EAGER: Fertilizing the Tree of Life with novel taxa from deep-sea vent microbial metagenomes collected over time and space

Portland State University, Portland OR

Investigators

Abstract

Deep-sea hot springs occurring along mid-ocean ridges or in deep-sea volcanoes, are some of the most poorly explored environments on Earth. When the very hot gas-filled and mineral-rich water mixes with the cold seawater at depths greater than 1500 meters (>1 mile), the minerals precipitate out of solution producing porous rocks often referred to as ‘chimneys’. These structures are colonized by a very rich diversity of heat-loving microbial life, much of which is new to science. The researchers will use cutting-edge genomic technology to sequence the genomes of the microbes in these high temperature ecosystems from samples collected over the past 25 years in the Atlantic, Pacific and Indian oceans. The research will transform our understanding of the extent and complexity of life on Earth and will provide insights into how life thrives and evolves under these extreme conditions. Further, the genomic information unlocked in this study can be used to search for future biotechnological and industrial applications. Additionally, data generated in this research will serve as a microbial genomic resource for the UN High Seas agreement adopted in June 2023, which in part aims prevent biodiversity loss in the high seas. The overall goal of the research is to synthesize the spatial and temporal dynamics of archaeal and bacterial environmental genomes in deep-sea hydrothermal vent deposits. This approach is transformative as it will be possible to develop an extensive temporal framework of microbial genomic biodiversity from deep-sea hydrothermal vent deposits in the Pacific, Atlantic and Indian Oceans, and provide further taxonomic and diversity insights into poorly represented lineages from deep-sea vents. Specifically, representative deep-sea hydrothermal vent metagenomes and culture collection genomes will be characterized by integrating recent metagenomes with those obtained through this research, spanning data from 1999-2018. Reference (type) metagenome assembled genomes (MAGs) of new genera, families, orders, classes, and phyla from deep-sea vent environments will be curated, named and deposited in Genbank, the Genome Taxonomy Database (GTDB) and in the recently developed SeqCode. These genomes will be integrated into taxonomic characterization and synthesis of the clades such has the Aquificota, Aciduliprofundales and Desulfurellales (Hippea spp.) and the taxonomic revision of the Thermoprotei. Using metagenomic approaches, the research will explore whether functional and/or phylogenomic changes have occurred over time from single and global sites, and address outstanding questions in microbial taxonomy, such as how or whether type-strain environmental genomes evolve over time, or even spatially; key processes to understanding the evolution of life on Earth. 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.