Research in the Meredith Lab aims to resolve the microbial imprint on ecosystem processes and atmospheric chemistry. Trace gases are important, but often overlooked, microbial metabolites, and microbial processes can have a leading order impact on atmospheric composition of trace gases. We constrain genetic traits for trace gas metabolism by linking microbial taxa, genes, and trace gas production and consumption kinetics in predictive trait models. Although microbes voraciously cycle trace gases in the complex soil matrix, it is challenging to measure gases at scales that capture variability in time (‘hot moments’) and space (‘hot spots’, gradients). We develop new tools to constrain microbial gas cycling in the subsurface, including novel soil gas probing systems and sensors. Even after microbial processes are understood at the small scale, they must be scaled-up and considered alongside other interacting biotic and abiotic processes in ecosystems and landscapes. We use experimental ecosystems to directly evaluate the emergent outcomes of environmental forcings on ecosystems and collaborate with land surface modelers to implement and improve representation of microbial processes.

Projects:

A volatile environment: How volatile mediated plant and microbial interactions extend the rhizosphere and enhance soil carbon storage

Understanding that many VOCs are ubiquitous in both the atmosphere and soil, we propose these compounds represent a significant and oft neglected component of the soil carbon pool. In this project, we are working to quantify the direct and indirect contributions of microbial and plant VOCs in both soil carbon cycling and stabilization, as well as investigate the mechanisms that regulate these processes.

We hypothesize that root VOCs and those that pass through the soil metabolic ‘microbial loop’ directly contribute to soil carbon cycling and stabilization. Moreover, as VOCs can act as signaling molecules that tether soil microbes, plants, and higher-order organisms together, we predict that VOCs can indirectly influence carbon stabilization through these teleconnections. Finally, due to the uniquely large ‘zone of influence’ soil VOC metabolites possess, compared to their non-volatile counterparts, we expect to identify the role of VOC movement between otherwise separated regions of soil that further enhance the conversion of VOCs into stable soil carbon pools.

“[This] work will represent the first quantification of the potential impact of direct, indirect, and teleconnection roles of root VOCs on soil carbon pools. If VOC contributions are significant, this project will directly impact conceptual and numerical models that aim to enhance the understanding of soil carbon cycling and stabilization and contribute to a new frontier in microbial systems science that embraces VOCs as integral components of the suite of organic compounds present in an ecosystem.”

– DOE 2022 Awards Announcement Summary

Principal Investigator: Laura Meredith

Co-Investigators: Malak Tfaily (University of Arizona), Rob Roscioli (Aerodyne Research, Inc.), Eoin Brodie, Kolby Jardine, and Romy Chakraborry (Lawrence Berkeley National Laboratory)

Funding: Department of Energy Systems Biology–Enabled Microbiome Research to Facilitate Predictions of Interactions and Behavior in the Environment Awards: DE-FOA-0002602.

Posters and presentations: Transformations of soil organic matter induced by volatile organic compounds (Meredith et al., 2024, EGU General Assembly Oral – Vienna, Austria)

Press: A volatile environment – Meredith awarded DOE grant to study VOCs and carbon storage in soil (2022)

Laura Meredith co-created and -led an international research campaign with Christiane Werner (University of Freiburg) and Nemiah Ladd (University of Basel) in the Biosphere 2 Tropical Rainforest biome. The Water, Atmosphere, and Life Dynamics (WALD, meaning ‘forest’ in German) campaign was a 5-month (Sept 2019 – Jan 2020) controlled whole-ecosystem drought and recovery experiment involving >90 participants from 14 institutions and 5 countries, $5M in instrumentation, and >20 media interviews. Our first results were just published in Science (Werner, Meredith, and Ladd, et al., 2021) with an accompanying perspective (Eisenhauer and Weigelt, 2021).

The overarching goal of the experiment was to fully track the forest’s response to drought from molecules to the ecosystem. We accomplished this by measuring multiple ecosystem compartments (atmosphere, leaf, stem, root, soil) online with 133 online gas sampling locations sampled by clusters of gas analyzers for water (H2O) isotopes, carbon dioxide (CO2) isotopes, volatile organic compounds (VOCs), and other trace gases (20 online gas analyzers total) and 290 additional environmental sensors. Moreover, we used the glass and steel structure enclosing the rainforest biome to precisely control the rainfall regime, and also to deliver stable isotope labeling at unprecedented ecosystem scales including whole atmosphere 13C-CO2 pulse labeling to track the speed and fate of C allocation under drought and control conditions and deep water 2H-H2O labeling to trace the role of plant deep water access.

There are many stories emerging from WALD. Our group leads the interpretation drought and rewet responses in volatile organic compound (VOC) and nitrous oxide (N2O, see below) cycling in soil and roots through integration with genomics. We also use measurements of carbonyl sulfide (OCS) to trace stomatal responses to drought.

Leadership: Laura Meredith, Christiane Werner, Nemiah Ladd. Contributions of all team members detailed in the B2 WALD Participation List.

Awards: 2020 University of Arizona Team Award for Excellence for effectiveness, service, and inclusive excellence; 2021 SNRE International Collaboration Award to Meredith; and 2021 College Research Faculty of the Year Award to Meredith.

Funding: Financial support from the Philecology Foundation to Biosphere 2 (Laura Meredith). European Research Council Consolidator Grant #647008 (VOCO2, Christiane Werner). DOE Facilities Integrating Collaborations for User Science (Malak Tfaily, article). SBIR DOE BER Phase II SBIR DE-SC0018459 (Rob Roscioli, Laura Meredith)

Press: Science Magazine News (2019); #B2WALD on Twitter, full list of news coverage

Peter Moma and Jan Fudyma sampling soil
Jess Graham in one of the three soil pits.
Juliana Gil Loiaza flagging soil sampling sites
Marissa Clover surveying leaf chambers during VOC cartridge sampling.
Emily Espelage excavating roots from Piper sp. plants
Roya AminiTabrizi evaluating meter-long soil cores from around the B2 tropical rainforest
Soil sampling flagging team Laura Meredith, Marissa Clover, Juliana Gil Loiaza, Jane Fudyma, and Alex Cueva

Microbial drivers of carbonyl sulfide (OCS) soil exchange

OCS is an atmospheric trace gas with potential to constrain estimates of global photosynthesis. Better understanding of OCS soil exchange is needed to use this tracer to dissect biosphere carbon cycling processes.

We build on our findings (Meredith et al., 2018) that fungi dominate microbe-mediated soil uptake of OCS via their carbonic anhydrase (CA) enzymes. We ask whether including fungal CA and OCS reaction rates can improve soil OCS representation in land-atmosphere models. We investigate this question in Boreal and Arctic sites in Alaska, where fungi are key to soil biomass and function and projecting changing components of the carbon cycle is critical.

Team: Laura Meredith (PI), fungal ecologist Jana U’Ren (Co-PI at University of Arizona), atmospheric chemist Roísín Commane (Co-PI at Columbia University), land surface modelers Ian Baker (Co-PI at Colorado State University) and Aleya Kaushik (NOAA). UA

Funding: NSF AGS Atmospheric Chemistry Award No. 1933280

C. Allison Newton (PhD Student) measuring soil OCS fluxes in a taiga ecosystem at the Healy NEON site (photo: Laura Meredith)

Unearthing the role of belowground biology in biosphere-atmosphere VOC exchange

The role of soil in biosphere-to-atmosphere volatile organic compound (VOC) exchange is elusive and underestimated. VOCs impact air quality and climate, and are projected to increase in response to global change. To help fill gaps in understanding of the belowground drivers of VOC biosphere-atmosphere exchange, this project will address the following research questions: “Which organisms and metabolic pathways drive belowground cycling of different VOCs?”; “How do soil microbes, roots, and root-microbe interactions affect soil VOC cycling?”; and “What factors control how soil VOC production vs. consumption scale to net soil fluxes?”

The project also includes an integrated education plan designed to bridge gaps in learning, research engagement, and training that currently divide atmospheric chemistry and ecosystem science education at the University of Arizona. To do so, the will develop: 1) a team-based undergraduate research program as a Vertically Integrated Project ; 2) a hands-on course in atmospheric and ecosystem science measurements; and 3) an industry training program.

Leadership: Laura Meredith (PI)

Funding: NSF CAREER AGS Atmospheric Chemistry and BIO Ecosystem Sciences Award No. 2045332

Related pubs: Honeker et al, 2021

Using subsurface sensors to decode volatile signals in the soils

In an academia-industry collaboration with scientists at QuantAQ, Inc. and Aerodyne Research, Inc., we are developing sensors for volatile organic compounds (VOCs) that can be integrated with soil gas probes. This collaboration leverages multifaceted expertise across the team in sensor design, sensor networks, and machine-learning analytics (QuantAQ); high precision VOC monitoring and quantification (Aerodyne); and biological trace gas cycling in soil (UA). The team’s long-term vision motivating this project is to achieve low-cost, subsurface VOC sensor networks that reveal biological interactions in soil with direct relevance to soil health.

This project was been continued in 2022 and is still ongoing under an additional DOE proposal named: Direct Routes for Microbial Carbon Stabilization of Volatile Organic Compounds in Soil. We are currently using the methods and sensors developed from our prior work to now determine how root-VOCs and VOCs metabolized by the soil microbiome contribute to soil carbon cycling and stabilization. We seek to determine the direct pathways and contributions this subset of VOCs has on these processes. Specifically, we will work to identify VOC-consuming microbes, the genetic traits related to VOC consumption, and the pathways that lead to VOC carbon stabilization using time-resolved VOC stable isotope labeling combined with our soil incubations systems refined previously.

Leadership: Laura Meredith (PI), sensor design and machine learning (Co-PIs David Hagan and Eben Cross, QuantAQ), high sensitivity VOC detection and interpretation (Co-PI Jordan Krechmer, Aerodyne).

Funding: NSF Signals in the Soil in BIO Ecosystem Sciences Award No. 2034192. DOE Office of Science, Office of Biological and Environmental Research (BER), grant nos. DE-SC0023189

Developing soil gas probes for monitoring trace gas messengers of microbial activity

In an academia-industry collaboration with scientists at Aerodyne Research, Inc., we develop soil gas probing systems to characterize microbial activity through spatially-resolved belowground trace gas measurements. We focus on detecting nitrogen gases and their stable isotopes including nitrous oxide (N2O), nitric oxide (NO), and nitrogen containing volatile organic compounds (N-VOCs), which represent key intermediates and terminal products of complex nitrogen transformations in soil. To demonstrate the performance of our novel probe materials and sample transfer system, we have deployed this system in two field campaigns including WALD (see above) and at the Maricopa Agricultural Center (MAC).

At MAC, we investigate the belowground genotype-phenotype controls on nitrogen use efficiency of a sorghum bioenergy crop. At the site, a large gantry characterizes plant phenotypes from overhead, which are the observable plant characteristics that arise from interactions between the plant (genotype) and its environment. We hypothesize that distinct sorghum genotypes will also differ in their below-ground phenotypes in ways that differentially influence N cycling. We use soil gas probes beneath the sorghum plants and root/rhizosphere analyses to dissect the plant-microbe interactions influencing nitrogen cycling.

Leadership: Joseph R. Roscioli (PI), Joanne Shorter (Co-PI), and Jordan Krechmer (Co-PI) at Aerodyne Research, Inc. and Laura Meredith (Co-PI) at University of Arizona.

Funding: DOE BER Phase I & II SBIR DE-SC0018459

Green infrastructure impacts on soil health and ecosystem function

Urban Rainwater Harvesting. Impacts on Soil Microbial Communities and Function Including Gas Fluxes. Urban soils are often degraded compared to their natural counterparts, and in this study we ask how microbial community composition and function are altered upon green infrastructure (GI) installation. The GI systems we study passively and actively utilize rainwater captured from roof run-off during the monsoon and winter storms, and grey water systems are fed annually by laundry water. As water is the limiting factor in arid environments, we anticipate that these treatments will dramatically re-shape microbial communities and lead to altered biogeochemical cycling.

Leadership: Laura Meredith (PI)

Funding: UA Provost Investment Fund, RII Faculty Seed Grant, RII Accelerate for Success

Related pubs: Buzzard et al., 2021