Education & Certifications


  • Ph.D., School of Earth, Energy and Environmental Sciences, Earth System Science (2020)
  • BS (Honors), Stanford University, Earth Systems - Biosphere (2014)

All Publications


  • Depth distributions of Nitrite Reductase (nirK) Gene Variants Reveal Spatial Dynamics of Thaumarchaeal Ecotype Populations in Coastal Monterey Bay. Environmental microbiology Reji, L., Tolar, B. B., Smith, J. M., Chavez, F. P., Francis, C. A. 2019

    Abstract

    Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1111/1462-2920.14753

    View details for PubMedID 31330081

  • Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column ISME JOURNAL Reji, L., Tolar, B. B., Smith, J. M., Chavez, F. P., Francis, C. A. 2019; 13 (5): 1144–58
  • Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column. The ISME journal Reji, L., Tolar, B. B., Smith, J. M., Chavez, F. P., Francis, C. A. 2019

    Abstract

    Ecological factors contributing to depth-related diversification of marine Thaumarchaeota populations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity-water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters-were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeota and heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobia and Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and Nitrospina OTUs. Even at depths where WCB-like Thaumarchaeota dominated, Nitrospina OTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.

    View details for PubMedID 30610232