Dr. Ella Sieradzki

Ella Sieradzki
Marie Sklodowska-Curie Fellow

Laboratoire Ampère
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
France







ella.shir@gmail.com

Research Interests

I’m a microbial ecologist interested in the contribution of microbiomes and viral communities to biogeochemical cycles. I’ve worked in both marine and soil environments and studied a variety of pathways with which microbes and viruses affect their habitat, such as extracellular proteases, light harvesting mechanisms and oil degradation. I believe that soil viruses can have a tremendous effect on carbon sequestration by releasing microbial organic matter that binds to minerals, which is why I hope my future research will focus on soil bacteriophages.

Curriculum Vitae

  • Postdoc, UC Davis Emerson lab, 2022
  • Postdoc, UC Berkeley Firestone & Banfield labs, 2018-2022

Education

  • PhD, University of Southern California Fuhrman lab, 2018
  • M.Sc. Tel Aviv University Ilan lab, 2009
  • B.Sc. Tel Aviv University, 2007

Current Projects

  • DIVOBIS: Determining impact of viruses on biogeochemical processes in soil

Publications

  1. Sieradzki, E.T., Morando, M., Fuhrman, J.A. (2021). Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater. mSystems (impact factor 6.3), DOI: https://doi.org/10.1128/mSystems.00245-21
  2. Lee, S., Sieradzki, E.T., Nicolas, A.M., Walker, R.L., Firestone, M.K., Hazard, C. and Nicol, G.W. (2021). Methane-derived carbon flow through host-virus trophic networks in soil. PNAS (impact factor 11.2), DOI: 10.1073/pnas.2105124118.
  3. Hungate, B., J. Marks, M. Power, E. Schwartz, K.J. van Groenigen, S. Blazewicz, Chuckran P., Dijkstra P., B. Finley, M.K. Firestone, M. Foley, A. Greenlon, M. Hayer, K. Hofmockel, B.J. Koch, M. Mack, R. Mau, S. Miller, E. Morrissey, J. Propster, A. Purcell, E.T. Sieradzki, E.P. Starr, B. Stone, C. Terrer and Pett-Ridge, J. (2021). The Functional Significance of Bacterial Predators. mBio DOI: 10.1128/mBio.00466-21 (impact factor 6.8).
  4. Tully B.J. *, Buongiorno J., Cohen A.B., Cram J.A., Garber A.I., Hu S.K., Krinos A.I., Leftwich P.T., Marshall A.J., Sieradzki E.T., Speth D.R., Suter E.A., Trivedi C.B, Valentin-Alvarado L.E. and Weissman J.L. The Bioinformatics Virtual Coordination Network: an open-source and interactive learning environment. Frontiers in Education (impact factor 1.85). DOI: 10.3389/feduc.2021.711618
  5. Sieradzki, E.T., Koch, B.J., Greenlon, A., Sachdeva, R., Malmstrom, R.R., Mau, R.L., Blazewicz, S.J., Firestone, M.K., Hofmockel, K., Schwartz, E., Hungate, B.A. and Pett-Ridge, J. (2020). Measurement error and resolution in quantitative stable isotope probing: implications for experimental design. mSystems (impact factor 6.3). DOI: 10.1128/mSystems.00151-20.
  6. Sieradzki, E.T., Ignacio-Espinoza, J.C., Needham, D.M., Fichot, E.B., Fuhrman, J.A. (2019). Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nature Communications (impact factor 14.9). DOI: 1038/s41467-019-09106-z. 
  7. Sieradzki, E.T., Fuhrman, J.A., Rivero-Calle, S., Gómez-Consarnau, L. (2018). Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. DOI: 10.7717/peerj.5798.
  8. Yeh, Y.C., Needham, D.M., Sieradzki, E.T., Fuhrman, J.A. (2018) taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run. mSystems. DOI: 1128/mSystems.00023-18.
  9. Novak, L., Lopez-Legentil, S., Sieradzki, E.T., Shenkar, N. (2017) Rapid establishment of the non-indigenous ascidian Styela plicata and its associated bacteria in marinas and fishing harbors along the Mediterranean coast of Israel. Mediterranean Marine Science. DOI: 12681/mms.2135.
  10. Sieradzki, E.T., Nuccio, E.E., Pett-Ridge, J. and Firestone, M.K. (In revision, ISME J). Transcription of protease and chitinase genes provides a window onto macromolecular organic nitrogen decomposition in soil. bioRxiv DOI:  2020.12.14.422732
  11. Greenlon, A., Sieradzki, E.T., …, Jillian F. Banfield (In revision, mSystems). Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. bioRxiv DOI: 2022.05.02.490339
  12. Chukran, P., Flagg, C., Propster, J., Rutherford, W., Sieradzki, E.T., Blazewicz, S.J., Hungate, B.A., Pett-Ridge, J., Schwartz, E and Dijkstra, P (In revision, ISME J). Edaphic controls on genome size and GC content of bacteria in soil microbial communities.
  13. Durham D.M.*, Sieradzki, E.T.*, ter Horst, A.M., Santos-Medellin C., Bess, W.A., Geonczy, S.E. and Emerson, J.B. (in revision, ISME comms). Substantial differences in soil viral community composition within and among four Northern California habitats. bioRxiv DOI: 2022.05.26.493654 *equal contribution
  14. Sieradzki, E.T., Greenlon, A., Firestone, M.K., Pett-Ridge, J., Blazewicz, S.J., Banfield, J.F. (Submitted). Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history. bioRxiv DOI: 2022.06.28.498032
  15. Lee, S., Sieradzki, E.T., Hazard, C., Nicol, G.W. (Submitted). Viruses of soil ammonia oxidising archaea identified using a novel DNA stable isotope probing approach for low GC mol% genomes. bioRxiv DOI: 2022.08.13.503859
  16. Nicolas, A.*, Sieradzki, E.T.*, Estera-Molina K., Pett-Ridge, J., Firestone, M.K., Banfield, J.F., Blazewicz, S.J. (In prep). Functional genomics of replicating microbes and viruses following rewetting of a Mediterranean grassland soil. *equal contribution
  17. Sieradzki, E.T., Nuccio, E. E., Pett-Ridge, J., Firestone, M. K. (In prep). Nitrogen transformations in rhizosphere and detritusphere soil from time resolved microbial metatranscriptomes.

Select Invited Seminars

  1. A needle in a stack of needles: using stable isotope probing to focus on active taxa in microbial ecology studies, ISME18, invited speaker, 2022
  2. Nitrogen acquisition in the microbiome of wild oat roots through a metatranscriptomic lens, Changing Microbiomes symposium, invited speaker, 2022
  3. Succession of microbes and viruses throughout a soil rewetting time-series. Microbiome Centers Consortium Seminar, 2022. https://osu.zoom.us/rec/play/f8kYaFcgOLTHMoIEq03jNj69z2Qxu3MAHmS031msAoqFghLaB-j4fi4vLuS8QfW50grZRyYks09_dkp0.RcjxfDpnBhUnkpsv?continueMode=true
  4. A needle in a haystack: How to study active organisms in complex environments with stable isotopes and metagenomics. Illumina webinar series, 2021. https://www.illumina.com/events/webinar/2021/active-organisms-metagenomics.html
  5. Nitrogen breakdown and assimilation pathways in rhizosphere and detritusphere soil from time resolved microbial metatranscriptomes. ISME MicroSeminar series, 2020. https://www.youtube.com/watch?v=3LFQYp_WRno
  6. Metatranscriptomes: system-level dynamics, differential expression and viruses. JBIMS Data Science Workshop: Microbiome, 2020.
  7. Insights into polycyclic aromatic hydrocarbon biodegradation in a chronically polluted site. Isotope geochemistry seminar series, UC Berkeley, CA. 2019

Presentation in Scientific Conferences

  1. Sieradzki, E.T.*, Ecophysiological traits underlying microbial succession after rewetting of soil from different precipitation regimes, EGU, 2022, Talk
  2. Sieradzki, E.T.*, Nuccio, E., Starr, E.P., Banfield, J.F., Firestone, M.K. and Pett-Ridge, J. (2020). Microbial and Viral Niche-Differentiation in Time-Resolved Metatranscriptomes from Rhizosphere and Detritusphere Soil. DOE Genomic Sciences PI meeting, Washington DC. Poster
  3. Sieradzki, E.T.*, Ignacio-Espinoza, J.C., Needham, D.M., Fichot, E.B., Fuhrman, J.A. (2019). Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. ASM Microbe, San Francisco, CA. Talk
  4. Sieradzki, E.T.*, Sachdeva, R., Koch, B., Mau, R., Hayer, M., Dijkstra, P., Schwartz, E., Hungate, B., Hofmockel, K., Bell, S., Fuhrman, J., Morrisey, E., Blazewicz, S., Nuccio, E., Malmstrom, R., Banfield, J., Firestone, M., Pett-Ridge, J. (2018) Stable isotope probing – a fraction saved is a fraction earned. ISME17, Leipzig, Germany. Poster
  5. Sieradzki, E.T.*, Fuhrman, J. (2016) Biodegradation of polycyclic aromatic hydrocarbons in naturally occurring marine microbial communities. ISME16, Montreal, Canada. Poster
  6. Sieradzki, E.T.*, Fuhrman, J. (2016) High resolution detection of taxa capable of PAHs degradation in a marine coastal system using SIP-tag and metagenomics. IsoEcol, Tokyo, Japan. Poster
  7. Sieradzki, E.T.*, Sachdeva, R., Fichot, E., Parada, A., Wroobel, I., Fuhrman, J. (2015) Human impact on marine microbial community composition. ASLO, Granada, Spain. Poster

University and Community Service

  1. Session Convener American Geophysical Union, Geovirology session. San Francisco, CA, December 2019, 2020.
  2. ScienceAbroad regional coordinator; Berkeley
  3. Organizing community activities for local Israeli scientists
  4. Women in Science planning committee member; University of California, Berkeley
  5. Inviting speakers, setting up events, applying for funding
  6. Invited seminar committee; University of Southern California
  7. Organizing panels, inviting speakers, applying for funding, handling reimbursements