2023 Kravis Department of Integrated Sciences Publications and Grants

*Indicates student co-author.

Defrenne, Camille E., Jessica A. M. Moore, Colin L. Tucker, Louis J. Lamit, Evan S. Kane, Randall K. Kolka, Rodney A. Chimner, Jason K. Keller, and Erik A. Lilleskov. “Peat Loss Collocates With a Threshold in Plant–Mycorrhizal Associations in Drained Peatlands Encroached by Trees.” New Phytologist, vol. 240, issue 1, 2023, pp. 412-425.


  • Drainage-induced encroachment by trees may have major effects on the carbon balance of northern peatlands, and responses of microbial communities are likely to play a central mechanistic role.
  • We profiled the soil fungal community and estimated its genetic potential for the decay of lignin and phenolics (class II peroxidase potential) along peatland drainage gradients stretching from interior locations (undrained, open) to ditched locations (drained, forested).
  • Mycorrhizal fungi dominated the community across the gradients. When moving towards ditches, the dominant type of mycorrhizal association abruptly shifted from ericoid mycorrhiza to ectomycorrhiza at c. 120 m from the ditches. This distance corresponded with increased peat loss, from which more than half may be attributed to oxidation. The ectomycorrhizal genus Cortinarius dominated at the drained end of the gradients and its relatively higher genetic potential to produce class II peroxidases (together with Mycena) was positively associated with peat humification and negatively with carbon-to-nitrogen ratio.
  • Our study is consistent with a plant–soil feedback mechanism, driven by a shift in the mycorrhizal type of vegetation, that potentially mediates changes in aerobic decomposition during postdrainage succession. Such feedback may have long-term legacy effects upon postdrainage restoration efforts and implication for tree encroachment onto carbon-rich soils globally.

Keller, Jason, Scott D. Bridgham, Kimberly K. Takagi, Cassandra A. Zalman, Jessica E. Rush, Crisand A. Anderson, Jessica M. Mosolf, and Kristin N. Gabriel. “Microbial Organic Matter Reduction Regulates Methane and Carbon Dioxide Production Across an Ombrotrophic-Minerotrophic Peatland Gradient.” Soil Biology and Biochemistry, vol. 182, 2023, 109045.

Abstract: Unraveling the mechanistic controls of methane (CH4) cycling in northern peatland ecosystems is crucial for understanding peatland-climate feedbacks. Growing evidence indicates that the microbial reduction of organic matter as a terminal electron acceptor can be a key regulator of CH4 production in peatlands, but the role of microbial organic matter reduction in different peatlands has not been well explored. Using an electron shuttling capacity assay, we investigated the relationship between the microbial reduction of organic matter and anaerobic CH4 and carbon dioxide (CO2) production in peatland soils in three experiments. In the first experiment, we surveyed the importance of microbial organic matter reduction in six soils representing the ombrotrophic-minerotrophic peatland gradient. In the second experiment, we further explored the reduction of solid-phase organic electron acceptors in a minerotrophic fen and compared these results to previously published values from an ombrotrophic bog (the end members of the initial gradient surveyed). Results from these experiments suggest that microbial organic matter reduction suppresses CH4 production, especially in ombrotrophic peat soils, likely helping to explain low CH4 production in bog-like soils. In contrast, the pool of oxidized organic matter was quickly reduced in minerotrophic peat soils which subsequently exhibited higher rates of CH4 production. In the final experiment, we investigated the effect of temperature on microbial organic matter reduction in the same ombrotrophic bog soil, demonstrating that warmer temperatures resulted in both a faster reduction of solid-phase organic matter and an apparent increase in the size of the organic electron acceptor pool that can be reduced by microbes. Future work should explore the drivers of the observed differences in microbial organic matter reduction in different peatland soils to provide a stronger mechanistic explanation for how this process will regulate peatland greenhouse gas dynamics in the face of global change, including increases in temperature.

Song, Tianze, Yutong Liu, Max Kolton, Rachel M. Wilson, Jason Keller, Jose L. Rolando, Jeffery P. Chanton, and Joel E. Kostka. “Porewater Constituents Inhibit Microbially Mediated Greenhouse Gas Production (Ghg) and Regulate the Response of Soil Organic Matter Decomposition to Warming in Anoxic Peat From a Sphagnum-Dominated Bog.” FEMS Microbiology Ecology, vol. 99, issue 7, 2023 fiad060.

Abstract: Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Liu, Nuo, Tonatiuh A. Gonzalez, Jacob Fischer, Chan Hong, Michelle Johnson, Ross Mawhorter, Fabrizia Mugnatto, Rachael Soh, Shifa Somji, Joseph S. Wirth, Ran Libeskind-Hadas, and Eliot C. Bush. “XenoGI 3: Using the DTLOR Model to Reconstruct the Evolution of Gene Families in Clades of Microbes.” BMC Bioinformatics, vol. 24, 2023, article no. 295.

Abstract: To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are geared toward a complete reconstruction for all families in an entire clade. Here we describe an update to the xenoGI software package which allows users to perform such an analysis using the newly developed DTLOR (duplication-transfer-loss-origin-rearrangement) reconciliation model starting from genome sequences as input.

External Grant: Wiley, Emily (PI). "Pathways to 'Learning Science Through Research' in Croatia." Fulbright Scholar Award, 2023-2024. 

Abstract: This project will identify curricular models that engage university students in learning science through doing research, and it will elucidate barriers and solutions to implementing those approaches broadly in Croatia. With colleagues at the University of Split, we will develop a framework for working collaboratively, within Croatia and with US institutions, on strategies to meet shared challenges. Pathways will open for engaging more Croatian students in early scientific research - providing skills and motivation to pursue science and technology careers. Outcomes shared through publication will advance theories and frameworks for science teaching practices used around the globe.

Kershaw, James, Joseph A. Stewart, Ivo Strawson, Maria Luiza de Carvalho Ferreira, Laura F. Robinson, Katherine R. Hendry, Ana Samperiz, Andrea Burke, James W.B. Rae, Rusty D. Day, Peter J. Etnoyer, Branwen Williams, and Vreni Häussermann. “Ba/Ca of Stylasterid Coral Skeletons Records Dissolved Seawater Barium Concentrations.” Chemical Geology, vol. 622, 2023, 121355.

Abstract: The concentration of dissolved barium in seawater ([Ba]SW) is influenced by both primary productivity and ocean circulation patterns. Reconstructing past subsurface [Ba]SW can therefore provide important information on processes which regulate global climate. Previous Ba/Ca measurements of scleractinian and bamboo deep-sea coral skeletons exhibit linear relationships with [Ba]SW, acting as archives for past Ba cycling. However, skeletal Ba/Ca ratios of the Stylasteridae – a group of widely distributed, azooxanthellate, hydrozoan coral – have not been previously studied.

Here, we present Ba/Ca ratios of modern stylasterid (aragonitic, calcitic and mixed mineralogy) and azooxanthellate scleractinian skeletons, paired with published proximal hydrographic data. We find that [Ba]SW and sample mineralogy are the primary controls on stylasterid Ba/Ca, while seawater temperature exerts a weak secondary control. [Ba]SW also exerts a strong control on azooxanthellate scleractinian Ba/Ca. However, Ba-incorporation into scleractinian skeletons varies between locations and across depth gradients, and we find a more sensitive relationship between scleractinian Ba/Ca and [Ba]SW than previously reported.

Paired Sr/Ca measurements suggest that this variability in scleractinian Ba/Ca may result from the influence of varying degrees of Rayleigh fractionation during calcification. We find that these processes exert a smaller influence on Ba-incorporation into stylasterid coral skeletons, a result consistent with other aspects of their skeletal geochemistry. Stylasterid Ba/Ca ratios are therefore a powerful, novel archive of past changes in [Ba]SW, particularly when measured in combination with temperature sensitive tracers such as Li/Mg or Sr/Ca. Indeed, with robust [Ba]SW and temperature proxies now established, stylasterids have the potential to be an important new archive for palaeoceanographic studies.

External Grant: Williams, Branwen. “MCA Pilot PUI: Proxy-Model Comparison Using Carbon Isotopes From Annually Banded Marine Calcifiers and Ocean Circulation Inverse Models to Evaluate Coastal Carbon Cycle Processes.” National Science Foundation CO #2322042, 2023.

Abstract: The ocean is a large sink of anthropogenic carbon from the atmosphere. Thus, calculating the movement of carbon into the oceans is important to understand future atmospheric carbon dioxide concentrations. Ocean climate models are a powerful tool to understand the processes that control carbon cycling. However, large discrepancies exist among data estimates and an ocean circulation inverse model (OCIM) that models carbon isotopes in the ocean. This project will use data obtained from proxy archives to perform a model-proxy data comparison as an independent test of the model-simulated carbon isotopes. The research would provide the first proxy data ? model output comparison of carbon isotope records from marine carbonates and simulations from OCIMs to better understand carbon cycling in the coastal regions of the North Atlantic and North Pacific Oceans. The comparison would address offsets and timing differences due to proxy archive and model biases related to seasonality, air-sea gas exchange, proxy archive chronological uncertainty, and broader environmental/climatic processes not constrained in the model.This project will analyze discrepancies between model output and proxy data to better constrain the carbon cycling processes critical to understanding the removal of anthropogenic carbon dioxide from the atmosphere and into the oceans. Thus, this work will contribute to societally relevant understanding of the processes that mitigate ongoing climate change. The project will support a mid-career researcher at a primary undergraduate institution. At the interface of societally relevant climate science and numerical modeling, this project will train undergraduate students through research experiences and will incorporate content into the curriculum of the new science department, thus providing an investment in workforce capabilities that will extend beyond the project duration.

Thippabhotla, Sirisha, Ben Liu, Adam Podgorny, Shibu Yooseph, Youngik Yang, Jun Zhang, and Cuncong Zhong. “Integrated de Novo Gene Prediction and Peptide Assembly of Metagenomic Sequencing Data.” NAR Genomics and Bioinformatics, vol. 5, issue 1, 2023, lqad023.

Abstract: Metagenomics is the study of all genomic content contained in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling and peptide assembly. Unfortunately, their information dependency has been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the information dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled metagenomic reads, achieving a 92–97% recall rate at a high precision level (>85%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.