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PubMed2004

A comparison of random draw and locally neutral models for the avifauna of an English woodland.

BACKGROUND: Explanations for patterns observed in the structure of local assemblages are frequently sought with reference to interactions between species, and between species and their local environment. However, analyses of null models, where non-interactive local communities are assembled from regional species pools, have demonstrated that much of the structure of local assemblages remains in simulated assemblages where local interactions have been excluded. Here we compare the ability of two null models to reproduce the breeding bird community of Eastern Wood, a 16-hectare woodland in England, UK. A random draw model, in which there is complete annual replacement of the community by immigrants from the regional pool, is compared to a locally neutral community model, in which there are two additional parameters describing the proportion of the community replaced annually (per capita death rate) and the proportion of individuals recruited locally rather than as immigrants from the regional pool. RESULTS: Both the random draw and locally neutral model are capable of reproducing with significant accuracy several features of the observed structure of the annual Eastern Wood breeding bird community, including species relative abundances, species richness and species composition. The two additional parameters present in the neutral model result in a qualitatively more realistic representation of the Eastern Wood breeding bird community, particularly of its dynamics through time. The fact that these parameters can be varied, allows for a close quantitative fit between model and observed communities to be achieved, particularly with respect to annual species richness and species accumulation through time. CONCLUSION: The presence of additional free parameters does not detract from the qualitative improvement in the model and the neutral model remains a model of local community structure that is null with respect to species differences at the local scale. The ability of this locally neutral model to describe a larger number of woodland bird communities with either little variation in its parameters or with variation explained by features local to the woods themselves (such as the area and isolation of a wood) will be a key subsequent test of its relevance.

Animals↗
PubMed2002

Community genetics in the Northwestern Atlantic intertidal.

Our ability to make inferences about the processes acting upon a biological system can be dramatically improved through integration of information from other fields. In particular, this is true of the field of phylogeography, a discipline that attempts to describe geographical variation in species using neutral genetic diversity as a correlate of time. Through comparisons of information from multiple species, as well as background information about the abiotic environment and how it has changed over time, we should be able to reassemble many of the forces that were important in assembling the communities and community interactions found in a given region. Here I review the information available for coastal species in the northwestern Atlantic, and argue that an integration of ecological, genetic, geological and oceanographic information can illustrate emergent patterns of community genetics.

Animals↗
PubMed2003

[Epidemiologic monitoring of tick-borne encephalitis in Rimov in Southern Bohemia].

Southern Bohemia is one of the extensive natural foci of tick-borne encephalitis (TE) in the Czech Republic. Some professionals hold the view that people living in the focus of infection acquire naturally herd immunity and are the protected against the infection and thus it is not necessary to vaccinate them against TE. Several serious cases of the disease in temporal sequence in Rímov in the district of Ceské Budĕjovice led the authors to examine more closely the problem of TE in this locality. Available epidemiological data were analyzed. A group of subjects with permanent residence in the community was assembled who were interested to participate in the trial. In these serological examinations were made to assess antibodies against TE. Analysis of the assembled data proved that during permanent residence in Rímov 6.07% of the investigated group during their life in Rímov developed the manifest form of TE, 9.64% developed the inapparent form and 15% subjects had antibodies after previous vaccination. The ratio of manifest and inapparent cases is 6.07:9.64, i.e. roughly 2:3. The total seroprevalence after the disease (manifest and inapparent) is 16%. Persons with a negative result of the examination were offered vaccination. The vaccination rate increased due to the authors' intervention from 15% to 65% in the given community.

Adolescent↗
PubMed2006

Sequentially assembled food webs and extremum principles in ecosystem ecology.

1. Successional changes during sequential assembly of food webs were examined. This was carried out by numerical methods, drawing one species at a time from a species pool and obtaining the permanent (persistent) community emerging at each step. Interactions among species were based on some simple rules about body sizes of consumers and their prey, and community dynamics were described in terms of flows of biomass density. 2. Sequential assembly acted as a sieve on the communities, assembled communities having many properties different on average from those of feasible, stable communities taken at random from the species pools. 3. Time-series of community development were consistent with certain functions thought to go to an extremum (maximum or minimum) in ecosystem ecology, including a rapid early increase in net primary productivity and ascendency, although a clear trend in total biomass density was not evident and resilience decreased rather than increased. 4. In addition, more gradual changes in food web structure took place during succession to which the ecosystem goal functions were relatively insensitive. These changes included gradual increases in the number of species, invasion resistance, number of loops of length > 2 and number of prey species per consumer species. 5. We therefore argue that ecosystem and community dynamics can offer complementary insights into the process of ecological succession. The extremum principles of ecosystem ecology highlight some of the major properties of succession, whereas the community ecology sheds light on some more subtle changes taking place within the networks.

Animals↗
PubMedDate not supplied

Lung cancer's persistent association with population density in Los Angeles County communities.

119 community clusters assembled from contiguous census tracts are investigated in an ecologic study, using as the dependent variable age-adjusted lung cancer in both sexes, 1970 (CA); independent variables are: population density (PD), % white (Anglo) (WH), % Spanish surname (SP), % black (BL), % Oriental (OR), mean income per capita (IN), % of dwelling units with 1+ persons/room (CR), % annoyed by air pollution 1956 (AP), and male/female population ages 55-64 (M/F). Except for CA and AP all data are from 1970 census, compiled by John Chapman and Anne Coulson. Variables given in percent except for AP are arcsine transformed in order to more closely approximate Gaussian normality. AP is approximately normal already. The association of CA with AP is negative and small, and inclusion of other variables and structures never leads to an interesting or significant association. Positive associations with CA are with PD (r = 0.300) and WH (0.228). M/F has the highest negative association with CA (-0.285), and is positively associated with WH (0.273) and IN (0.388). M/F has a strong negative association with PD (-0.549). CR is negatively associated with CA (-0.173). In testing for the independent contribution of PD, we use the strategy of testing whether divergent methods give convergent results. Path analysis is used to reflect a number of structural assumptions among independent variables, and the association of CA and PD remains consistent and positive. After recoding the variables PD, WH, SP, BL, OR, IN, and CR into five classes of 20 and one of 19, a multiple classification analysis (MCA) is performed, using MF as a continuous co-variable. Although the unadjusted PD has a slightly greater eta than the other variables, WH and IN have a larger beta after adjustment, and the multiple R is similar to that found by path analysis, reflecting explained variance of about 0.5. The deviations of PD, CR, and BL are not monotonic but those of WH and IN are. Analysis is repeated for the 20 communities with highest IN and for the 20 with lowest IN, and the correlations (r) of CA with PD are 0.561 and 0.376 respectively. For the 20 communities with highest proportion SP, the association is a non-significant 0.108, for the 20 with highest BL, it is 0.196 and for the the 40 highest WH, the CA association with PD is 0.772. Data for the 40 most white communities are presented in a path analysis.(ABSTRACT TRUNCATED AT 400 WORDS)

Female↗
PubMed2004

Land management in the American southwest: a state-and-transition approach to ecosystem complexity.

State-and-transition models are increasingly being used to guide rangeland management. These models provide a relatively simple, management-oriented way to classify land condition (state) and to describe the factors that might cause a shift to another state (a transition). There are many formulations of state-and-transition models in the literature. The version we endorse does not adhere to any particular generalities about ecosystem dynamics, but it includes consideration of several kinds of dynamics and management response to them. In contrast to previous uses of state-and-transition models, we propose that models can, at present, be most effectively used to specify and qualitatively compare the relative benefits and potential risks of different management actions (e.g., fire and grazing) and other factors (e.g., invasive species and climate change) on specified areas of land. High spatial and temporal variability and complex interactions preclude the meaningful use of general quantitative models. Forecasts can be made on a case-by-case basis by interpreting qualitative and quantitative indicators, historical data, and spatially structured monitoring data based on conceptual models. We illustrate how science- based conceptual models are created using several rangeland examples that vary in complexity. In doing so, we illustrate the implications of designating plant communities and states in models, accounting for varying scales of pattern in vegetation and soils, interpreting the presence of plant communities on different soils and dealing with our uncertainty about how those communities were assembled and how they will change in the future. We conclude with observations about how models have helped to improve management decision-making.

Conservation of Natural Resources↗
PubMed2004

The role of biofilms in otolaryngologic infections.

PURPOSE OF REVIEW: Bacterial biofilms have recently been shown to be important in diseases of the head and neck. Because the concept of biofilms is novel to most practitioners, it is important to gain a basic understanding of biofilms and to recognize that strategies developed to treat planktonic bacteria are ineffective against bacteria in a biofilm. RECENT FINDINGS: Bacteria preferentially exist in complex, surface-attached organizations known as biofilms. Bacteria in biofilms express a different set of genes than their planktonic counterparts and have markedly different phenotypes. Biofilm bacteria communicate with each other, and have mechanisms to diffuse nutrients and dispose of waste. Biofilms provide bacteria with distinct advantages, including antimicrobial resistance and protection from host defenses. Thus, bacteria exist in a far more complex fashion than previously thought and can best be thought of as "self-assembling multicellular communities." Although a focus on the planktonic form of bacteria has been useful in understanding acute infections, chronic infections are much better understood as biofilm illnesses. Biofilms have been shown to be involved in chronic otitis media, chronic tonsillitis, cholesteatoma, and device-associated infections. SUMMARY: Now that basic research has demonstrated that the vast majority of bacteria exist in biofilms, the biofilm concept of disease is beginning to spread throughout the clinical world. Understanding that many of the infections that affect structures of the head and neck are actually biofilm related is fundamental to developing rational strategies for treatment and prevention.

Bacterial Infections↗
PubMed2026

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗
PubMed1997

Public informatics resources for rice and other grasses.

As an emerging model system, rice will benefit from an informatics infrastructure which organizes genome data and makes it available worldwide. RiceGenes and other Internet-accessible resources are evolving to meet these goals. Grass crops such as rice, maize, millet, sorghum and wheat are closely related but are represented by independent database projects; interlinking these resources would create a broad view of grass genetics and make it easier to compare data across genomes. The future success of grass informatics depends on the development of new comparative mapping displays as well as the participation of the research community in assembling and curating comparative map data.

Databases, Factual↗
PubMed2005

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community.

Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of approximately 10(6) cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.

Bacteria↗
PubMed2004

Human genetics, environment, and communities of color: ethical and social implications.

A conference titled "Human Genetics, Environment, and Communities of Color: Ethical and Social Implications" and a workshop symposium titled "Human Genetics and Environmental Justice" were held by West Harlem Environmental Action, Inc., with cosponsorship by the National Institute of Environmental Health Sciences (NIEHS), the Community Outreach and Education Program of the NIEHS P30 Center for Environmental Health at the Mailman School of Public Health at Columbia University, New York, and the U.S. Environmental Protection Agency. The conference and symposium took place at Columbia University in New York City on 4-5 February 2002. Expert panels composed of public health practitioners, genetic researchers, ethicists, lawyers, social scientists, and community organizations were assembled to explore how genetic research will affect communities of color, specifically in environmental health research. The goal of the conference was to educate participants on the science and ethics of genetic research and to explore the potential benefits and pitfalls of genetic research vis-à-vis new trends in environmental health research, specifically with reference to communities of color. The goal of the symposium was to discuss the major perceptions and concerns for community-based environmental justice advocates and other communities of color regarding environmental health genetic research. The conference and symposium drew more than 300 participants and articulated important perspectives on the opportunities and challenges for environmental justice advocates and other communities of color posed by rapid advances in environmental health genetic research and toxicogenomics.

Biomedical Research↗
PubMed2026

Functional convergence of rTCA-related carbon-fixation potential and biochemical residue accumulation in seagrass sediments.

Seagrass meadows are globally significant blue carbon ecosystems, yet the microbial and biochemical mechanisms driving sediment organic carbon (SOC) accumulation remain poorly understood. To address this, we employed an integrated approach combining metagenomic sequencing, biochemical assays, and structural equation modeling to investigate carbon cycling in the seagrass and adjacent unvegetated sediments of Swan Lake, China. A total of 115,179 carbon fixation genes and 119,615 decomposition genes were identified, revealing distinct microbial community structures among the habitats. Seagrass sediments harbored more diverse carbon-fixing (CFMs) and decomposing microorganisms (CDMs), with 83 medium-to high-quality metagenome-assembled genomes (MAGs) recovered. While neutral community model analysis indicated that stochastic processes predominantly governed community assembly, functional analyses highlighted specific drivers of sequestration. The reductive tricarboxylic acid (rTCA) cycle emerged as the dominant carbon fixation pathway, with key genes (e.g., aclA, korA) showing strong positive correlations with SOC. Conversely, decomposition pathways for starch and lignin were negatively associated with SOC. Furthermore, seagrass sediments exhibited elevated concentrations of total amino sugars (TAS) and lignin phenols (TLP), which linked significantly to carbon fixation rather than decomposition. PLS-SEM revealed statistically significant associations among seagrass traits, environmental variables, microbial carbon-fixation potential, biochemical residue pools, and SOC, supporting a mechanistic pathway in which enhanced microbial functional potential drives the accumulation of recalcitrant biochemical residues, thereby facilitating long-term carbon retention in sediments. These findings emphasize the pivotal role of microbial anabolism and the accumulation of biosynthetic residues in sediment carbon storage, suggesting a functional convergence in seagrass-driven carbon sinks.

Metagenomics↗
PubMed2002

Can we tell how a community was constructed? A comparison of five evenness indices for their ability to identify theoretical models of community construction.

Evenness indices provide a simple measure of community structure. It might therefore be possible to use them to identify the process by which a community has been assembled. To test whether this is practicable, we constructed simulated community samples using five stochastic models of community construction, proposed by Tokeshi. We then examined the ability of five evenness indices to identify the model under which the community samples were produced. Each model produced samples with a range of evenness values, but mean evenness differed between the models. The dominance decay (DD) model produced community samples with the greatest evenness, followed by MacArthur fraction (MF). Evenness was lowest under the dominance pre-emption (DP) model. The differences between models were quite consistent across indices and consistent between 5-species and 15-species communities. Samples produced under the DD and MF models varied least in evenness between 5-species and 15-species samples, and those produced under the random assortment (RA) model varied most, irrespective of the evenness index used. Evenness varied considerably between replicate samples, as expected with stochastic processes. In 5-species communities, the greatest robustness in evenness across replicates was seen using indices O or E'. In 15-species communities, O and E(Q) were the most robust. The index best able to identify the model which had generated the sample differed between models and with species richness. If the model of interest is not known in advance, the best index for identifying the generating model is E(var) for communities of more than 10 species for RF, RA and DP models and O for other communities. The number of samples required in a data set before it could be effectively identified was, for example, more than 30 for 5-species samples produced under the random fraction (RF) model, and 3 for 15-species RF samples. In contrast, a 5-species DD data set could be effectively identified when it contained 15 or more samples. We conclude that evenness can be used to identify the process by which the community has been constructed, out of the five models considered here. The best evenness index for doing this varies with the species richness and the evenness of the community but we can suggest the use of O without knowing the model because its the more stable one against species richness and the more robust and unbiased against simulated samples and it encompass a good discriminating power between the models in most of the cases studied.

Abstracting and Indexing↗
PubMed1994

Community-level competition: asymmetrical dominance.

Ecological competition between entire communities of species occurs only when geographic barriers are suddenly removed. Recent empirical analysis suggests that, following the disappearance of a barrier, one community may swamp a second community, causing most or all of its species to go extinct. I provide theoretical insight into this result by showing that two "naive" competition communities mix randomly following the removal of a barrier. However, if the two communities have been "assembled," or self-organized, through a history of competitive exclusion, the communities are likely to battle as coordinated armies, with one or the other side ultimately claiming the entire landscape.

Animals↗
PubMed1996

Durability of tobacco control activities in 11 north American communities: life after the Community Intervention Trial for Smoking Cessation (COMMIT).

Durability of tobacco control activities in the 11 intervention sites of the Community Intervention Trial for Heavy Smokers (COMMIT) was examined. Although continuation of COMMIT activities was not a major goal, all communities made plans to continue some tobacco control activity. Information was gathered at focus groups of former COMMIT volunteers and staff who were assembled in each community and asked to describe tobacco control activities in their communities during the past 12-16 months-the period after the termination of COMMIT funding. It was found that a tobacco coalition, board or other structure was still operating in nine of the 11 communities and 10 had some level of paid staff dedicated to smoking control. There was also substantial activity in three of the four channels that COMMIT used as an intervention framework: worksites, public education and cessation resources. Many communities were currently engaged in considerable smoking control activity aimed at youth, an area that was intentionally de-emphasized by COMMIT. Implications for the durability of health promotion programs by communities are discussed.

Adolescent↗
PubMed2004

Emergence of community structure in terrestrial mammal-dominated ecosystems.

We present a paper that combines empirical and theoretical research about the trophic organization of biological communities. Some regularities are observed in the analysis of the relationship between the trophic structure (how the species are distributed among a set of feeding groups) of a number of African large mammal communities and the type of ecosystem. Different types of ecosystems are characterized by specific patterns in the trophic structure of the mammal community. In order to explain the origin of these patterns, we propose a model defining the underlying dynamic of mammal-dominated ecosystems. The main aim of this study is to show that it is possible to obtain a dynamic explanation of those patterns. The model is shown to spontaneously define different types of structures in community organization, related to those observed. We propose a model that could help to explain the correlation between different environmental factors and the abundance or diversity of herbivores, and which establishes a general mechanism that makes it possible to understand how some rules constrain the assembly of the communities. In addition, the proposed model leads us to see how biological communities can operate in an integrated way, which allows for the acceptance of their changes on large time-scales as evolutionary. In summary, we suggest that communities are unitary structures with coherent properties that result from the self-organizing dynamic of the whole system.

Animals↗
PubMed2003

[Advances in plant ecophysiological studies on re-vegetation of degraded ecosystem].

Natural force and human intervention lead to many local, regional, and sometimes global changes in plant community patterns. Regardless of the cause and intensity of these changes, ecosystem can recover most of their attributes through natural succession, or can be repaired by human assistance. The essentiality of restoration of degraded ecosystem is community succession, a process during which an ecosystem evolves from primary stage to advanced stage, and its structure and function change from simple to complex plant. Ecophysiological study could explain some macroscopical phenomena of the ecology of re-vegetation of degraded ecosystem, and provide a scientific base for assembling pioneering plant community. The advances in plant ecophysiological study on re-vegetation of degraded ecosystems were reviewed in this paper.

Biomass↗