Density functional theory meta-GGA + U study of water incorporation in the metal-organic framework material Cu-BTC.

Water absorption in the metal-organic framework (MOF) material Cu-BTC, up to a concentration of 3.5 H2O per Cu ion, is studied via density functional theory at the meta-GGA + U level. The stable arrangements of water molecules show chains of hydrogen-bonded water molecules and a tendency to form closed cages at high concentration. Water clusters are stabilized primarily by a combination of water-water hydrogen bonding and Cu-water oxygen interactions. Stability is further enhanced by van der Waals interactions, electric field enhancement of water-water bonding, and hydrogen bonding of water to framework oxygens. We hypothesize that the tendency to form such stable clusters explains the particularly strong affinity of water to Cu-BTC and related MOFs with exposed metal sites.

Fine-root system development and susceptibility to pathogen colonization.

Root development may exert control on plant-pathogen interactions with soil-borne pathogens by shaping the spatial and temporal availability of susceptible tissues and in turn the impact of pathogen colonization on root function. To evaluate the relationship between root development and resistance to apple replant disease (ARD) pathogens, pathogen abundance was compared across root branching orders in a bioassay with two rootstock genotypes, M.26 (highly susceptible) and CG.210 (less susceptible). Root growth, anatomical development and secondary metabolite production were evaluated as tissue resistance mechanisms. ARD pathogens primarily colonized first and second order roots, which corresponded with cortical tissue senescence and loss in second and third order roots. Defense compounds were differentially allocated across root branching orders, while defense induction or stress response was only detected in first order and pioneer roots. Our results suggest disease development is based largely on fine-root tip attrition. In accordance, the less susceptible rootstock supported lower ARD pathogen abundance and altered defense compound production in first order and pioneer roots and maintained higher rates of root growth in both the ARD soil and pasteurized control compared to the more susceptible. Thus, this rootstock's ability to maintain shoot growth in replant soil may be attributable to relative replant pathogen resistance in distal root branches as well as tolerance of infection based on rates of root growth.

Disease-Suppressive Vermicompost Induces a Shift in Germination Mode of Pythium aphanidermatum Zoosporangia.

Compost amendments to soils can minimize losses from soilborne plant pathogens, yet the mechanisms by which this occurs have not been well elucidated. In the present study, developmental responses of Pythium aphanidermatum zoosporangia to vermicomposts were observed to better understand how suppression of Pythium seedling disease is expressed. Mature zoosporangia were exposed to vermicompost extracts (VCEs) and monitored using time-lapse photomicroscopy. Sterile and nonsterile VCEs inhibited indirect germination and viable zoospore production whereas zoosporangia germinated directly in VCE to produce germ tubes. Additional treatments were tested to determine factors that promote direct over indirect germination. The pH (5 to 9 at 0.001 M) and ionic strength (0.1 to 0.0001 at pH 6) of potassium phosphate buffer did not alter zoosporogenesis compared with sterile water. Decreasing osmotic potentials in glucose and sucrose from -248 to -2,712 kPa or in polyethylene glycol 8000 from -0.335 to -105 kPa led to a decrease in indirect germination with a corresponding increase in direct germination. Significant levels of seed infection were observed within 1 h of exposure to zoospores (produced in sterile water) or to germ tubes (produced in sucrose solution). Our data demonstrate that VCEs suppress zoosporogenesis and stimulate direct germination; however, this did not result in the suppression of germ tube growth and seed infection.

Duloxetine in the treatment of binge eating disorder with depressive disorders: a placebo-controlled trial.

OBJECTIVE: This study evaluated duloxetine in the treatment of binge eating disorder (BED) with comorbid current depressive disorders. METHOD: In this 12-week, double-blind, placebo-controlled trial, 40 patients with Diagnostic and Statistical Manual of Mental Disorders-IV-TR BED and a comorbid current depressive disorder received duloxetine (N = 20) or placebo (N = 20). The primary outcome measure was weekly binge eating day frequency. RESULTS: In the primary analysis, duloxetine (mean 78.7 mg/day) was superior to placebo in reducing weekly frequency of binge eating days (p = .04), binge eating episodes (p = .02), weight (p = .04), and Clinical Global Impression-Severity of Illness ratings for binge eating (p = .02) and depressive disorders (p = .01). Changes in body mass index and measures of eating pathology, depression, and anxiety did not differ between the two groups. DISCUSSION: Duloxetine may be effective for reducing binge eating, weight, and global severity of illness in BED with a comorbid current depressive disorder, but this finding needs confirmation in larger, placebo-controlled trials.

Microbial-induced carbon competition in the spermosphere leads to pathogen and disease suppression in a municipal biosolids compost.

The aim of this study was to understand whether competition for fatty acids in plant seed exudates by compost-derived seed-colonizing microbial communities could explain the suppression of plant infections initiated by sporangia of Pythium ultimum. The germination behavior of P. ultimum sporangia in response to cucumber seeds was measured to determine the impact of seed-colonizing microbes on pathogen suppression. Seed-colonizing microbial communities from municipal biosolids compost utilized cucumber seed exudates and linoleic acid in vitro, reducing the respective stimulatory activity of these elicitors to P. ultimum sporangial germination. However, when sporangia were observed directly in the spermosphere of seeds sown in the compost medium, levels of germination and sporangial emptying did not differ from the responses in sand. The percentage of aborted germ tubes was greater after incubating sporangia in compost medium for 12-h than the level of germ tube abortion when sporangia were incubated in sand. Abortion did not occur if previously germinated sporangia were supplemented with cucumber seed exudate. Furthermore, removal of cucumber seed exudate after various stages of germ tube emergence resulted in an increase in aborted germ tubes over time. Adding increasing levels of glucose directly to the compost medium alleviated germ tube abortion in the spermosphere and also eliminated disease suppression. These data fail to support a role for linoleic acid competition in Pythium seedling disease suppression but provide evidence for general carbon competition mediated by seed-colonizing microbial communities as a mechanism for the suppression of Pythium seed infections in municipal biosolids compost.

Seed-colonizing bacterial communities associated with the suppression of Pythium seedling disease in a municipal biosolids compost.

This study was designed to characterize seed-colonizing microbial communities that were previously shown to be involved in the suppression of seedling disease caused by Pythium ultimum in a municipal biosolids compost. Selective microbial inhibitors were employed to inactivate portions of the microbial community associated with seed germinated in a compost medium to evaluate their impact on disease suppression. After initial screenings for toxicity to both cucumber and P. ultimum, six selective inhibitors were eventually used to assess the impact of seed treatment on the reduction of bacterial and fungal populations and on disease suppression. Rifampicin was the most effective inhibitor for inactivating disease suppression. Bacterial communities that colonized cucumber seed sown in compost medium for 8 h and seed sown in compost medium for 8 h followed by a 3-h treatment of either rifampicin at 500 ppm or water were dislodged from seed surfaces and subjected to RNA extraction and reverse transcription to cDNA. Differences in the composition of seed-colonizing bacterial communities were assessed using terminal restriction fragment length polymorphisms (T-RFLP) of polymerase chain reaction-amplified 16S rDNA genes. T-RFLP profiles revealed a diversity of distinct bacterial taxa, a number of which dominate seed surfaces within 8 h of sowing. Analysis of similarity (ANOSIM) using terminal restriction fragment (T-RF) presence or absence showed that community profiles of nontreated and water-treated seed were quite similar whereas community profiles from rifampicin-treated seed were distinct. Differences in community profiles based on T-RF abundance (peak height and peak area) indicated that all treatments were unique (ANOSIM, all pairwise comparisons P < 0.05) Peaks heights and areas of relatively few T-RFs were reduced to zero following rifampicin treatment and 34 T-RFs explained 85% of the observed difference between treatments. Tentative taxon assignments for each of the T-RFs that contributed to the treatment differences revealed a preponderance of sequences with affinities to the α-, ß-, and γ-Proteobacteria and Firmicutes. Limited sequencing of clones associated with water-treated and rifampicin-treated seed revealed the presence of similar taxa dominated by members of the γ-Proteobacteria. Many species within these taxa (such as Pseudomonas spp., Enterobacter spp., and Bacillus spp.) are known to be suppressive to Pythium diseases. Results of our study have confirmed that Pythium disease suppression in a municipal biosolids compost is mediated by compost-associated bacteria that colonize seed within hours after sowing. By focusing on actively growing microbes in the infection court during important stages of pathogen infection, we believe we can more efficiently determine the mechanisms of disease suppression and the microbes involved. Although specific to this pathosystem and compost, our results have a much broader scope of inference and illustrate the utility of such a targeted approach in identifying a relatively small subset of microbial taxa from complex communities likely to be involved in disease suppression.

Temporal release of fatty acids and sugars in the spermosphere: impacts on Enterobacter cloacae-induced biological control.

The aim of this study was to determine the temporal release of fatty acids and sugars from corn and cucumber seeds during the early stages of seed germination in order to establish whether sugars found in exudate can prevent exudate fatty acid degradation by Enterobacter cloacae. Both saturated (long-chain saturated fatty acids [LCSFA]) and unsaturated (long-chain unsaturated fatty acids [LCUFA]) fatty acids were detected in corn and cucumber seed exudates within 15 min after seed sowing. LCSFA and LCUFA were released at a rate of 26.1 and 6.44 ng/min/seed by corn and cucumber seeds, respectively. The unsaturated portion of the total fatty acid pool from both plant species contained primarily oleic and linoleic acids, and these fatty acids were released at a combined rate of 6.6 and 0.67 ng/min/seed from corn and cucumber, respectively. In the absence of seed exudate sugars, E. cloacae degraded linoleic acid at rates of 29 to 39 ng/min, exceeding the rate of total fatty acid release from seeds. Sugars constituted a significant percentage of corn seed exudate, accounting for 41% of the total dry seed weight. Only 5% of cucumber seed exudate was comprised of sugars. Glucose, fructose, and sucrose were the most abundant sugars present in seed exudate from both plant species. Corn seeds released a total of 137 microg/seed of these three sugars within 30 min of sowing, whereas cucumber seeds released 0.83 microg/seed within the same time frame. Levels of glucose, fructose, and sucrose found in corn seed exudate (90 to 342 microg) reduced the rate of linoleic acid degradation by E. cloacae to 7.5 to 8.8 ng/min in the presence of either sugar, leaving sufficient concentrations of linoleic acid to activate Pythium ultimum sporangia Our results demonstrate that elevated levels of sugars in the corn spermosphere can prevent the degradation of LCUFA by E. cloacae, leading to its failure to suppress P. ultimum sporangial activation, germination, and subsequent disease development.

Differential interference with Pythium ultimum sporangial activation and germination by Enterobacter cloacae in the corn and cucumber spermospheres.

Differential protection of plants by Enterobacter cloacae was studied by investigating early sensing and response behavior of Pythium ultimum sporangia toward seeds in the presence or absence of E. cloacae. Ten percent of P. ultimum sporangia were activated within the first 30 min of exposure to cucumber seeds. In contrast, 44% of the sporangia were activated as early as 15 min after exposure to corn seeds with over 80% sporangial activation by 30 min. Germ tubes emerged from sporangia after 2.5 and 1.0 h in the cucumber and corn spermospheres, respectively. Seed application of the wild-type strain of E. cloacae (EcCT-501R3) reduced sporangial activation by 45% in the cucumber spermosphere, whereas no reduction was observed in the corn spermosphere. Fatty acid transport and degradation mutants of E. cloacae (strains EcL1 and Ec31, respectively) did not reduce sporangial activation in either of the spermospheres. Although wild-type or mutant strains of E. cloacae failed to reduce seed colonization incidence, pathogen biomass on cucumber seeds was reduced in the presence of E. cloacae strains EcCT-501R3 and Ec31 by 4 and 8 h after sowing, respectively. By 12 h, levels of P. ultimum on cucumber seeds treated with E. cloacae EcCT-501R3 did not differ from levels on noninoculated seeds. On corn seeds, P. ultimum biomass was not affected by the presence of any E. cloacae strain. When introduced after sporangial activation had occurred, E. cloacae failed to reduce P. ultimum biomass on cucumber seeds compared with that on nontreated seeds. Also, increasing numbers of sporangia used to inoculate seeds yielded increased pathogen biomass at each sampling time. This indicates a direct link between the level of seed-colonizing biomass of P. ultimum and the number of activated and germinated sporangia in the spermosphere, suggesting that E. cloacae suppresses P. ultimum seed infections by reducing sporangial activation and germination within the first 30 to 90 min after sowing.

Soil conditioning effects of Phragmites australis on native wetland plant seedling survival.

Interactions between introduced plants and soils they colonize are central to invasive species success in many systems. Belowground biotic and abiotic changes can influence the success of introduced species as well as their native competitors. All plants alter soil properties after colonization but, in the case of many invasive plant species, it is unclear whether the strength and direction of these soil conditioning effects are due to plant traits, plant origin, or local population characteristics and site conditions in the invaded range. Phragmites australis in North America exists as a mix of populations of different evolutionary origin. Populations of endemic native Phragmites australis americanus are declining, while introduced European populations are important wetland invaders. We assessed soil conditioning effects of native and non-native P. australis populations on early and late seedling survival of native and introduced wetland plants. We further used a soil biocide treatment to assess the role of soil fungi on seedling survival. Survival of seedlings in soils colonized by P. australis was either unaffected or negatively affected; no species showed improved survival in P. australis-conditioned soils. Population of P. australis was a significant factor explaining the response of seedlings, but origin (native or non-native) was not a significant factor. Synthesis: Our results highlight the importance of phylogenetic control when assessing impacts of invasive species to avoid conflating general plant traits with mechanisms of invasive success. Both native (noninvasive) and non-native (invasive) P. australis populations reduced seedling survival of competing plant species. Because soil legacy effects of native and non-native P. australis are similar, this study suggests that the close phylogenetic relationship between the two populations, and not the invasive status of introduced P. australis, is more relevant to their soil-mediated impact on other plant species.

Microbial dynamics and interactions in the spermosphere.

The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.

Virulence of oomycete pathogens from Phragmites australis-invaded and noninvaded soils to seedlings of wetland plant species.

Soil pathogens affect plant community structure and function through negative plant-soil feedbacks that may contribute to the invasiveness of non-native plant species. Our understanding of these pathogen-induced soil feedbacks has relied largely on observations of the collective impact of the soil biota on plant populations, with few observations of accompanying changes in populations of specific soil pathogens and their impacts on invasive and noninvasive species. As a result, the roles of specific soil pathogens in plant invasions remain unknown. In this study, we examine the diversity and virulence of soil oomycete pathogens in freshwater wetland soils invaded by non-native Phragmites australis (European common reed) to better understand the potential for soil pathogen communities to impact a range of native and non-native species and influence invasiveness. We isolated oomycetes from four sites over a 2-year period, collecting nearly 500 isolates belonging to 36 different species. These sites were dominated by species of Pythium, many of which decreased seedling survival of a range of native and invasive plants. Despite any clear host specialization, many of the Pythium species were differentially virulent to the native and non-native plant species tested. Isolates from invaded and noninvaded soils were equally virulent to given individual plant species, and no apparent differences in susceptibility were observed between the collective groups of native and non-native plant species.

Differential Suppression of Damping-off Caused by Pythium aphanidermatum, P. irregulare, and P. myriotylum in Composts at Different Temperatures.

The suppressiveness of compost amendments to pre-emergence damping-off of cucumber incited by isolates of Pythium aphanidermatum, P. myriotylum, and P. irregulare was studied. Growth chamber experiments were designed to examine the effects of temperature (20, 24, 28, and 32°C), compost type (municipal biosolids [MC] and leaves [LC]), and compost dose (40, 80, 160, and 320 mg/cm3) on suppression of damping-off (i.e., increase in seedling stands) caused by different Pythium isolates obtained from different hosts. In dose-response experiments, LC was suppressive at dosage rates ≥80 mg compost/cm3 of sand, whereas MC was suppressive at rates ≥40 mg/cm3. Damping-off severity induced by each of the three Pythium spp. was temperature-dependent. For example, P. aphanidermatum and P. myriotylum caused damping-off at each of the four temperatures tested, whereas P. irregulare caused disease only at 20 and 24°C. MC was suppressive to P. aphanidermatum at 20 and 24°C, whereas LC was suppressive at 28 and 32°C. Both composts significantly suppressed damping-off caused by P. irregulare at 20°C (85% suppression in MC and 60% suppression in LC) and at 24°C (approximately 60% suppression in both composts), and by P. myriotylum at all temperatures tested. In experiments with a variable temperature cycle (32°C for 14 h, day and 22°C for 10 h, night), only P. aphanidermatum and P. myriotylum caused damping-off of cucumber seedlings. Under these conditions, LC significantly suppressed damping-off caused by P. aphanidermatum (20% suppression) or P. myriotylum (37% suppression) but MC was not suppressive. In experiments where the two composts were mixed, a significant negative interaction between the two composts was observed for the suppression of P. myriotylum and P. irregulare at 20°C and of P. irregulare at 24°C, but not for P. aphanidermatum at any of the tested temperatures. There was no difference in aggressiveness among isolates within each of the three Pythium spp., regardless of their host origin. However, a significant variation in suppressiveness of LC was observed among isolates of P. aphanidermatum (11 isolates) derived from the same host, but not for P. irregulare (9 isolates) or P. myriotylum (7 isolates).

Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands.

Soil pathogens are believed to be major contributors to negative plant-soil feedbacks that regulate plant community dynamics and plant invasions. While the theoretical basis for pathogen regulation of plant communities is well established within the plant-soil feedback framework, direct experimental evidence for pathogen community responses to plants has been limited, often relying largely on indirect evidence based on above-ground plant responses. As a result, specific soil pathogen responses accompanying above-ground plant community dynamics are largely unknown. Here, we examine the oomycete pathogens in soils conditioned by established populations of native noninvasive and non-native invasive haplotypes of Phragmites australis (European common reed). Our aim was to assess whether populations of invasive plants harbor unique communities of pathogens that differ from those associated with noninvasive populations and whether the distribution of taxa within these communities may help to explain invasive success. We compared the composition and abundance of pathogenic and saprobic oomycete species over a 2-year period. Despite a diversity of oomycete taxa detected in soils from both native and non-native populations, pathogen communities from both invaded and noninvaded soils were dominated by species of Pythium. Pathogen species that contributed the most to the differences observed between invaded and noninvaded soils were distributed between invaded and noninvaded soils. However, the specific taxa in invaded soils responsible for community differences were distinct from those in noninvaded soils that contributed to community differences. Our results indicate that, despite the phylogenetic relatedness of native and non-native P. australis haplotypes, pathogen communities associated with the dominant non-native haplotype are distinct from those of the rare native haplotype. Pathogen taxa that dominate either noninvaded or invaded soils suggest different potential mechanisms of invasion facilitation. These findings are consistent with the hypothesis that non-native plant species that dominate landscapes may "cultivate" a different soil pathogen community to their rhizosphere than those of rarer native species.

Diversity of peronosporomycete (oomycete) communities associated with the rhizosphere of different plant species.

Peronosporomycete (oomycete) communities inhabiting the rhizospheres of three plant species were characterized and compared to determine whether communities obtained by direct soil DNA extractions (soil communities) differ from those obtained using baiting techniques (bait communities). Using two sets of Peronosporomycete-specific primers, a portion of the 5' region of the large subunit (28S) rRNA gene was amplified from DNA extracted either directly from rhizosphere soil or from hempseed baits floated for 48 h over rhizosphere soil. Amplicons were cloned, sequenced, and then subjected to phylogenetic and diversity analyses. Both soil and bait communities arising from DNA amplified with a Peronosporomycetidae-biased primer set (Oom1) were dominated by Pythium species. In contrast, communities arising from DNA amplified with a Saprolegniomycetidae-biased primer set (Sap2) were dominated by Aphanomyces species. Neighbor-joining analyses revealed the presence of additional taxa that could not be identified with known Peronosporomycete species represented in GenBank. Sequence diversity and mean sequence divergence (Theta pi) within bait communities were lower than the diversity within soil communities. Furthermore, the composition of Peronosporomycete communities differed among the three fields sampled and between bait and soil communities based on F(st) and parsimony tests. The results of our study represent a significant advance in the study of Peronosporomycetes in terrestrial habitats. Our work has shown the utility of culture-independent approaches using 28S rRNA genes to assess the diversity of Peronosporomycete communities in association with plants. It also reveals the presence of potentially new species of Peronosporomycetes in soils and plant rhizospheres.

Compost-induced suppression of Pythium damping-off is mediated by fatty-acid-metabolizing seed-colonizing microbial communities.

Leaf composts were studied for their suppressive effects on Pythium ultimum sporangium germination, cottonseed colonization, and the severity of Pythium damping-off of cotton. A focus of the work was to assess the role of fatty-acid-metabolizing microbial communities in disease suppression. Suppressiveness was expressed within the first few hours of seed germination as revealed by reduced P. ultimum sporangium germination, reduced seed colonization, and reduced damping-off in transplant experiments. These reductions were not observed when cottonseeds were sown in a conducive leaf compost. Microbial consortia recovered from the surface of cottonseeds during the first few hours of germination in suppressive compost (suppressive consortia) induced significant levels of damping-off suppression, whereas no suppression was induced by microbial consortia recovered from cottonseeds germinated in conducive compost (conducive consortia). Suppressive consortia rapidly metabolized linoleic acid, whereas conducive consortia did not. Furthermore, populations of fatty-acid-metabolizing bacteria and actinobacteria were higher in suppressive consortia than in conducive consortia. Individual bacterial isolates varied in their ability to metabolize linoleic acid and protect seedlings from damping-off. Results indicate that communities of compost-inhabiting microorganisms colonizing cottonseeds within the first few hours after sowing in a Pythium-suppressive compost play a major role in the suppression of P. ultimum sporangium germination, seed colonization, and damping-off. Results further indicate that fatty acid metabolism by these seed-colonizing bacterial consortia can explain the Pythium suppression observed.

Differential inactivation of seed exudate stimulation of Pythium ultimum sporangium germination by Enterobacter cloacae influences biological control efficacy on different plant species.

This study was initiated to understand whether differential biological control efficacy of Enterobacter cloacae on various plant species is due to differences in the ability of E. cloacae to inactivate the stimulatory activity of seed exudates to Pythium ultimum sporangium germination. In biological control assays, E. cloacae was effective in controlling Pythium damping-off when placed on the seeds of carrot, cotton, cucumber, lettuce, radish, tomato, and wheat but failed to protect corn and pea from damping-off. Seeds from plants such as corn and pea had high rates of exudation, whereas cotton and cucumber seeds had much lower rates of exudation. Patterns of seed exudation and the release of P. ultimum sporangium germination stimulants varied among the plants tested. Seed exudates of plants such as carrot, corn, lettuce, pea, radish, and wheat were generally more stimulatory to P. ultimum than were the exudates of cotton, cucumber, sunflower, and tomato. However, this was not directly related to the ability of E. cloacae to inactivate the stimulatory activity of the exudate and reduce P. ultimum sporangium germination. In the spermosphere, E. cloacae readily reduced the stimulatory activity of seed exudates from all plant species except corn and pea. Our data have shown that the inability of E. cloacae to protect corn and pea seeds from Pythium damping-off is directly related to its ability to inactivate the stimulatory activity of seed exudates. On all other plants tested, E. cloacae was effective in suppressing damping-off and inactivating the stimulatory activity of seed exudates.