2023 O.N. Allen Soil and Environmental Microbiology Small Grants Program Awardees

Grace Cagle (Soil Science)

Does plant diversity affect microbial carbon use efficiency in a grassland managed for livestock forage?
Soil microbial diversity influences the rate of carbon (C) decomposition and assimilation. As microbial C assimilation supports soil C sequestration, a better understanding of how soil microbial diversity influences C turnover in soil under differing land management practices can help to maximize the carbon sequestration potential of agricultural systems. Grasslands managed for livestock feed and grazing represent 77% of agricultural lands, presenting an opportunity to utilize management practices that reduce the contribution of agriculture to climate change and increase soil carbon sequestration. Rates of carbon sequestration in ecosystems as well as energy and material transfer to higher trophic levels are highly correlated with microbial carbon use efficiency (CUE), a measure of how much carbon is incorporated into microbial biomass vs being respired and lost as CO2. The literature indicates that plant species richness and microbial diversity play a role in CUE and ultimately soil carbon storage, but how plant species richness influences CUE in grasslands managed for livestock forage has not been studied. I will measure CUE under “low” and “high” plant diversity and identify the diversity of microbial taxa involved C degradation in conjunction with a three-year study on C stocks being conducted at the Prairie du Sac Agricultural Research Station (U.S. Dept. of Agriculture). I hypothesize that greater plant diversity corresponds with greater CUE and a higher diversity of taxa involved in C degradation. This work will provide an opportunity for undergraduate research experience and the results will be disseminated to the USDA for inclusion in their study on carbon stocks.

Isabella Muscettola (Soil Science)

Uncovering Bacterial Ecological Memory to Repeated Fire
Fire is a key natural disturbance that shapes the structure and function of forested ecosystems. However, across the western US, the past hundred years of fire exclusion have left forests vulnerable to higher severity and larger fires. A community’s resilience, or ability to return to pre-disturbance conditions, may be informed by its “ecological memory” of previous compositional and functional states. At the ecosystem level, frequency of fire can influence community resilience. For example, in forests that historically have had frequent fires, maintaining the frequent fire regime can maintain the forest’s resilience to future fire. Belowground, the impact of repeated fire on soil bacterial community resilience is understudied. Repeated fires also have compounding effects on soil physical and chemical properties, including the production of pyrogenic organic matter (PyOM), a highly aromatic, non-preferentially degraded form of carbon. These changes to the soil environment impart compositional shifts to microbial communities that can persist for years. However, shifts in community composition do not always confer changes to overall soil microbial functions such as nutrient cycling. To further understand whether soil bacterial communities from soils with differing fire histories have an ecological memory of past fire disturbances, we will conduct a manipulative study to test (1) the rate of return to pre-fire composition and (2) the community’s ability to degrade PyOM. Forest soils from fire-excluded (100+ years without fire) and recent history of fire (at least 1 fire in the past 20 years) sites will be sampled, burned, and mixed with PyOM in mesocosms where carbon dioxide fluxes will be measured. Temporal sampling of the burned cores and subsequent community characterization using 16S rRNA amplicon sequencing will test community resilience. I hypothesize that soil microbial communities with a history of fire will more effectively degrade PyOM shortly after being burned and will have greater community resilience to fire.

Priscila Pinto & Erica Shoenberger (Agronomy, Soil Science)

Soil organic matter in different cropping systems: how are the stocks and turnover of the particulate and mineral-associated fractions?
Carbon sequestration in soil organic matter (SOM) is a key ecosystem service to mitigate climate change, whereas SOM decomposition provides nutrients to plants and energy to the soil biota, which can support climate change adaptation. SOM formation and decomposition occur simultaneously and depend on environmental conditions, plant litter inputs, and soil biota activity. Agroecosystems usually lead to SOM depletions because they have low inputs to soil due to harvest outputs, low root productivity targeted by cash crop breeding, and low diversity compared with the undisturbed ecosystem. Replacement of annual crops by perennial crops or intercrops can lead to changes in SOM formation, persistence, and function. Since SOM is heterogeneous in composition and turnover, there is a widespread agreement for separating total SOM into components with contrasting behavior: particulate organic matter (POM) and mineral-associated organic matter (MAOM). POM is largely made up of lightweight fragments that are relatively undecomposed, whereas MAOM consists of single molecules or microscopic fragments of organic material that are chemically or physically associated with soil minerals. MAOM has greater protection from microbial decomposition through this association, whereas POM has relatively less. Combining the study of the stock and turnover of these fractions can allow us to see changes in the short term: the use of 13C isotopes is useful to trace the origin of the SOM and allow the estimation of the formation and decomposition rates of each fraction, and the N released from labile compounds, which are part of both POM and MAOM fractions, can be estimated by 7-d anaerobic incubations. This project aims to evaluate the effect of perennial crops and intercropping on soil organic matter. We hypothesize 1) SOM formation is higher in perennial crops than in annual crops because the former has higher belowground inputs to the soil, 2) intercropping perennial grasses with legumes limits the POM accumulation because the N availability triggers the decomposition of lightweight fragments that are composed the POM, 3) intercropping perennial grasses with legumes increases MAOM accumulation because high production of labile compounds favor microorganisms growth that ends up forming MAOM when they die, 4) perennial crops leads higher N released from SOM than annual crops, mainly due to increases in N released from MAOM in the intercropping systems.

Brooke Propson (Soil Science)

Measuring the expression of fungal genes associated with mediating soil carbon storage during forest recovery from anthropogenic nitrogen deposition: the keystone of a genes to ecosystem story
Increased anthropogenic nitrogen (N) deposition to historically N-limited forests has resulted in their increased capacity to store soil carbon (C). This increase in soil C is attributable to changes in microbial function, namely the suppression of the activity of microbial extracellular enzymes that are associated with the breakdown of soil organic matter (OM), which ultimately results in reduced rates of leaf litter and soil OM decomposition. This suppression in enzyme activity occurs in the absence of a compositional shift in metabolically active fungi and is instead driven by the reduced expression of genes that encode the production of extracellular enzymes that underlie the slowed OM decay and consequential buildup of soil C. However, since the implementation of the Clean Air Act Amendments in the United States in 1990, anthropogenic emissions have greatly declined, and with them the deposition of atmospheric N has also significantly decreased. As a result, it is imperative to better understand how forest ecosystems, and the terrestrial C sink that they support, recover from historically high rates of atmospheric N deposition. For the first chapter of my Ph.D. dissertation, I determined that the previously documented increase in forest floor C is no longer present in our study system 5-years after experimental N additions, which lasted 24-years, ceased. Additionally, the previously documented suppression in forest floor peroxidase enzyme activity is also no longer present 5-years post-fertilization termination and instead exhibit marginally significant increases. The objective of my proposed project is to assess if the reductions in soil C storage and increases in extracellular enzyme activity I have observed post-termination of fertilization can be explained by increases in the expression of genes encoding enzymes that govern the fate of this critical C pool. The results of this study will aid in our understanding of the fate of soil C storage in forests across the U.S. and Europe as they recover from historically high rates of N deposition

Ella Schmidt (Freshwater & Marine Science)

Predicting phenological trends of under-ice microbial communities in boreal freshwater bog lakes
Freshwater bog lakes in temperate climates display cyclic seasonal patterns (phenology) of carbon storage and emission that future climatic conditions may alter. Bog microbial communities are known to show high resilience to disturbances (Shade et al 2012), but they display high sensitivity to disturbances in temperature and dissolved oxygen. Because microbial diversity directly impacts ecosystem productivity and emissions, shifts in microbial metabolism affect whether a body of water acts as a net carbon sink or source. Preliminary analysis of open-water 16S community composition found potential seasonal patterns in community composition, which may be driven by the under-ice community’s ability to buffer against changes in environmental conditions. Furthermore, identifying the relative abundance of under-ice methanotrophs and methanogens improves models of methane emissions under future warming climate conditions.
My research aims to 1) identify long-term seasonal and interannual trends in open-water bog microbial communities associated with changes in environmental drivers and 2) determine if changes in under-ice microbial communities determine open-water community composition and diversity. Our study system, Trout Bog, is part of the Long-Term Ecological Research (LTER) network and has been sampled regularly since 2005 for both microbial community and environmental factors. We are conducting biweekly sampling spanning the onset of ice through spring melt and water column turnover to compare with ongoing biweekly open-water sampling. The results will provide novel insight into the winter community structure of bog lakes and associations between under-ice and open water carbon cycles.

Cecelia Stokes (Botany)

Murderous to metazoans or fatal to fungi: re-examining the ecology of the death cap mushroom
Amanita phalloides is an invasive, ectomycorrhizal mushroom (ECM) within the clade of “lethal amanitas” that has become widespread in the endemic, old growth coastal live oak woodlands of Point Reyes National Seashore in California. The death cap produces highly toxic secondary metabolites, such as amatoxins, that are thought to have integral roles in its ecology. The long-standing hypothesis focuses on the toxins acting as a defense against antagonistic animals, specifically insects and other invertebrates. However, no one has explicitly tested this hypothesis and very little is known of how the toxins influence interactions with other fungi. I will investigate the potential for amatoxins to function as defense mechanisms against invertebrates and document the competitive dynamics between native fungi and A. phalloides to determine the role of toxic secondary metabolites in the death cap’s ecology. In fields sites located in Point Reyes, California and Toulouse, France (one of the death cap’s native ranges), cap tissue and invertebrates will be collected from A. phalloides mushrooms, and surrounding soil will be collected as well. Similar samples will be collected from native lethal and non-lethal Amanita for comparison. DNA will be extracted from each sample and undergo metabarcoding using high-throughput amplicon sequencing to determine the microbial and invertebrate community compositions. To understand the environmental scope of amatoxins, I will test their distribution throughout the soil, below-ground mycelium, and root tissues of their symbionts using AMATOX tests. Amatoxin sensitivity assays will be conducted on several species of fungi and invertebrates using culture and feeding media amended with amatoxins to assess direct impacts of the toxins. My research will characterize the fungal, bacterial, and invertebrate communities associated with A. phalloides in its native and invasive ranges to evaluate potential advantages during an invasion. Furthermore, investigating the antagonistic effects of amatoxins on invertebrates and ECM species will lead to a better understanding of how a toxic invasive mushroom disrupts native microbial biodiversity and community composition.