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Phylogenetic clustering and overdispersion in bacterial communities.

Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

Bacteria↗

Environmental fluctuations facilitate species co-existence and increase decomposition in communities of wood decay fungi.

A fluctuating environment may facilitate co-existence of species, and high species richness may be important for maintaining ecosystem processes under changing environmental conditions. A positive relationship has been found between species richness and primary production in many experiments, and there is now an increasing interest whether similar relationships also apply to microorganisms and decomposition. Basidiomycete fungi are the primary decomposers of wood with the functional groups brown and white rot fungi, which differ with respect to decay strategy. In this study, 16 species of boreal wood decay fungi, 8 brown rot fungi and 8 white rot fungi, were assembled in artificial communities. The aims were to study species persistence, wood decomposition and metabolic efficiency in fungal communities of increasing levels of species richness under constant and fluctuating temperature regimes. Species persistence was generally low, but temperature fluctuations facilitated co-existence of species. Decomposition was highest at intermediate diversity levels under the fluctuating temperature regime. Metabolic efficiency, estimated as the amount of fungal mycelium formed per amount of degraded wood, decreased with increasing community complexity under the fluctuating temperature regime. Brown and white rot fungi differed in decomposition rates and metabolic efficiency, but no synergistic effects were found where the two functional groups were mixed. This study demonstrates how niche differentiation in a variable environment may act to maintain diversity and function. In our experiment, differences in functional responses to the varying temperature rather than resource partitioning between brown and white rot fungi had significant effects. Niche differentiation is likely to be particularly important in maintaining species diversity in communities of wood decaying fungi, which are known from previous studies to be characterised by intense competition, and where otherwise metabolically costly interactions lead to species exclusion and dominance by highly competitive species.

Basidiomycota↗

Black-tailed prairie dogs and the structure of avian communities on the shortgrass plains.

We tested the hypothesis that black-tailed prairie dogs (Cynomys ludovicianus) influence avian community structure on the shortgrass prairie. We surveyed 36 prairie dog towns and 36 paired sites without prairie dogs during summer and fall of 1997, 1998, and 1999 in the Oklahoma Panhandle. Our surveys totaled 9,040 individual observations for 73 avian species. Significantly distinct avian communities were present on prairie dog towns when compared to sites within four different macrohabitats of the surrounding landscape: open rangeland, scrub/sandsage (Artemisia filifolia) habitats, Conservation Reserve Program (CRP) plots, and fallow crop fields. Relative densities of all bird species combined was higher on prairie dog towns versus paired sites in summer and fall. Mean species richness of birds was significantly higher on prairie dog towns than paired sites during summer, but there were no significant differences in fall. Open rangeland had the highest mean species richness in fall. Assemblages of avian communities differed significantly between prairie dog towns and the four macrohabitat types during summer. Burrowing owls (Athene cunicularia), killdeer (Charadrius vociferous), horned larks (Eremophila alpestris), and meadowlarks (Sturnella spp.) were positively and significantly associated with prairie dog towns during summer, while horned larks and ferruginous hawks (Buteo regalis) were significantly associated with prairie dog towns during fall. Even in their current remnant state, black-tailed prairie dogs continue to play a significant role in the assembly of ecological communities across the Great Plains. Conservation of prairie dogs goes well beyond a single species, and is an important strategy for the preservation of the prairie ecosystem as a whole.

Animals↗

[Health promotion and education: a diagnosis of sanitation conditions using participatory research and community education (São João dos Queiróz - Quixadá/Ceará, Brazil)].

This study was conducted in a rural community, São João dos Queiróz, a township in the county of Quixadá, Ceará, Brazil, using a combination of participatory research and community education in compliance with the health promotion reference and principles of the 1986 Ottawa Charter. The project was joined by representatives of several local government institutions and organizations from the grassroots community movement. The theme generating the research, as defined by an assembly meeting of the community association, was a diagnosis of sanitation conditions in the community. The starting point was the assessment of local conditions. Results showed adverse local conditions in sanitation, literacy, income, and employment. Suggestions for solving the problems were organized so as to be included in the planning agenda for local health policies. Evaluation was procedural and enriched with daily research activities. The problem-solving pedagogical approach developed during the educational process contributed to a critical reconstruction, appropriation, and sharing of the resulting knowledge.

Adolescent↗

A master regulator for biofilm formation by Bacillus subtilis.

Wild strains of Bacillus subtilis are capable of forming architecturally complex communities of cells known as biofilms. Critical to biofilm formation is the eps operon, which is believed to be responsible for the biosynthesis of an exopolysaccharide that binds chains of cells together in bundles. We report that transcription of eps is under the negative regulation of SinR, a repressor that was found to bind to multiple sites in the regulatory region of the operon. Mutations in sinR bypassed the requirement in biofilm formation of two genes of unknown function, ylbF and ymcA, and sinI, which is known to encode an antagonist of SinR. We propose that these genes are members of a pathway that is responsible for counteracting SinR-mediated repression. We further propose that SinR is a master regulator that governs the transition between a planktonic state in which the bacteria swim as single cells in liquid or swarm in small groups over surfaces, and a sessile state in which the bacteria adhere to each other to form bundled chains and assemble into multicellular communities.

Amino Acid Sequence↗

Diversity patterns from ecological models at dynamical equilibrium.

We study a dynamic model of ecosystems where an immigration flux assembles the species community and maintains its biodiversity. This framework is particularly relevant for insular ecosystems. Population dynamics is represented either as an individual-based model or as a set of deterministic equations for population abundances. Local extinctions and immigrations balance at a statistically stationary state where biodiversity fluctuates around a constant mean value. We find a number of scaling laws characterizing this stationary state. In particular, the number of species increases as a power law of the immigration rate. With additional assumptions on the immigration flux, we obtain species-area relationships in agreement with observations for archipelagos. We also find power-law distributions for species abundances and lifetimes.

Animals↗

Agranulocytosis associated with calcium dobesilate clinical course and risk estimation with the case-control and the case-population approaches.

OBJECTIVE: Calcium dobesilate is used in the treatment of diabetic retinopathy, chronic venous insufficiency, haemorrhoids and other ill-defined vascular conditions. It has been associated with agranulocytosis in anecdotal reports. We describe the clinical course of a series of patients who developed agranulocytosis while taking this drug, and we estimate the risk by means of both a case-control and a case-population strategy. METHODS: All cases of agranulocytosis meeting strict predefined diagnostic criteria in an area of 3.3 to 3.9 x 106 inhabitants in the period 1980-1998 were identified. Cases and age-, gender- and hospital-matched controls were interviewed with a structured questionnaire including a detailed drug history. Each case was reviewed and confirmed by a haematologist, who was blind with respect to drug exposures. Consumption data were used to estimate the risk of agranulocytosis associated with calcium dobesilate using a case-population approach in which the incidence of agranulocytosis among users of calcium dobesilate was compared with that among the non-exposed population. RESULTS: After a follow up of 68.55 x 10(6) person-years, 345 cases of agranulocytosis (242 community cases) were assembled. Reliable information was obtained from 216 cases. Two patients exhibited positive rechallenge. Twelve cases (5.6%) and 5 of 1380 controls (0.4%) had taken calcium dobesilate in the week before. With the case-control approach, the odds ratio was 23.66 [95% confidence interval (CI), 7.54-74.24], the attributable risk was 5.3% (95% CI, 3.0-9.4), and the number of cases attributable to dobesilate in the study area during the study period was 12.8. The case-population estimates were an incidence of 121.03 cases per 10(6) patient-years, a relative risk of 39.55 (95% CI, 17.96-77.49), an attributable risk of 6.73% (CI 3.4-12.9), and 16.30 cases attributable to dobesilate in the study area during the study period. DISCUSSION: This study adds to evidence indicating that the case-population method is adequate for the study of rare type B adverse drug reactions. An additional advantage of this approach is that the incidence of the disease of interest among those exposed to the drug can be estimated. The risk of agranulocytosis associated with calcium dobesilate should be considered in relation to poor evidence of its clinical efficacy.

Aged↗

Agranulocytosis induced by pyrithyldione, a sedative hypnotic drug.

OBJECTIVE: Pyrithyldione, a sedative-hypnotic drug with a poor clinical pharmacological development, was associated with anecdotal cases of agranulocytosis in the 1940s in the USA, in the 1960s and 1970s in the ex-Democratic Republic of Germany and in the 1980s in Japan. We describe the estimation of the risk of agranulocytosis associated with its use in Spain, which led to its withdrawal from the market. METHODS: In collaboration with the haematology units of all the hospitals in a defined area (3.3-3.9 x 10(6) inhabitants), all cases of agranulocytosis meeting strict diagnostic criteria were identified. Each case - defined as an episode of agranulocytosis - was reviewed by a haematologist without knowledge of previous drug exposures. Cases and age-, gender- and hospital-matched controls were interviewed with a structured questionnaire about previous drug exposures. In addition, in order to estimate the risk of pyrithyldione-associated agranulocytosis through a case-population approach, its consumption among the cases was compared with its consumption among the general population. RESULTS: After a follow-up of 66.5 x 10(6) person-years, 330 cases of agranulocytosis (230 community cases) were assembled. Reliable information on previous exposures was obtained for 204 cases. They were compared with 1314 controls. Eleven patients (14 cases, 6.9%) and zero controls had been exposed to pyrithyldione. The adjusted OR was 200.11 (CI 95% 22. 62-infinity). All patients were female; none had a fatal outcome; three exhibited positive rechallenge; and all had concomitantly taken other drugs. Although pyrithyldione was a prescription-only medicine, only 8% had been dispensed with medical prescriptions. Assuming the worst case, i.e. that all the exposed cases could be attributed to pyrithyldione, the incidence was 35.6 cases per 100, 000 patient-years (95% CI, 18.9-60.9), which gives a risk ratio estimate of 109.6 (57.5-191.5) if compared with the incidence of agranulocytosis among the non-exposed population [3.26 cases (CI 95% 2.83-3.71) per 10(6) inhabitants and per year]. DISCUSSION: Pyrithyldione was viewed by pharmacists as a mild hypnotic, and apparently this had conferred to this drug an unjustified image of safety. The National Commission of Pharmacovigilance recommended to the Ministry of Health its withdrawal from the market when eight cases of agranulocytosis had been identified. However, it took more than 2 years to withdraw it, and six additional cases occurred in the study area. This illustrates the need for quick regulatory action when pharmacoepidemiological data suggest an unfavourable benefit/risk ratio.

Adult↗

Toward an ecological synthesis: a case for habitat selection.

Habitat selection, and its associated density and frequency-dependent evolution, has a profound influence on such vital phenomena as population regulation, species interactions, the assembly of ecological communities, and the origin and maintenance of biodiversity. Different strategies of habitat selection, and their importance in ecology and evolution, can often be revealed simply by plots of density in adjacent habitats. For individual species, the strategies are closely intertwined with mechanisms of population regulation, and with the persistence of populations through time. For interacting species, strategies of habitat selection are not only responsible for species coexistence, but provide one of the most convenient mechanisms for measuring competition, and the various community structures caused by competitive interactions. Other kinds of interactions, such as those between predators and prey, demonstrate that an understanding of the coevolution of habitat-selection strategies among strongly interacting species is essential to properly interpret their spatial and temporal dynamics. At the evolutionary scale, the frequency dependence associated with habitat selection may often allow populations to diverge and diversify into separate species. Habitat selection thereby demonstrates how we can map microevolutionary strategies in behavior onto their population and community consequences, and from there, onto macroevolutionary patterns of speciation and adaptive radiation. We can anticipate that future studies of habitat selection will not only help us complete those maps, but that they will also continue to enrich the panoply of ideas that shape evolutionary ecology.

Animals↗

Barium alginate cell-delivery systems: correlation between technological parameters.

The most recent trends for the development of several in vitro cell cultures have been oriented towards the cell immobilisation in 3-dimensional scaffolds and cell encapsulation. In fact, an important requirement of cell survival is self-assembly in functional communities, in the presence of an artificial extracellular matrix. In our research, a previously described technique for spermatozoa encapsulation was applied to obtain capsules loaded with an opaque agent as a model, and to perform a formulative study. A process variable, barium ion concentration, was correlated to some capsule properties, such as weight, gel thickness, total and core diameter. Ion concentration can be modified to obtain capsules with predictable characteristics.

Alginates↗

The phylogenetics of Desmognathine salamander populations across the southern Appalachians.

Salamanders in the genus Desmognathus (Caudata: Plethodontidae) are distributed along an aquatic to terrestrial habitat gradient in the southern Appalachian Mountains. The spatial distribution of species is believed to have formed as aquatic ancestors displaced lineages by competition and predatory interactions into less optimal terrestrial habitats. Aquatic and terrestrial species may also display different patterns of genetic diversity due to the differing likelihood of gene flow via aquatic corridors. To determine whether phylogenetic patterns were consistent with these hypotheses, we sequenced portions of the cytochrome oxidase I and 12S rRNA genes of the mitochondrial genome from 96 individuals belonging to 10 species in the genus Desmognathus. In addition, we combined our dataset with an earlier published dataset for the 12S rRNA genes. The order of species divergence is consistent with aquatic ancestors having displaced taxa into more terrestrial habitats, but the major lineages within the genus Desmognathus arose suddenly, and therefore, the specific sequence of events is not well resolved. The phylogenetic analyses among species suggest that direct-development and a terrestrial lifestyle are ancestral in the genus Desmognathus, but the degree of adult terrestriallity is labile, with some species having re-invaded terrestrial habitats. We present evidence of a clade of Desmognathus quadramaculatus from North Carolina that is distinct from the D. quadramaculatus/Desmognathus marmoratus clade. Within species, estimates of Tajima's D and Fu and Li's statistics suggest the species experienced population expansions at different times in the past. Current levels of sequence diversity in northern populations, therefore, reflect different arrival times, and hence, differences in the opportunity for among population divergence. The recent arrival of most species over large portions of their geographic ranges suggests that most extant communities have been assembled, a posteriori, by the recent assortment of species along the aquatic to terrestrial gradient according to their ecologies.

Animals↗

Neutral theory: the stability of forest biodiversity.

The unified neutral theory of biodiversity and biogeography provides a dynamic null hypothesis for the assembly of natural communities. It is also useful for understanding the influence of speciation, extinction, dispersal and ecological drift on patterns of relative species abundance, species-area relationships and phylogeny. Clark and McLachlan argue that neutral drift is inconsistent with the palaeorecord of stability in fossil pollen assemblages of the Holocene forests of southern Canada. We show here that their analysis is based on a partial misunderstanding of neutral theory and that their data alone cannot unambiguously test its validity.

Biodiversity↗

Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period.

The adult human gut microbiota is dominated by two divisions of Bacteria, the Bacteroidetes and the Firmicutes. Assembly of this community begins at birth through processes that remain largely undefined. In this report, we examine the adaptations of Bacteroides thetaiotaomicron, a prominent member of the adult distal intestinal microbiota, during the suckling and weaning periods. Germ-free NMRI mice were colonized at birth from their gnotobiotic mothers, who harbored this anaerobic Gram-negative saccharolytic bacterium. B. thetaiotaomicron was then harvested from the ceca of these hosts during the suckling period (postnatal day 17) and after weaning (postnatal day 30). Whole genome transcriptional profiles were obtained at these two time points using custom B. thetaiotaomicron GeneChips. Transcriptome-based in silico reconstructions of bacterial metabolism and gas chromatography-mass spectrometry and biochemical assays of carbohydrate utilization in vivo indicated that in the suckling gut B. thetaiotaomicron prefers host-derived polysaccharides, as well as mono- and oligosaccharides present in mother's milk. After weaning, B. thetaiotaomicron expands its metabolism to exploit abundant, plant-derived dietary polysaccharides. The bacterium's responses to postnatal alterations in its nutrient landscape involve expression of gene clusters encoding environmental sensors, outer membrane proteins involved in binding and import of glycans, and glycoside hydrolases. These expression changes are interpreted in light of a phylogenetic analysis that revealed unique expansions of related polysaccharide utilization loci in three human alimentary tract-associated Bacteroidetes, expansions that likely reflect the evolutionary adaptations of these species to different nutrient niches.

Animals↗

Ionic interconversion of pacemaker and nonpacemaker cultured chick heart cells.

Trypsin-dispersed cells from hearts (ventricles) of 7 to 8 day chick embryos were cultured 3 to 21 days. The cells became attached to the culture dish and assembled into monolayer communities. By means of a bridge circuit, one microelectrode was used for simultaneously passing current and recording membrane potentials (V(m)). The input resistance, calculated by the measured DeltaV(m) for a known step of current, averaged 10 M ohm. Electrotonic depolarization of nonpacemaker cells had no effect on frequency of firing. Within 2 min after addition of Ba(++) (5 to 10 mM) to the Tyrode bath, the cells became partially depolarized and quiescent nonpacemaker cells developed oscillations in V(m) which led to action potentials. With time, the depolarization became nearly complete and the input resistance increased 2 to 10 times. During such sustained depolarizations, action potentials were no longer produced and often tiny oscillations were observed; however, large action potentials developed during hyperpolarizing pulses. Thus, the automaticity of the depolarized cell became apparent during artificial repolarization. Sr(++) (5 to 10 mM) initially produced hyperpolarization and induced automaticity in quiescent nonpacemaker cells. Elevated [K(+)](o) (20 to 30 mM) suppressed automaticity of pacemaker cells and decreased R(m) concomitantly. Thus, Ba(++) probably converts nonpacemaker cells into pacemaker cells independently of its depolarizing action. Ba(++) may induce automaticity and depolarization by decreasing g(K), and elevated [K(+)](o) may depress automaticity by increasing g(K). The data support the hypothesis that the level of g(K) determines whether a cell shall function as a pacemaker.

Animals↗

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.

Comparative studies have been of invaluable importance to the understanding of evolutionary biology. The evolution of developmental programs can be studied in nematodes at a single cell resolution given their fixed cell lineage. We have established Pristionchus pacificus as a major satellite organism for evolutionary developmental biology relative to Caenorhabditis elegans, the model nematode. Online genomic information to support studies in this satellite system can be accessed at http://www.pristionchus.org. Our web resource offers diverse content covering genome browsing, genetic and physical maps, similarity searches, a community platform and assembly details. Content will be continuously improved as we annotate the P.pacificus genome, and will be an indispensable resource for P.pacificus genomics.

Animals↗

Treatment of behavioral emergencies: a summary of the expert consensus guidelines.

OBJECTIVES: Behavioral emergencies are a common and serious problem for consumers, their communities, and the healthcare settings on which they rely, but there is little research to guide provider responses to this challenge. Key constructs such as agitation have not been adequately operationalized so that the criteria defining a behavioral emergency are vague. A significant number of deaths of patients in restraint has focused government and regulators on these issues, but a consensus about key elements in the management of behavioral emergencies has not yet been articulated by the provider community. The authors assembled a panel of 50 experts to define the following elements: the threshold for emergency interventions, the scope of assessment for varying levels of urgency and cooperation, guiding principles in selecting interventions, and appropriate physical and medication strategies at different levels of diagnostic confidence and for a variety of etiologies and complicating conditions. METHOD: A written survey with 808 decision points was completed by 50 experts. A modified version of the RAND Corporation 9-point scale for rating appropriateness of medical decisions was used to score options. Consensus on each option was defined as a non-random distribution of scores by chi-square "goodness-of-fit" test. We assigned a categorical rank (first line/preferred choice, second line/ alternate choice, third line/usually inappropriate) to each option based on the 95% confidence interval around the mean rating. Guideline tables were constructed describing the preferred strategies in key clinical situations. RESULTS: The expert panel reached consensus on 83% of the options. The relative appropriateness of emergency interventions was ascertained for a continuum of behaviors. When asked about the frequency with which emergency interventions (parenteral medication, restraint, seclusion) were required in their services, 47% of the experts reported that such interventions were necessary for 1%-5% of patients seen in their services and 32% for 6%-20%. In general, the consensus of this panel lends support to many elements of recent regulations from the Health Care Financing Administration (now the Centers for Medicare and Medicaid Services), including the timing of clinician assessment and reassessment and the intensity of nursing care. However, the panel did not endorse the concept of "chemical restraint," instead favoring the idea that medications are treatments for target behaviors in behavioral emergencies even when the causes of these behaviors are not well understood. Control of aggressive behavior emerged as the highest priority during the emergency; however, preserving the physician-patient relationship was rated a close second and became the top priority in the long term. Oral medications, particularly concentrates, were clearly preferred if it is possible to use them. Benzodiazepines alone were top rated in 6 of 12 situations. High-potency conventional antipsychotics used alone never received higher ratings than benzodiazepines used alone. A combination of a benzodiazepine and an antipsychotic was preferred for patients with suspected schizophrenia, mania, or psychotic depression. There was equal support for high-potency conventional or atypical antipsychotics (particularly liquids) in oral combinations with benzodiazepines. Droperidol emerged in fourth place in some situations requiring an injection. CONCLUSIONS: To evaluate many of the treatment options in this survey, the experts had to extrapolate beyond controlled data. Within the limits of expert opinion and with the expectation that future research data will take precedence, these guidelines provide some direction for addressing common clinical dilemmas in the management of psychiatric emergencies and can be used to inform clinicians in acute care settings regarding the relative merits of various strategies.

Journal Article↗

Habitat selection determines abundance, richness and species composition of beetles in aquatic communities.

Distribution and abundance patterns at the community and metacommunity scale can result from two distinct mechanisms. Random dispersal followed by non-random, site-specific mortality (species sorting) is the dominant paradigm in community ecology, while habitat selection provides an alternative, largely unexplored, mechanism with different demographic consequences. Rather than differential mortality, habitat selection involves redistribution of individuals among habitat patches based on perceived rather than realized fitness, with perceptions driven by past selection. In particular, habitat preferences based on species composition can create distinct patterns of positive and negative covariance among species, generating more complex linkages among communities than with random dispersal models. In our experiments, the mere presence of predatory fishes, in the absence of any mortality, reduced abundance and species richness of aquatic beetles by up to 80% in comparison with the results from fishless controls. Beetle species' shared habitat preferences generated distinct patterns of species richness, species composition and total abundance, matching large-scale field patterns previously ascribed to random dispersal and differential mortality. Our results indicate that landscape-level patterns of distribution and species diversity can be driven to a large extent by habitat selection behaviour, a critical, but largely overlooked, mechanism of community and metacommunity assembly.

Animals↗

Biogeography and ecological setting of Indian Ocean hydrothermal vents.

Within the endemic invertebrate faunas of hydrothermal vents, five biogeographic provinces are recognized. Invertebrates at two Indian Ocean vent fields (Kairei and Edmond) belong to a sixth province, despite ecological settings and invertebrate-bacterial symbioses similar to those of both western Pacific and Atlantic vents. Most organisms found at these Indian Ocean vent fields have evolutionary affinities with western Pacific vent faunas, but a shrimp that ecologically dominates Indian Ocean vents closely resembles its Mid-Atlantic counterpart. These findings contribute to a global assessment of the biogeography of chemosynthetic faunas and indicate that the Indian Ocean vent community follows asymmetric assembly rules biased toward Pacific evolutionary alliances.

Animals↗