Juan M. Lopez-Bautista




  • Postdoctoral research: University of Louisiana
  • PhD, Plant Biology, Louisiana State University, 2000

Research Interests

My principal research interests are in Phycology. My research program is focused on the biodiversity, phylogenomics, molecular systematics, and evolution of algae. My current projects are on algal plastid genomes and two NSF-funded Tree of Life projects in Green and Red algae. Other related projects are seaweed biodiversity in the Gulf of Mexico and the subaerial microchlorophytes from tropical rainforests.

GRAToL: Assembling the Green Algal Tree of Life. This project will assemble a Tree of Life for the green algae. A minimum estimate of diversity of the group is a little more 14,000, with species distributed on all continents and across virtually every habitat type on Earth. Although recently molecular studies have revealed two major clades of green algae (marine groups and several freshwater and marine unicellular lineages in one group, and several freshwater groups plus embryophytes as the second), the relationships among major lineages within the green algae are poorly known. Moreover, within the major groups, relationships and monophyly of many traditionally defined groups are poorly resolved. Our collaborative research team will use an approach that is a hybrid of PCR-based multi-gene sequencing and next-generation sequencing methods. We will assemble a green algal tree of life by sequencing 10 genes for +400 taxa. Next-generation sequencing will be used for a subset of 16 taxa to study deep phylogenetic relationships in the green algae, find genes for detailed analysis of particular groups, and examine organellar genome evolution in the green algae. A global analysis will be used to make a reclassification for all green algae.

REDToL: Phylogenetic and Genomic Approaches to Reconstructing the Red Algal (Rhodophyta) Tree of Life. Rhodophyta (red algae) are key members of aquatic environments and sources for important human foods and have a multitude of pharmaceutical and industrial uses. Rhodophyta played an important role in the evolution of our planet through secondary endosymbiosis. A red alga was the ancient donor of the plastid in groups such as dinoflagellates, brown algae, and diatoms (among others). Our project is aiming to: 1) reconstruct a robust phylogeny of 471 red algal species using a concatenated dataset of 2 nuclear, 4 plastid, and 2 mitochondrial encoded gene markers, 2) sequence plastid genomes and generate transcriptome databases for 16 key taxa that represent the phylogenetic (e.g., class- and order-level) breadth of the red algae, 3) make freely available red algal multi-gene and genome data via release to GenBank and a project-specific web site. The robust phylogenetic framework resulting from our study will be the basis for a comprehensive taxonomic revision of the red algae and provide the basis for interpreting key innovations during red algal evolution.

These Rhodophyta and Chlorophyta AToL projects will integrate data with other AToL projects (heterokonts, liverworts and other embryophytes) to identify core genes for broad phylogenetic analyses. These investigations will also provide a common framework for a future comprehensive eukaryotic tree.

SUBAERIAL MICROCHLOROPHYTES FROM TROPICAL RAINFORESTS. Our laboratory has been investigating the subaerial representatives of the orders Trentepohliales, Klebsormidiales and Cladophorales. Molecular systematics and phylogenetic analyses along with morphology-based classification hypotheses have been our tools to unravel biological and evolutionary trends. Gene sequencing techniques and computerized data analyses of nuclear and plastid genes as well as ultrastructure has been used in this research. My particular interest in the Trentepohliales is centered in the phylogenetic relationships among the genera and species as well as the species concept in the order. We are investigating the taxonomy and systematics of Klebsormidium by a combination of morphological studies and sequencing of the rbcL gene. Our results so far indicate that a great deal of genetic diversity is hidden behind the simple morphology of these subaerial microchlorophytes, and that the current concepts of several common species will probably need to be reassessed. Biodiversity surveys are also part of our current interest, in particular from tropical rainforests. A comparison with other tropical regions is showing that our floristic accounts are very high figure. Thus, we have able to conclude that French Guiana and Panama are biodiversity hotspots for subaerial algae.

SEAWEED DIVERSITY. The macroalgal biodiversity of the Gulf of Mexico has been the spotlight of my research during several decades. We are currently studying the benthic marine algae from the North Central Gulf of Mexico and Cuba. We are developing a digital database of seaweeds from these areas. Changes in the floristic composition related to human-induced changes in the environment as well as detection of non-indigenous species has been the focal point in our current investigations.

Selected Publications

  • Cabrera, R., O’Shields, B., Diaz-Larrea, J. and J. Lopez-Bautista. 2020. Molecular phylogenetic analyses of the genus Hypnea (Cystocloniaceae, Rhodophyta) in Cuba. Caribbean Journal of Science 50 (1): 74-85.
  • Garcia-Soto, G. and J. Lopez-Bautista. 2019. Laurencia natalensis (Ceramiales, Rhodophyta): a new record for the Atlantic Ocean. Caribbean Journal of Science 49(2-3):201-208.
  • Stefanidou, N., Genitsaris, S., Lopez-Bautista, J. and M. Moustaka-Gouni. 2019. Response of a coastal Baltic Sea diatom-dominated phytoplankton community to experimental heat shock and changing salinity. Oecologia 191(2):461-474
  • Garcia-Soto, G. and J. Lopez-Bautista. 2019. Acanthophora dendroides (Rhodomelaceae), a new record for the Atlantic and Pacific Oceans. Check List 15:509.
  • Chávez-Sánchez, T., Piñón-Gimate, A., Melton III, J. T., López-Bautista, J. M., & Casas-Valdez, M..2019. First report, along with nomenclature adjustments, of Ulva ohnoi, U. tepida and U. torta (Ulvaceae, Ulvales, Chlorophyta) from northwestern Mexico. Botanica Marina 62(2):113-123
    Cremen, M. C. M., Leliaert, F., West, J., Lam, D. W., Shimada, S., Lopez-Bautista, J. M., & Verbruggen, H. 2019. Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses. Molecular phylogenetics and evolution, 130, 397-405.
  • Stefanidou, N., Genitsaris, S., Lopez-Bautista, J., Sommer, U., & Moustaka-Gouni, M. 2018. Unicellular eukaryotic community response to temperature and salinity variation in mesocosm experiments. Frontiers in Microbiology, 9, 24-44.
  • Stefanidou, N., Genitsaris, S., Lopez-Bautista, J., Sommer, U., & Moustaka-Gouni, M. 2018. Effects of heat shock and salinity changes on coastal Mediterranean phytoplankton in a mesocosm experiment. Marine Biology, 165(10), 154.
    García-Soto, G., & Lopez-Bautista, J. 2018.
  • Taxonomic notes on the genus Alsidium C. Agardh, including the merging of Bryothamnion Kützing (Rhodomelaceae). Algae, 33(3), 215-229
  • Lemes-da-Silva, N., Safrankova, M., Branco, L.H. and J. Lopez-Bautista. 2018. A new and cryptic species of Trentepohlia (Ulvophyceae, Chlorophyta) from Brazilian mixed forests. Phycologia (accepted)
  • Hoffman, R., Wynne, M., Schils, T., Lopez-Bautista, J. and H. Verbruggen. 2018. Codium pulvinatum (Bryopsidales, Chlorophyta), a new species form the Arabian Sea, recently introduced into the Mediterranean Sea. Phycologia 57(1):79-89.
  • Chavez-Sanchez, T., Piñon-Gimate, A., Serviere-Zaragoza, E., Lopez-Bautista, J. and M. Casas-Valdez. 2018. Ulva blooms in the Southwestern Gulf of California: Reproduction and biomass. Estuarine, Coastal and Shelf Science 200:202-211.
  • Cortona, A., Lelieaert, F., Bogaert, K., Turmel, M., Boedeker, C., Janouskovec, J., Lopez-Bautista, J., Verbruggen, H., Vandepoele, K. Clerkc, Ol. 2017. The Plastid Genome in Cladophorales Green Algae is Encoded by Hairpin Plasmids. doi: https://doi.org/10.1101/145037
    Lam, D. and J. Lopez-Bautista. 2016. Complete chloroplast genome for Caulerpa racemosa (Bryopsidales, Chlorophyta) and comparative analyses of siphonous green seaweed plastomes. Cymbella II(2):23-32 Access here
  • Lopez-Bautista,J. 2016. Reseña libro: Macroalgas marinas de Cuba. Algas 51:90-91.
  • Garcia-Soto, G., Sole-Sempere, M. and J. Lopez-Bautista. 2016. Catalogo Sistematico de las macroalgas marinas de isla Zapara, Estado Zulia, Venezuela. ALGA 51:52-62.
  • Melton J.T. III, Gabriela Garcia-Soto, and Juan M. Lopez-Bautista. 2016. A new record of the bloom-forming green algal species Ulva ohnoi Hiraoka & S. Shimada, 2004 (Ulvales, Chlorophyta) in the Caribbean Sea. ALGAS 51:62-64.
  • Lelieart, F., Tronholm, A., Lemieux, C., Turmel, M. Depriest, M., Bhattacharya, D., Karol, K., Fredericq, S., Zechman, F. and J. Lopez-Bautista. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae nov. Scientific Reports 6:25367 DOI:10.1038/srep25367.
  • Melton, J.T. III, Collado-Vides, L., and J. Lopez-Bautista. 2016. Molecular identification and nutrient analysis of the green tide species Ulva ohnoi (Ulvophyceae, Chlorophyta), a new report and likely nonnative species in the Western Atlantic. Aquatic Invasions 11(3): 225-237. DOI: 10.3391/ai.2016.11.3.01
  • Zi-Min Hu, De-Lin Duan and J. Lopez-Bautista. 2016. Seaweed phytogeography from 1994 to 2014: An Overview. In: Zi-Min, Hu and C. Craser (Eds.) Seaweed Phytogeography: Adaptation and Evolution of Seaweeds under Environmental Change, Springer, Netherlands, pp. 3-22.
  • Melton, T. and J. Lopez-Bautista. 2015. De novo assembly of the mitochondrial genome of Ulva fasciata Delile (Ulvophyceae, Chlorophyta), a distromatic blade-forming green macroalga. Mitochondrial DNA Part A. DOI: 10.3109/1940736.2015.1082095 PDF
  • Cardosi, J., Blackwell, J. Leliaert, F., Ginzbarg, S. and J. Lopez-Bautista. 2015. Digitizing the algal herbarium at The University of Alabama (UNA). Joshua, Accepted March 2, 2015
  • Melton, T., Leliaert, F., Tronholm, A. and J. Lopez-Bautista. 2015. The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta). PLOSONE,DOI: 10.1371/journal.pone.0121020, Published: April 7, 2015 PDF
  • Leliaert, F. and J. Lopez-Bautista. 2015. The chloroplast genomes of Bryopsis plumosa and Tydemania expeditionis (Bryopsidales, Chlorophyta). BMC Genomic 16:204, DOI: 10.1186/s12864-015-1418-3 PDF
  • Leliaert F, Lopez-Bautista JM, De Clerck O. 2015. Class Ulvophyceae K. R. Mattox & K. D. Stewart. In: (Frey, W., Ed.) Syllabus of Plant Families (A. Engler’s Syllabus der Pflanzenfamilien, 2/1 Eukaryotic Algae, 13th ed., ISBN 978-3-443-01083-6, 324 pp., 67 figs., Borntraeger, Germany
  • Fucikova, K. Leliaert, F., Cooper, E., Skaloud, P. D’Hondt, S., DeClerck, O., Gurgel, C., Lewis, C., Lewis, P., Lopez-Bautista, J., Delwiche, F., and H. Verbruggen. 2014. New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence datasets. Frontiers in Ecology and Evolution 2(63):1-12 PDF
  • Lam, D. and J. Lopez-Bautista. 2014. Epiphytic diversity of the Raleighvallen rainforest (Suriname, South America) based on environmental DNA sequences. Bol. Soc. Mex. Ficologia 5:36-45. PDF
  • DePriest, S., Bhattacharya, D., and J. Lopez-Bautista. 2014. The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae. Biol. Bull. 227(2): in press.PDF
  • Leliaert, F., Verbruggen, H., D’Hondt, S., Lopez-Bautista, J. and O. DeClerck. 2014. The forgotten genus Pseudoderbesia (Bryopsidales, Chlorophyta). Cryptogamie Algologie 35(3):207-219.PDF
  • Allali, H. Ward, D. and Lopez-Bautista. 2014. The use of metagenomics to infer algal diversity in a subaerial community from an African tropical rainforest, “Les Monts de Cristal” national park, Gabon. Bol. Soc. Mex. Ficologia 3:6-19 PDF
  • Frederik Leliaert, Heroen Verbruggen, Pieter Vanormelingen, Frederique Steen, Juan M. López -Bautista, Giuseppe C. Zuccarello, Olivier De Clerck. 2014. DNA-based species delimitation in algae. European J. Phycol. 49(2):179-196PDF
  • Zi-Min Hu, Lopez-Bautista, J. and De-Lin Duan. 2014. How to rectify the misuse of scientific names in bioscience? Chinese Science Bull. 59(13):1479-1481.PDF
  • Zi-Min Hu, Lopez-Bautista Juan. 2014. Adaptation mechanisms and ecological consequences of seaweed invasions: a review case of agarophyte Gracilaria vermiculophylla. Biological Invasions 16:967-976PDF
  • DePriest, M., Bhattacharya, D. and J. Lopez-Bautista. 2013. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS ONE8(7): e68246. doi:10.1371/journal.pone.0068246 PLOS ONE
  • Young, R., von Salm, J., Amsler, M., Lopez-Bautista, J., Amsler, C., McClintock, J.., and B. Baker. 2013. Site-specific variability in the chemical diversity of the Antarctic red alga Plocamium cartilagineum. Mar. Drugs. 11:2126-2139. PDF
  • Zi-Min, H., Zhang, J., Lopez-Bautista, J. and D. De-Lin. 2013. Assymetric genetic exchange in the brown seaweed Sargassum fusiforme (Phaeophyceae) driven by oceanic currents. Marine Biology 160(6):1407-1414  PDF
  • Allali, H., Rindi, F. and J. Lopez-Bautista. 2013. Biodiversity of Trentepohliales (Ulvophyceae, Chlorophyta) in Gabon, central Africa. Nova Hedwigia 96(3-4):309-324 PDF