The Holden Arboretum

Vermilion-on-the-Lake, OH, United States

The Holden Arboretum

Vermilion-on-the-Lake, OH, United States
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Gupta V.,University of Toronto | Smemo K.A.,The Holden Arboretum | Smemo K.A.,Kent State University | Yavitt J.B.,Cornell University | Basiliko N.,University of Toronto
Microbial Ecology | Year: 2012

The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and 13C-DNA stable-isotope probing (SIP) to measure methane (CH 4) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH 4 oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated 13C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH 4 oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating 13C in 16S rDNA; however, its phylogenetic similarity to other CO 2-utilizing archaea probably indicates that this organism is not directly involved in CH 4 oxidation in peat. © 2011 Springer Science+Business Media, LLC.


Welsh A.K.,Texas State University | Burke D.J.,The Holden Arboretum | Hamerlynck E.P.,U.S. Department of Agriculture | Hahn D.,Texas State University
Plant and Soil | Year: 2010

Seasonal variation of arbuscular mycorrhizal fungi (AMF) in roots of the high salt marsh plant Spartina patens, the diversity of nitrogen-fixing bacteria in the rhizosphere and plant growth performance was studied at key stages of the growing season coinciding with major plant phenological stages, i.e., vegetative growth, reproduction and senescence. AMF colonization was highest during vegetative growth, with values declining during the growing season to the same level seen at plant dormancy. AMF colonization was reduced at lower depths in the sediments where anoxic conditions were observed and in plants treated with the systemic fungicide Benomyl. Only small changes in diversity of nitrogen-fixing bacteria in general and more specifically of those belonging to the ε-subdivision of Proteobacteria were detected during the season or between treatments by PCR-RFLP of nifH gene fragments with DNA as template for amplification; however, greater seasonal changes were displayed when cDNA was used as template for amplification as a proxy for gene expression and thus active bacteria. DGGE analyses of nifH gene fragments representing nitrogen-fixing bacteria of the ε-subdivision of Proteobacteria using both using DNA and cDNA as template showed highly diverse profiles that changed during the season and in response to treatment. Seasonal changes were observed for a suite of plant growth attributes and differences were observed between treatments, with higher values generally obtained on non-treated plants compared to Benomyl-treated plants. These differences were most pronounced during vegetative growth; however, differences between non-treated and Benomyl-treated plants were reduced seasonally and disappeared by the onset of senescence. This study demonstrates seasonal changes in AMF colonization on S. patens and in the community structure of nitrogen-fixing members of the ε-subdivision of Proteobacteria in the plant root zone. Plant growth performance changed seasonally with some effects of Benomyl-treatment. © Springer Science + Business Media B.V. 2009.


Burke D.J.,The Holden Arboretum | Burke D.J.,Case Western Reserve University | Smemo K.A.,The Holden Arboretum | Smemo K.A.,Kent State University | Hewins C.R.,The Holden Arboretum
Soil Biology and Biochemistry | Year: 2014

We examined whether ectomycorrhizal and saprotrophic fungi produce extracellular enzymes in culture and whether leaf litter addition affected production. We found little consistency in enzyme production among ECM fungi. Most fungi produced substantial levels of acid phosphatase and levels for many ECM fungi were equivalent to saprotrophic fungi. However, saprotrophic fungi had higher chitinase levels than ECM fungi. Some ECM fungi (e.g. Russula) produced levels of oxidative enzymes that were equivalent to saprotrophic fungi. © 2013 Elsevier Ltd.


Krynak K.L.,Case Western Reserve University | Burke D.J.,The Holden Arboretum | Benard M.F.,Case Western Reserve University
Biological Conservation | Year: 2016

Due to ease of global transportation, disease threats to amphibians are expected to increase. Therefore it is crucial that we improve our understanding of factors which may depress disease resistance so that we can incorporate this information into long-term conservation planning. Amphibians are protected from disease-causing pathogens by two skin-associated immune defense traits: the skin microbiome and the antimicrobial peptides found within natural peptide secretions (NPS) produced by the skin. Particular environmental characteristics may alter these amphibian immune defense traits and potentially affect disease resistance. We surveyed the skin-associated microbial communities (microbiome) and natural peptide secretions (NPS) of Blanchard's cricket frogs (. Acris blanchardi), at each of eleven sites across the species' declining range. We utilized an AICc model selection and model averaging approach to test for potential environmental influence on these traits. We found that populations differed in microbiomes and NPS production, but not NPS bioactivity against Bd (. Batrachochytrium dendrobatidis). The microbiome was associated with water conductivity, ratio of natural to managed land, and latitude. Additionally the microbiome was affected by interactions between frog sex and latitude, between frog sex and water surface area, and between the ratio of natural to managed land and water surface area. NPS production was influenced by an interaction between water surface area and conductivity. We found no evidence that NPS influence the microbiome; however, Bd growth rate in culture was positively associated with NPS production. This study indicates that environmental characteristics influence amphibian immune defense traits and may explain population differences in pathogen resistance. © 2015 Elsevier Ltd.


DeForest J.L.,Ohio University | Smemo K.A.,The Holden Arboretum | Smemo K.A.,Kent State University | Burke D.J.,The Holden Arboretum | And 3 more authors.
Biogeochemistry | Year: 2012

Although northern temperate forests are generally not considered phosphorus (P) limited, ecosystem P limitation may occur on highly weathered or strongly acidic soils where bioavailable inorganic P is low. In such environments, soil organisms may compensate by increasing the utilization of organic P via the production of extracellular enzymes to prevent limitation. In this study, we experimentally increased available P and/or pH in several acidic eastern deciduous forests underlain by glaciated and unglaciated soils in eastern Ohio, USA. We hypothesized that where inorganic P is low; soil microbes are able to access organic P by increasing production of phosphatase enzymes, thereby overcoming biogeochemical P limitations. We measured surface soil for: available P pools, N mineralization and nitrification rates, total C and N, enzymes responsible for C, N, and P hydrolysis, and microbial community composition (PLFA). Increasing surface soil pH a whole unit had little effect on microbial community composition, but increased N cycling rates in unglaciated soils. Phosphorus additions suppressed phosphatase activities over 60% in the unglaciated soils but were unchanged in the glaciated soils. All treatments had minimal influence on microbial biomass, but available pools of P strongly correlated with microbial composition. Microbes may be dependent on sources of organic P in some forest ecosystems and from a microbial perspective soil pH might be less important overall than P availability. Although our sampling was conducted less than 1 year after treatment initiation, microbial community composition was strongly influenced by available P pools and these effects may be greater than short-term increases in soil pH. © 2011 Springer Science+Business Media B.V.


Pendergast T.H.,University of Pittsburgh | Burke D.J.,The Holden Arboretum | Burke D.J.,Case Western Reserve University | Carson W.P.,University of Pittsburgh
New Phytologist | Year: 2013

Feedbacks between soil communities and plants may determine abundance and diversity in plant communities by influencing fitness and competitive outcomes. We tested the core hypotheses of soil community feedback theory: plant species culture distinct soil communities that alter plant performance and the outcome of interspecific competition. We applied this framework to inform the repeated dominance of Solidago canadensis in old-field communities. In glasshouse experiments, we examined the effects of soil communities on four plant species' performance in monoculture and outcomes of interspecific competition. We used terminal restriction fragment length polymorphism (TRFLP) analysis to infer differences in the soil communities associated with these plant species. Soil community origin had strong effects on plant performance, changed the intensity of interspecific competition and even reversed whether plant species were limited by conspecifics or heterospecifics. These plant-soil feedbacks are strong enough to upend winners and losers in classic competition models. Plant species cultured significantly different mycorrhizal fungal and bacterial soil communities, indicating that these feedbacks are likely microbiotic in nature. In old-fields and other plant communities, these soil feedbacks appear common, fundamentally alter the intensity and nature of plant competition and potentially maintain diversity while facilitating the dominance of So. canadensis. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.


Burke D.J.,The Holden Arboretum | Burke D.J.,Case Western Reserve University | Zhu S.,Case Western Reserve University | Pablico-Lansigan M.P.,Case Western Reserve University | And 2 more authors.
Biology and Fertility of Soils | Year: 2014

We examined the effect of TiO2 nanoparticles (NPs) on the growth of maize and soybean plants and associated soil microbial communities. Plants were grown in a greenhouse, and low levels of undoped or nitrogen-doped TiO2 NPs were applied. Plant growth and nutrient content were determined, and effects of NPs on composition of soil microbial communities were examined using terminal restriction fragment length polymorphism analysis (TRFLP) of rDNA. We found no significant effects of TiO2 NPs on plant growth, nutrient content, or the composition of bacterial communities within the rhizosphere. However, arbuscular mycorrhizal fungal communities were affected by application of undoped and nitrogen-doped TiO2 NPs. This observation may be partially attributed to the small but significant TiO2 NP uptake levels in the root tissues of both plants. Our results suggest that even low concentrations of TiO2 NPs may influence some important groups of soil microbes, such as mycorrhizal fungi, but changes in the composition of microbial communities may not affect plant growth under conditions of adequate moisture and nutrients. © 2014, Springer-Verlag Berlin Heidelberg.


Preston M.D.,University of Toronto | Smemo K.A.,The Holden Arboretum | Smemo K.A.,Kent State University | McLaughlin J.W.,Ontario Ministry of Natural Resources | Basiliko N.,University of Toronto
Frontiers in Microbiology | Year: 2012

Northern peatlands are a large repository of atmospheric carbon due to an imbalance between primary production by plants and microbial decomposition. The James Bay Lowlands (JBL) of northern Ontario are a large peatland-complex but remain relatively unstudied. Climate change models predict the region will experience warmer and drier conditions, potentially altering plant community composition, and shifting the region from a long-term carbon sink to a source. We collected a peat core from two geographically separated (ca. 200 km) ombrotrophic peatlands (Victor and Kinoje Bogs) and one minerotrophic peatland (Victor Fen) located nearVictor Bog within the JBL. We characterized (i) archaeal, bacterial, and fungal community structure with terminal restriction fragment length polymorphism of ribosomal DNA, (ii) estimated microbial activity using community level physiological profiling and extracellular enzymes activities, and (iii) the aeration and temperature dependence of carbon mineralization at three depths (0-10, 50-60, and 100-110 cm) from each site. Similar dominant microbial taxa were observed at all three peatlands despite differences in nutrient content and substrate quality. In contrast, we observed differences in basal respiration, enzyme activity, and the magnitude of substrate utilization, which were all generally higher at Victor Fen and similar between the two bogs. However, there was no preferential mineralization of carbon substrates between the bogs and fens. Microbial community composition did not correlate with measures of microbial activity but pH was a strong predictor of activity across all sites and depths. Increased peat temperature and aeration stimulated CO2 production but this did not correlate with a change in enzyme activities. Potential microbial activity in the JBL appears to be influenced by the quality of the peat substrate and the presence of microbial inhibitors, which suggests the existing peat substrate will have a large influence on future JBL carbon dynamics. © 2012 Preston, Smemo, McLaughlin and Basiliko.


Becklin K.M.,University of Kansas | Medeiros J.S.,The Holden Arboretum | Sale K.R.,University of Kansas | Ward J.K.,University of Kansas
Ecology Letters | Year: 2014

Assessing family- and species-level variation in physiological responses to global change across geologic time is critical for understanding factors that underlie changes in species distributions and community composition. Here, we used stable carbon isotopes, leaf nitrogen content and stomatal measurements to assess changes in leaf-level physiology in a mixed conifer community that underwent significant changes in composition since the last glacial maximum (LGM) (21 kyr BP). Our results indicate that most plant taxa decreased stomatal conductance and/or maximum photosynthetic capacity in response to changing conditions since the LGM. However, plant families and species differed in the timing and magnitude of these physiological responses, and responses were more similar within families than within co-occurring species assemblages. This suggests that adaptation at the level of leaf physiology may not be the main determinant of shifts in community composition, and that plant evolutionary history may drive physiological adaptation to global change over recent geologic time. © 2014 John Wiley & Sons Ltd/CNRS.


Valverde-Barrantes O.J.,Kent State University | Smemo K.A.,The Holden Arboretum | Feinstein L.M.,Kent State University | Kershner M.W.,Kent State University | Blackwood C.B.,Kent State University
Journal of Ecology | Year: 2013

Large variation in tree root architecture and morphology has been reported for temperate forest communities. However, it is not clear whether this variation represents adaptation of species to specific soil properties, alternative resource acquisition strategies among co-occurring species, or canalized traits without a strong impact on the success of individuals in different environments. Here, our goal was to test these alternative hypotheses and quantify how community-aggregated and intraspecific root trait variations are explained by biotic versus abiotic mechanisms in a temperate deciduous forest. We conducted our study in an Acer-Fagus-dominated forest in north-east Ohio, USA. Using molecular barcoding techniques, we identified 738 root systems belonging to 14 tree species. We measured seven functional root traits related to root architecture and morphology at the species and community-aggregated levels. Although we found significant relationships between soil resource gradients and root trait distributions, intrinsic differences between coexisting species were more important than soil factors in explaining the distribution of root traits in the community. Additionally, root trait variation at the species level was also influenced by the presence of other species within cores. Community-aggregated variation was more influenced by the combination of species present than soil properties in each sample, suggesting that biotic interactions play an important role in controlling community root trait distribution. Synthesis. We propose that root trait differentiation between coexisting species is the result of inherent differences between species and plasticity-mediated responses to neighbours. Hence, the large variation in root traits reported in temperate forest seems to reflect alternative evolutionary pathways that allow individuals to exploit distinct niches in relatively close proximity. © 2013 The Authors. Journal of Ecology © 2013 British Ecological Society.

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