MIcrobial Diversity Training for New Problems in a New Era

The Microbial Biodiversity Advanced Research Training Course at the Marine Biological Laboratory (MBL) is a highly regarded, intensive six-week experience. For over 50 years, it has been instrumental in training generations of early career researchers in the field of advanced microbial sciences. The primary objective of the program is to equip students with the modern experimental skills necessary to investigate microbiological questions across various biological scales, ranging from the study of single microbial cells, populations, or ecosystems. The Microbial Biodiversity course is dedicated to cultivating the next generation of microbial scientists in modern experimental techniques and interdisciplinary approaches to understand and predict the function of microbial communities in ecosystems health and the impact of microbiota on the planet. This training prepares students to contribute to a variety of research careers, including those in the biotechnology sector and life sciences medicine. The course investigates microbial biodiversity in rich natural freshwater and intertidal ecosystems including a) Trunk River, a brackish intertidal inlet; b) the Great Sippewissett Salt Marsh; c) the acidic, freshwater Cedar Swamp; and d) the School Street Marsh, a phototrophic and iron- oxidizing layered community. Students isolate collections and develop genomic in-house datasets that are made publicly available for current and future courses to delve into evolutionary and ecological processes. Focused training includes: (i) genome-enabled laboratory isolations emphasizing the functional analyses of understudied bacteria, archaea, microbial eukaryotes, and viruses (ii); in situ physiological and imaging approaches to quantify spatial and temporal microbial dynamics in local habitats; (iii) single cell and population-based approaches to quantify genetic and phenotypic heterogeneity and evolutionary mechanisms creating and maintaining biodiversity in microbial populations; and (iv) analyze disparate data sets from field/lab work with machine learning / statistical learning approaches (i.e., artificial intelligence) to reveal new connections in microbial ecology exploration. The new curriculum includes theoretical, practical and computational training in microbiology, cell biology, and microbial ecology with research in genetic mechanisms that generate microbial biodiversity. Junior faculty and other early-career researchers, who will be mentored in teaching pedagogy, will lead research projects. Through these interactions trainees develop and broaden their research network to support future training and collaborations. Objective 1. Equip the next generation of microbiologists with skills in metagenomics-enabled cultivation and in developing new non-model genetic systems for isolates and consortia. The course integrates comprehensive theoretical and practical training in microbial physiology, metabolism, and genomics, with a focus on cutting-edge techniques for cultivating bacteria, archaea, microbial eukaryotes, and their associated viruses. Objective 2. Identifying and understanding microbial biogeochemical transformations and cryptic pathways using functional genomic, biochemical, and imaging approaches. Advanced training in modern biochemical, genetic, and cell biological approaches to investigate biological innovation and novel biogeochemical pathways. Emphasize experimental approaches for both population- based and single-cell techniques, including FACS-based single-cell genomics (SAG) and single-cell transcriptomics. Objective 3. Initiate field and/or lab work that asks how one field component, microbiota, influences another component, e.g., geochemistry and apply predictive machine learning and statistical learning (ML/SL) tools to correlate seemingly disparate data sets to reveal unforeseen relationships. Integrate both theoretical and practical training in molecular microbial ecology with advanced computational tools to find solutions to complex problems. The Microbial Biodiversity Course offers an unparalleled opportunity for immersive research and transformative professional growth for students in both fundamental and applied topics in Microbial Biodiversity. Students thrive with hands-on practical training, close mentorship, and exposure to cutting-edge research through interactions with renowned visiting scientists. Participants engage in cross-disciplinary collaborations through lectures and symposia shared with other MBL training courses. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.