Projects & Collaborations

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DRought Impacts on soil microbial metabolism in European foRests (DRIER)

Soil is a critical storage pool for carbon in Earth’s surface. How carbon cycling will change in soils as a result of anthropogenic climate forcing remains unclear, in part because of limited mechanistic understanding of how microbial metabolism and diversity combine to affect carbon portioning between microbial biomass and respiration (known as carbon use efficiency or CUE). In central Europe, increased drought frequency and intensity is likely to impact carbon cycling and CUE in soils in the near future, due to changes in the availability of organic matter as moisture content decreases, and to changes in the composition of organic matter input from plants. To improve our process-based understanding of how carbon cycling will change in the soils of central European forests under drought, I propose to develop and apply a novel tool to quantify changes in the central carbon metabolism of soil microbial communities, based on compound-specific hydrogen isotope measurements of phospholipid-derived fatty acids (PLFAs), which are contained in the lipid membranes of living microbes.

Studies with cultured microbes have demonstrated that the hydrogen isotope composition of lipids is highly sensitive to central metabolism, with lipids produced from tricarboxylic acid cycle precursors and intermediates having d²H values that are up to 250 ‰ higher than those from sugar-based metabolisms. Lipid d²H values thus have great potential as indicators of the activity of central metabolic pathways, but have thus far only been employed in aquatic settings and microbial mats, not in soils.

In DRIER, I will initially test the suitability of d²H values of PLFAs as a proxy for net soil microbial metabolism through a series of increasingly complex laboratory experiments beginning with simple co-cultures inoculated with two model bacterial species and progressing to small mesocosms of natural microbiomes from local forest soils. I will then conduct several larger soil mesocosm experiments, evaluating how the metabolism and substrates used by different microbial groups change under drought, and how these changes are influenced by the presence of living plant roots or leaf litter additions. In addition to measuring d²H values of PLFAs from these mesocosms, I will characterize changes in the quality of soil organic matter and the abundance of specific metabolites through high-resolution mass spectrometry, changes in the microbial community composition through 16S amplicon sequencing, and changes in microbial gene expression through metatranscriptomic analyses. Finally, I will determine how soil microbial metabolism changes during a long-term water exclusion experiment in a natural forest at the Swiss Canopy Crane II site in Hölstein, BL. I will collect soil cores at multiple time points from drought and control plots and apply the approach developed in the soil mesocosms to assess shifts in microbial metabolism in response to sustained, multi-year droughts and place these shifts in the context of long-term changes is soil respiration and CUE. I will also conduct full metagenomic analyses from the soil cores to determine how long-term drought affects overall soil microbial community structure, and how this impacts the overall CUE potential of soils over time. Through this cutting-edge, combined multi-omics approach, DRIER will reveal unique insights about the interactions of soil organic matter and microbial metabolism during drought in central European forests and will likely establish PLFA d²H values as a novel, integrated proxy for central metabolism in soil microbes at the community level.

Algal Dynamics And Productivity through Time (ADAPT)

Research Project | 4 Project Members

Although individually small, algae have the collective power to change the composition of Earth's atmosphere, oceans, and climate, thereby influencing virtually all other forms of life. Human disruptions to the carbon and nitrogen cycles impact waters in which algae live and cause changes to phytoplankton distributions and productivity. These changes can drive feedback loops with unforeseen consequences for Earth's oceans and atmosphere, thereby impacting the environment and resources needed for the continued human prosperity. Understanding algal community dynamics and responses to environmental change is therefore key for constraining their feedbacks to climatic and biogeochemical perturbations. One of the best ways to understand these dynamics is to analyze the ways in which algae have responded to the diverse conditions that have existed over geologic time. However, our ability to gain information from past changes is only as good as the tools we have to detect these changes because direct observations are limited to the tiniest sliver of Earth's history. As a consequence, we must rely on indirect indicators - proxies - of past ecologic and environmental change. The proposed ADAPT project will lead to a comprehensive, innovative, multi-proxy toolkit that can be applied to resolve outstanding questions about phytoplankton dynamics on diverse geographic and temporal scales. This will allow us to reconstruct phytoplankton community dynamics and interactions with nutrient cycling in the geologic past, and better predict feedbacks between phytoplankton and climate in the future. In this context, ADAPT will focus on developing and applying three organic geochemical proxies: relative distributions of diagnostic lipid biomarkers, the difference in nitrogen isotope ratios between bulk organic matter and chlorophyll degradation products, and the difference in hydrogen isotope ratios among different classes of algal lipids. The organic geochemical proxies will be integrated with, and calibrated through, sedimentary ancient DNA ( seda DNA) analyses. Seda DNA is another emerging tool to reconstruct past ecological changes, but is limited to more recent timescales than the organic geochemical proxies. The underlying goals of ADAPT are to reconstruct phytoplankton community dynamics and interactions with nutrient cycling in the geologic past, and to develop the tools needed to better understand how they impact the atmosphere, global ecosystems, and climate system. In order to achieve these goals I have developed a five-year plan divided into three phases. In the first phase of ADAPT, I will validate and cross-calibrate proxies for phytoplankton ecology using samples collected every second week from the water column of a small lake in Switzerland with large seasonal variability in the distribution of different types of algae. In the second phase, I will determine how lacustrine phytoplankton communities responded to known anthropogenic forcings in the modern era (20 th and 21 st centuries) and in antiquity (ancient Romans). In the third phase of ADAPT, I will reconstruct the composition of phytoplankton communities over the Holocene in temperate lakes in order to establish baseline values for natural rates of change and frequency of harmful algal blooms. I choose to focus on lakes because in contrast to oceans their relatively small size means they can react quickly to perturbations, facilitating the development of a mechanistic understanding of how algal populations respond to changing conditions, and how those signals are transferred to sedimentary proxy indicators.