Our research is focused on the discovery of novel bacterial, archaeal and eukaryotic microbes and viruses in environmental sequence data. We use multi-omics (metagenomics, metatranscriptomics, single cell genomics and phylogenomics) and machine learning to identify new divergent lineages and expand the Tree of Life. We then investigate the coding potential to find novel functions that may impact microbiome structure and biogeochemical cycles.
Research Team
 |
 |
 |
 |
| Frederik Schulz, PI, Research Scientist | Tomas Tyml, Project Scientist | Juan Villada, Postdoc | Clarence Le, Affiliate Researcher |
| [email protected] | [email protected] | [email protected] | [email protected] |
| More about Frederik. | Tomas uses traditional cultivation methods along with microscopy and genomics to study endosymbiotic associations within microbial eukaryotes. He hopes to broaden our understanding of the roles these associations play in the evolutionary history of life. | Juan uses approaches at the interface of evolutionary genomics and systems biology to discover novel microbial lineages, predict their lifestyle, and investigate their effects on the environment | Clarence identifies and analyzes novel clades of RNA viruses and determines novel viral gene functions that may impact hosts and host populations. |
 |
 |
 |
 |
| Marianne Buscaglia, Affiliate Researcher | Miguel Romero Gutierrez, Postdoc | Petra Byl, Affiliate Researcher | Arianna Krinos, Affiliate Researcher |
| [email protected] | [email protected] | [email protected] | [email protected] |
| Marianne uses metagenomics to study giant viruses in cold marine environments and is interested in analyzing genes that can impact the metabolism of their hosts. | Miguel is looking for previously uncharacterized lineages of protists using molecular phylogenetics, genomics, and metagenomics. His aim is to understand the phylogenetic and metabolic diversity that these novel taxa harbor and how they have been shaped by the environment. | Petra cultivates marine algae infected by giant viruses from subtropical, oligotrophic ocean gyres. She uses genomic and transcriptomic sequencing along with laboratory manipulations to understand how nutrient stress impacts virus-host interaction. | Arianna explores the effect of aquatic protistan taxonomy and genetic diversity on physiology and ecosystem functioning through a combination of transcriptomic, metatranscriptomic, and metagenomic approaches. |
Global diversity of Giant Viruses. Image credit: Zosia Rostomian, LBNL
Selected Publications
A complete publication list available at Google Scholar.
- Schulz, C Abergel, T Woyke (2022) Giant virus biology and diversity in the era of genome-resolved metagenomics. Nature Reviews Microbiology volume 20, 721–736
- JC Villada, F Schulz (2022) The endosymbiotic box of protective tricks. Nature Reviews Microbiology 20 (5), 255-255
- Schulz et al. (2020) Giant virus diversity and host interactions through global metagenomics. Nature. 578 (7795), 432-436
- Schulz et al. (2020) Advantages and limits of metagenomic assembly and binning of a giant virus. mSystems. 5 (3)
- Schulz et al. (2018) Hidden diversity of soil giant viruses. Nature Communications. 9 (1), 1-9
- Schulz et al. (2017) Towards a balanced view of the bacterial tree of life. Microbiome. 5 (1), 1-6
- Schulz et al. (2017) Giant viruses with an expanded complement of translation system components. Science, 356 (6333), 82-85
- Schulz et al. (2016) A Rickettsiales symbiont of amoebae with ancient features. Environmental Microbiology. 18 (8), 2326-2342
The NeLLi team at Mt Diablo State Park
- Schulz and Horn (2015) Intranuclear bacteria: inside the cellular control center of eukaryotes. Trends in cell biology. 25 (6), 339-346
- Schulz et al. (2015) Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria. Scientific reports. 5 (1), 1-10
- Schulz et al. (2014) Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae. The ISME Journal. 8 (8), 1634-1644
