Sean M. Schaeffer

• Ph. D.
• Professor (Associate) at University of Tennessee at Knoxville

Leachate from litter and vegetation penetrates permafrost surface soils during thaw before being exported to aquatic systems. We know this leachate is critical to ecosystem function downstream and hypothesized that thaw leachate inputs would also drive terrestrial microbial activity and nutrient uptake. However, we recognized two potential endpoint...

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about m...

Rapid temperature and precipitation changes in High Arctic tundra ecosystems are altering the biogeochemical cycles of carbon (C) and nitrogen (N), but in ways that are difficult to predict. The challenge grows from the uncertainty of N cycle responses and the extent to which shifts in soil N are coupled with the C cycle and productivity of tundra...

A major thrust of terrestrial microbial ecology is focused on understanding when and how the composition of the microbial community affects the functioning of biogeochemical processes at the ecosystem scale (meters-to-kilometers and days-to-years). While research has demonstrated these linkages for physiologically and phylogenetically “narrow” proc...

Climate‐smart agricultural practices, such as no‐tillage (NT) and cover cropping, have been widely adopted and are anticipated to yield multiple benefits, including soil carbon sequestration, enhancing soil health, and crop yield stability. However, their influence on nitrous oxide (N2O) emissions varies, with the potential of both increasing and d...

Viruses are ubiquitous and abundant in soil and play crucial roles in shaping the diversity and activity of microbial host communities. Viral lytic activity yields intracellular matter to the dissolved pool and produces macromolecular microbial necromass, which may be a critical pathway for carbon sequestration. For a complete understanding of the...

Cover cropping is a promising strategy to improve soil health, but it may also trigger greenhouse gas emissions, especially nitrous oxide (N2O). Beyond nitrogen (N) availability, cover crop residue decomposition may accelerate heterotrophic respiration to limit soil O2 availability, hence promote N2O emissions from denitrification under sub-optimal...

Biodegradable mulch films (BDMs) are a sustainable and promising alternative to non-biodegradable polyethylene mulches used in crop production systems. Nitrogen amendments in the form of fertilizers are used by growers to enhance soil and plant-available nutrients; however, there is limited research on how these additions impact the biodegradation...

Micro and nanoplastics (MPs and NPs, respectively) in agricultural soil ecosystems represent a pervasive global environmental concern, posing risks to soil biota and crops, hence soil health and food security. This review provides a comprehensive and current summary of the literature on sources and properties of MNPs in agricultural ecosystems, met...

Biodegradable mulch films (BDMs) are a sustainable and promising alternative to non-biodegradable polyethylene mulches used in crop production systems. Nitrogen amendments in the form of fertilizers are used by growers to enhance soil and plant-available nutrients, however, there is limited research on how these additions impact biodegradation of B...

Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic...

Soil bacterial communities are critical for stability and function of terrestrial ecosystems. Viruses are ubiquitous in soils and have significant impacts on the structure and functions of bacterial host communities. However, little is known concerning the impact of various land use management practices on bacterial and viral communities. This stud...

Accurate predictions of crop yield are an integral part of effective agricultural tactical and strategic management decisions to sustain yield without adversely impacting the environment. Process-based simulation models are widely used to predict crop yields, but their application remains limited by the requirements of substantial expertise, intens...

Input of plant residue carbon (C) stimulates microbial growth and activity, and thus may alter native soil organic matter (SOM) mineralization. The partition of plant residue C between microbial growth and respiration, and priming effect on soil organic C (SOC) are affected by initial SOM levels and plant residue types. However, how the interaction...

In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are u...

Raindrop impact and wetting-drying cycles of soil strongly influence aggregate breakdown and reformation, but these mechanisms have not been examined simultaneously under field conditions. This study examined soil breakdown and aggregation in situ following rain events and inter-event soil moisture variations (referred herein as wetting-drying cycl...

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil ph...

The active layer of permafrost in Ny Ålesund, Svalbard (79°N) around the Bayelva River in the Leirhaugen glacier moraine is measured as a small net carbon sink at the brink of becoming a carbon source. In many permafrost-dominating ecosystems, microbes in the active layers have been shown to drive organic matter degradation and greenhouse gas produ...

Over the past 25 or so years soil health has been broadly studied, sometimes justly criticized, but commonly accepted and appreciated by stakeholders. Rather than follow the approach from over the last 10 to 15 years of concentrating on details of soil health indicators and agglomerated indices, recent publications have instead begun to analyze bro...

In the age of big data, soil data are more available than ever, but -outside of a few large soil survey resources- remain largely unusable for informing soil management and understanding Earth system processes outside of the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to context...

Climate change is predicted to induce more frequent and intense drying-wetting disturbances in soils. Although the response of soil microbial communities and the functions they perform during, or shortly after, drying-wetting disturbances is well documented, the recovery of these components several weeks after the disturbances is still largely unkn...

Plastic polyethylene mulch has been widely used in crop production, but also causes environmental pollution if plastic residues accumulate in soil. Biodegradable plastic mulches (BDM) are a potential solution to problems caused by polyethylene mulches, as BDMs are designed be tilled into the soil after the growing season and then biodegrade. Howeve...

The labile organic carbon (C) pool plays a vital role in soil biogeochemical transformation and can be used as a sensitive indicator of the response of soil quality to agricultural practice. However, little is known about how residue type and soil fertilization affect the incorporation of residue C into labile organic C pools. A 360-day laboratory...

Understanding how conservation agricultural management improves soil nitrogen (N) stability in the face of climate change can help increase agroecosystem productivity and mitigate runoff, leaching and downstream water quality issues. We conducted a 2-year field study in a 36-year-old rain-fed cotton production system to evaluate the impacts of chan...

Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS,...

The effect of modified biochar on the greenhouse gas emission in soil is not clear until now. In this study, biochar (BC) was modified by phosphoric acid (P) and further combined with nano-zero-valent iron (nZVI) to form nZVI-P-BC composite. The P modified biochar could significantly increase the available phosphorus in soil. The release of CO2 and...

Biodegradable plastic mulch films (BDMs) are essential in the production of vegetable and specialty crops due to their promotion of increased crop yield and quality. Unlike conventional polyethylene (PE) mulches, BDMs can be tilled into the soil after crop harvest to undergo biodegradation, thereby leading to minimal environmental impact. Agricultu...

There is an increased interest in the use of soil-biodegradable plastic mulch due to limited disposal options for conventional polyethylene mulch. However, information about the impact of continuous use of soil-biodegradable plastic mulch on the environment is limited. Here, we show the effects on soil and groundwater quality from the use of soil-b...

Understanding the mechanisms of carbon (C) stabilization in soil under the influence of moisture pulses is essential for predicting the stability of terrestrial C in the face of climate change. Conservation agricultural management is widely recognized to mitigate climate change through soil C stabilization or retention. We conducted a 24-day mesoco...

The global use of agricultural plastic films, which provide multiple benefits for food production, is expected to grow by 59% from 2018 to 2026. Disposal options for agricultural plastics are limited and a major global concern, as plastic fragments from all sources ultimately accumulate in the sea. Biodegradable plastic mulches could potentially al...

Emerging evidence indicates that, similar to aquatic ecosystems, viral infection may act as a top-down control on microbial communities in terrestrial systems. Bacteriophage have been shown to shift to a lytic reproductive cycle in response to host stress and/or environmental cues. During the lytic cycle, viruses actively reproduce and weaken the h...

Genetic engineering has been used to decrease the lignin content and to change the lignin composition of switchgrass ( Panicum virgatum L.) to decrease cell wall recalcitrance to enable more efficient cellulosic biofuel production. Previous greenhouse and field studies showed that downregulation of the gene encoding switchgrass caffeic acid O -meth...

Decomposition provides a critical mechanism for returning nutrients to the surrounding environment. In terrestrial systems, animal carcass, or carrion, decomposition results in a cascade of biogeochemical changes. Soil microbial communities are stimulated, resulting in transformations of carbon (C) and nitrogen (N) sourced from the decaying carrion...

Plastic mulch films are employed in the production of vegetables and other specialty crops worldwide due to the benefits they provide, such as reduction of weeds and water loss by evaporation, and control of soil temperature. The benefits can lead to better product quality and yield, and to a more efficient utilization of agricultural inputs such a...

Background and aims Under the scenario of global change, continuous ¹³C-enriched CO2 labeling is a powerful tool for evaluating the interaction between plants and soil, especially the influence of elevated CO2 on the input of plant-derived C (new C) into soil in the short term. However, the methodological validity concerning the acquisition of isot...

Purpose Soil organic carbon (SOC) dynamics are central to understanding the effects of environmental change on the carbon cycle of ecosystems. Vegetation and soil stable carbon isotope composition (δ¹³C), especially the difference of δ¹³C between surface soils and source vegetation (Δδ¹³C), can provide useful information about the SOC dynamics. The...

Understanding the processes controlling amino sugar accumulation in soil is essential for predicting the contribution of microbial residues to soil organic matter (SOM). The accumulation of amino sugars in soil is affected by multiple factors. Seldom are those factors examined together. We measured amino sugar concentration, extracellular enzyme ac...

Plastic is ubiquitous in modern life, but most conventional plastic is non-biodegradable and accumulates as waste after use. Biodegradable plastic is a promising alternative to conventional plastic. However, biodegradable plastics must be thoroughly evaluated to ensure that they undergo complete degradation and have no adverse impact on the environ...

Soil organic carbon (SOC) sequestration is influenced by incorporation of maize straw and application of fertilizers, in intensive agricultural regions. However, there is a limited understanding of the transformation and stabilization of the newly added carbon (C) in soils applied with different amounts of straw residue. The aim of this study was t...

Arctic tundra ecosystems are warming disproportionately in the winter, including a delayed autumn soil freeze‐up. Because microbial processes are extremely sensitive to change in temperature below freezing, overwinter warming strongly stimulates decomposition and nutrient mineralization and ultimately promotes the conversion of sedge‐dominated tuss...

The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)‐bioreduction and achieves detoxification of organic/inorganic contaminants. Though much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage‐host interactions and virus co...

Aims Crop nitrogen (N) and phosphorus (P) stoichiometry can influence food nutritive quality and many ecosystem processes. However, how and why N and P stoichiometry respond to long-term agricultural management practices (e.g., N fertilization and film mulching) are not clearly understood. Methods We collected maize tissues (leaf, stem, root, and s...

Decomposition provides a critical mechanism for returning nutrients to the surrounding environment. In terrestrial systems, animal carcass, or carrion, decomposition results in a cascade of biogeochemical changes. Soil microbial communities are stimulated, resulting in transformations of carbon (C) and nitrogen (N) sourced from the decaying carrion...

Microbial activity promotes the formation of water stable soil aggregates, which are critical for soil carbon (C) storage. Repeated re-wetting and drying of the soil causes physical disruption (i.e., slaking) of aggregates, but also induces a physiological stress response that can decrease microbial activity. The balance between physicochemical de-...

Viruses play an important yet largely unexplored ecological role in soil. The relationship between soil virus dynamics (abundance, burst size, lysogenic potential) and other biogeochemical properties (microbial biomass and carbon (C) use efficiency, soil respiration, nitrogen (N) pools) has not previously been quantified. We investigated how such p...

Plastic pollution in agricultural soils, caused by the incomplete removal of polyethylene mulch after usage, is a growing environmental concern. There has therefore been increased interest in biodegradable plastic mulches as alternative to polyethylene mulch; however, little is known about their impact on soil health. We evaluated the effects of fo...

In situ bioremediation to achieve immobilization of toxic metals and radionuclides or detoxification of chlorinated solvents relies on electron donor additions. This practice promotes microbial Fe(III)-oxide mineral reduction that could change soil pore structure, release soil colloids, alter matrix surface properties, and cause the formation of se...

Soil moisture controls microbial activity and soil carbon cycling. Because microbial activity decreases as soils dry, decomposition of soil organic matter (SOM) is thought to decrease with increasing drought length. Yet, microbial biomass and a pool of water‐extractable organic carbon (WEOC) can increase as soils dry, perhaps implying microbes may...

Although the fertilization effect on soil microbial communities have been studied extensively, its influence combined with plastic-film mulching on seasonal variations of bacterial communities remains unknown. High throughput sequencing was used to explore seasonal bacterial communities in a long-term fertilization experiment that commenced in 1987...

Hotspots represent the ephemeral introduction of nutrients into an environment, and occur in both the modern and geologic past. The annual deposition of deciduous leaves in temperate forests, tree falls, animal excrement, and vertebrate carcass deposition all result in the pulsed introduction of nutrients to an ecosystem. Hotspots are critical for...

Crop yield response to nitrogen (N) application has been well documented, but quantitatively tracing the distribution of exogenous straw derived N (straw-N) in a soil-plant system amended by plastic film mulching and fertilizers is poorly understood. Focus on this, we used a ¹⁵N tracer, applied as maize straw, into a monoculture maize field experim...

The balance between loss of C to the atmosphere, and the accumulation of soil organic matter is directly controlled by soil microorganisms. A key driver of microbial activity is soil moisture, but it is unclear how microbial C cycling responds to spatiotemporal shifts in hydrological conditions across a heterogeneous, dynamic landscape. We explored...

The effect of simulated and agricultural weathering in two diverse US regions: Tennessee (TN) and Washington (WA), on the physicochemical properties of three commercially available biodegradable plastic mulch films (BDMs), and an experimental polylactic acid/polyhydroxyalkanoate (PLA/PHA) mulch was investigated to assess the potential impact of wea...

Páramo grasslands are important carbon sinks in the Ecuadorian Andes. Although carbon content of páramo Andisols is correlated with high water retention, the effects of differences in soil moisture under different types of land use on soil carbon processes have not been explicitly tested in the Ecuadorian Andes. This study assessed the relationship...

Cell wall recalcitrance poses a major challenge on cellulosic biofuel production from feedstocks such as switchgrass (Panicum virgatum L.). Since lignin is a known contributor of recalcitrance, transgenic switchgrass plants with altered lignin have been produced by downregulation of caffeic acid O-methyltransferase (COMT). Field trials of COMT-down...

Mean annual precipitation and consecutive dry day lengths are projected to increase in the Southeastern United States and cause dramatic changes to the natural soil moisture regimes of non-irrigated land. Changes to moisture content can strongly affect the production of soil-respired carbon dioxide (CO2) and the structure of soil microbial communit...

Two tick-borne diseases with expanding case and vector distributions are ehrlichiosis (transmitted by Amblyomma americanum) and rickettiosis (transmitted by A. maculatum and Dermacentor variabilis). There is a critical need to identify the specific habitats where each of these species is likely to be encountered to classify and pinpoint risk areas....

Datasets. Data files for MANOVA and ANOVA analyses. (ZIP)

DCA results. DCA results indicated habitat types were distinguishable based on vegetation measures; two vegetation habitat types (grassland and forest) instead of four (grassland, bottomland deciduous, upland deciduous, and coniferous). (TIF)

PCA results. PCA results depict how sites and habitat groups differed with respect to the different predictor variables, but not to examine their relationship. (TIF)

Microorganisms mediate the decomposition of straw residue in soil, but how soil fertility levels affect microbial incorporation of straw C remains unclear in many ecosystems. The objectives of this study were to quantify the contribution of straw C to microbial organic C (MBC), and to evaluate the effect of different soil fertility levels on the di...

There is strong evidence of an increasing trend of severe drought and precipitation events in the Unites States (US) due to greenhouse gas emissions. However, there is a considerable knowledge gap between these severe weather events and soil microbial respiration. The objective of this study was to quantify soil microbial respiration and assess mic...

In the early 1940’s, during the early stages of the Manhattan Project (WWII), of rural communities in Anderson County, Tennessee was rapidly converted into laboratory facilities and the city of Oak Ridge. The environment that became Oak Ridge not only experienced pollutants from the laboratory activities, but also alterations from the land-use chan...

The rate and extent of decomposition of soil organic carbon (SOC) is dependent, among other factors, on substrate chemistry and microbial dynamics. Our objectives were to understand the influence of substrate chemistry on microbial decomposition of carbon (C), and to use model fitting to quantify differences in pool sizes and mineralization rates....

Background/Question/Methods Microbial activity varies in time in response to changes in environmental and biogeochemical conditions. Describing these responses in mathematical models is complicated by the fact that exogenous environmental forcing and nonlinearities describing the endogenous dynamics result in variability and excitations over many...

The rate and extent of decomposition of soil organic carbon (SOC) is dependent on substrate chemistry and microbial dynamics. Our objectives were to understand the influence of substrate chemistry on microbial processing of carbon (C), and to use model fitting to quantify differences in pool sizes and mineralization rates. We conducted an incubatio...

Soil microorganisms play a critical role in biogeochemical cycles that affects crop production through nutrient regulation and availability, plant health, soil structure and organic matter dynamics. This project aimed to characterize the microbial community size, structure and activity as affected by tillage (till and no-till), nitrogen (N) fertili...

A method was developed to measure delta13C of soil CO2 from soil gas samples injected directly into the sample air stream of a tunable diode laser (TDL) spectrometer. Measurement precision was ±0.20/00, and each measurement required two minutes. An open chamber design was also evaluated for use with the TDL. Comparison of Keeling plot intercepts fr...