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Huber spent her youth in Chicago and has cited frequent visits to the local Shedd Aquarium as part of her inspiration to pursue a career in oceanography.^[5] Huber was an undergraduate student at Eckerd College in St. Petersburg, Florida, and received her B.S. in marine science in 1998.^[6] She received her Ph.D. in biological oceanography from the University of Washington in 2004 for work with oceanographer and astrobiologist John Baross on the microbial ecology of underwater volcanoes.^[5][6]

Huber began work as a postdoctoral fellow at the Marine Biological Laboratory, a facility in Woods Hole, Massachusetts affiliated with the University of Chicago, in 2005; she became an assistant scientist there in 2007. She joined the faculty at Brown University as an assistant professor of ecology and evolutionary biology in 2008.^[1] She became an associate scientist at MBL and the associate director of the Josephine Bay Paul Center in 2013, and an associate professor at Brown in 2014.^[6] She moved her laboratory to Woods Hole Oceanographic Institution in June 2017.

Since 2015 Huber has served on the editorial board of the scientific journal Environmental Microbiology and as a senior editor of mSystems, an open-access journal published by the American Society for Microbiology.^[6] Huber is also active in public outreach and science communication.^[5]

In 2025 Huber was elected a Fellow of the American Academy of Microbiology.^[7]

Huber’s research group studies the microbial ecology of the deep ocean, particularly the habitat formed beneath the sea floor and the contributions of microbes to marine biogeochemistry.^[1]