Evaluation of an Antimicrobial Stewardship Decision Support for Pediatric Infections

OBJECTIVES

Clinical decision support (CDS) has promise for the implementation of antimicrobial stewardship programs (ASPs) in the emergency department (ED). We sought to assess the usability of a newly developed automated CDS to improve guideline-adherent antibiotic prescribing for pediatric community-acquired pneumonia (CAP) and urinary tract infection (UTI).

METHODS

We conducted comparative usability testing between an automated, prototype CDS-enhanced discharge order set and standard order set, for pediatric CAP and UTI antibiotic prescribing. After an extensive user-centered design process, the prototype CDS was integrated into the electronic health record, used passive activation, and embedded locally adapted prescribing guidelines. Participants were randomized to interact with three simulated ED scenarios of children with CAP or UTI, across both systems. Measures included task completion, decision-making and usability errors, clinical actions (order set use and correct antibiotic selection), as well as objective measures of system usability, utility, and workload using the National Aeronautics and Space Administration Task Load Index (NASA-TLX). The prototype CDS was iteratively refined to optimize usability and workflow.

RESULTS

Usability testing in 21 ED clinical providers demonstrated that, compared to the standard order sets, providers preferred the prototype CDS, with improvements in domains such as explanations of suggested antibiotic choices (p < 0.001) and provision of additional resources on antibiotic prescription (p < 0.001). Simulated use of the CDS also led to overall improved guideline-adherent prescribing, with a 31% improvement for CAP. A trend was present toward absolute workload reduction. Using the NASA-TLX, workload scores for the current system were median 26, interquartile ranges (IQR): 11 to 41 versus median 25, and IQR: 10.5 to 39.5 for the CDS system (p = 0.117).

CONCLUSION

Our CDS-enhanced discharge order set for ED antibiotic prescribing was strongly preferred by users, improved the accuracy of antibiotic prescribing, and trended toward reduced provider workload. The CDS was optimized for impact on guideline-adherent antibiotic prescribing from the ED and end-user acceptability to support future evaluative trials of ED ASPs.

Under pressure to exercise: a cross-sectional study of characteristics and predictors of compulsive exercise in early adolescents

BACKGROUND

To investigate the frequency of compulsive exercise among early adolescents, and determine the associated impact of sex, physical activity level, exercise habits, motivational regulation, dieting behaviour and health-related quality of life (HRQoL) on compulsive exercise.

METHODS

Cross-sectional design with 8th grade adolescents (n = 572, mean ± SD age 13.9 ± 0.3 yrs). Outcome assessment was compulsive exercise (Compulsive Exercise Test, CET). Total CET score ≥ 15 was defined as clinical CET score. Further assessment included exercise motivation (Behavioural Regulation of Exercise Questionnaire-2), HRQoL (KIDSCREEN 27), accelerometer-assessed physical activity and Andersen test for cardiorespiratory fitness. Exercise obsession was defined as clinical CET score and < 60 min/day with moderate-to-vigorous objectively assessed physical activity.

RESULTS

Small sex differences were found for CET total score. Seven percent of the adolescents were classified with clinical CET score, and four percent with exercise obsession. Adolescents with clinical CET score had higher body mass index, more weight loss attempts, and lower physical fitness compared to adolescents with non-clinical CET score. Being a boy, higher scores on introjected motivational regulation and HRQOL subscale parent relation and autonomy, use of exercise monitoring tool, and number of weight loss attempt the past 12 months explained 39% of the total CET score variance. Physical activity level did not predict compulsive exercise.

CONCLUSIONS

Compulsive exercise in early adolescents was predicted by exercise motivation, exercise habit, and dieting, but not physical activity level. This implicates a distinction of obsessive cognitions about physical activity from performed physical activity in adolescents, and that such cognitions must be addressed in future initiatives that aim to improve adolescents' general physical activity level, health, and wellbeing. Trial registration ClinicalTrials.gov: NCT03906851. Although there is a huge concern about adolescents being insufficiently physically active, there are also adolescents who struggle with issues of compulsive exercise. The issues of compulsive exercise have been rarely studied in adolescents. We therefore aimed to describe compulsive exercise and factors that were associated with and could explain presence of compulsive exercise. A total of 572 8th graders (age 13.9 ± 0.3 yrs) responded to this study. We found that the score on compulsive exercise was higher in boys than in girls, and that adolescents with high score on compulsive exercise had higher body mass index, more weight loss attempts, and lower physical fitness compared to adolescents with low score on compulsive exercise. Also, we found that exercise obsessions, i.e., thinking of exercise without actually exercising, was present in four percent of the respondents. Being a boy, attempting weight loss, exercising to avoid shame/guilt, and exercising for the perceived value of exercise predicted compulsive exercise. Awareness of the compulsive exercise and exercise obsessions is important in public health initiatives that aim to increase adolescents' physical activity level.

Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica

Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.

Seventy-two-hour Return Initiative: Improving Emergency Department Discharge to Decrease Returns

Unscheduled return visits within 72 hours of discharge account for 4% of pediatric emergency department (ED) visits each year and are a quality indicator of ED care. This project aimed to reduce the unexpected 72-hour return visit rate for a network of ED and urgent cares (UC) by improving discharge processes.

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone

The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.

Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth?

Here we describe recent breakthroughs in our understanding of microbial life in dry volcanic tephra ("soil") that covers much of the surface area of the highest elevation volcanoes on Earth. Dry tephra above 6000 m.a.s.l. is perhaps the best Earth analog for the surface of Mars because these "soils" are acidic, extremely oligotrophic, exposed to a thin atmosphere, high UV fluxes, and extreme temperature fluctuations across the freezing point. The simple microbial communities found in these extreme sites have among the lowest alpha diversity of any known earthly ecosystem and contain bacteria and eukaryotes that are uniquely adapted to these extreme conditions. The most abundant eukaryotic organism across the highest elevation sites is a Naganishia species that is metabolically versatile, can withstand high levels of UV radiation and can grow at sub-zero temperatures, and during extreme diurnal freeze-thaw cycles (e.g. - 10 to + 30 °C). The most abundant bacterial phylotype at the highest dry sites sampled (6330 m.a.s.l. on Volcán Llullaillaco) belongs to the enigmatic B12-WMSP1 clade which is related to the Ktedonobacter/Thermosporothrix clade that includes versatile organisms with the largest known bacterial genomes. Close relatives of B12-WMSP1 are also found in fumarolic soils on Volcán Socompa and in oligotrophic, fumarolic caves on Mt. Erebus in Antarctica. In contrast to the extremely low diversity of dry tephra, fumaroles found at over 6000 m.a.s.l. on Volcán Socompa support very diverse microbial communities with alpha diversity levels rivalling those of low elevation temperate soils. Overall, the high-elevation biome of the Atacama region provides perhaps the best "natural experiment" in which to study microbial life in both its most extreme setting (dry tephra) and in one of its least extreme settings (fumarolic soils).

The Caregiver Perspective on Unscheduled 72-Hour Return Visits to Pediatric Acute Care Sites: A Focus on Discharge Processes

OBJECTIVE

To characterize pediatric caregivers' reasons for 72-hour emergency department (ED) and urgent care (UC) returns.

METHODS

A sample of caregivers returning within 72 hours of initial visit to a pediatric ED or affiliated UC site was surveyed from November 2014 to June 2015; patients evaluated at outside ED/UC, scheduled for return, or non-English/Spanish speaking were excluded. Caregiver surveys underwent item generation, validation, and pilot testing. Survey items included caregiver reasons for unscheduled returns, with a specific assessment of delivery of key components of discharge instructions (diagnosis, duration of illness, home care, return precautions). Complete delivery of instructions was defined by caregiver reported receipt of instructions on all 4 components.

RESULTS

Of the 500 caregiver surveys analyzed 495 children received a 72-hour return ED/UC visit. Mean age of caregivers was 33 years, 62% completed college. Children were 2 years of age or younger (47%), male (52%), Caucasian (55%), and publicly insured (64%). Reported reasons for ED/UC return included belief that their child's illness had not resolved (51%) or worsened (41%). Many caregivers (41%) were not instructed on all key components of discharge. Almost half of caregivers (47%) were not educated on anticipated duration of illness. Complete delivery of discharge instructions was associated with ED/UC satisfaction (odds ratio, 5.7; 95% confidence interval, 3.8-8.5).

CONCLUSIONS

Among caregivers of children returning for an unscheduled ED/UC visit, most do not receive complete discharge instructions at initial visit. Improving delivery of key components of discharge instructions has the potential to increase ED/UC satisfaction and reduce unscheduled 72-hour returns.

Degradation of juglone by soil bacteria

Bacteria that can degrade juglone (5-hydroxy-1,4-naphthoquinone) were isolated from soil beneath black walnut trees. Autecological studies with one of these bacteria (Pseudomonas J1), demonstrated that it could grow rapidly using juglone as its sole source of carbon and energy. Using nonlinear regression analysis and the Monod equation, it was determined that this bacterium had a high affinity for juglone (K s = 0.95 μg/ml).Pseudomonas J1 can also utilize other aromatic compounds from plants as its sole source of carbon and energy. Compounds such as chlorogenic acid, ferulic acid, gallic acid, and 2-hydroxy-1,4-naphthoquinone (Lawson) were rapidly degraded byPseudomonas J1. The rapid degradation of juglone and other suspected allelochemicals by soil bacteria make it unlikely that these compounds are important mediators of plant-plant interactions under natural conditions.

Phylogeny and biogeography of an uncultured clade of snow chytrids

Numerous studies have shown that snow can contain a diverse array of algae known as 'snow algae'. Some reports also indicate that parasites of algae (e.g. chytrids) are also found in snow, but efforts to phylogenetically identify 'snow chytrids' have not been successful. We used culture-independent molecular approaches to phylogenetically identify chytrids that are common in long-lived snowpacks of Colorado and Europe. The most remarkable finding of the present study was the discovery of a new clade of chytrids that has representatives in snowpacks of Colorado and Switzerland and cold sites in Nepal and France, but no representatives from warmer ecosystems. This new clade ('Snow Clade 1' or SC1) is as deeply divergent as its sister clade, the Lobulomycetales, and phylotypes of SC1 show significant (P < 0.003) genetic-isolation by geographic distance patterns, perhaps indicating a long evolutionary history in the cryosphere. In addition to SC1, other snow chytrids were phylogenetically shown to be in the order Rhizophydiales, a group with known algal parasites and saprotrophs. We suggest that these newly discovered snow chytrids are important components of snow ecosystems where they contribute to snow food-web dynamics and the release of nutrients due to their parasitic and saprotrophic activities.

Antimicrobial effects of murine mesenchymal stromal cells directed against Toxoplasma gondii and Neospora caninum: role of immunity-related GTPases (IRGs) and guanylate-binding proteins (GBPs)

Mesenchymal stromal cells (MSCs) have a multilineage differentiation potential and provide immunosuppressive and antimicrobial functions. Murine as well as human MSCs restrict the proliferation of T cells. However, species-specific differences in the underlying molecular mechanisms have been described. Here, we analyzed the antiparasitic effector mechanisms active in murine MSCs. Murine MSCs, in contrast to human MSCs, could not restrict the growth of a highly virulent strain of Toxoplasma gondii (BK) after stimulation with IFN-γ. However, the growth of a type II strain of T. gondii (ME49) was strongly inhibited by IFN-γ-activated murine MSCs. Immunity-related GTPases (IRGs) as well as guanylate-binding proteins (GBPs) contributed to this antiparasitic effect. Further analysis showed that IFN-γ-activated mMSCs also inhibit the growth of Neospora caninum, a parasite belonging to the apicomplexan group as well. Detailed studies with murine IFN-γ-activated MSC indicated an involvement in IRGs like Irga6, Irgb6 and Irgd in the inhibition of N. caninum. Additional data showed that, furthermore, GBPs like mGBP1 and mGBP2 could have played a role in the anti-N. caninum effect of murine MSCs. These data underline that MSCs, in addition to their regenerative and immunosuppressive activity, function as antiparasitic effector cells as well. However, IRGs are not present in the human genome, indicating a species-specific difference in anti-T. gondii and anti-N. caninum effect between human and murine MSCs.

Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica

High-elevation valleys in dry areas of the Himalayas are among the most extreme, yet least explored environments on Earth. These barren, rocky valleys are subjected to year-round temperature fluctuations across the freezing point and very low availability of water and nutrients, causing previous workers to hypothesize that no photoautotrophic life (primary producers) exists in these locations. However, there has been no work using modern biogeochemical or culture-independent molecular methods to test the hypothesis that photoautotrophs are absent from high Himalayan soil systems. Here, we show that although microbial biomass levels are as low as those of the Dry Valleys of Antarctica, there are abundant microbial photoautotrophs, displaying unexpected phylogenetic diversity, in barren soils from just below the permanent ice line of the central Himalayas. Furthermore, we discovered that one of the dominant algal clades from the high Himalayas also contains the dominant algae in culture-independent surveys of both soil and ice samples from the Dry Valleys of Antarctica, revealing an unexpected link between these environmentally similar but geographically very distant systems. Phylogenetic and biogeographic analyses demonstrated that although this algal clade is globally distributed to other high-altitude and high-latitude soils, it shows significant genetic isolation by geographical distance patterns, indicating local adaptation and perhaps speciation in each region. Our results are the first to demonstrate the remarkable similarities of microbial life of arid soils of Antarctica and the high Himalayas. Our findings are a starting point for future comparative studies of the dry valleys of the Himalayas and Antarctica that will yield new insights into the cold and dry limits to life on Earth.

Coexisting bacterial populations responsible for multiphasic mineralization kinetics in soil

Experiments were conducted to study populations of indigenous microorganisms capable of mineralizing 2,4-dinitrophenol (DNP) in two soils. Previous kinetic analyses indicated the presence of two coexisting populations of DNP-mineralizing microorganisms in a forest soil (soil 1). Studies in which eucaryotic and procaryotic inhibitors were added to this soil indicated that both populations were bacterial. Most-probable-number counts with media containing different concentrations of DNP indicated that more bacteria could mineralize low concentrations of DNP than could metabolize high concentrations of it. Enrichments with varying concentrations of DNP and various combinations of inhibitors consistently resulted in the isolation of the same two species of bacteria from soil 1. This soil contained a large number and variety of fungi, but no fungi capable of mineralizing DNP were isolated. The two bacterial isolates were identified as a Janthinobacterium sp. and a Rhodococcus sp. The Janthinobacterium sp. had a low mu(max) and a low K(m) for DNP mineralization, whereas the Rhodococcus sp. had much higher values for both parameters. These differences between the two species of bacteria were similar to differences seen when soil was incubated with different concentrations of DNP. Values for mu(max) from soil incubations were similar to mu(max) values obtained in pure culture studies. In contrast, K(s) and K(m) values showed greater variation between soil and pure culture studies. The results of this study help to confirm predictions that two physiologically distinct bacterial populations are responsible for the multiphasic mineralization kinetics observed in the soil studied.

Microbial activity and diversity during extreme freeze-thaw cycles in periglacial soils, 5400 m elevation, Cordillera Vilcanota, Perú

High-elevation periglacial soils are among the most extreme soil systems on Earth and may be good analogs for the polar regions of Mars where oligotrophic mineral soils abut with polar ice caps. Here we report on preliminary studies carried out during an expedition to an area where recent glacial retreat has exposed porous mineral soils to extreme, daily freeze-thaw cycles and high UV fluxes. We used in situ methods to show that inorganic nitrogen (NO(3) (-) and NH(4) (+)) was being actively cycled even during a period when diurnal soil temperatures (5 cm depth) ranged from -12 to 27 degrees C and when sub-zero, soil cooling rates reached 1.8 degrees C h(-1) (the most rapid soil cooling rates recorded to date). Furthermore, phylogenetic analyses of microbial phylotypes present at our highest sites (5410 m above sea level) showed the presence of nitrifying bacteria of the genus Nitrospira and newly discovered nitrite-oxidizing Betaproteobacteria. These soils were overwhelmingly dominated (>70% of phylotypes) by photosynthetic bacteria that were related to novel cyanobacteria previously found almost exclusively in other plant-free, high-elevation soils. We also demonstrated that soils from our highest sites had higher potential for mineralizing glutamate and higher microbial biomass than lower elevation soils that had been more recently covered by ice. Overall, our findings indicate that a diverse and robustly functioning microbial ecosystem is present in these previously unstudied high-elevation soils.

The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils

Global climate change has accelerated the pace of glacial retreat in high-latitude and high-elevation environments, exposing lands that remain devoid of vegetation for many years. The exposure of 'new' soil is particularly apparent at high elevations (5000 metres above sea level) in the Peruvian Andes, where extreme environmental conditions hinder plant colonization. Nonetheless, these seemingly barren soils contain a diverse microbial community; yet the biogeochemical role of micro-organisms at these extreme elevations remains unknown. Using biogeochemical and molecular techniques, we investigated the biological community structure and ecosystem functioning of the pre-plant stages of primary succession in soils along a high-Andean chronosequence. We found that recently glaciated soils were colonized by a diverse community of cyanobacteria during the first 4-5 years following glacial retreat. This significant increase in cyanobacterial diversity corresponded with equally dramatic increases in soil stability, heterotrophic microbial biomass, soil enzyme activity and the presence and abundance of photosynthetic and photoprotective pigments. Furthermore, we found that soil nitrogen-fixation rates increased almost two orders of magnitude during the first 4-5 years of succession, many years before the establishment of mosses, lichens or vascular plants. Carbon analyses (pyrolysis-gas chromatography/mass spectroscopy) of soil organic matter suggested that soil carbon along the chronosequence was of microbial origin. This indicates that inputs of nutrients and organic matter during early ecosystem development at these sites are dominated by microbial carbon and nitrogen fixation. Overall, our results indicate that photosynthetic and nitrogen-fixing bacteria play important roles in acquiring nutrients and facilitating ecological succession in soils near some of the highest elevation receding glaciers on the Earth.

Phylogeny and ecophysiology of opportunistic "snow molds" from a subalpine forest ecosystem

Mats of coenocytic "snow molds" are commonly observed covering the soil and litter of alpine and subalpine areas immediately following snow melt. Here, we describe the phylogenetic placement, growth rates, and metabolic potential of cold-adapted fungi from under-snow mats in the subalpine forests of Colorado. SSU rDNA sequencing revealed that these fungi belong to the zygomycete orders Mucorales and Mortierellales. All of the isolates could grow at temperatures observed under the snow at our sites (0 degrees C and -2 degrees C) but were unable to grow at temperatures above 25 degrees C and were unable to grow anaerobically. Growth rates for these fungi were very high at -2 degrees C, approximately an order of magnitude faster than previously studied cold-tolerant fungi from Antarctic soils. Given the rapid aerobic growth of these fungi at low temperatures, we propose that they are uniquely adapted to take advantage of the flush of nutrient that occurs at the soil-snow interface beneath late winter snow packs. In addition, extracellular enzyme production was relatively high for the Mucorales, but quite low for the Mortierellales, perhaps indicating some niche separation between these fungi beneath the late winter snow pack.

Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil

Soil microbial communities have the metabolic and genetic capability to adapt to changing environmental conditions on very short time scales. In this paper we combine biogeochemical and molecular approaches to reveal this potential, showing that microbial biomass can turn over on time scales of days to months in soil, resulting in a succession of microbial communities over the course of a year. This new understanding of the year-round turnover and succession of microbial communities allows us for the first time to propose a temporally explicit N cycle that provides mechanistic hypotheses to explain both the loss and retention of dissolved organic N (DON) and inorganic N (DIN) throughout the year in terrestrial ecosystems. In addition, our results strongly support the hypothesis that turnover of the microbial community is the largest source of DON and DIN for plant uptake during the plant growing season. While this model of microbial biogeochemistry is derived from observed dynamics in the alpine, we present several examples from other ecosystems to indicate that the general ideas of biogeochemical fluxes being linked to turnover and succession of microbial communities are applicable to a wide range of terrestrial ecosystems.

Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution

Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.

Molecular and metabolic characterization of cold-tolerant alpine soil Pseudomonas sensu stricto

Alpine soils undergo dramatic temporal changes in their microclimatic properties, suggesting that the bacteria there encounter uncommon shifting selection gradients. Pseudomonads constitute important members of the alpine soil community. In order to characterize the alpine Pseudomonas community and to assess the impact of shifting selection on this community, we examined the ability of cold-tolerant Pseudomonas isolates to grow on a variety of carbon sources, and we determined their phylogenetic relationships based on 16S ribosomal DNA sequencing. We found a high prevalence of Pseudomonas in our soil samples, and isolates from these soils exhibited extensive metabolic diversity. In addition, our data revealed that many of our isolates form a unique cold-adapted clade, representatives of which are also found in the Swedish tundra and Antarctica. Our data also show a lack of concordance between the metabolic properties and 16S phylogeny, indicating that the metabolic diversity of these organisms cannot be predicted by phylogeny.

Disruption of narH, narJ, and moaE inhibits heterotrophic nitrification in Pseudomonas strain M19

Interruptions in three nitrate reductase-related genes, narH, narJ, and moaE, inhibited heterotrophic nitrification in Pseudomonas strain M19. No nitrate was detected in the medium, and nitrification proceeded in the presence of a nitrate reductase inhibitor. Heterotrophic nitrification was greatly stimulated by the addition of nitrate.

Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt

Previous work in an alpine dry meadow in the Front Range of the Rocky Mountains has shown that microbial biomass is high during winter and declines rapidly as snow melts in the spring, and that this decline is associated with changes in temperature regime and substrate availability. In this study we tested the hypothesis that the summer and winter microbial communities differ in function and composition. Shifts in species composition between pre- and post-snowmelt communities were detected using reciprocal hybridization of community DNA; DNA extracted from soils sampled at different times was significantly less homologous relative to spatial replicates sampled at the same time. Fungal/bacterial ratios, as measured by direct microscopic counts and by substrate-induced respiration experiments with specific inhibitors, were higher in winter soils. Specific activity of cellulase (absolute cellulase activity per unit microbial biomass C) was higher in the winter soils than in summer soils, while specific amylase activity was not different between winter and summer. Based on most-probable number measurements, the use of the phenolic compound vanillic acid was highest in the winter, while the use of the amino acid glycine was lowest in the winter. Winter and summer soil respiration responded differently to temperature; at 0 degrees C, winter soils respired at a higher proportion of the 22 degrees C rate than did summer soils.

Colonization of contaminated soil by an introduced bacterium: effects of initial pentachlorophenol levels on the survival of Sphingomonas chlorophenolica strain RA2

The survival of a Sphingomonas species that was introduced into pentachlorophenol (PCP)-contaminated soil was monitored with two complementary methods, a respiration-based assay and a most probable number (MPN) technique. Sphingomonas chlorophenolicastrain RA2 is a PCP-mineralizing bacterium that was introduced into soil contaminated with a range of PCP concentrations (0-300 &mgr;g PCP g(-1) soil). The population of introduced microorganisms was followed for 170 days using a substrate-induced growth-response method and a MPN assay that specifically targets PCP-mineralizing bacteria. Varying the initial PCP concentration resulted in the emergence of three distinct patterns of survival. In soil contaminated with 300 &mgr;g PCP g(-1) the population of S. chlorophenolica strain RA2 immediately declined following introduction, increased by 200-fold and leveled off by the end of the 170-day incubation. In contrast, populations of S. chlorophenolica strain RA2 declined to levels below detection limits in uncontaminated soil by the end of the experiment. Intermediate PCP concentrations (10-100 &mgr;g PCP g(-1) soil) resulted in the establishment of S. chlorophenolica strain RA2 that slowly declined in numbers. These results indicate that Sphingomonas chlorophenolica strain RA2 is an effective colonizer of PCP-contaminated soil but will not persist in the absence of PCP.

Functional expression of a novel human neurokinin-3 receptor homolog that binds [3H]senktide and [125I-MePhe7]neurokinin B, and is responsive to tachykinin peptide agonists

In 1992, Xie et al. identified a cDNA sequence in the expression cloning search for the kappa opioid receptor. When the cDNA was expressed in Cos-7 cells, binding of opioid compounds was observed to be of low affinity and without kappa, mu, or delta selectivity [Xie, G.-X., Miyajima, A. and Goldstein, A. (1992) Proc. Natl. Acad. Sci. USA 89, 4124-4128]. This cDNA was highly homologous to the human neurokinin-3 (NK-3) receptor sequence, and displayed lower homology to NK-1 and NK-2 sequences. This sequence was stably expressed in Chinese hamster ovary cells, which do not express neurokinin receptors naturally, and ligand binding and second messenger characteristics were compared with a human NK-3 receptor. The NK-3 receptor homolog bound [3H] senktide with a Kd of 39 nM, similar to that of the NK-3 receptor. The rank order of tachykinin peptides competing for [3H]senktide binding at the NK-3 receptor homolog was [MePhe7]neurokinin B > senktide > substance P = neurokinin A > neurokinin B. This cell line also bound [125I-MePhe7]neurokinin B; however, neurokinin B was an effective competitor. Tachykinin peptides stimulated both inositol phospholipid hydrolysis and arachidonic acid release at NK-3 and NK-3 receptor homolog cell lines, with similar rank orders of potency of [MePhe7] neurokinin B = neurokinin B = senktide > NKA = substance P. These results indicate that expression of the NK-3 receptor homolog cDNA in the Chinese hamster ovary cell system induces the expression of a receptor site with many similarities but certain key differences from that of the human NK-3 receptor. The results are discussed with reference to the existence of a novel human tachykinin receptor.

Use of a pentachlorophenol degrading bacterium to bioremediate highly contaminated soil

A Sphingomonas species that mineralizes high concentrations of pentachlorophenol (PCP) was isolated from a PCP-contaminated EPA Superfund site. This bacterium, identified as Sphingomonas sp. strain RA2, is able to degrade PCP at concentrations of up to 300 micrograms/mL in liquid culture. This organism was tested for its ability to degrade high concentrations of PCP in a soil that did not contain organisms capable of degrading high concentrations of PCP. When inoculated into contaminated soil, Sphingomonas sp. RA2 mineralized PCP at concentrations of 300, 600, 900, and 1200 micrograms PCP/g of soil, but was unable to mineralize 1500 micrograms PCP/g of soil. Only very minimal loss of PCP was seen in uninoculated soils. The results of this study demonstrate that Sphingomonas sp. RA2 may be a useful organism for remediation of sites contaminated with high concentrations of PCP.

A simple method for quantifying activity and survival of microorganisms involved in bioremediation processes

We have developed a substrate-induced growth response (SIGR) method for quantifying activity and population dynamics of microorganisms involved in bioremediation processes in soil and bioreactors. The biomass of organisms that can mineralize a given chemical can be estimated based on the concentration of that chemical needed to induce the growth of the standing population. Estimates of population size are obtained by using nonlinear regression techniques to fit a simple model of microbial population dynamics to biodegradation curves. Using this approach we obtain estimates of values for parameters such as initial population size and growth rate of organisms carrying out biodegradative processes. Our approach was validated by comparing model parameter estimates with independent estimates of the same parameters from the same bioremediation systems. Examples studied include pentachlorophenol degraders introduced into soil and 2,4-dinitrophenol degrading organisms in a bioreactor.

Characterization of a novel Pseudomonas sp. that mineralizes high concentrations of pentachlorophenol

A pentachlorophenol (PCP)-mineralizing bacterium was isolated from polluted soil and identified as Pseudomonas sp. strain RA2. In batch cultures, Pseudomonas sp. strain RA2 used PCP as its sole source of carbon and energy and was capable of completely degrading this compound as indicated by radiotracer studies, stoichiometric release of chloride, and biomass formation. Pseudomonas sp. strain RA2 was able to mineralize a higher concentration of PCP (160 mg liter-1) than any previously reported PCP-degrading pseudomonad. At a PCP concentration of 200 mg liter-1, cell growth was completely inhibited and PCP was not degraded, although an active population of Pseudomonas sp. RA2 was still present in these cultures after 2 weeks. The inhibitory effect of PCP was partially attributable to its effect on the growth rate of Pseudomonas sp. strain RA2. The highest specific growth rate (mu = 0.09 h-1) was reached at a PCP concentration of 40 mg liter-1 but decreased at higher or lower PCP concentrations, with the lowest mu (0.05 h-1) occurring at 150 mg liter-1. Despite this reduction in growth rate, total biomass production was proportional to PCP concentration at all PCP concentrations degraded by Pseudomonas sp. RA2. In contrast, final cell density was reduced to below expected values at PCP concentrations greater than 100 mg liter-1. These results indicate that, in addition to its effect as an uncoupler of oxidative phosphorylation, PCP may also inhibit cell division in Pseudomonas sp. strain RA2.(ABSTRACT TRUNCATED AT 250 WORDS)

Interactions of bacteria and microflagellates in sequencing batch reactors exhibiting enhanced mineralization of toxic organic chemicals

Community level interactions were studied in non-axenic sequencing batch reactors (SBRs) being used to treat 2,4-dinitrophenol (DNP). Increasing the influent DNP concentrations from 1 to 10 µg ml(-1) eliminated large predatory organisms such as rotifers and ciliated protozoa from the SBRs. Under steady-state conditions at a DNP concentration of 10 µg ml(-1), supplemental additions of glucose enhanced DNP degradation and led to the establishment of a microbial community consisting of five species of bacteria and a variety of microflagellates. The bacteria and flagellates exhibited oscillating population dynamics in this system, possibly indicating predator-prey interactions between these two groups. Only two of the five bacteria isolated from this system could utilize glucose as a growth substrate, and one of these two species was the only organism that could mineralize DNP in the system. The other three bacteria could grow using metabolic by-products of one of the glucose-utilizing strains (Bacillus cereus) found in the reactors. Supplemental glucose additions increased the average size of bacterial floc particles to 172 µm, compared with 41 µm in SBRs not receiving glucose. It is theorized that the enhanced mineralization of DNP in this non-axenic system was attributable to increased community interactions resulting in increased bacterial flocculation in SBRs receiving supplemental glucose additions.

Supplemental Substrate Enhancement of 2,4-Dinitrophenol Mineralization by a Bacterial Consortium

A Janthinobacterium sp. and an actinomycete, both capable of mineralizing 2,4-dinitrophenol (DNP), were used to construct a consortium to mineralize DNP in nonaxenic bench-scale sequencing batch reactors (SBRs). Average K m values for DNP mineralization by pure cultures of the Janthinobacterium sp. and the actinomycete were 0.01 and 0.13 μg/ml, respectively, and the average maximum specific growth rate (μ max ) values for them were 0.06 and 0.23/h, respectively. In the presence of NH 4 Cl, nitrite accumulation in pure culture experiments and in the SBRs was stoichiometric to initial DNP concentration and the addition of nitrogen enhanced DNP mineralization in the SBRs. Mineralization of 10 μg of DNP per ml was further enhanced in SBRs by the addition of glucose at concentrations of 100 and 500 μg/ml but not at 10 μg/ml. Possible mechanisms for this enhanced DNP mineralization in SBRs were suggested by kinetic analyses and biomass measurements. Average μ max values for DNP mineralization in the presence of 0, 10, 100, and 500 μg of glucose per ml were 0.33, 0.13, 0.42, and 0.59/h, respectively. In addition, there was greater standing biomass in reactors amended with glucose. At steady-state operation, all SBRs contained heterogeneous microbial communities but only one organism, an actinomycete, that was capable of mineralizing DNP. This research demonstrates the usefulness of supplemental substrates for enhancing the degradation of toxic chemicals in bioreactors that contain heterogeneous microbial communities.

Dynamics of microbial populations in soil: Indigenous microorganisms degrading 2,4-dinitrophenol

The mineralization of 2,4-dinitrophenol (DNP) and changes in the DNP-mineralizing population over a wide range of DNP concentrations were monitored to evaluate the dynamics of the DNP-mineralizing populations in two soils (soils 1 and 2). Curves of CO2 evolution were analyzed using nonlinear regression analysis and models incorporating parameters for population size and growth rate. The results of these analyses were compared to independent estimates of the DNP-mineralizing population from most-probable-number (MPN) determinations. The combined results of these analyses showed that 0.1μg of DNP g(-1) of soil was too low a concentration to support maintenance or growth of the DNP-mineralizing population, whereas all higher concentrations supported either maintenance or growth of the population in soil 1. Independent estimates of population size showed good agreement between the nonlinear regression and MPN techniques, especially at initial DNP concentrations below 100μg g(-1). Estimates of both population size and maximum specific growth rate varied with concentration, possibly indicating the existence of two different DNP-mineralizing populations in soil 1. In the other soil tested (soil 2), the population of DNP-mineralizers was much lower than in the first soil, and no evidence of two populations was obtained. In soil 2, good agreement between the nonlinear regression and MPN estimates of population size was also obtained. Results of this study demonstrate the power of using testable models of population dynamics to obtain useful estimates of parameters of microbial growth and survival in soil.

Kinetics of p-nitrophenol mineralization by a Pseudomonas sp.: effects of second substrates

The kinetics of simultaneous mineralization of p-nitrophenol (PNP) and glucose by Pseudomonas sp. were evaluated by nonlinear regression analysis. Pseudomonas sp. did not mineralize PNP at a concentration of 10 ng/ml but metabolized it at concentrations of 50 ng/ml or higher. The Ks value for PNP mineralization by Pseudomonas sp. was 1.1 micrograms/ml, whereas the Ks values for phenol and glucose mineralization were 0.10 and 0.25 micrograms/ml, respectively. The addition of glucose to the media did not enable Pseudomonas sp. to mineralize 10 ng of PNP per ml but did enhance the degradation of higher concentrations of PNP. This enhanced degradation resulted from the simultaneous use of glucose and PNP and the increased rate of growth of Pseudomonas sp. on glucose. The Monod equation and a dual-substrate model fit these data equally well. The dual-substrate model was used to analyze the data because the theoretical assumptions of the Monod equation were not met. Phenol inhibited PNP mineralization and changed the kinetics of PNP mineralization so that the pattern appeared to reflect growth, when in fact growth was not occurring. Thus, the fitting of models to substrate depletion curves may lead to erroneous interpretations of data if the effects of second substrates on population dynamics are not considered.

Models for the kinetics of biodegradation of organic compounds not supporting growth

We developed 12 models of kinetics to describe the metabolism of organic substrates that are not supporting bacterial growth. These models can be used to describe the biodegradation of organic compounds that are not supporting growth when the responsible populations are growing logistically, logarithmically, or linearly or are not increasing in numbers. Nonlinear regression analysis was used to fit patterns of mineralization by two bacteria to these kinetic models. Pseudomonas acidovorans mineralized 1 ng of phenol per ml while growing exponentially at the expense of uncharacterized organic carbon in a synthetic medium. Phenol at a concentration of 1 ng/ml did not affect the growth of P. acidovorans. These data were best fit by the model that incorporates the equation for logarithmic growth and assumes a concentration of test substrate well below its Km value. In the absence of a second substrate, glucose at concentrations below those supporting growth was mineralized by Salmonella typhimurium in a manner best described by pseudo first-order kinetics. In the presence of different concentrations of arabinose, however, the kinetics of glucose mineralization by S. typhimurium reflected linear, logistic, or logarithmic growth of the population on arabinose. We conclude that the kinetics of mineralization of organic compounds at concentrations too low to support growth are best described either by the first-order model or by models that incorporate expressions for the kinetics of growth of the metabolizing population on other substrates. When growth is at the expense of other substrates, the kinetics observed reflect such growth, as well as the concentration of the substrate of interest.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of dissolved organic carbon and second substrates on the biodegradation of organic compounds at low concentrations

Pseudomonas acidovorans and Pseudomonas sp. strain ANL but not Salmonella typhimurium grew in an inorganic salts solution. The growth of P. acidovorans in this solution was not enhanced by the addition of 2.0 micrograms of phenol per liter, but the phenol was mineralized. Mineralization of 2.0 micrograms of phenol per liter by P. acidovorans was delayed 16 h by 70 micrograms of acetate per liter, and the delay was lengthened by increasing acetate concentrations, whereas phenol and acetate were utilized simultaneously at concentrations of 2.0 and 13 micrograms/liter, respectively. Growth of Pseudomonas sp. in the inorganic salts solution was not affected by the addition of 3.0 micrograms each of glucose and aniline per liter, nor was mineralization of the two compounds detected during the initial period of growth. However, mineralization of both substrates by this organism occurred simultaneously during the latter phases of growth and after growth had ended at the expense of the uncharacterized dissolved organic compounds in the salts solution. In contrast, when Pseudomonas sp. was grown in the salts solution supplemented with 300 micrograms each of glucose and aniline, the sugar was mineralized first, and aniline was mineralized only after much of the glucose carbon was converted to CO2. S. typhimurium failed to multiply in the salts solution with 1.0 micrograms of glucose per liter. It grew slightly but mineralized little of the sugar at 5.0 micrograms/liter, but its population density rose at 10 micrograms of glucose per liter or higher. The hexose could be mineralized at 0.5 micrograms/liter, however, if the solution contained 5.0 mg of arabinose per liter.(ABSTRACT TRUNCATED AT 250 WORDS)