Gupta V.,University of Toronto |
Smemo K.A.,Holden Arboretum |
Smemo K.A.,Kent State University |
Yavitt J.B.,Cornell University |
And 3 more authors.
Environmental Science and Technology | Year: 2013
Peatlands are an important source of the atmospheric greenhouse gas methane (CH4). Although CH4 cycling and fluxes have been quantified for many northern peatlands, imprecision in process-based approaches to predicting CH4 emissions suggests that our understanding of underlying processes is incomplete. Microbial anaerobic oxidation of CH 4 (AOM) is an important CH4 sink in marine sediments, but AOM has only recently been identified in a few nonmarine systems. We used 13C isotope tracers and followed the fate of 13C into CO2 and peat in order to study the geographic extent, relative importance, and biogeochemistry of AOM in 15 North American peatlands spanning a ∼1500 km latitudinal transect that varied in hydrology, vegetation, and soil chemistry. For the first time, we demonstrate that AOM is a widespread and quantitatively important process across many peatland types and that anabolic microbial assimilation of CH4-C occurs. However, AOM rate is not predicted by CH4 production rates and the primary mechanism of C assimilation remains uncertain. AOM rates are higher in fen than bog sites, suggesting electron acceptor constraints on AOM. Nevertheless, AOM rates were not correlated with porewater ion concentrations or stimulated following additions of nitrate, sulfate, or ferric iron, suggesting that an unidentified electron acceptor(s) must drive AOM in peatlands. Globally, we estimate that AOM could consume a large proportion of CH4 produced annually (1.6-49 Tg) and thereby constrain emissions and greenhouse gas forcing. © 2013 American Chemical Society.
Burke D.J.,Holden Arboretum |
Burke D.J.,Case Western Reserve University |
Chan C.R.,Holden Arboretum
Canadian Journal of Microbiology | Year: 2010
We compared the effects of the invasive plant Alliaria petiolata (garlic mustard) and 2 native plants on soil bacterial communities in a mature mesophytic forest. Soil samples were collected from plant patches containing either Alliaria or the native plants Allium tricoccum (wild leek) and Gallium triflorum (bedstraw). Since Alliaria litter contains secondary compounds that have reported antimicrobial properties, soil was collected outside the root zone of the plants but within the plant patches such that the soil would have been influenced by the litter of the respective plant species but not by plant roots. DNA was extracted from the soil samples and used to amplify the 16S rRNA gene region using bacterial specific primers. Terminal restriction fragment length polymorphism (TRFLP) profiles of each bacterial community were used to examine differences in bacterial communities among the plant species and between August and April sampling. Bacterial richness, evenness, and diversity were not significantly affected by plant species. Non-metric multidimensional scaling (NMS) suggested that differences existed between August and April sampling, but that plant species litter exerted a much weaker effect on soil bacterial communities. Soil physiochemical conditions were significantly correlated with soil bacterial communities and may underlie the observed seasonal changes in bacterial communities.
Burke D.J.,Holden Arboretum |
Burke D.J.,Case Western Reserve University |
Weintraub M.N.,University of Toledo |
Hewins C.R.,Holden Arboretum |
Kalisz S.,University of Pittsburgh
Soil Biology and Biochemistry | Year: 2011
Soil fungi are highly diverse and act as the primary agents of nutrient cycling in forests. These fungal communities are often dominated by mycorrhizal fungi that form mutually beneficial relationships with plant roots and some mycorrhizal fungi produce extracellular and cell-bound enzymes that catalyze the hydrolysis of nitrogen (N)- and phosphorus (P)- containing compounds in soil organic matter. Here we investigated whether the community structure of different types of mycorrhizal fungi (arbuscular and ectomycorrhizal fungi) is correlated with soil chemistry and enzyme activity in a northern hardwood forest and whether these correlations change over the growing season. We quantified these relationships in an experimental paired plot study where white-tailed deer (access or excluded 4.5 yrs) treatment was crossed with garlic mustard (presence or removal 1 yr). We collected soil samples early and late in the growing season and analyzed them for soil chemistry, extracellular enzyme activity and molecular analysis of both arbuscular mycorrhizal (AM) and ectomycorrhizal/saprotrophic fungal communities using terminal restriction fragment length polymorphism (TRFLP). AM fungal communities did not change seasonally but were positively correlated with the activities of urease and leucine aminopeptidase (LAP), enzymes involved in N cycling. The density of garlic mustard was correlated with the presence of specific AM fungal species, while deer exclusion or access had no effect on either fungal community after 4.5 yrs. Ectomycorrhizal/saprotrophic fungal communities changed seasonally and were positively correlated with most soil enzymes, including enzymes involved in carbon (C), N and P cycling, but only during late summer sampling. Our results suggest that fine scale temporal and spatial changes in soil fungal communities may affect soil nutrient and carbon cycling. Although AM fungi are not generally considered capable of producing extracellular enzymes, the correlation between some AM taxa and the activity of N acquisition enzymes suggests that these fungi may play a role in forest understory N cycling. © 2011 Elsevier Ltd.
Krynak K.L.,Case Western Reserve University |
Burke D.J.,Holden Arboretum |
Benard M.F.,Case Western Reserve University
PLoS ONE | Year: 2015
Recent global declines, extirpations and extinctions of wildlife caused by newly emergent diseases highlight the need to improve our knowledge of common environmental factors that affect the strength of immune defense traits. To achieve this goal, we examined the influence of acidification and shading of the larval environment on amphibian skin-associated innate immune defense traits, pre and post-metamorphosis, across two populations of American Bullfrogs (Rana catesbeiana), a species known for its wide-ranging environmental tolerance and introduced global distribution. We assessed treatment effects on 1) skinassociated microbial communities and 2) post-metamorphic antimicrobial peptide (AMP) production and 3) AMP bioactivity against the fungal pathogen Batrachochytrium dendrobatidis (Bd). While habitat acidification did not affect survival, time to metamorphosis or juvenile mass, we found that a change in average pH from 7 to 6 caused a significant shift in the larval skin microbial community, an effect which disappeared after metamorphosis. Additionally, we found shifts in skin-associated microbial communities across life stages suggesting they are affected by the physiological or ecological changes associated with amphibian metamorphosis. Moreover, we found that post-metamorphic AMP production and bioactivity were significantly affected by the interactions between pH and shade treatments and interactive effects differed across populations. In contrast, there were no significant interactions between treatments on post-metamorphic microbial community structure suggesting that variation in AMPs did not affect microbial community structure within our study. Our findings indicate that commonly encountered variation in the larval environment (i.e. pond pH and degree of shading) can have both immediate and long-term effects on the amphibian innate immune defense traits. Our work suggests that the susceptibility of amphibians to emerging diseases could be related to variability in the larval environment and calls for research into the relative influence of potentially less benign anthropogenic environmental changes on innate immune defense traits. © 2015 Krynak et al.
Carrino-Kyker S.R.,Holden Arboretum |
Carrino-Kyker S.R.,Case Western Reserve University |
Smemo K.A.,Holden Arboretum |
Smemo K.A.,Kent State University |
And 2 more authors.
BMC Microbiology | Year: 2013
Background: Human activities have greatly increased nitrogen (N) levels in natural habitats through atmospheric N deposition and nutrient leaching, which can have large effects on N cycling and other ecosystem processes. Because of the significant role microorganisms play in N cycling, high inputs of nitrogenous compounds, such as nitrate (NO3-), into natural ecosystems could have cascading effects on microbial community structure and the metabolic processes that microbes perform. To investigate the multiple effects of NO3- pollution on microbial communities, we created two shotgun metagenomes from vernal pool microcosms that were either enriched with a solution of 10 mg NO3 - N (+NO3-) or received distilled water as a control (-N). Results: After only 20 hours of exposure to NO 3-, the initial microbial community had shifted toward one containing a higher proportional abundance of stress tolerance and fermentation environmental gene tags (EGTs). Surprisingly, we found no changes to N metabolism EGTs, even though large shifts in denitrification rates were seen between the +NO3- and -N microcosms. Thus, in the absence of NO 3- addition, it is plausible that the microbes used other respiratory pathways for energy. Respiratory pathways involving iron may have been particularly important in our -N microcosms, since iron acquisition EGTs were proportionally higher in the -N metagenome. Additionally, we noted a proportional increase in Acidobacteria and Alphaproteobacteria EGTs in response to NO3- addition. These community shifts in were not evident with TRFLP, suggesting that metagenomic analyses may detect fine-scale changes not possible with community profiling techniques. Conclusions: Our results suggest that the vernal pool microbial communities profiled here may rely on their metabolic plasticity for growth and survival when certain resources are limiting. The creation of these metagenomes also highlights how little is known about the effects of NO3- pollution on microbial communities, and the relationship between community stability and function in response to disturbance. © 2013 Carrino-Kyker et al.; licensee BioMed Central Ltd.
News Article | December 16, 2015
"These Blanchard's cricket frogs have nearly gone extinct in their northern range, so we're almost forensically trying to understand what happened," said Mike Benard, a biology professor at Case Western Reserve. "This study suggests that changes we are making to the environment have the potential to make animals more susceptible to diseases and therefore may lead to population declines." Scientists found that habitat characteristics explained the differences in immune defense traits of frogs between populations. They found that the skin microbiomes ?symbiotic bacterial and fungal communities on the skin ?of frogs from disturbed sites, like residential and agricultural lands, were different from the skin microbiomes of frogs from more natural habitats. They also found natural peptide secretions—proteins frogs secrete from their skin that protect against pathogens—differed between frogs from different environments. Both changes potentially alter the amphibian's immune defense capabilities. These findings and more are published in the journal Biological Conservation. Research is increasingly showing that microbiomes in the gut and on the skin and antimicrobial peptides excreted by humans and other animals play important roles in fighting infection and disease. "We're seeing a lot of disease-related declines among amphibians, not to mention other groups of animals, such as bats plagued with white-nose syndrome and bees suffering from colony collapse disorder," said Katherine Krynak, a postdoctoral scholar in Case Western Reserve's Department of Biology and leader of the study. "This research shows that land use—farming or treating lawns with herbicides, pesticides and fertilizers—can influence traits that protect animals from disease." Blanchard's cricket frogs are about an inch long. They had once been widely spread across Wisconsin, Michigan and northern Ohio, but now only pockets remain in this northern region. Frogs used in the study were from ponds in various habitats: natural ponds surrounded by forest or prairie, or more disturbed ponds surrounded by houses, on farmed land or near athletic fields, parking lots and golf courses. In addition to considering the physical differences, the researchers tested water chemistry and quality in each pond. With permission from the states of Ohio and Michigan, Krynak, Benard and David Burke, a scientist and research chair at Holden Arboretum in Kirtland, Ohio, examined samples Krynak had collected from the frogs. Krynak used Q-tip like swabs to obtain samples of the skin microbiome, and then placed the frogs in a solution that gently induced the animals to secrete the antimicrobial peptides. Krynak and Burke then used molecular methods to examine the community of microbes on the frogs' skin. Burke, who studies symbiotic interactions between plants and microbial communities, is also an adjunct assistant professor of biology at Case Western Reserve. Krynak and Burke also examined the amount of peptides the frogs produced and how effective the peptides were against an amphibian pathogen they cultured in the lab. The researchers found microbiome differences between frogs that live in natural areas, such as a pond owned by the Nature Conservancy, and those in ponds surrounded by highly "managed" land, such as farmland or residential properties. "What we're seeing is the bacteria on the skin can vary markedly, depending on what people are doing to the environment that the frogs are living in," Burke said. A pond's latitude, conductivity—a proxy for chemical runoff—and size also appear to affect the microbiome. The amount of natural peptide secretions produced from the frogs' skin also varied across sites and was influenced by both the size of the pond and the conductivity of the water. Some of the skin secretions have been shown to fight off fungal infections, Krynak said. But in petri dishes in the lab, the growth rate of chytrid fungus, which has been linked to devastating population declines in amphibians worldwide, climbed with increasing Blanchard's cricket frog natural peptide secretions. The researchers will further investigate why higher concentrations of peptides appear to allow the killer fungus to grow faster in this species. "This pattern suggests that in areas where land use increases the amount of the peptides these frogs produce, this particular pathogen could have devastating effects" Krynak said. The team will also look more directly at how the environment interacts with a population's genes, changing the expression of traits. "Not only may the environment be altering traits now, but it may be dampening the ability of a population to adapt in the future," Krynak said. They are also experimentally isolating factors such as how a commonly used and commercially available glyphosate-based herbicide may alter these immune defense traits. Environmental alteration of defense traits may explain why different amphibian populations show different levels of resistance to infection and disease. Krynak said there's a strong chance that the environment is affecting these traits in other amphibians and wildlife in general. "By improving our understanding of the factors influencing immune defense traits capabilities, we are given the opportunity to make changes to our land management practices to better protect wildlife health" she said "and in all likelihood, our own health as a consequence". Explore further: Skin microbiome may hold answers to protect threatened gold frogs from lethal fungus
Medeiros J.S.,Holden Arboretum |
Pockman W.T.,University of New Mexico
American Journal of Botany | Year: 2014
• Premise of the study: The impact of changing temperature regime on plant distributions may depend on the nature of physiological variation among populations. The arid-land genus Larrea spans habitats with a range of freezing frequency in North and South America. We hypothesized that variation in xylem anatomy among populations and species within this genus is driven by plasticity and trade-offs between safety from freeze-thaw embolism and water transport efficiency. • Methods: We measured vessel density and diameter distributions to predict freeze-thaw embolism and water transport capacity for high and low latitude populations of three Larrea species grown in the field and a greenhouse common garden. • Key results: Among field-grown L. divaricata, low latitude plants had larger mean vessel diameter and greater predicted freeze-thaw embolism, but higher water transport capacity compared with high latitude plants. Though high latitude L. tridentata and L. nitida had abundant smaller vessels, these plants also produced very large vessels and had semi ring-porous wood structure. Thus, their predicted embolism and water transport capacity were comparable to those of low latitude plants. Differences among field-grown and common-garden-grown plants demonstrate that plasticity contributes to population differentiation in xylem characters, though high latitude L. divaricata exhibited relatively lower plasticity. • Conclusions: Our results indicate that a trade-off between transport safety and efficiency contributes substantially to variation in xylem structure within the genus Larrea. In addition, we suggest that xylem plasticity may play a role in negotiating these trade-offs, with implications for responses to future climate change. © 2014 Botanical Society of America.
Stoler A.B.,University of Pittsburgh |
Stoler A.B.,Rensselaer Polytechnic Institute |
Burke D.J.,Holden Arboretum |
Relyea R.A.,University of Pittsburgh |
Relyea R.A.,Rensselaer Polytechnic Institute
Ecology | Year: 2016
Research suggests that a positive relationship exists between diversity and ecological function, yet the multi-trophic effects of biodiversity remain poorly understood. The resource complementarity hypothesis suggests that increasing the trait diversity of resources provides a more complete diet for consumers, elevating consumer feeding rates. Whereas previous tests of this mechanism have measured trait diversity as the variation of single traits or the richness of functional groups, we employed a multivariate trait index to manipulate the chemical diversity of temperate tree litter species in outdoor pond mesocosms. We inoculated outdoor mesocosms with diverse and multi-trophic communities of microbial and macro-consumer species that rely on leaf litter for energy and nutrients. Litter was provided at three levels of chemical trait diversity, a constant level of species richness, and an equal representation of all litter species. Over three months, we measured more than 65 responses, and assessed the effects of litter chemical diversity and chemical trait means (i.e., community-weighted means). We found that litter chemical diversity positively correlated with decomposition rate of leaf litter, but had no effect on biomass or density of producers and consumers. However, the pond communities often responded to chemical trait means, particularly those related to nutrients, structure, and defense. Our results suggest that resource complementarity does have some effect on the release of energy and nutrients from decomposing substrates in forest ponds, but does not have multi-trophic effects. Our results further suggest that loss of tree biodiversity could affect forest ecosystem functionality, and particularly the processes occurring in and around ponds and wetlands. © 2016 by the Ecological Society of America.
Medeiros J.S.,Holden Arboretum |
Ward J.K.,University of Kansas
New Phytologist | Year: 2013
Changes in atmospheric carbon dioxide concentration ([CO2]) affect plant carbon/water tradeoffs, with implications for drought tolerance. Leaf-level studies often indicate that drought tolerance may increase with rising [CO2], but integrated leaf and xylem responses are not well understood in this respect. In addition, the influence of the low [CO2] of the last glacial period on drought tolerance and xylem properties is not well understood. We investigated the interactive effects of a broad range of [CO2] and plant water potentials on leaf function, xylem structure and function and the integration of leaf and xylem function in Phaseolus vulgaris. Elevated [CO2] decreased vessel implosion strength, reduced conduit-specific hydraulic conductance, and compromised leaf-specific xylem hydraulic conductance under moderate drought. By contrast, at glacial [CO2], transpiration was maintained under moderate drought via greater conduit-specific and leaf-specific hydraulic conductance in association with increased vessel implosion strength. Our study involving the integration of leaf and xylem responses suggests that increasing [CO2] does not improve drought tolerance. We show that, under glacial conditions, changes in leaf and xylem properties could increase drought tolerance, while under future conditions, greater productivity may only occur when higher water use can be accommodated. © 2013 New Phytologist Trust.
Krebs S.,Holden Arboretum
Acta Horticulturae | Year: 2013
A replicated field trial containing Rhododendron cultivars, species, and experimental hybrids was repeatedly flooded during one growing season to test for resistance to Phytophthora cinnamomi under stress conditions. At the end of the season root rot disease scores were assigned based on visual assessment of root, crown, and shoot necrosis using a numerical rating scale of 1 (healthy fine roots) to 5 (dead plant). Under flooding conditions, the average disease score of three resistant cultivars (controls used as benchmarks) was 4.1, which was a 90 percent increase above their previously determined average of 2.2 under non-flooded conditions. In contrast, disease scores of the resistant species R. hyperythrum were 35 percent higher under flooded (2.7) than non-flooded (2.0) treatments. Eight F1 hybrids derived from R. hyperythrum had an average disease score of 3.3 and were significantly less diseased than the resistant benchmark cultivars under flooded field conditions. Loss of root rot resistance in flooded soils could result from conditions that favor pathogen development and infection and from physiological changes in host plants that predispose them to disease. Under flooding conditions, R. hyperythrum appears to be less predisposed to root rot than resistant genotypes with different genetic backgrounds. While the basis for this difference in stress response is not currently known, it appears to be heritable in the F1 generation and represents a valuable trait for root rot resistance breeding. © ISHS 2013.