scholarly journals The Best of All Worlds: Streptococcus pneumoniae Conjunctivitis through the Lens of Community Ecology and Microbial Biogeography

2019 ◽  
Vol 8 (1) ◽  
pp. 46 ◽  
Author(s):  
Lawson Ung ◽  
Paulo J. M. Bispo ◽  
Noelle C. Bryan ◽  
Camille Andre ◽  
James Chodosh ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Community Ecology ◽  
Disease Transmission ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Microbial World ◽  
Next Generation Sequencing Technology ◽  
Microbial Biogeography ◽  
Ecological Principles ◽  
Population Structures

The study of the forces which govern the geographical distributions of life is known as biogeography, a subject which has fascinated zoologists, botanists and ecologists for centuries. Advances in our understanding of community ecology and biogeography—supported by rapid improvements in next generation sequencing technology—have now made it possible to identify and explain where and why life exists as it does, including within the microbial world. In this review, we highlight how a unified model of microbial biogeography, one which incorporates the classic ecological principles of selection, diversification, dispersion and ecological drift, can be used to explain community dynamics in the settings of both health and disease. These concepts operate on a multiplicity of temporal and spatial scales, and together form a powerful lens through which to study microbial population structures even at the finest anatomical resolutions. When applied specifically to curious strains of conjunctivitis-causing, nonencapsulated Streptococcus pneumoniae, we show how this conceptual framework can be used to explain the possible evolutionary and disease-causing mechanisms which allowed these lineages to colonize and invade a separate biogeography. An intimate knowledge of this radical bifurcation in phylogeny, still the only known niche subspecialization for S. pneumoniae to date, is critical to understanding the pathogenesis of ocular surface infections, nature of host-pathogen interactions, and developing strategies to curb disease transmission.

Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques

2010 ◽  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Community Ecology ◽  
Community Dynamics ◽  
Spatial Scales ◽  
River Mouth ◽  
Extrinsic Factors ◽  
Local Species Richness ◽  
Community Convergence ◽  
Local Filters

<em>Abstract</em>.—Community ecology increasingly seeks to integrate the influences of regional and historical processes with species interactions within local habitats. This broadened perspective is largely based on comparative approaches that employ “natural experiments” to identify factors shaping community structure. Because coastal rivers are separated from one another by insurmountable barriers (oceans or land), freshwater fishes are particularly well suited for comparative analyses of factors that influence fish community organization. In this chapter, we review how this comparative approach shed light on large-scale biodiversity gradients, community saturation, community convergence, density compensation, and the role of intrinsic and extrinsic factors in community dynamics. The main factors (e.g., river mouth discharge and history) empirically related to species richness of a river are well identified, and metacommunity ecology provides a fruitful conceptual framework for understanding how regional (river) species richness translates into local species richness. Much work remains to identify factors explaining differences among whole river basin assemblages with regard to ecological traits (e.g., trophic status and life history) composition and to assess whether trait-related environmental and biotic local filters act similarly over large spatial scales. One important conclusion that can be drawn from the studies reviewed here is that history cannot be neglected whatever the scale of investigation (global, river, or site). A second conclusion is that historical effects are not strong enough to blur the occurrence of qualitatively repeatable patterns of community structure over large spatial scale, which is encouraging because it suggests development of general predictive models of community structure is an attainable goal.

scholarly journals Dispersal and Land Cover Contribute to Pseudorabies Virus Exposure in Invasive Wild Pigs

EcoHealth ◽  
2021 ◽  
Author(s):  
Felipe A. Hernández ◽  
Amanda N. Carr ◽  
Michael P. Milleson ◽  
Hunter R. Merrill ◽  
Michael L. Avery ◽  
...  
Keyword(s):  
Land Cover ◽  
Disease Transmission ◽  
Wildlife Conservation ◽  
Pseudorabies Virus ◽  
Spatial Scales ◽  
Information Criterion ◽  
Small Scale ◽  
Wild Pigs ◽  
Bacterial Agent ◽  
Open Canopy

AbstractWe investigated the landscape epidemiology of a globally distributed mammal, the wild pig (Sus scrofa), in Florida (U.S.), where it is considered an invasive species and reservoir to pathogens that impact the health of people, domestic animals, and wildlife. Specifically, we tested the hypothesis that two commonly cited factors in disease transmission, connectivity among populations and abundant resources, would increase the likelihood of exposure to both pseudorabies virus (PrV) and Brucella spp. (bacterial agent of brucellosis) in wild pigs across the Kissimmee Valley of Florida. Using DNA from 348 wild pigs and sera from 320 individuals at 24 sites, we employed population genetic techniques to infer individual dispersal, and an Akaike information criterion framework to compare candidate logistic regression models that incorporated both dispersal and land cover composition. Our findings suggested that recent dispersal conferred higher odds of exposure to PrV, but not Brucella spp., among wild pigs throughout the Kissimmee Valley region. Odds of exposure also increased in association with agriculture and open canopy pine, prairie, and scrub habitats, likely because of highly localized resources within those land cover types. Because the effect of open canopy on PrV exposure reversed when agricultural cover was available, we suggest that small-scale resource distribution may be more important than overall resource abundance. Our results underscore the importance of studying and managing disease dynamics through multiple processes and spatial scales, particularly for non-native pathogens that threaten wildlife conservation, economy, and public health.

Biological processes in modelling soil functions – a balancing act between too complex and too simple

2021 ◽  
Author(s):  
Sara König ◽  
Ulrich Weller ◽  
Thomas Reitz ◽  
Bibiana Betancur-Corredor ◽  
Birgit Lang ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Microbial Activity ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Simulation Models ◽  
Microbial Processes ◽  
Biological Processes ◽  
Soil Functions ◽  
Management Options ◽  
The Impact

&lt;p&gt;Mechanistic simulation models are an essential tool for predicting soil functions such as nutrient cycling, water filtering and storage, productivity and carbon storage as well as the complex interactions between these functions. Most soil functions are driven or affected by soil organisms. Yet, biological processes are often neglected in soil function models or implicitly described by rate parameters. This can be explained by the high complexity of the soil ecosystem with its dynamic and heterogeneous environment, and by the range of temporal and spatial scales these processes are taking place at. On the other hand, the technical capabilities to explore microbial activity and communities in soil has greatly improved, resulting in new possibilities to understand soil microbial processes on various scales.&lt;/p&gt;&lt;p&gt;However, to integrate such biological processes in soil modelling, we need to find the right level of detail. Here, we present a systemic soil model approach to simulate the impact of different management options and changing climate on soil functions integrating biological activity on the profile scale. We use stoichiometric considerations to simulate microbial processes involved in different soil functions without explicitly describing community dynamics or functional groups. With this approach we are able to mechanistically describe microbial activity and its impact on the turnover of organic matter and nutrient cycling as driven by agricultural soil management.&lt;/p&gt;&lt;p&gt;Further, we discuss general challenges and ongoing developments to additionally consider, e.g., microbe-fauna-interactions or microbial feedback with soil structure dynamics.&lt;/p&gt;

Plant-Herbivore Interactions

2001 ◽  
Author(s):  
Denise Dealing
Keyword(s):  
Community Dynamics ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Secondary Compounds ◽  
Nutritional Composition ◽  
Secondary Chemistry ◽  
Niwot Ridge ◽  
Herbivore Interactions ◽  
Ultimate Objective ◽  
Plant Herbivore

The alpine provides a tremendous opportunity for studying plant-herbivore interactions at the population, community, and ecosystem levels. For herbivores, variations in topography and microclimate result in a relatively large amount of spatial variation in plant communities within short distances (chapter 6). A large community of herbivores, from nematodes to grasshoppers to elk, occurs on Niwot Ridge. Furthermore, given the low rates of nutrient availability in alpine soils (Fisk and Schmidt 1995; chapter 12) combined with the slow-growing perennial habit of the vegetation, alpine plants should, in theory, invest heavily in defense against herbivores (Coley et al. 1985). The goal of this chapter is to provide: (1) a summary of the feeding behaviors of the herbivores on Niwot Ridge, (2) information on the nutritional and secondary chemistry of plants on Niwot Ridge as it relates to herbivory, and (3) a review of hypotheses on community dynamics of herbivores and plants relevant to the alpine. The ultimate objective is to provide a synthesis of information that will stimulate interest in alpine tundra as a system for studying the dynamics of plant-herbivore interactions at all levels of ecological organization. The flora of Niwot Ridge has been divided into six communities (May and Webber 1982; chapter 6). Regardless of community association, nearly all of the plant species occurring on the ridge are perennials and several are very long lived (May and Webber 1982). Communities can change across small spatial scales (meters), and community origin and maintenance are believed to be largely determined by abiotic factors (Walker et al. 1994; chapter 6). However, several studies suggest that biotic factors such as herbivory may have a significant impact on plant community dynamics (Huntly et al. 1986; Davies 1994). There is significant variation in the nutritional composition of plants on Niwot Ridge. Generally, and in the absence of plant secondary compounds, species that are high in nitrogen and low in fiber are presumed to be the most desirable as forage. Based solely on these nutritional variables, the clover Trifolium parryi is hypothesized to be one of the more-preferred forages, whereas alpine sandwort, Minuartia obtusiloba, should be one of the less-preferred food items.

scholarly journals Viruses of Polar Aquatic Environments

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 189 ◽  
Author(s):  
Sheree Yau ◽  
Mansha Seth-Pasricha
Keyword(s):  
Community Dynamics ◽  
Spatial Scales ◽  
Extreme Environments ◽  
Cold Climate ◽  
Polar Regions ◽  
Microbial Life ◽  
The North ◽  
Cellular Life ◽  
Antarctic Continent ◽  
Cycling Of Nutrients

The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.

scholarly journals Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype

2009 ◽  
Vol 276 (1661) ◽  
pp. 1495-1506 ◽  
Author(s):  
William E Kunin ◽  
Philippine Vergeer ◽  
Tanaka Kenta ◽  
Matthew P Davey ◽  
Terry Burke ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Physical Distance ◽  
Population Variation ◽  
Regional Patterns ◽  
Range Margin ◽  
Arabidopsis Lyrata ◽  
Perennial Plant ◽  
Temperature Regimes ◽  
Population Structures ◽  
Genetic Profiles

Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.

Multi-scale spatial analysis of human alveolar echinococcosis risk in China

Parasitology ◽  
2003 ◽  
Vol 127 (S1) ◽  
pp. S133-S141 ◽  
Author(s):  
F. M. DANSON ◽  
A. J. GRAHAM ◽  
D. R. J. PLEYDELL ◽  
M. CAMPOS-PONCE ◽  
P. GIRAUDOUX ◽  
...  
Keyword(s):  
Spatial Data ◽  
Disease Transmission ◽  
Spatial Scales ◽  
Regional Scale ◽  
Central China ◽  
Spatial Data Analysis ◽  
Transmission Risk ◽  
Spatial Proximity ◽  
Human Populations ◽  
Remotely Sensed Data

Risk factors for the transmission of Echinococcus multilocularis to humans operate at a range of spatial scales. Over a large area, such as China, regional scale risk is correlated with variation in climatic conditions because of its effect on the spatial distribution of landscapes that can support E. multilocularis transmission in wildlife hosts and the probability of egg survival. At a local scale of a few kilometres, or tens of kilometres, transmission risk is related to the spatial proximity of human populations and landscapes with active transmission. At the patch scale, when considering individual villages or households, human behavioural factors are important and for individuals genetic and immunological factors play a role. Satellite remote sensing can provide landscape information at a range of spatial scales and provide a spatial framework within which to examine transmission patterns. This paper reviews the application of remotely sensed data and spatial data analysis to develop a better understanding of disease transmission and shows how such data have been used to examine human alveolar echinocossosis infection patterns, at a range of spatial scales, in an endemic area in central China.

scholarly journals Defining marine microbial biomes from environmental and dispersal filtered metapopulations

2017 ◽  
Author(s):  
Markus V. Lindh
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Spatial Scales ◽  
Dispersal Limitation ◽  
Global Ocean ◽  
Microbial Populations ◽  
Microbial Biogeography ◽  
Metapopulation Theory ◽  
Mock Communities

SummaryEnergy and matter fluxes essential for all life1 are modulated by spatial and temporal shifts in microbial community structure resulting from environmental and dispersal filtering2,3, emphasizing the continued need to characterize microbial biogeography4,5. Yet, application of metapopulation theory, traditionally used in general ecology for understanding shifts in biogeographical patterns among macroorganisms, has not been tested extensively for defining marine microbial populations filtered by environmental conditions and dispersal limitation at global ocean scales. Here we show, from applying metapopulation theory on two major global ocean datasets6,7, that microbial populations exhibit core- and satellite distributions with cosmopolitan compared to geographically restricted distributions of populations. We found significant bimodal occupancy-frequency patterns (the different number of species occupying different number of patches) at varying spatial scales, where shifts from bimodal to unimodal patterns indicated environmental and dispersal filtering. Such bimodal occupancy-frequency patterns were validated in Longhurst’s classical biogeographical framework and in silico where observed bimodal patterns often aligned with specific biomes and provinces described by Longhurst and where found to be non-random in randomized datasets and mock communities. Taken together, our results show that application of metapopulation theory provides a framework for determining distinct microbial biomes maintained by environmental and dispersal filtering.

scholarly journals Scaling up biodiversity–ecosystem functioning relationships: the role of environmental heterogeneity in space and time

2021 ◽  
Vol 288 (1946) ◽  
pp. 20202779
Author(s):  
Patrick L. Thompson ◽  
Sonia Kéfi ◽  
Yuval R. Zelnik ◽  
Laura E. Dee ◽  
Shaopeng Wang ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Ecosystem Functioning ◽  
Environmental Heterogeneity ◽  
Community Dynamics ◽  
Formal Model ◽  
Spatial Scales ◽  
Scale Dependence ◽  
Space And Time ◽  
Number Of Species

The biodiversity and ecosystem functioning (BEF) relationship is expected to be scale-dependent. The autocorrelation of environmental heterogeneity is hypothesized to explain this scale dependence because it influences how quickly biodiversity accumulates over space or time. However, this link has yet to be demonstrated in a formal model. Here, we use a Lotka–Volterra competition model to simulate community dynamics when environmental conditions vary across either space or time. Species differ in their optimal environmental conditions, which results in turnover in community composition. We vary biodiversity by modelling communities with different sized regional species pools and ask how the amount of biomass per unit area depends on the number of species present, and the spatial or temporal scale at which it is measured. We find that more biodiversity is required to maintain functioning at larger temporal and spatial scales. The number of species required increases quickly when environmental autocorrelation is low, and slowly when autocorrelation is high. Both spatial and temporal environmental heterogeneity lead to scale dependence in BEF, but autocorrelation has larger impacts when environmental change is temporal. These findings show how the biodiversity required to maintain functioning is expected to increase over space and time.

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