey Komissarov, Jason C. Kwan, et al.) Scientific Data (2020)

Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum ...

Complete genome sequence of microcystis aeruginosa FD4, isolated from a subtropical river in Southwest Florida (Hidetoshi Urakawa, Taylor L. Hancock, Jacob H. Steele, et al.) Microbiology Resource Announcements (2020)

We report the first complete genome of Microcystis aeruginosa from North America. A harmful bloom that occurred in the Caloosahatchee River in 2018 led to a state of emergency declaration in Florida. Although strain FD4 ...

Microbial Community Shift Under Exposure of Dredged Sediments From a Eutrophic Bay (Juliana R. Nascimento, Cole Easson, Diogo de A. Jurelevicius, et al.) Environmental Monitoring and Assessment (2020)

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different ...

Combined eDNA and Acoustic Analysis Reflects Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico (Cole G. Easson, Kevin M. Boswell, Nicholas Tucker, et al.) Frontiers in Marine Science (2020)

Oceanic diel vertical migration (DVM) constitutes the daily movement of various mesopelagic organisms migrating vertically from depth to feed in shallower waters and return to deeper water during the day. Accurate classification of taxa that ...

Detecting Personal Microbiota Signatures at Artificial Crime Scenes (Jarrad T. Hampton-Marcell, Peter Larsen, Tifani Anton, et al.) Forensic Science International (2020)

When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We ...

Host Population Genetics and Biogeography Structure the Microbiome of the Sponge Cliona delitrix (Cole Easson, Andia Chaves-Fonnegra, Robert W. Thacker, et al.) Ecology and Evolution (2020)

Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between ...

Gut Microbiome Diversity Is Associated with Sleep Physiology in Humans (Robert Smith, Cole Easson, Sarah M. Lyle, et al.) PLoS One (2019)

The human gut microbiome can influence health through the brain-gut-microbiome axis. Growing evidence suggests that the gut microbiome can influence sleep quality. Previous studies that have examined sleep deprivation and the human gut microbiome have ...

Gut Microbiome Diversity is Associated with Sleep Physiology in Humans (Robert P Smith, Cole G Easson, Sarah M Lyle, et al.) PLoS One (2019)

The human gut microbiome can influence health through the brain-gut-microbiome axis. Growing evidence suggests that the gut microbiome can influence sleep quality. Previous studies that have examined sleep deprivation and the human gut microbiome have ...

Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment (Lydia Baker, Lindsay L Freed, Cole Easson, et al.) eLife (2019)

Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that ...

Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of mexico (Lindsay L Freed, Cole Easson, Lydia Baker, et al.) FEMS Microbiology Ecology (2019)

The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) ...