Bio


I am a geobiologist and am generally interested in the connections between microbial ecology and biogeochemical cycling.

I grew up in the foothills of the Cascade mountains in Oregon. For my undergraduate degree, I attended Amherst College (Amherst, MA) and majored in Biology. After graduating, I spent three years working in diverse lab settings. I interned at the Sanibel-Captiva Conservation Foundation (SCCF) Marine Lab in Florida, worked for a year in a plant-microbe symbiosis lab at UCSB, and then worked for a year at MIT studying cyanobacteria. All these experiences increased my interest in microbial ecology and the co-evolution of life and Earth.

Currently, I am pursuing a PhD at Stanford in the Earth System Sciences department. I study nitrogen-cycling microbial communities in San Francisco Bay in the Francis Lab.

Honors & Awards


  • Amherst College Fellowship, Amherst College (2016, 2017, 2018)
  • Graduate Research Fellowship Program (GRFP), NSF (September 2016-2021)
  • Best Session Talk, Research Review Stanford Earth (April 2018)

Education & Certifications


  • BA, Amherst College, Biology (2013)

Service, Volunteer and Community Work


  • GSAC Advocacy Cochair, Stanford Earth (4/2018 - 6/2019)

    Stanford Earth Graduate Student Advisory Committee representative for ESS. Generally planned graduate student community building events and hosted departmental student town halls. As cochair I organized meetings with the Dean, led initiatives to redefine GSAC roles and responsibilities, and organized GSAC retreats. https://gsac.stanford.edu/

    Location

    Stanford, CA, USA

  • GSAC Secretary, Stanford University (4/2017 - 4/2018)

    Stanford Earth Graduate Student Advisory Counsel representative. Plan graduate student community building events and host departmental student town halls.

    Location

    Stanford, CA, USA

  • WES executive board, Stanford University (4/2017 - 4/2018)

    Women in Earth Science

    Location

    Stanford, CA, USA

  • RiSE working group (2/2018 - 10/2018)

    Respect in Stanford Earth

    Location

    Stanford, CA, USA

Current Research and Scholarly Interests


I am generally interested in the co-evolution of life and Earth, and am particularly interested in the ecology of Earth's smallest constituents: microbes. Along my path towards graduate school, I become particularly interested in marine microbes, especially bacteria and archaea, and how they impact global biogeochemical cycles. My current graduate research is focused on microbes in the highly polluted San Francisco Bay estuary. I am interested in using DNA-based and biogeochemical techniques to understand the ecology of nitrogen-cycling bacteria and archaea (organisms that can eat or breathe various nitrogen compounds such as ammonia or nitrate). I generally focus on some of my favorite organisms, Thaumarchaea, which use electrons from ammonia in their energy metabolism and produce nitrite in the process. Thaumarchaea are also called ammonia-oxidizing archaea and carry out the first step of nitrification (the conversion of ammonia to nitrate).

All Publications


  • Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus ELIFE Berube, P. M., Rasmussen, A., Braakman, R., Stepanauskas, R., Chisholm, S. W. 2019; 8

    Abstract

    Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing intraspecific allocation of ecologically important functions. Nitrate assimilation genes are absent in basal lineages but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, gene loss, and homologous recombination. By mapping this process onto a model of Prochlorococcus' macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.

    View details for DOI 10.7554/eLife.41043

    View details for Web of Science ID 000458353700001

    View details for PubMedID 30706847

    View details for PubMedCentralID PMC6370341