CAREER: Characterizing the phylogenetic lineages and genomic factors enabling adaptation in free-living marine nematodes

University Of Georgia Research Foundation Inc, Athens GA

Investigators

Abstract

Free-living nematodes are one of the most abundant microbial phyla found in benthic habitats worldwide, representing 70-90% of metazoan life forms in marine sediments and performing key functions such as nutrient cycling and sediment stability. Yet, their unexplored diversity—and the extreme paucity of taxonomic and molecular data from benthic marine ecosystems— represents one of the major challenges in biology and currently limits our capacity to understand the accelerating consequences of environmental change. This project uses cutting-edge -Omics approaches in conjunction with classical morphological taxonomy to characterize patterns regarding the biodiversity, evolution, and ecology of free-living marine nematodes and their host-associated microbiomes. First, this work uses eDNA metabarcoding to determine how overall meiofaunal biodiversity changes across marine habitat transitions (depth, salinity) and gradients of environmental stress (pollution, oxygen availability). Second, the project identifies key nematode lineages which maintain “cosmopolitan” distributions across key marine gradients, and lineages which can tolerate the most extreme environmental stressors. Finally, this work characterizes the nematode genomic adaptations and host-associated microbiome patterns that may facilitate nematode dispersal and adaptation to extreme environmental stress. Educational activities are being strongly integrated with data generation and analysis of nematode -Omics datasets. The investigator leads an effort to build foundational computational skill sets in undergraduate and graduate students at the University of Georgia, establishing and growing a local bioinformatics community of practice. Weeklong summer hackathons aimed at intermediate bioinformatics learners merge data visualization and science communication tools and teach participants how to “tell stories through data”. Finally, this project engages undergraduate researchers in “sediments to species” workflows, providing interdisciplinary education in classical molecular systematics, bioinformatics, and science communication. The goal of this project is to carry out the first large-scale investigation of free-living marine nematodes that that collects molecular data across marine habitat transitions (salinity, depth) and gradients of environmental stress (pollution, oxygen availability), providing a comparative dataset for the existing body of historical (morphological) taxonomic studies. This research uses a novel approach that combines traditional light microcopy, environmental DNA sequencing, and single-worm genome sequencing in order to advance scientific knowledge of free-living nematodes and their ecological and evolutionary roles in marine habitats worldwide. The resulting datasets produce an important baseline of global nematode biodiversity in shallow-water and deep-sea marine habitats, and illuminate “dark areas” in the Nematode Tree of Life (lineages which are currently poorly sampled and lack molecular DNA barcodes). This project combines interdisciplinary research themes spanning marine nematode systematics, bioinformatics, and microbial ecology, with a strong integration of computational training and science communication for undergraduate and graduate students across all project aims. Research outputs are rapidly advancing our knowledge of the structure and function of seafloor habitats worldwide, and molecular datasets lay the groundwork for future genome-enabled studies of diverse free-living nematode groups. 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.