Yannick Zander

Projection Description

The main objective of my work focusses on microbes in deep, hot sediments from the Guaymas Basin, investigating the interplay of microbial life via lipidomics, supplemented by contextual parameters by leveraging common metabolomics machine learning techniques. This last aspect gives rise to a secondary objective: developing a framework for analyzing and clustering MALDI data.

My PhD project is part of the DFG project “Impact of temperature on microbial activity and carbon flow in deep hot sediments of the Guaymas Basin, Gulf of California (IODP Expedition 385)” at MARUM - Centre for Marine Environmental Sciences in Bremen. The research unit “T-GUAYMAS” focuses on microbial life in hot, deep sediments in the Guaymas basin. the basin is situated in an active spreading margin, resulting in large temperature gradients with depth as well as volcanic sill intrusions, causing organic matter in the sediment to form hydrocarbons that are hydrothermally cycled (Teske et al., 2020). During the expedition, more than 4 km of core were recovered. Due to steep temperature gradients in the tectonically weakened crust, the acquired cores cover temperatures of up to 120°C (the current known maximum temperature tolerated by microbes (Takai et al., 2008)) and due to basaltic sill intrusions, hosts a great variety of microbial species (Teske et al., 2014). The concentration of microorganisms and their phylogeny as well as the reactions at play are still largely unknown. In the course of my three-year position, I will be investigating links between environmental parameters and microbial abundances in the Guaymas basin via established lipidomics workflows as well as combining obtained data with environmental and contextual parameters to apply meta-analysis.

The deep marine biosphere is estimated to account for about 15 % of the biomass worldwide (Bar-On, 2018) and has an impact on oceanic geochemical conditions such as elemental cycling of C, H, O, N, Fe, Mn, S and methane oxidation (Orcutt et al., 2013). Furthermore, some of the oldest chemolithotrophic lineages can be found in the deep biosphere, which makes them interesting for investigating the origins of life (Drake and Reiners, 2021). The site under investigation is special since microbes usually found over large stretches of areas can be found on comparably small spatial extents (Engelen et al., 2021).

This research will be conducted within the broader context of complementary data, including temperature variations, endospore abundance, acetate levels, and other pertinent factors. Leveraging machine learning algorithms, I aim to unveil the compositions of microorganism communities and identify the conditions that give rise to different microbial communities.

Another part of  my PhD project is Mass spectrometry imaging (MSI). MSI has recently been established in geoscientific applications (e.g. Liu et al., 2022, Alfken et al., 2020 and Alfken et al. 2021) and is becoming increasingly important for high-resolution lipidomics. Since those datasets have been created for many sites already (among others the Guaymas Basin) there is demand for well-established workflows. The datasets generated in this way are huge, offering potential for datamining approaches and to resolve microorganism interactions on the micrometer scale (e.g. Wörmer et al., 2020).

One challenge is to combine different kinds of measurements (for example, µXRF with MSI or X-Ray data) due to deformations occurring during the sample preparations. Employing image segmentation and registration techniques will allow to integrate different kinds of measurements on a micrometer scale, ultimately resulting in more comprehensive datasets for investigating investigating localization of microbial communities and possibly identifying novel biomarkers based on their relation to known ones. 

References

Alfken, S., Wörmer, L., Lipp, J. S., Wendt, J., Schimmelmann, A., & Hinrichs, U. (2020). Mechanistic Insights Into Molecular Proxies Through Comparison of Subannually Resolved Sedimentary Records With Instrumental Water Column Data in the Santa Barbara Basin, Southern California. Paleoceanography and Paleoclimatology, 35(10), e2020PA004076. https://doi.org/10.1029/2020PA004076

Alfken, S., Wörmer, L., Lipp, J. S., Napier, T., Elvert, M., Wendt, J., Schimmelmann, A., & Hinrichs, U. (2021). Disrupted Coherence Between Upwelling Strength and Redox Conditions Reflects Source Water Change in Santa Barbara Basin During the 20th Century. Paleoceanography and Paleoclimatology, 36(12), e2021PA004354. https://doi.org/10.1029/2021PA004354

Drake, H., & Reiners, P. W. (2021). Thermochronologic perspectives on the deep-time evolution of the deep biosphere. Proceedings of the National Academy of Sciences, 118(45), e2109609118. https://doi.org/10.1073/pnas.2109609118

Engelen, B., Nguyen, T., Heyerhoff, B., Kalenborn, S., Sydow, K., Tabai, H., Peterson, R. N., Wegener, G., & Teske, A. (2021). Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.710881

Liu, W., Alfken, S., Wörmer, L., Lipp, J. S., & Hinrichs, K. (2022). Hidden molecular clues in marine sediments revealed by untargeted mass spectrometry imaging. Frontiers in Earth Science, 10, 931157. https://doi.org/10.3389/feart.2022.931157

M., Y., Phillips, R., & Milo, R. (2018). The biomass distribution on Earth. Proceedings of the National Academy of Sciences, 115(25), 6506-6511. https://doi.org/10.1073/pnas.1711842115

Orcutt, B. N., LaRowe, D. E., Biddle, J. F., Colwell, F. S., Glazer, B. T., Reese, B. K., Kirkpatrick, J. B., Lapham, L. L., Mills, H. J., Sylvan, J. B., Wankel, S. D., & Wheat, C. G. (2013). Microbial activity in the marine deep biosphere: Progress and prospects. Frontiers in Microbiology, 4. https://doi.org/10.3389/fmicb.2013.00189

Takai, K., Nakamura, K., Toki, T., Tsunogai, U., Miyazaki, M., Miyazaki, J., Hirayama, H., Nakagawa, S., Nunoura, T., & Horikoshi, K. (2008). Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10949–10954. https://doi.org/10.1073/pnas.0712334105

Teske, A., Callaghan, A., & LaRowe, D. (2014). Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00362

Teske, A., Lizarralde, D., Höfig, T. W., Aiello, I. W., Ash, J. L., Bojanova, D. P., ... & Zhuang, G. (2020). International Ocean Discovery Program, Expedition 385 Preliminary Report: Guaymas Basin Tectonics and Biosphere; 15 September–15 November 2019.

Wörmer, L., Gajendra, N., Schubotz, F., Matys, E. D., Evans, T. W., Summons, R. E., & Hinrichs, U. (2020). A micrometer-scale snapshot on phototroph spatial distributions: Mass spectrometry imaging of microbial mats in Octopus Spring, Yellowstone National Park. Geobiology, 18(6), 742-759. https://doi.org/10.1111/gbi.12411

Curriculum Vitae