Papers by Jennifer DeBruyn
mSphere
Conservation agriculture practices that promote soil health have distinct and lasting effects on ... more Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer.
Soil Microbial Communities Associated With Biodegradable Plastic Mulch Films
Frontiers in Microbiology
Characterizing the postmortem human bone microbiome from surface-decomposed remains
PLOS ONE
Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. Howe... more Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobac-teria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.
PeerJ
Plastic mulch films are used globally in crop production but incur considerable disposal and envi... more Plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to polyethylene (PE)-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However, insufficient research regarding the impacts of repeated soil incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA, USA. Treatments included four plastic BDMs (three commercially available and one experimental film), a biodegradable cellulose paper mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA gene amplicon sequencing revealed...
0927 - Quantifying and Characterizing Poly-lactic Acid Degradation by the Soil Microbes Bacillus pumilus and Rhodococcus yunnanensis
Scientific Reports
During carcass decomposition, tissues undergo biochemical changes: Cells autolyze, enteric microb... more During carcass decomposition, tissues undergo biochemical changes: Cells autolyze, enteric microbes ferment cellular products, and tissues degrade. Ultimately, decomposition fluids are released as an ephemeral nitrogen (N) and carbon source to the surrounding environment. However, decomposition fluids are δ 15 N-enriched relative to body tissues, leading to a disconnect between starting tissue composition and ending fluid composition. It remains largely unknown when or if tissues exhibit δ 15 N enrichment postmortem despite the importance of tissue stable isotopes to ecologists. to test our hypothesis that tissues would become progressively δ 15 N-enriched during decay, soft tissues and bone were collected from beaver carcasses at five time points. All soft tissues, including muscle, were significantly δ 15 N-enriched compared to fresh tissues, but were not as enriched as decomposition fluids. Tissue breakdown is initially dominated by anaerobic autolysis and later by microbe and insect infiltration, and partly explains decay fluid isotopic enrichment. We speculate that after rupture, preferential volatilization of δ 15 N-depleted compounds (especially ammonia) contributes to further enrichment. These results constrain the timing, rate, and potential mechanisms driving carcass isotopic enrichment during decay, and suggest that found carcasses (e.g., road kill) should be used with caution for inferring trophic ecology as decay can result in significant postmortem δ 15 N enrichment. Vertebrate tissue isotopic composition is widely used by ecologists to address questions related to broader ecosystem functioning, including population dynamics, animal migrations or ranges, provenance, age, and diet, which can be used to infer trophic-level interactions 1-5. For animals that are difficult to observe directly in nature or for archaeological communities, these types of chemical fingerprints are invaluable for understanding ecosystems 6,7. As a general rule, a 2 to 4‰ enrichment in tissue nitrogen (N) stable isotopic composition (δ 15 N) above the diet value is expected, resulting in increasing δ 15 N with increasing trophic level 8-10. Under nutritional stress and/or shifts in the animal's nitrogen balance, nitrogen enrichment patterns begin to deviate 11,12 , however this is usually only observed under the most extreme conditions (i.e., fasting, suboptimal health) 13,14. Anabolic states, where protein synthesis increases (e.g. during pregnancy), leads to an overall decrease in hair δ 15 N values 15 , while catabolic states or starvation and high protein diets lead to δ 15 N-enrichment 11,16. Despite the potential for N balance and nutritional stress to alter tissue δ 15 N composition, stable isotopes still provide an important tool for ecological research. Prior studies evaluating animal ecology using stable isotopes have relied on the use of three broad types of samples: (1) Primary samples (i.e., muscle, hair, feces) collected from live animals or animals with a known time of death; (2) Found samples (i.e., salvaged road kill, scat, hair or feathers) with an unknown duration of exposure or postmortem interval; and (3) Previously collected and archived samples (i.e., bones and hair in lab or museum collections). Each sample type-primary, found, or archived-provides critical information about ecological interactions. Stable isotope analyses from primary samples from living animals, particularly those that are threatened or endangered, provide critical insights into habitat use, diet, and niche partitioning between species. For example, fur stable isotopic composition of wild-captured mouse lemurs revealed geographical differences in diet 2. For animals that are difficult to track or with low population densities, found samples are the only viable materials available. For example, the coyote diet was reconstructed using stable isotopic composition of road kill and scat 5. The use of archived specimens, often collected over decades and potentially from difficult to access localities or from endangered species, may represent the only viable sample
Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation
Environmental Microbiology
Biogeosciences Discussions
Decomposition provides a critical mechanism for returning nutrients to the surrounding environmen... more 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 soft tissues, 5 changes to soil pH and electrical conductivity as microbial communities release CO 2 and mineralize organic N, and significant changes to oxygen availability. Over time, microbial communities transform ammonium to nitrate and potentially N 2 O through nitrification and denitrification. While many of the rapid changes to soil biogeochemistry observed during carrion decomposition return to background or starting conditions shortly after soft tissues are degraded, 10 some biogeochemical parameters, particularly bulk soil stable δ 15 N isotopic composition, have the potential to exhibit prolonged perturbations, extending for several years. The goal of this study was to evaluate the lateral and vertical changes to soil stable isotopic composition one year after carrion decomposition in a forest ecosystem. Lateral transects extending 140 cm from three decomposition "hotspots" were sampled at 20 cm intervals, and subsurface cores were collected 15 beneath each hotspot to a depth of 50 cm. Bulk soil stable isotopic composition (δ 15 N and δ 13 C) indicated that one year after complete soft tissue removal and decay, soils were significantly 15 Nenriched compared to control soils up to 60 cm from the hotspot center, and enrichment extended to a depth of 10 cm. Our results demonstrate that carrion decomposition has the potential to result in long-term changes to soil biogeochemistry, up to at least one year after soft tissue 20 degradation, and to contribute to bulk soil stable isotopic composition.
Frontiers in Microbiology
Agricultural plastic mulch films are widely used in specialty crop production systems because of ... more Agricultural plastic mulch films are widely used in specialty crop production systems because of their agronomic benefits. Biodegradable plastic mulches (BDMs) offer an environmentally sustainable alternative to conventional polyethylene (PE) mulch. Unlike PE films, which need to be removed after use, BDMs are tilled into soil where they are expected to biodegrade. However, there remains considerable uncertainty about longterm impacts of BDM incorporation on soil ecosystems. BDMs potentially influence soil microbial communities in two ways: first, as a surface barrier prior to soil incorporation, indirectly affecting soil microclimate and atmosphere (similar to PE films) and second, after soil incorporation, as a direct input of physical fragments, which add carbon, microorganisms, additives, and adherent chemicals. This review summarizes the current literature on impacts of plastic mulches on soil biological and biogeochemical processes, with a special emphasis on BDMs. The combined findings indicated that when used as a surface barrier, plastic mulches altered soil microbial community composition and functioning via microclimate modification, though the nature of these alterations varied between studies. In addition, BDM incorporation into soil can result in enhanced microbial activity and enrichment of fungal taxa. This suggests that despite the fact that total carbon input from BDMs is minuscule, a stimulatory effect on microbial activity may ultimately affect soil organic matter dynamics. To address the current knowledge gaps, long term studies and a better understanding of impacts of BDMs on nutrient biogeochemistry are needed. These are critical to evaluating BDMs as they relate to soil health and agroecosystem sustainability.
Frontiers in microbiology, 2017
The elevational pattern of soil microbial diversity along mountain slopes has received considerab... more The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level. Elevational patterns of the relative abundance of specific microbial taxa could be partially explained by the oligotrophic-copiotrophic theory. Specifically, two dark-coniferous forests, located at mid-elevation sites, were considered to be oligotrophic habitats, with relatively higher soil C/N ratio and [Formula: see text]-N concentrations. As expected, oligotrophic microbial taxa, belonging to the bacte...
Frontiers in microbiology, 2017
Conservation tillage is an extensively used agricultural practice in northern China that alters s... more Conservation tillage is an extensively used agricultural practice in northern China that alters soil texture and nutrient conditions, causing changes in the soil microbial community. However, how conservation tillage affects rhizosphere and bulk soil fungal communities during plant growth remains unclear. The present study investigated the effect of long-term (6 years) conservation (chisel plow, zero) and conventional (plow) tillage during wheat growth on the rhizosphere fungal community, using high-throughput sequencing of the internal transcribed spacer (ITS) gene and quantitative PCR. During tillering, fungal alpha diversity in both rhizosphere and bulk soil were significantly higher under zero tillage compared to other methods. Although tillage had no significant effect during the flowering stage, fungal alpha diversity at this stage was significantly different between rhizosphere and bulk soils, with bulk soil presenting the highest diversity. This was also reflected in the phy...
PeerJ, 2017
The human microbiome has demonstrated an importance for the health and functioning in living indi... more The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = - 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) signif...
PloS one, 2016
Research on the human microbiome, the microbiota that live in, on, and around the human person, h... more Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes of decomposing human cadavers, focusing on the skin microbiota found in the nasal and ear canals. We then developed several models of statistical regression to establish an algorithm for predicting the PMI of microbial samples. We found that the complete data set, rather than a curated list of indicator species, was preferred fo...
Soil Degradation of Polylactic Acid/Polyhydroxyalkanoate-Based Nonwoven Mulches
Journal of Polymers and the Environment, 2015
ABSTRACT The soil degradation of fully biobased agricultural mulches prepared from polylactic aci... more ABSTRACT The soil degradation of fully biobased agricultural mulches prepared from polylactic acid (PLA) and blends of PLA and poly3-hydroxybutyrate-co-4-hydroxybutyrate (polyhydroxyalkanoate, or PHA) using nonwoven textile technology was compared to that of a commercial biodegradable mulch film, BioTelo (Dubois Agrinovation, Waterford, Canada). The addition of PHA to PLA to the feedstock blend produced nonwovens that possessed lower tensile strength and molecular weight and increased the average fiber diameter of mulches. A meltblown (MB) nonwoven mulch prepared from a PLA-PHA 72/28 w/w blend underwent the greatest degradation, achieving a 78 % loss of tensile strength and a 25.9 % decrease of weight-averaged molecular weight during 10 and 30 week of soil burial, respectively. The mass fraction of PHA decreased during soil burial, suggesting the preferential microbial assimilation of PHA over PLA. BioTelo underwent a 29 % loss of tensile strength but no appreciable change of molecular weight for its chloroform-soluble components. In contrast, spunbond (SB) PLA mulches did not undergo any appreciable degradation during the 30 week soil burial studies. The results suggest that the MB-PLA + PHA nonwoven may serve as a potentially valuable biodegradable agricultural mulch, and that SB-PLA may be useful as a compostable material for long-term agricultural applications, such as row covers and landscape fabrics. A soil degradation study of MB-PLA + PHA that directly compared untreated compost-enriched soil to sterilized soil-compost mixture demonstrated that the loss of tensile strength occurred only in the unsterilized soil, suggesting this event is directly associated with soil microorganisms.
Changing tides for Lake Erie: the biogeochemical evolution of a Laurentian Great Lake and implications for biological communities of the future
Estimating Time Since Death from Postmortem Human Gut Microbial Communities
Journal of Forensic Sciences, 2015
Postmortem succession of human-associated microbial communities (&amp... more Postmortem succession of human-associated microbial communities ("human microbiome") has been suggested as a possible method for estimating postmortem interval (PMI) for forensic analyses. Here we evaluate human gut bacterial populations to determine quantifiable, time-dependent changes postmortem. Gut microflora were repeatedly sampled from the proximal large intestine of 12 deceased human individuals as they decayed under environmental conditions. Three intestinal bacterial genera were quantified by quantitative PCR (qPCR) using group-specific primers targeting 16S rRNA genes. Bacteroides and Lactobacillus relative abundances declined exponentially with increasing PMI at rates of Nt = 0.977e(-0.0144t) (r(2) = 0.537, p < 0.001) and Nt = 0.019e(-0.0087t) (r(2) = 0.396, p < 0.001), respectively, where Nt is relative abundance at time (t) in cumulative degree hours. Bifidobacterium relative abundances did not change significantly: Nt = 0.003e(-0.002t) (r(2) = 0.033, p = 0.284). Therefore, Bacteroides and Lactobacillus abundances could be used as quantitative indicators of PMI.
The Dead and Their Microbes
Microbe Magazine, 2016
Distribution and dynamics of pyrene-degrading Mycobacteria in freshwater sediments contaminated with polycyclic aromatic hydrocarbons
Microbial biodegradation of polycyclic aromatic hydrocarbons (PAHs) is the primary means of atten... more Microbial biodegradation of polycyclic aromatic hydrocarbons (PAHs) is the primary means of attenuation of these toxic and carcinogenic compounds from contaminated soils and sediments. The documented toxicity and carcinogenicity of many PAHs demands remedial action for ...
Environmental Science and Technology, May 1, 2009
Despite a long history of anthropogenic contamination of Lake Erie sediments, little work has bee... more Despite a long history of anthropogenic contamination of Lake Erie sediments, little work has been done to understand the potential for PAH biodegradation by indigenous microbial communities. Pyrene-degrading Mycobacterium are prevalent in many polycyclic aromatic hydrocarbon (PAH)-contaminated freshwater sediments, and are of interest for their ability to degrade environmentally recalcitrant high molecular weight PAHs. This work tested the hypothesis that pyrene-degrading mycobacteria are prevalent in Lake Erie; an additional aim was to gain a baseline picture of the sediment microbial communities through sequencing a 16S rDNA clone library. Biodegradation potential of Lake Erie Mycobacterium populations was assessed through quantification of pyrene dioxygenase genes (nidA) and mycobacteria 16S rDNA genes using quantitative real time PCR. nidA was detected at all seven sampling sites across Lake Erie, with abundances ranging from 2.09 to 70.4 × 10 6 copies per gram sediment, with highest abundances at the most PAH-contaminated site (Cleveland Harbor). This is in contrast to naphthalene dioxygenase genes commonly used as biomarkers of PAH degradation: nahAc (from γ-proteobacteria) was not detected anywhere, and nagAc (from -proteobacteria) was detected only in Cleveland Harbor, despite dominance by proteobacteria in Lake Erie sediment 16S rDNA clone libraries (>50% of clones). The prevalence of Mycobacterium nidA genotypes corroborated previous studies indicating that PAH-degrading mycobacteria have a cosmopolitan distribution and suggests they play an important but overlooked role in natural attenuation and cycling of PAHs in Lake Erie.
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Papers by Jennifer DeBruyn