Links within this page: Extremophiles and Rare Microorganisms Workshop: isolation, culturing and characterization | Microbial Genomes, Metagenomics, and Transcriptomics | Metagenomic Analyses of Microbial Communities from Extreme Environments | Ecology and Conservation of the Aquatic Box Turtle (Terrapene coahuila) | Remote Sensing and Landscape Modeling for Desert Environments | Field trip: Geological and hydrogeological features of the Cuatro Ciénegas Basin and mountains
Date: May 26 & 27th, 2025
Location: Laboratorio Génesis, Cuatro Ciénegas, Coahuila.
Led by: Dr. Nahui Olin Medina-Chavez and Dr. Susana De la Torre Zavala
Capacity: 15 participants
Through a combination of theoretical talks and hands-on lab work, participants will learn sampling strategies, pre-treatment methods, and both traditional and modern “culturomics” approaches for isolating, characterizing, and preserving microorganisms. With a focus on extremotolerant microbes and the thresholds they endure, attendees will gain insights into why culturing remains vital for advancing microbiological research. This workshop offers a unique opportunity to explore the microbial frontier where evolution and harsh environmental conditions intersect.
Date: May 26 & 27, 2025
Location: Laboratorio Génesis, Cuatro Ciénegas, Coahuila
Led by: Dr. Cuauhtémoc Licona-Cassani
Capacity: 15 participants
In this workshop, participants will explore both the theoretical and practical aspects of preparing DNA and RNA from environmental and purified samples for sequencing. Through hands-on lab work, attendees will learn key sampling strategies, best practices for quantification and quality control, and how to select the most suitable isolation techniques based on research goals. Discussions will address choosing appropriate sequencing platforms—metagenomic or transcriptomic—and designing effective analysis pipelines to assess data quality and interpret results. This immersive experience offers insight into the full workflow of microbial genomics research, from field sampling to advanced bioinformatic processing.
Date: May 27, 2025
Location: Laboratorio Génesis, Cuatro Ciénegas, Coahuila
Led by: Dr. Maribel Hernandez and Dr. Manuel Barrios
Capacity: 15 participants
In this workshop, participants will learn essential skills for processing metagenomic sequencing data, including: microbial species identification, metagenome assembly and metagenome annotation. This workshop provides a unique opportunity to explore the microbial diversity of extreme environments, bridging the gap between raw data and ecological insights.
Date: May 26 & 27, 2025
Location: Field sites and Hotel Marielena, Cuatro Ciénegas, Coahuila
Led by: Dr. Gamaliel Castañeda Gaytán,Universidad Juárez del estado de Durango (UJED)
Capacity: 10 participants
This workshop focuses on the ecology and evolutionary status of the Coahuilan box turtle—an endangered species uniquely adapted to aquatic habitats. Participants will learn about its natural history, behavior, and habitat use in Cuatro Ciénegas, as well as ongoing environmental protection efforts. Through field observations and interactive discussions, attendees will gain insight into why this “Tortuga bisagra” spends most of its life in water, setting it apart from other Terrapene species. This hands-on experience offers a rare opportunity to understand and support critical conservation strategies for one of Mexico’s most distinctive endemic reptiles.
Date: May 26 & 27, 2025
Location: Hotel Marielena, Cuatro Ciénegas, Coahuila
Led by: M.Sc. Plinio Guzmán
Capacity: 15 attendees
This workshop provides practical tools to access and process satellite data for evaluating surface water bodies and desert landscapes. Participants will explore computer vision and machine learning techniques to analyze remote sensing data, enabling them to extract valuable insights for research and resource management. While the session involves coding in Python, it is designed for non-programmers interested in applying these tools in their own work.
To ensure tailored content, registrants are required to submit a short paragraph describing their experience with satellite imagery and programming for data analytics, along with their goals for attending the session. Participants must bring their own laptop.
Date: June 1, 2025, from 7:00 am to 6:00 pm
Location: This field trip will start from Hotel Marielena, Cuatro Ciénegas, Coahuila
Led by: Dr. Mariano Cerca, Dr. Jorge Aranda Gómez, Dr. Dora Carreón Freyre, and Dr. Gabriel Chávez Cabello
Capacity: 15 attendees
This trip is about exploring the unique geological features of the Cuatro Ciénegas Basin, discussing the hydrogeological implications, and immersing yourself in the unique experience of exploring the mountains surrounding the basin. It focuses on the unique geological site of the Cuatro Ciénegas Basin. During the field trip, we will visit selected sites of geological relevance, from marine sedimentary rocks to a set of mafic scoria cones and associated lava flows that occur in the valley located between the towns of Cuatro Ciénegas and Ocampo in Coahuila. The stratigraphy of the Cuatro Cienegas region spans from the Early Cretaceous to the Recent. The geological evolution of the area is linked to the breakup of Pangea and the establishment of a passive margin during most of the Cretaceous. The mountains surrounding the Cuatro Cienegas valley, such as the Menchaca, La Fragua, La Madera, and San Marcos ranges, show a spectacular record of the shortening deformation that affected the area during the Late Cretaceous and Early Paleogene.
The valley of Cuatro Cienegas hosts a highly sensitive hydrogeological system where water loss in the last years has led to catastrophic biodiversity decline. Understanding the geological evolution of the region can give insight into the aquifer flow dynamics. The participants will explore the region's geological history and its relation with the sedimentary filling of the basin. We will finish the day exploring gypsum dunes and discussing a hydrogeological conceptual model for the Cuatro Cienegas Basin. The excursion will provide a hands-on experience and insights into the interplay between geology, hydrology, and biodiversity in this extraordinary desert oasis.
The cost will be $60 US DLL. What is included
- Transportation in vehicles adequate for the field trip,
- lunch during the field trip
- including one drink
- expert geologists and geomorphologists.
BiGEvo 2025 invites researchers, practitioners, and students to contribute to an interdisciplinary forum exploring the connections between bioinformatics, evolution, and geology. This event will provide a unique opportunity to showcase scientific advancements, foster collaboration, and engage in rich discussions that bridge disciplines.
Why Submit? BiGEvo 2025 will feature an exciting scientific programme including keynote presentations, talks selected from submitted abstracts, poster sessions, and pre-conference workshops. Contributing your work ensures visibility, collaboration, and the chance to advance meaningful discussions across the scientific community.
Topics of Interest Include:
- Computational Evolutionary Biology
- Evolutionary Biology and Astrobiology
- Geology and Evolution
- Climate Change and Environmental Impacts
- Ecology of Stromatolites, Microbialites, and Microbial Mats
- Evolutionary Genomics and Metagenomics
- Bioprospection for Novel Discoveries
- Wetland Conservation
- Hydrogeology
- Geomicrobiology
- Environmental Paleoecology, DNA from Soils and Sediments (sed- and sedaDNA), and Paleoclimatology
- Extremophiles and Adaptation
- Geospatial & Geophysical Studies of Semiarid Environments
- Lacustrine Environments in Arid Areas
- Biogeochemistry
Submission Guidelines
- Abstracts must not exceed 500 words. Submissions will be considered for poster sessions ONLY.
- All abstracts should clearly outline the research objectives, methods, key results, and conclusions.
- The official language of the conference will be English.
Don’t miss your chance to contribute to this dynamic scientific gathering! Submit your abstract today and be part of a program that drives interdisciplinary research forward.
Deadline for Late-poster Abstract Submission: 1 May 2025
Join us at BiGEvo 2025 to share your work, spark new collaborations, and shape the future of research at the intersection of bioinformatics, evolution, and geology!
Links within this page: Steering Committee
Steering Committee
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Héctor Arocha Director Museo Génesis Cuatrociénegas, Coahuila |
Dora Carreón-Freyre Senior Researcher at the Institute of Geosciences, UNAM Head of the Laboratory of Mechanics of Geosystems Past-Chair of the UNESCO International Initiative of Land Subsidence |
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Mariano Cerca Instituto de Geociencias UNAM |
Susana De la Torre Zavala Profesora Investigadora Laboratorio 9, Instituto de Biotecnología Facultad de Ciencias Biológicas UANL |
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Octavio García Director Grupo T ITRASIG México |
Felipe García Oliva Instituto de Investigaciones en Ecositemas y Sustenabilidad UNAM |
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Maribel Hernández Bioinformatics & Complex Networks Lab Cinvestav Unidad Irapuato |
Diane E. Kovats ISCB Chief Executive Officer United States |
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Bárbara Moguel Associate Professor Universidad de las Américas Puebla |
Gabriela Olmedo Alvarez Lab Mol. Biol. and Microbial Ecology Cinvestav Unidad Irapuato |
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Links within this page: Elizabeth Chacón Baca | Devaki Bhaya | Daniel Carrizo | Karen Lloyd | Laxmi Parida | João Carlos Setubal | Joel Stavans | Valeria Souza
Elizabeth Chacón Baca
Universidad Autónoma de Nuevo León
Mexico
Dr. Elizabeth Chacón is a paleontologist specializing in biogeochemical and geobiological studies of ancient ecosystems, particularly Cretaceous stromatolites and microfossils. Her research integrates paleontology, geochemistry, and astrobiology, contributing to our understanding of early life on Earth. She has conducted international research stays at UC Santa Barbara, University of Göttingen, and Harvard University, collaborating on exobiology and planetary biology. Currently a professor at UANL. She actively promotes science communication and has served as President of the Mexican Society of Paleontology (SOMEXPAL, 2020–2023). Recently, she was accepted into the Mexican Academy of Sciences (Geosciences, 2024). Her research has contributed to understanding ancient ecosystems and their relevance to modern conservation and planetary science.
Fosil and Recent Mcrobialites, a multiscalar study
Through the fossil record organosedimentary rocks known as microbialites have been continuously forming mainly as microbial carbonates. Such microbial carbonates result from multiple microbial-mineral interactions among a great diversity of microbial communities and under a wide range of environmental conditions. Not only microbialites are the oldest paleontological evidence of life on Earth but also a rich source of biosignatures with the greatest potential preservation potential on extraterrestrial surfaces. This talk includes relevant aspects on the microscopical characterization of the thrombolites from Cuatro Cienegas as modern analogues where geobiological processes act at different scales
Devaki Bhaya
Carnegie Institution for Science
United States
My research group studies extremophile microbial communities in the hot springs of Yellowstone National Park, seeking to understand how microbial diversity and dynamics correlate with gradients of temperature and light. We employ comparative genomics, meta-omics data, and single amplified genomes to quantify the role of genomic micro-diversity, horizontal gene transfer, host-phage coevolution, and metabolic versatility in these communities. I will frame our findings within the broader context of how collaborations with computational and evolutionary biologists have enriched our understanding of phototrophic community dynamics, highlighting how physical parameters (e.g., light), in combination with genetic diversity, shape the microbial world.
Tracking diversity and defense in phototrophic communities
The colorful microbial mats in the hot springs of Yellowstone National Park represent stratified biofilms where 16S rRNA diversity has been correlated with environmental gradients of temperature, oxygen and light. These extremophile phototrophic communities are ideally suited to gain deeper insights into how microbial diversity, dynamics and defense strategies are correlated with environmental gradients. In particular, we are interested in how microbial communities cooperate and also how they deal with biotic and abiotic stressors. To do so, we use various bioinformatic and molecular approaches including comparative genomics, diel transcriptomics, metagenomics (based on short and long read datasets) and information gained from single amplified genomes. I will describe our strategies to quantify and understand the role of genomic micro-diversity, horizontal gene transfer, host-phage coevolution and metabolic versatility in these communities. I will emphasize how collaborations with computational and evolutionary biologists has enhanced our understanding of the diversity and dynamics of phototrophic communities and how physical parameters (such as light) and biotic stressors (such as phage attack) shape the microbial world.
Supported by National Science Foundation, Carnegie Institution, DOE Joint Genome Institute, and Environmental Molecular Sciences Laboratory.
Daniel Carrizo
Centro de Astrobiología, CSIC-INTA
Spain
Daniel Carrizo holds a PhD in Environmental Analytical Chemistry (Barcelona, Spain). He has a multidisciplinary background (biogeochemistry, analytical chemistry, environmental chemistry, atmospheric chemistry) with extensive laboratory (5 post-doctoral contracts in Australia, Sweden, Portugal, Spain and UK) and field experience (campaigns in the Arctic, Atlantic Ocean, Antarctica, Atacama Desert, Andes Mountains, Iceland, etc.). He has experience in the development and application of analytical techniques (GC-MS, HPLC, IRMS, GC-IRMS, IR, Raman, metabolomics) for the investigation of the fate, partitioning and taphonomic processes of organic compounds and their associated stable isotopes (C, H, etc.) in the environment. Since 2021, he has been a Senior Scientist at the Center for Astrobiology, INTA, and directs the “Biogeochemistry of Extreme Environments” laboratory at the CAB.
Biomarkers, molecular fossils and stable isotopes as powerful tools to decipher life in extreme environments: from deep ocean to Mars
Extreme environments, from the deep ocean to extraterrestrial landscapes like Mars, present unique challenges for detecting and understanding life. Biomarkers, molecular fossils, and stable isotopes serve as powerful tools for studying these environments, providing chemical signatures that reveal past and present biological activity. Lipids biomarkers offer insights into microbial life forms that adapt to extreme conditions, while molecular fossils preserve traces of ancient organisms, even in environments where traditional fossils cannot survive. Stable isotope analysis further enhances our understanding by identifying biological fractionation patterns that distinguish biotic from abiotic processes as well different metabolic pathways involved in the synthesis of these lipid compounds. By integrating biomarker research, molecular fossil analysis, and isotope geochemistry, we can reconstruct past and present biosignatures, offering profound implications about how and under what environmental conditions life arose and evolved on Earth, as well as implications to search for life beyond Earth. In this presentation we are going to talk about our research experience in lipids biomarkers and their isotopic composition and how these tools can help us to infer microbial communities structures, metabolic pathways or paleoenvironmental conditions in different extreme environments on Earth.
Karen Lloyd
University of Tennessee
United States
Karen G. Lloyd is the Wrigley Chair in Environmental Studies and Professor of Earth Sciences at the University of Southern California. She explores the undiscovered world of subsurface microbiology and how these ecosystems interact with Earth’s geochemical cycles. Her work covers deep-sea methane seeps and mud volcanoes, volcanic arcs, and deeply-buried Arctic permafrost. Her first book, called Intraterrestrials: Discovering the Strangest Life on Earth will be published in May 2025.
Hot springs as windows into the deep biosphere
Many natural springs flush deep subsurface microbes up to the surface. This allows us to obtain a landscape scale view of the subsurface biosphere and determine how it might be supported by deep volcanic volatile emissions. These deep volatiles include carbon, hydrogen, sulfur and nitrogen compounds that can serve as biomass and energy resources for a deep subsurface biosphere. I will present recent research establishing these relationships across the Costa Rican subduction zone.
Dr. Laxmi Parida is an IBM Fellow, Master Inventor, and the head of Computational Genomics at IBM T.J. Watson Research Center. She is a recognized expert in computational biology, applied mathematics, and machine learning, with extensive contributions to genomics, network science, and topological data analysis. A member of the Mathematical Sciences Council and the IBM Academy of Technology, she also serves as a visiting professor at NYU’s Courant Institute of Mathematical Sciences. With over 200 peer-reviewed publications, 50 US patents, and several prestigious awards—including the Cacao Innovator Award—Dr. Parida is a leader in advancing computational approaches in biology. She also plays an active role on advisory boards and editorial committees in bioinformatics and computational sciences.
The Changing Landscape of Computing in Life Sciences
AI, particularly Foundation models and Generative AI, has many success stories in a wide arena of applications, including biology. Does AI solve it all? I will discuss some problems that are not very suitable for AI. I will give a quick introduction to topological data analysis (TDA) and describe the application of TDA to these problems. In the final part of the talk I will discuss an exploration we are currently doing with the emerging technology of Quantum Computing.
João Carlos Setubal
Universidade de São Paulo
Brazil
João Carlos Setubal is a Brazilian researcher in bioinformatics, specializing in the computational analysis of genomic, transcriptomic, and proteomic data. His work aims to improve our understanding of organisms and their evolutionary histories by developing and applying advanced computational tools to process large-scale biological data. As a professor at the University of São Paulo (USP), he leads a research group focused on creating bioinformatics solutions that have applications in medicine, agriculture, energy, and environmental science. His current research includes studying microbiomes in diverse environments, reconstructing genomes from metagenomic data, and developing computational tools for microbiome analysis. He is involved in several major projects, such as the FAPESP-funded Center for Research in Bacterial and Bacteriophage Biology (CEPID B3) and the CNPq-supported bigDiscovery (bigD) project in bioinformatics and genomics. His team also investigates the metagenomics of the São Paulo Zoo microbiota and gene expression in angiogenesis. Through these projects, Setubal contributes to advancing genomic research and its applications in health, biodiversity, and environmental sustainability.
Species and strain diversity of bacterial genera in large-scale metagenomic datasets
We have developed a computational tool that can mine large-scale metagenomic datasets for their species and strain diversity given user-specified bacterial genera. In our tests, this tool provides more accurate results than general-purpose taxonomic classification programs. In this talk I will describe the tool and show results for a few genera, such as Xanthomonas, Acinetobacter, and Stutzerimonas.
Joel Stavans
Weizmann Institute of Science
Israel
We study different aspects of bacteria and their lifestyles from quantitative and physics points of view using various approaches, both experimental and theoretical. The focus of our studies ranges from genetic networks at the single cell level and the influence of intrinsic noise, search processes within cells during horizontal gene transfer, to morphogenesis, pattern formation and synchronization of circadian clocks in multicellular cyanobacteria. Most recently we have turned our attention to the systems ecology of multispecies bacterial communities such as those from Cuatro Ciénegas and in particular, their self-organization in the water column under the influence of oxygen gradients and gravity.
Spatial segregation during oxytaxis-driven bioconvection in multispecies planktonic bacterial communities
Large groups of agents often exhibit self-organized, collective motion and the emergence of coherent spatial structures whose characteristic scales largely exceed the size of the agents themselves. Prime examples covering many length scales range from mammal herds, fish schools and bird flocks, to insect and robot swarms. Despite significant advances in understanding the behavior of large homogeneous groups in the last decades, little is known about the self-organization and dynamics of heterogeneous groups.
Under oxygen gradients, oxytactic (aerotactic) motile bacteria can swim in auto-organized, flows called bioconvection, whose spatial scales exceed the bacterial size by three orders of magnitude. I will present results of bioconvection experiments with multispecies suspensions of wild-type bacteria collected from the hyper-diverse bacterial communities of Cuatro Ciénegas in Mexico, whose origin date to the pre-Cambrian. Our real time fluorescence microscopy experiments show that these bacteria display a plethora of amazing dynamical behaviors, including inter-species spatial segregation in shallow suspensions. The mechanisms giving rise to these complex behaviors stem both from biological and physical inter-species interactions.
The results advance our understanding of heterogeneity in the dynamics of complex planktonic microbial ecological communities and the role of oxygen in the water column, bringing profound insights into their spatial organization and collective behavior.
Dr. Souza has spent over two decades investigating how and why diverse microbial species coexist, focusing particularly on the oasis of Cuatro Ciénegas. Her research examines the evolutionary, physiological, and ecological processes that drive speciation and shape microbial communities. A recognized authority on the preservation of Cuatro Ciénegas, her work highlights the interplay between fundamental science and conservation efforts, with an emphasis on understanding ecological and evolutionary dynamics, species coexistence, and the development of conservation strategies based on scientific research. In addition to her research, she has been deeply committed to education and outreach, engaging with students in Cuatro Ciénegas to promote scientific literacy and environmental awareness.
Cuatro Ciénegas: What have we learned in 25 years?
We arrived at Cuatro Ciénegas in 1999, brought by NASA to study it as a model of the sea in the Early Cambrian and possibly early Mars, and what we found was far more fantastic than expected. The San Marcos y Pinos Mountains hold a magmatic pocket in their depths, forcing a deep aquifer rich in viruses, bacteria, and ancient archaea to rise to the wetland, where they form microbial mats and stromatolites. As a result of this "sampling" of a vast gene pool, we observed that each sample is different, yet metabolically complementary. The lineages are highly diverse and generally exhibit long branches, suggesting a lost world that isolated itself from the rest of the world in the mountains and experienced, in isolation, its own evolutionary processes. However, Churince, Pozas Rojas, and Domos del Arqueano are three systems that have been studied over time. Two of them are already dry, and we hope that Pozas Rojas can function as a reservoir and as a "vent," a site where the primary productivity of the deep microbiome can photosynthesize before returning to the depths and, by infiltrating, feed the enormous diversity found in the deep aquifer. It is a tragedy that this aquifer is overexploited, and we hope that new conservation and awareness-raising actions will lead to the conservation of this unique site.
Mike Travisano
University of Minnesota Twin Cities
United States
Dr. Travisano’s research spans from the origin of life to the fundamental mechanisms driving biological diversity and complexity. His work has expanded from studying single bacterial and archaeal species to exploring predator-prey dynamics, cooperative microbial interactions, and the transition to multicellular life. With a deep interest in evolutionary biology, his lab examines how adaptation unfolds in real time and how simple biological systems evolve into more complex forms. Using experimental evolution, he investigates how ecological interactions drive the evolution of multicellularity.
Experimental Evolution and the Origins of Complexity
I will present insights from experimental evolution studies that explore how simple microbial systems evolve complexity. Our research reveals how ecological interactions and selection pressures shape the emergence of multicellularity. By studying microbial communities over thousands of generations, my research group offers a window into the mechanisms driving biological innovation.