SPRUCE S1 Bog Tree Basal Area and Understory Community Composition Assessed in the Southern and Northern Ends of the S1 Bog

DOE Data Explorer

Iversen, C. M. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Garrett, A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Martin, A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Turetsky, M. R. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Norby, R. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Childs, J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Ontl, T. A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A

2017-01-01

The composition and cover of woody and understory species, along with the timing of stem growth, were characterized near minirhizotron installations at the south and north ends of the S1 bog in order to understand the relationship between root dynamics and the surrounding plant communities. There are three data streams: (1) Woody species basal area -- the number, basal area, and distance from the center point of all trees within a 5-m radius of each minirhizotron pair, which were quantified in 2011, (2) Understory cover -- the understory vascular plant community composition and percent cover, which were surveyed in 1 m2 areas at four cardinal directions adjacent to each pair of minirhizotrons in June 2011, and (3) Stem growth -- the basal area increment (stem growth) of nearby trees, which was quantified using automated or manual dendrobands in 2011 and 2012, respectively.

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system

PubMed Central

Zhao, Wang; Liu, Guang-Feng; Wang, Jiang-Yong

2017-01-01

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling. PMID:28787009

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

PubMed

Jiang, Jing-Zhe; Zhao, Wang; Liu, Guang-Feng; Wang, Jiang-Yong

2017-01-01

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.

Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera.

PubMed

Hsiang, Allison Y; Elder, Leanne E; Hull, Pincelli M

2016-04-05

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct 'look' to communities--making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera--an abundant group in the marine fossil record--and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic. © 2016 The Authors.

The effect of elevated atmospheric CO2 concentration on gross nitrogen and carbon dynamics in a permanent grassland: A field pulse-labeling study

NASA Astrophysics Data System (ADS)

Moser, Gerald; Gorenflo, André; Keidel, Lisa; Brenzinger, Kristof; Elias, Dafydd; McNamara, Niall; Maček, Irena; Vodnik, Dominik; Braker, Gesche; Schimmelpfennig, Sonja; Gerstner, Judith; Müller, Christoph

2014-05-01

To predict ecosystem reactions to elevated atmospheric CO2 (eCO2) it is essential to understand the interactions between plant carbon input, microbial community composition and activity and associated nutrient dynamics. Long-term observations (> 14 years) within the Giessen Free Air Carbon dioxide Enrichment (Giessen FACE) study on permanent grassland showed next to an enhanced biomass production an unexpected strong positive feedback effect on ecosystem respiration and nitrous oxide (N2O) production. The overall goal of this study is to understand the long-term effects of eCO2 and carbon input on microbial community composition and activity as well as the associated nitrogen dynamics, N2O production and plant N uptake in the Giessen FACE study on permanent grassland. A combination of 13CO2 pulse labelling with 15N tracing of 15NH4+ and 15NO3- was carried out in situ. Different fractions of soil organic matter (recalcitrant, labile SOM) and the various mineral N pools in the soil (NH4+, NO3-), gross N transformation rates, pool size dependent N2O and N2 emissions as well as N species dependent plant N uptake rates and the origin of the CO2 respiration have been quantified. Microbial analyses include exploring changes in the composition of microbial communities involved in the turnover of NH4+, NO3-, N2O and N2, i.e. ammonia oxidizing, denitrifying, and microbial communities involved in dissimilatory nitrate reduction to ammonia (DNRA). mRNA based analyses will be employed to comparably evaluate the long-term effects of eCO2 on the structure and abundance of these communities, while transcripts of these genes will be used to target the fractions of the communities which actively contribute to N transformations. We quantified the contribution of mycorrhizae on N2O emissions and observed the phenological development of the mycorrhizae after the labeling.

Delineating ecological regions in marine systems: Integrating physical structure and community composition to inform spatial management in the eastern Bering Sea

NASA Astrophysics Data System (ADS)

Baker, Matthew R.; Hollowed, Anne B.

2014-11-01

Characterizing spatial structure and delineating meaningful spatial boundaries have useful applications to understanding regional dynamics in marine systems, and are integral to ecosystem approaches to fisheries management. Physical structure and drivers combine with biological responses and interactions to organize marine systems in unique ways at multiple scales. We apply multivariate statistical methods to define spatially coherent ecological units or ecoregions in the eastern Bering Sea. We also illustrate a practical approach to integrate data on species distribution, habitat structure and physical forcing mechanisms to distinguish areas with distinct biogeography as one means to define management units in large marine ecosystems. We use random forests to quantify the relative importance of habitat and environmental variables to the distribution of individual species, and to quantify shifts in multispecies assemblages or community composition along environmental gradients. Threshold shifts in community composition are used to identify regions with distinct physical and biological attributes, and to evaluate the relative importance of predictor variables to determining regional boundaries. Depth, bottom temperature and frontal boundaries were dominant factors delineating distinct biological communities in this system, with a latitudinal divide at approximately 60°N. Our results indicate that distinct climatic periods will shift habitat gradients and that dynamic physical variables such as temperature and stratification are important to understanding temporal stability of ecoregion boundaries. We note distinct distribution patterns among functional guilds and also evidence for resource partitioning among individual species within each guild. By integrating physical and biological data to determine spatial patterns in community composition, we partition ecosystems along ecologically significant gradients. This may provide a basis for defining spatial management units or serve as a baseline index for analyses of structural shifts in the physical environment, species abundance and distribution, and community dynamics over time.

Networks of energetic and metabolic interactions define dynamics in microbial communities.

PubMed

Embree, Mallory; Liu, Joanne K; Al-Bassam, Mahmoud M; Zengler, Karsten

2015-12-15

Microorganisms form diverse communities that have a profound impact on the environment and human health. Recent technological advances have enabled elucidation of community diversity at high resolution. Investigation of microbial communities has revealed that they often contain multiple members with complementing and seemingly redundant metabolic capabilities. An understanding of the communal impacts of redundant metabolic capabilities is currently lacking; specifically, it is not known whether metabolic redundancy will foster competition or motivate cooperation. By investigating methanogenic populations, we identified the multidimensional interspecies interactions that define composition and dynamics within syntrophic communities that play a key role in the global carbon cycle. Species-specific genomes were extracted from metagenomic data using differential coverage binning. We used metabolic modeling leveraging metatranscriptomic information to reveal and quantify a complex intertwined system of syntrophic relationships. Our results show that amino acid auxotrophies create additional interdependencies that define community composition and control carbon and energy flux through the system while simultaneously contributing to overall community robustness. Strategic use of antimicrobials further reinforces this intricate interspecies network. Collectively, our study reveals the multidimensional interactions in syntrophic communities that promote high species richness and bolster community stability during environmental perturbations.

Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management.

PubMed

Malmstrom, Carolyn M; Butterfield, H Scott; Planck, Laura; Long, Christopher W; Eviner, Valerie T

2017-01-01

Invasive weeds threaten the biodiversity and forage productivity of grasslands worldwide. However, management of these weeds is constrained by the practical difficulty of detecting small-scale infestations across large landscapes and by limits in understanding of landscape-scale invasion dynamics, including mechanisms that enable patches to expand, contract, or remain stable. While high-end hyperspectral remote sensing systems can effectively map vegetation cover, these systems are currently too costly and limited in availability for most land managers. We demonstrate application of a more accessible and cost-effective remote sensing approach, based on simple aerial imagery, for quantifying weed cover dynamics over time. In California annual grasslands, the target communities of interest include invasive weedy grasses (Aegilops triuncialis and Elymus caput-medusae) and desirable forage grass species (primarily Avena spp. and Bromus spp.). Detecting invasion of annual grasses into an annual-dominated community is particularly challenging, but we were able to consistently characterize these two communities based on their phenological differences in peak growth and senescence using maximum likelihood supervised classification of imagery acquired twice per year (in mid- and end-of season). This approach permitted us to map weed-dominated cover at a 1-m scale (correctly detecting 93% of weed patches across the landscape) and to evaluate weed cover change over time. We found that weed cover was more pervasive and persistent in management units that had no significant grazing for several years than in those that were grazed, whereas forage cover was more abundant and stable in the grazed units. This application demonstrates the power of this method for assessing fine-scale vegetation transitions across heterogeneous landscapes. It thus provides means for small-scale early detection of invasive species and for testing fundamental questions about landscape dynamics.

Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management

PubMed Central

Butterfield, H. Scott; Planck, Laura; Long, Christopher W.; Eviner, Valerie T.

2017-01-01

Invasive weeds threaten the biodiversity and forage productivity of grasslands worldwide. However, management of these weeds is constrained by the practical difficulty of detecting small-scale infestations across large landscapes and by limits in understanding of landscape-scale invasion dynamics, including mechanisms that enable patches to expand, contract, or remain stable. While high-end hyperspectral remote sensing systems can effectively map vegetation cover, these systems are currently too costly and limited in availability for most land managers. We demonstrate application of a more accessible and cost-effective remote sensing approach, based on simple aerial imagery, for quantifying weed cover dynamics over time. In California annual grasslands, the target communities of interest include invasive weedy grasses (Aegilops triuncialis and Elymus caput-medusae) and desirable forage grass species (primarily Avena spp. and Bromus spp.). Detecting invasion of annual grasses into an annual-dominated community is particularly challenging, but we were able to consistently characterize these two communities based on their phenological differences in peak growth and senescence using maximum likelihood supervised classification of imagery acquired twice per year (in mid- and end-of season). This approach permitted us to map weed-dominated cover at a 1-m scale (correctly detecting 93% of weed patches across the landscape) and to evaluate weed cover change over time. We found that weed cover was more pervasive and persistent in management units that had no significant grazing for several years than in those that were grazed, whereas forage cover was more abundant and stable in the grazed units. This application demonstrates the power of this method for assessing fine-scale vegetation transitions across heterogeneous landscapes. It thus provides means for small-scale early detection of invasive species and for testing fundamental questions about landscape dynamics. PMID:29016604

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

The data not collected on community forestry

PubMed Central

Oldekop, Johan A.; Cronkleton, Peter; Etue, Emily; Newton, Peter; Russel, Aaron J.M.; Tjajadi, Januarti Sinarra; Zhou, Wen; Agrawal, Arun

2016-01-01

Abstract Conservation and development practitioners increasingly promote community forestry as a way to conserve ecosystem services, consolidate resource rights, and reduce poverty. However, outcomes of community forestry have been mixed; many initiatives failed to achieve intended objectives. There is a rich literature on institutional arrangements of community forestry, but there has been little effort to examine the role of socioeconomic, market, and biophysical factors in shaping both land‐cover change dynamics and individual and collective livelihood outcomes. We systematically reviewed the peer‐reviewed literature on community forestry to examine and quantify existing knowledge gaps in the community‐forestry literature relative to these factors. In examining 697 cases of community forest management (CFM), extracted from 267 peer‐reviewed publications, we found 3 key trends that limit understanding of community forestry. First, we found substantial data gaps linking population dynamics, market forces, and biophysical characteristics to both environmental and livelihood outcomes. Second, most studies focused on environmental outcomes, and the majority of studies that assessed socioeconomic outcomes relied on qualitative data, making comparisons across cases difficult. Finally, there was a heavy bias toward studies on South Asian forests, indicating that the literature on community forestry may not be representative of decentralization policies and CFM globally. PMID:27060464

Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera

PubMed Central

Hsiang, Allison Y.; Elder, Leanne E.; Hull, Pincelli M.

2016-01-01

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic. PMID:26977067

Seventy years of forest growth and community dynamics in an undisturbed northern hardwood forest

Treesearch

Jennifer Pontius; Joshua M. Halman; Paul G. Schaberg

2016-01-01

Long-term forest inventories provide a unique opportunity to quantify changes in forest structure and evaluate how changes compare with current stand development models. An examination of a 70 year record at the Bartlett Experimental Forest, New Hampshire, indicated that although species abundances have primarily changed as expected under natural succession, some...

The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs.

PubMed

Nenzén, Hedvig K; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.

The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs

PubMed Central

Nenzén, Hedvig K.; Montoya, Daniel; Varela, Sara

2014-01-01

Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities. PMID:25207754

Hillslope characterization: Identifying key controls on local-scale plant communities' distribution using remote sensing and subsurface data fusion.

NASA Astrophysics Data System (ADS)

Falco, N.; Wainwright, H. M.; Dafflon, B.; Leger, E.; Peterson, J.; Steltzer, H.; Wilmer, C.; Williams, K. H.; Hubbard, S. S.

2017-12-01

Mountainous watershed systems are characterized by extreme heterogeneity in hydrological and pedological properties that influence biotic activities, plant communities and their dynamics. To gain predictive understanding of how ecosystem and watershed system evolve under climate change, it is critical to capture such heterogeneity and to quantify the effect of key environmental variables such as topography, and soil properties. In this study, we exploit advanced geophysical and remote sensing techniques - coupled with machine learning - to better characterize and quantify the interactions between plant communities' distribution and subsurface properties. First, we have developed a remote sensing data fusion framework based on the random forest (RF) classification algorithm to estimate the spatial distribution of plant communities. The framework allows the integration of both plant spectral and structural information, which are derived from multispectral satellite images and airborne LiDAR data. We then use the RF method to evaluate the estimated plant community map, exploiting the subsurface properties (such as bedrock depth, soil moisture and other properties) and geomorphological parameters (such as slope, curvature) as predictors. Datasets include high-resolution geophysical data (electrical resistivity tomography) and LiDAR digital elevation maps. We demonstrate our approach on a mountain hillslope and meadow within the East River watershed in Colorado, which is considered to be a representative headwater catchment in the Upper Colorado Basin. The obtained results show the existence of co-evolution between above and below-ground processes; in particular, dominant shrub communities in wet and flat areas. We show that successful integration of remote sensing data with geophysical measurements allows identifying and quantifying the key environmental controls on plant communities' distribution, and provides insights into their potential changes in the future climate conditions.

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

PubMed

Kress, W John; Erickson, David L; Swenson, Nathan G; Thompson, Jill; Uriarte, Maria; Zimmerman, Jess K

2010-11-09

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Interpreting beta-diversity components over time to conserve metacommunities in highly dynamic ecosystems.

PubMed

Ruhí, Albert; Datry, Thibault; Sabo, John L

2017-12-01

The concept of metacommunity (i.e., a set of local communities linked by dispersal) has gained great popularity among community ecologists. However, metacommunity research mostly addresses questions on spatial patterns of biodiversity at the regional scale, whereas conservation planning requires quantifying temporal variation in those metacommunities and the contributions that individual (local) sites make to regional dynamics. We propose that recent advances in diversity-partitioning methods may allow for a better understanding of metacommunity dynamics and the identification of keystone sites. We used time series of the 2 components of beta diversity (richness and replacement) and the contributions of local sites to these components to examine which sites controlled source-sink dynamics in a highly dynamic model system (an intermittent river). The relative importance of the richness and replacement components of beta diversity fluctuated over time, and sample aggregation led to underestimation of beta diversity by up to 35%. Our literature review revealed that research on intermittent rivers would benefit greatly from examination of beta-diversity components over time. Adequately appraising spatiotemporal variability in community composition and identifying sites that are pivotal for maintaining biodiversity at the landscape scale are key needs for conservation prioritization and planning. Thus, our framework may be used to guide conservation actions in highly dynamic ecosystems when time-series data describing biodiversity across sites connected by dispersal are available. © 2017 Society for Conservation Biology.

Comparison of biofilm formation between major clonal lineages of methicillin resistant Staphylococcus aureus.

PubMed

Vanhommerig, Evelyn; Moons, Pieter; Pirici, Daniel; Lammens, Christine; Hernalsteens, Jean-Pierre; De Greve, Henri; Kumar-Singh, Samir; Goossens, Herman; Malhotra-Kumar, Surbhi

2014-01-01

Epidemic methicillin-resistant S. aureus (MRSA) clones cause infections in both hospital and community settings. As a biofilm phenotype further facilitates evasion of the host immune system and antibiotics, we compared the biofilm-forming capacities of various MRSA clones. Seventy-six MRSA classified into 13 clones (USA300, EMRSA-15, Hungarian/Brazilian etc.), and isolated from infections or from carriers were studied for biofilm formation under static and dynamic conditions. Static biofilms in microtitre plates were quantified colorimetrically. Dynamic biofilms (Bioflux 200, Fluxion, USA) were studied by confocal laser-scanning and time-lapse microscopy, and the total volume occupied by live/dead bacteria quantified by Volocity 5.4.1 (Improvision, UK). MRSA harbouring SCCmec IV produced significantly more biomass under static conditions than SCCmec I-III (P = 0.003), and those harbouring SCCmec II significantly less than those harbouring SCCmec I or III (P<0.001). In the dynamic model, SCCmec I-III harbouring MRSA were significantly better biofilm formers than SCCmec IV (P = 0.036). Only 16 strains successfully formed biofilms under both conditions, of which 13 harboured SCCmec IV and included all tested USA300 strains (n = 3). However, USA300 demonstrated remarkably lower percentages of cell-occupied space (6.6%) compared to the other clones (EMRSA-15 = 19.0%) under dynamic conditions. Time-lapse microscopy of dynamic biofilms demonstrated that USA300 formed long viscoelastic tethers that stretched far from the point of attachment, while EMRSA-15 consisted of micro-colonies attached densely to the surface. MRSA harbouring SCCmec types IV and I-III demonstrate distinct biofilm forming capacities, possibly owing to their adaptation to the community and hospital settings, respectively. USA300 demonstrated abundant biofilm formation under both conditions, which probably confers a competitive advantage, contributing to its remarkable success as a pathogen.

NDVI as a predictor of canopy arthropod biomass in the Alaskan arctic tundra.

PubMed

Sweet, Shannan K; Asmus, Ashley; Rich, Matthew E; Wingfield, John; Gough, Laura; Boelman, Natalie T

2015-04-01

The physical and biological responses to rapid arctic warming are proving acute, and as such, there is a need to monitor, understand, and predict ecological responses over large spatial and temporal scales. The use of the normalized difference vegetation index (NDVI) acquired from airborne and satellite sensors addresses this need, as it is widely used as a tool for detecting and quantifying spatial and temporal dynamics of tundra vegetation cover, productivity, and phenology. Such extensive use of the NDVI to quantify vegetation characteristics suggests that it may be similarly applied to characterizing primary and secondary consumer communities. Here, we develop empirical models to predict canopy arthropod biomass with canopy-level measurements of the NDVI both across and within distinct tundra vegetation communities over four growing seasons in the Arctic Foothills region of the Brooks Range, Alaska, USA. When canopy arthropod biomass is predicted with the NDVI across all four growing seasons, our overall model that includes all four vegetation communities explains 63% of the variance in canopy arthropod biomass, whereas our models specific to each of the four vegetation communities explain 74% (moist tussock tundra), 82% (erect shrub tundra), 84% (riparian shrub tundra), and 87% (dwarf shrub tundra) of the observed variation in canopy arthropod biomass. Our field-based study suggests that measurements of the NDVI made from air- and spaceborne sensors may be able to quantify spatial and temporal variation in canopy arthropod biomass at landscape to regional scales.

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance.

PubMed

Shade, Ashley; Read, Jordan S; Welkie, David G; Kratz, Timothy K; Wu, Chin H; McMahon, Katherine D

2011-10-01

For lake microbes, water column mixing acts as a disturbance because it homogenizes thermal and chemical gradients known to define the distributions of microbial taxa. Our first objective was to isolate hypothesized drivers of lake bacterial response to water column mixing. To accomplish this, we designed an enclosure experiment with three treatments to independently test key biogeochemical changes induced by mixing: oxygen addition to the hypolimnion, nutrient addition to the epilimnion, and full water column mixing. We used molecular fingerprinting to observe bacterial community dynamics in the treatment and control enclosures, and in ambient lake water. We found that oxygen and nutrient amendments simulated the physical-chemical water column environment following mixing and resulted in similar bacterial communities to the mixing treatment, affirming that these were important drivers of community change. These results demonstrate that specific environmental changes can replicate broad disturbance effects on microbial communities. Our second objective was to characterize bacterial community stability by quantifying community resistance, recovery and resilience to an episodic disturbance. The communities in the nutrient and oxygen amendments changed quickly (had low resistance), but generally matched the control composition by the 10th day after treatment, exhibiting resilience. These results imply that aquatic bacterial assemblages are generally stable in the face of disturbance. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

On Growth and Form of the Zebrafish Gut Microbiome

NASA Astrophysics Data System (ADS)

Jemielita, Matthew; Taormina, Michael; Rolig, Annah; Burns, Adam; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

2014-03-01

The vertebrate gut is home to a diverse microbial community whose composition has a strong influence on the development and health of the host organism. Researchers can identify the members of the microbiota, yet little is known about the spatial and temporal dynamics of these microbial communities, including the mechanisms guiding their nucleation, growth, and interactions. We address these issues using the larval zebrafish (Danio rerio) as a model organism, which are raised microbe-free and then inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging using light sheet fluorescence microscopy enables visualization of the gut's entire microbial population over the first 24 hours of colonization. Image analysis allows us to quantify microbial populations that range from a few individuals to tens of thousands of microbes, and analyze the structure and growth kinetics of gut bacterial communities. We find that genetically-identical microbes can show surprisingly different growth rates and colonization abilities depending on their order of arrival. This demonstrates that knowing only the constituents of the gut community is insufficient to determine their dynamics; rather, the history of colonization matters.

Tracking environmental dynamics and agricultural intensification in southern Mali

USGS Publications Warehouse

Tappan, G. Gray; McGahuey, M.

2007-01-01

The Office de la Haute Vallée du Fleuve Niger (OHVN) zone in southern Mali is a small but important agricultural production region. Against a background of environmental degradation including decades of declining rainfall, soil erosion, and human pressure on forest resources, numerous farming communities stand out through the use of improved soil and water management practices that have improved agricultural and environmental conditions. Field surveys conducted in 1998–2001 indicated that environmental and agricultural conditions have improved in the past decade. In an effort to better quantify environmental trends, we conducted a study using medium- and high-resolution remotely sensed images from 1965 to 2001 in order to analyze land use and land cover trends in 21 village territories. The trends show clear indications of agricultural intensification and diversification among villages that have received assistance from the OHVN agricultural development agency. Some communities have improved environmental conditions by protecting their forest resources through community management actions. Four decades of remotely sensed images played a practical role in tracking and quantifying environmental and agricultural conditions over time.

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

PubMed

Stein, Richard R; Bucci, Vanni; Toussaint, Nora C; Buffie, Charlie G; Rätsch, Gunnar; Pamer, Eric G; Sander, Chris; Xavier, João B

2013-01-01

The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka-Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli.

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

PubMed Central

Toussaint, Nora C.; Buffie, Charlie G.; Rätsch, Gunnar; Pamer, Eric G.; Sander, Chris; Xavier, João B.

2013-01-01

The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka–Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. PMID:24348232

Experiments in clustered neuronal networks: A paradigm for complex modular dynamics

NASA Astrophysics Data System (ADS)

Teller, Sara; Soriano, Jordi

2016-06-01

Uncovering the interplay activity-connectivity is one of the major challenges in neuroscience. To deepen in the understanding of how a neuronal circuit shapes network dynamics, neuronal cultures have emerged as remarkable systems given their accessibility and easy manipulation. An attractive configuration of these in vitro systems consists in an ensemble of interconnected clusters of neurons. Using calcium fluorescence imaging to monitor spontaneous activity in these clustered neuronal networks, we were able to draw functional maps and reveal their topological features. We also observed that these networks exhibit a hierarchical modular dynamics, in which clusters fire in small groups that shape characteristic communities in the network. The structure and stability of these communities is sensitive to chemical or physical action, and therefore their analysis may serve as a proxy for network health. Indeed, the combination of all these approaches is helping to develop models to quantify damage upon network degradation, with promising applications for the study of neurological disorders in vitro.

Consistent nutrient storage and supply mediated by diverse fish communities in coral reef ecosystems.

PubMed

Allgeier, Jacob E; Layman, Craig A; Mumby, Peter J; Rosemond, Amy D

2014-08-01

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish-mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g., overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans. © 2014 John Wiley & Sons Ltd.

Dynamics of Marine Microbial Metabolism and Physiology at Station ALOHA

NASA Astrophysics Data System (ADS)

Casey, John R.

Marine microbial communities influence global biogeochemical cycles by coupling the transduction of free energy to the transformation of Earth's essential bio-elements: H, C, N, O, P, and S. The web of interactions between these processes is extraordinarily complex, though fundamental physical and thermodynamic principles should describe its dynamics. In this collection of 5 studies, aspects of the complexity of marine microbial metabolism and physiology were investigated as they interact with biogeochemical cycles and direct the flow of energy within the Station ALOHA surface layer microbial community. In Chapter 1, and at the broadest level of complexity discussed, a method to relate cell size to metabolic activity was developed to evaluate allometric power laws at fine scales within picoplankton populations. Although size was predictive of metabolic rates, within-population power laws deviated from the broader size spectrum, suggesting metabolic diversity as a key determinant of microbial activity. In Chapter 2, a set of guidelines was proposed by which organic substrates are selected and utilized by the heterotrophic community based on their nitrogen content, carbon content, and energy content. A hierarchical experimental design suggested that the heterotrophic microbial community prefers high nitrogen content but low energy density substrates, while carbon content was not important. In Chapter 3, a closer look at the light-dependent dynamics of growth on a single organic substrate, glycolate, suggested that growth yields were improved by photoheterotrophy. The remaining chapters were based on the development of a genome-scale metabolic network reconstruction of the cyanobacterium Prochlorococcus to probe its metabolic capabilities and quantify metabolic fluxes. Findings described in Chapter 4 pointed to evolution of the Prochlorococcus metabolic network to optimize growth at low phosphate concentrations. Finally, in Chapter 5 and at the finest scale of complexity, a method was developed to predict hourly changes in both physiology and metabolic fluxes in Prochlorococcus by incorporating gene expression time-series data within the metabolic network model. Growth rates predicted by this method more closely matched experimental data, and diel changes in elemental composition and the energy content of biomass were predicted. Collectively, these studies identify and quantify the potential impact of variations in metabolic and physiological traits on the melee of microbial community interactions.

Climate change in our backyards: the reshuffling of North America's winter bird communities.

PubMed

Princé, Karine; Zuckerberg, Benjamin

2015-02-01

Much of the recent changes in North American climate have occurred during the winter months, and as result, overwintering birds represent important sentinels of anthropogenic climate change. While there is mounting evidence that bird populations are responding to a warming climate (e.g., poleward shifts) questions remain as to whether these species-specific responses are resulting in community-wide changes. Here, we test the hypothesis that a changing winter climate should favor the formation of winter bird communities dominated by warm-adapted species. To do this, we quantified changes in community composition using a functional index--the Community Temperature Index (CTI)--which measures the balance between low- and high-temperature dwelling species in a community. Using data from Project FeederWatch, an international citizen science program, we quantified spatiotemporal changes in winter bird communities (n = 38 bird species) across eastern North America and tested the influence of changes in winter minimum temperature over a 22-year period. We implemented a jackknife analysis to identify those species most influential in driving changes at the community level and the population dynamics (e.g., extinction or colonization) responsible for these community changes. Since 1990, we found that the winter bird community structure has changed with communities increasingly composed of warm-adapted species. This reshuffling of winter bird communities was strongest in southerly latitudes and driven primarily by local increases in abundance and regional patterns of colonization by southerly birds. CTI tracked patterns of changing winter temperature at different temporal scales ranging from 1 to 35 years. We conclude that a shifting winter climate has provided an opportunity for smaller, southerly distributed species to colonize new regions and promote the formation of unique winter bird assemblages throughout eastern North America. © 2014 John Wiley & Sons Ltd.

Quantifying long-term evolution of intra-urban spatial interactions

PubMed Central

Sun, Lijun; Jin, Jian Gang; Axhausen, Kay W.; Lee, Der-Horng; Cebrian, Manuel

2015-01-01

Understanding the long-term impact that changes in a city's transportation infrastructure have on its spatial interactions remains a challenge. The difficulty arises from the fact that the real impact may not be revealed in static or aggregated mobility measures, as these are remarkably robust to perturbations. More generally, the lack of longitudinal, cross-sectional data demonstrating the evolution of spatial interactions at a meaningful urban scale also hinders us from evaluating the sensitivity of movement indicators, limiting our capacity to understand the evolution of urban mobility in depth. Using very large mobility records distributed over 3 years, we quantify the impact of the completion of a metro line extension: the Circle Line (CCL) in Singapore. We find that the commonly used movement indicators are almost identical before and after the project was completed. However, in comparing the temporal community structure across years, we do observe significant differences in the spatial reorganization of the affected geographical areas. The completion of CCL enables travellers to re-identify their desired destinations collectively with lower transport cost, making the community structure more consistent. These changes in locality are dynamic and characterized over short timescales, offering us a different approach to identify and analyse the long-term impact of new infrastructures on cities and their evolution dynamics. PMID:25551142

Biodiversity effects of the predation gauntlet

NASA Astrophysics Data System (ADS)

Stier, Adrian C.; Stallings, Christopher D.; Samhouri, Jameal F.; Albins, Mark A.; Almany, Glenn R.

2017-06-01

The ubiquity of trophic downgrading has led to interest in the consequences of mesopredator release on prey communities and ecosystems. This issue is of particular concern for reef-fish communities, where predation is a key process driving ecological and evolutionary dynamics. Here, we synthesize existing experiments that have isolated the effects of mesopredators to quantify the role of predation in driving changes in the abundance and biodiversity of recently settled reef fishes. On average, predators reduced prey abundance through generalist foraging behavior, which, through a statistical sampling artifact, caused a reduction in alpha diversity and an increase in beta diversity. Thus, the synthesized experiments provide evidence that predation reduces overall abundance within prey communities, but—after accounting for sampling effects—does not cause disproportionate effects on biodiversity.

A family of interaction-adjusted indices of community similarity.

PubMed

Schmidt, Thomas Sebastian Benedikt; Matias Rodrigues, João Frederico; von Mering, Christian

2017-03-01

Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of β diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assessed the performance of two specific indices that are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity.

A family of interaction-adjusted indices of community similarity

PubMed Central

Schmidt, Thomas Sebastian Benedikt; Matias Rodrigues, João Frederico; von Mering, Christian

2017-01-01

Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of β diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assessed the performance of two specific indices that are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity. PMID:27935587

Contribution of sea ice microbial production to Antarctic benthic communities is driven by sea ice dynamics and composition of functional guilds.

PubMed

Wing, Stephen R; Leichter, James J; Wing, Lucy C; Stokes, Dale; Genovese, Sal J; McMullin, Rebecca M; Shatova, Olya A

2018-04-28

Organic matter produced by the sea ice microbial community (SIMCo) is an important link between sea ice dynamics and secondary production in near-shore food webs of Antarctica. Sea ice conditions in McMurdo Sound were quantified from time series of MODIS satellite images for Sept. 1 through Feb. 28 of 2007-2015. A predictable sea ice persistence gradient along the length of the Sound and evidence for a distinct change in sea ice dynamics in 2011 were observed. We used stable isotope analysis (δ 13 C and δ 15 N) of SIMCo, suspended particulate organic matter (SPOM) and shallow water (10-20 m) macroinvertebrates to reveal patterns in trophic structure of, and incorporation of organic matter from SIMCo into, benthic communities at eight sites distributed along the sea ice persistence gradient. Mass-balance analysis revealed distinct trophic architecture among communities and large fluxes of SIMCo into the near-shore food web, with the estimates ranging from 2 to 84% of organic matter derived from SIMCo for individual species. Analysis of patterns in density, and biomass of macroinvertebrate communities among sites allowed us to model net incorporation of organic matter from SIMCo, in terms of biomass per unit area (g/m 2 ), into benthic communities. Here, organic matter derived from SIMCo supported 39 to 71 per cent of total biomass. Furthermore, for six species, we observed declines in contribution of SIMCo between years with persistent sea ice (2008-2009) and years with extensive sea ice breakout (2012-2015). Our data demonstrate the vital role of SIMCo in ecosystem function in Antarctica and strong linkages between sea ice dynamics and near-shore secondary productivity. These results have important implications for our understanding of how benthic communities will respond to changes in sea ice dynamics associated with climate change and highlight the important role of shallow water macroinvertebrate communities as sentinels of change for the Antarctic marine ecosystem. © 2018 John Wiley & Sons Ltd.

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Trait-mediated assembly processes predict successional changes in community diversity of tropical forests.

PubMed

Lasky, Jesse R; Uriarte, María; Boukili, Vanessa K; Chazdon, Robin L

2014-04-15

Interspecific differences in relative fitness can cause local dominance by a single species. However, stabilizing interspecific niche differences can promote local diversity. Understanding these mechanisms requires that we simultaneously quantify their effects on demography and link these effects to community dynamics. Successional forests are ideal systems for testing assembly theory because they exhibit rapid community assembly. Here, we leverage functional trait and long-term demographic data to build spatially explicit models of successional community dynamics of lowland rainforests in Costa Rica. First, we ask what the effects and relative importance of four trait-mediated community assembly processes are on tree survival, a major component of fitness. We model trait correlations with relative fitness differences that are both density-independent and -dependent in addition to trait correlations with stabilizing niche differences. Second, we ask how the relative importance of these trait-mediated processes relates to successional changes in functional diversity. Tree dynamics were more strongly influenced by trait-related interspecific variation in average survival than trait-related responses to neighbors, with wood specific gravity (WSG) positively correlated with greater survival. Our findings also suggest that competition was mediated by stabilizing niche differences associated with specific leaf area (SLA) and leaf dry matter content (LDMC). These drivers of individual-level survival were reflected in successional shifts to higher SLA and LDMC diversity but lower WSG diversity. Our study makes significant advances to identifying the links between individual tree performance, species functional traits, and mechanisms of tropical forest succession.

Seasonal species interactions minimize the impact of species turnover on the likelihood of community persistence.

PubMed

Saavedra, Serguei; Rohr, Rudolf P; Fortuna, Miguel A; Selva, Nuria; Bascompte, Jordi

2016-04-01

Many of the observed species interactions embedded in ecological communities are not permanent, but are characterized by temporal changes that are observed along with abiotic and biotic variations. While work has been done describing and quantifying these changes, little is known about their consequences for species coexistence. Here, we investigate the extent to which changes of species composition impact the likelihood of persistence of the predator-prey community in the highly seasonal Białowieza Primeval Forest (northeast Poland), and the extent to which seasonal changes of species interactions (predator diet) modulate the expected impact. This likelihood is estimated extending recent developments on the study of structural stability in ecological communities. We find that the observed species turnover strongly varies the likelihood of community persistence between summer and winter. Importantly, we demonstrate that the observed seasonal interaction changes minimize the variation in the likelihood of persistence associated with species turnover across the year. We find that these community dynamics can be explained as the coupling of individual species to their environment by minimizing both the variation in persistence conditions and the interaction changes between seasons. Our results provide a homeostatic explanation for seasonal species interactions and suggest that monitoring the association of interactions changes with the level of variation in community dynamics can provide a good indicator of the response of species to environmental pressures.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

DOE PAGES

Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

2014-07-15

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

A Mechanistic Study of Plant and Microbial Controls over R* for Nitrogen in an Annual Grassland

PubMed Central

Levine, Jonathan M.; HilleRisLambers, Janneke

2014-01-01

Differences in species' abilities to capture resources can drive competitive hierarchies, successional dynamics, community diversity, and invasions. To investigate mechanisms of resource competition within a nitrogen (N) limited California grassland community, we established a manipulative experiment using an R* framework. R* theory holds that better competitors within a N limited community should better depress available N in monoculture plots and obtain higher abundance in mixture plots. We asked whether (1) plant uptake or (2) plant species influences on microbial dynamics were the primary drivers of available soil N levels in this system where N structures plant communities. To disentangle the relative roles of plant uptake and microbially-mediated processes in resource competition, we quantified soil N dynamics as well as N pools in plant and microbial biomass in monoculture plots of 11 native or exotic annual grassland plants over one growing season. We found a negative correlation between plant N content and soil dissolved inorganic nitrogen (DIN, our measure of R*), suggesting that plant uptake drives R*. In contrast, we found no relationship between microbial biomass N or potential net N mineralization and DIN. We conclude that while plant-microbial interactions may have altered the overall quantity of N that plants take up, the relationship between species' abundance and available N in monoculture was largely driven by plant N uptake in this first year of growth. PMID:25170943

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland

PubMed Central

Spotswood, Erica N.; Bartolome, James W.; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery. PMID:26222069

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

PubMed

Spotswood, Erica N; Bartolome, James W; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

Evolution of vulnerability of communities facing repeated hazards

PubMed Central

Guikema, Seth D.; Zhu, Laiyin; Igusa, Takeru

2017-01-01

The decisions that individuals make when recovering from and adapting to repeated hazards affect a region’s vulnerability in future hazards. As such, community vulnerability is not a static property but rather a dynamic property dependent on behavioral responses to repeated hazards and damage. This paper is the first of its kind to build a framework that addresses the complex interactions between repeated hazards, regional damage, mitigation decisions, and community vulnerability. The framework enables researchers and regional planners to visualize and quantify how a community could evolve over time in response to repeated hazards under various behavioral scenarios. An illustrative example using parcel-level data from Anne Arundel County, Maryland—a county that experiences fairly frequent hurricanes—is presented to illustrate the methodology and to demonstrate how the interplay between individual choices and regional vulnerability is affected by the region’s hurricane experience. PMID:28953893

Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils

PubMed Central

Pereira e Silva, Michele C.; Schloter-Hai, Brigitte; Schloter, Michael; van Elsas, Jan Dirk; Salles, Joana Falcão

2013-01-01

Background Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. Methodology/Principal Findings In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium , Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. Conclusions Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil. PMID:24058578

Effect of biostimulants on 2,4,6-trinitrotoluene (TNT) degradation and bacterial community composition in contaminated aquifer sediment enrichments.

PubMed

Fahrenfeld, Nicole; Zoeckler, Jeffrey; Widdowson, Mark A; Pruden, Amy

2013-04-01

2,4,6-Trinitrotoluene (TNT) is a toxic and persistent explosive compound occurring as a contaminant at numerous sites worldwide. Knowledge of the microbial dynamics driving TNT biodegradation is limited, particularly in native aquifer sediments where it poses a threat to water resources. The purpose of this study was to quantify the effect of organic amendments on anaerobic TNT biodegradation rate and pathway in an enrichment culture obtained from historically contaminated aquifer sediment and to compare the bacterial community dynamics. TNT readily biodegraded in all microcosms, with the highest biodegradation rate obtained under the lactate amended condition followed by ethanol amended and naturally occurring organic matter (extracted from site sediment) amended conditions. Although a reductive pathway of TNT degradation was observed across all conditions, denaturing gradient gel electrophoresis (DGGE) analysis revealed distinct bacterial community compositions. In all microcosms, Gram-negative γ- or β-Proteobacteria and Gram-positive Negativicutes or Clostridia were observed. A Pseudomonas sp. in particular was observed to be stimulated under all conditions. According to non-metric multidimensional scaling analysis of DGGE profiles, the microcosm communities were most similar to heavily TNT-contaminated field site sediment, relative to moderately and uncontaminated sediments, suggesting that TNT contamination itself is a major driver of microbial community structure. Overall these results provide a new line of evidence of the key bacteria driving TNT degradation in aquifer sediments and their dynamics in response to organic carbon amendment, supporting this approach as a promising technology for stimulating in situ TNT bioremediation in the subsurface.

Fire, flow and dynamic equilibrium in stream macroinvertebrate communities

USGS Publications Warehouse

Arkle, R.S.; Pilliod, D.S.; Strickler, K.

2010-01-01

The complex effects of disturbances on ecological communities can be further complicated by subsequent perturbations within an ecosystem. We investigated how wildfire interacts with annual variations in peak streamflow to affect the stability of stream macroinvertebrate communities in a central Idaho wilderness, USA. We conducted a 4-year retrospective analysis of unburned (n = 7) and burned (n = 6) catchments, using changes in reflectance values (??NBR) from satellite imagery to quantify the percentage of each catchment's riparian and upland vegetation that burned at high and low severity. For this wildland fire complex, increasing riparian burn severity and extent were associated with greater year-to-year variation, rather than a perennial increase, in sediment loads, organic debris, large woody debris (LWD) and undercut bank structure. Temporal changes in these variables were correlated with yearly peak flow in burned catchments but not in unburned reference catchments, indicating that an interaction between fire and flow can result in decreased habitat stability in burned catchments. Streams in more severely burned catchments exhibited increasingly dynamic macroinvertebrate communities and did not show increased similarity to reference streams over time. Annual variability in macroinvertebrates was attributed, predominantly, to the changing influence of sediment, LWD, riparian cover and organic debris, as quantities of these habitat components fluctuated annually depending on burn severity and annual peak streamflows. These analyses suggest that interactions among fire, flow and stream habitat may increase inter-annual habitat variability and macroinvertebrate community dynamics for a duration approaching the length of the historic fire return interval of the study area. ?? 2009 Blackwell Publishing Ltd.

Facilitative-Competitive Interactions in an Old-Growth Forest: The Importance of Large-Diameter Trees as Benefactors and Stimulators for Forest Community Assembly

PubMed Central

Fichtner, Andreas; Forrester, David I.; Härdtle, Werner; Sturm, Knut; von Oheimb, Goddert

2015-01-01

The role of competition in tree communities is increasingly well understood, while little is known about the patterns and mechanisms of the interplay between above- and belowground competition in tree communities. This knowledge, however, is crucial for a better understanding of community dynamics and developing adaptive near-natural management strategies. We assessed neighbourhood interactions in an unmanaged old-growth European beech (Fagus sylvatica) forest by quantifying variation in the intensity of above- (shading) and belowground competition (crowding) among dominant and co-dominant canopy beech trees during tree maturation. Shading had on average a much larger impact on radial growth than crowding and the sensitivity to changes in competitive conditions was lowest for crowding effects. We found that each mode of competition reduced the effect of the other. Increasing crowding reduced the negative effect of shading, and at high levels of shading, crowding actually had a facilitative effect and increased growth. Our study demonstrates that complementarity in above- and belowground processes enable F. sylvatica to alter resource acquisition strategies, thus optimising tree radial growth. As a result, competition seemed to become less important in stands with a high growing stock and tree communities with a long continuity of anthropogenic undisturbed population dynamics. We suggest that growth rates do not exclusively depend on the density of potential competitors at the intraspecific level, but on the conspecific aggregation of large-diameter trees and their functional role for regulating biotic filtering processes. This finding highlights the potential importance of the rarely examined relationship between the spatial aggregation pattern of large-diameter trees and the outcome of neighbourhood interactions, which may be central to community dynamics and the related forest ecosystem services. PMID:25803035

Facilitative-competitive interactions in an old-growth forest: the importance of large-diameter trees as benefactors and stimulators for forest community assembly.

PubMed

Fichtner, Andreas; Forrester, David I; Härdtle, Werner; Sturm, Knut; von Oheimb, Goddert

2015-01-01

The role of competition in tree communities is increasingly well understood, while little is known about the patterns and mechanisms of the interplay between above- and belowground competition in tree communities. This knowledge, however, is crucial for a better understanding of community dynamics and developing adaptive near-natural management strategies. We assessed neighbourhood interactions in an unmanaged old-growth European beech (Fagus sylvatica) forest by quantifying variation in the intensity of above- (shading) and belowground competition (crowding) among dominant and co-dominant canopy beech trees during tree maturation. Shading had on average a much larger impact on radial growth than crowding and the sensitivity to changes in competitive conditions was lowest for crowding effects. We found that each mode of competition reduced the effect of the other. Increasing crowding reduced the negative effect of shading, and at high levels of shading, crowding actually had a facilitative effect and increased growth. Our study demonstrates that complementarity in above- and belowground processes enable F. sylvatica to alter resource acquisition strategies, thus optimising tree radial growth. As a result, competition seemed to become less important in stands with a high growing stock and tree communities with a long continuity of anthropogenic undisturbed population dynamics. We suggest that growth rates do not exclusively depend on the density of potential competitors at the intraspecific level, but on the conspecific aggregation of large-diameter trees and their functional role for regulating biotic filtering processes. This finding highlights the potential importance of the rarely examined relationship between the spatial aggregation pattern of large-diameter trees and the outcome of neighbourhood interactions, which may be central to community dynamics and the related forest ecosystem services.

Remote Sensing for Hydrology: Surface Water Dynamics from Three Decades of Landsat Data

NASA Astrophysics Data System (ADS)

Tulbure, M. G.; Broich, M.; Kingsford, R.; Lucas, R.; Keith, D.

2014-12-01

Surface water is a vital resource affected by changes in climate and anthropogenic factors. Knowledge of surface water dynamics provides critical information for flood and drought management. Here we focused on the on the entire Murray-Darling Basin (MDB) of Australia, a large semi-arid region with scarce water resources, high hydroclimatic variability and competing water demands, impacted by climate change, altered flow regimes and land use changes. The MDB is also an area where substantial investment in environmental water allocation of large volumes of environmental flow was made. We used Landsat TM and ETM+ time series to synoptically map the dynamic of surface water extent with an internally consistent algorithm (Tulbure and Broich, 2013) over decades (1986-2011). We used a subset of Landsat path/rows for image training in both wet and dry years. Results show high interannual variability in number and size of flooded areas, with flooded areas during the Millennium Drought (until 2009) being substantially smaller than during the excessive 2010-2011 La Nina flooding. Flooding frequency in 2006, a very dry year was lower than in 2010, the La Nina year when extensive floods occurred. More developed areas of the basin showed different inter-annual patterns from natural areas of the basin. At Barmah-Millewa, the largest river red gum forest in the world, we also mapped flooded forest and tracked changes in NDVI. Higher NDVI values were found in areas more frequently flooded. Knowledge of the spatial and temporal dynamics of flooding and the response of riparian vegetation communities to flooding is important for management of floodplain wetlands and vegetation communities and for investigating effectiveness of environmental flows and flow regimes in the MDB. Existing maps of inundated areas are linked with river flow to quantify the relationship between river flow and inundated area in the MDB. Historic flood inundation extent mapped via remote sensing can be used to quantify spatially explicit changes in surface water dynamics and vegetation communities as outcomes of management scenarios in response to water management decisions. This methodology is globally applicable and relevant to areas prone to flooding with competing water demands and can be used for mapping water availability in data scarce regions.

Measuring and modeling stemflow by two xerophytic shrubs in the Loess Plateau: The role of dynamic canopy structure

NASA Astrophysics Data System (ADS)

Zhang, Y.; Li, X.; Li, W.; Shi, F.; Wu, H.; WU, X.; Pei, T.

2016-12-01

Stemflow plays an important role in hydrological processes in dryland shrubs, but it still remains poorly understood, especially regarding the effects of dynamic canopy structure on stemflow. This study aimed to measure and model the stemflow of two dominant xerophytic shrub (Hippophae rhamnoides and Spiraea pubescens) communities and to identify the key controlling factors of stemflow yield. We quantified and scaled-up stemflow from branches and leaves to stand levels. Correlations and stepwise regression analysis between stemflow and meteorological and biological factors indicated that at branch level, the rainfall amount and the branch diameter were the best variables for modelling and predicting stemflow for Hippophae rhamnoides, while the rainfall amount and the aboveground biomass were the best variables for modelling and predicting stemflow for Spiraea pubescens. At stand level, the stemflow yield is mostly affected by rainfall amount and leaf area index for both shrubs. The stemflow fluxes account for 3.5±0.9% of incident rainfall for H. rhamnoides community and 9.4±2.1% for S. pubescens community, respectively. The differences in percentages of stemflow between the two shrub communities was attributed to differences in canopy structures and water storage capacities. This evaluation of the effects of canopy structure dynamics on stemflow, and of the developed model, provided a better understanding of the effect of the canopy structure on the water cycles in dryland shrub ecosystems.

The dynamics of meaningful social interactions and the emergence of collective knowledge

PubMed Central

Dankulov, Marija Mitrović; Melnik, Roderick; Tadić, Bosiljka

2015-01-01

Collective knowledge as a social value may arise in cooperation among actors whose individual expertise is limited. The process of knowledge creation requires meaningful, logically coordinated interactions, which represents a challenging problem to physics and social dynamics modeling. By combining two-scale dynamics model with empirical data analysis from a well-known Questions & Answers system Mathematics, we show that this process occurs as a collective phenomenon in an enlarged network (of actors and their artifacts) where the cognitive recognition interactions are properly encoded. The emergent behavior is quantified by the information divergence and innovation advancing of knowledge over time and the signatures of self-organization and knowledge sharing communities. These measures elucidate the impact of each cognitive element and the individual actor’s expertise in the collective dynamics. The results are relevant to stochastic processes involving smart components and to collaborative social endeavors, for instance, crowdsourcing scientific knowledge production with online games. PMID:26174482

The dynamics of meaningful social interactions and the emergence of collective knowledge

NASA Astrophysics Data System (ADS)

Dankulov, Marija Mitrović; Melnik, Roderick; Tadić, Bosiljka

2015-07-01

Collective knowledge as a social value may arise in cooperation among actors whose individual expertise is limited. The process of knowledge creation requires meaningful, logically coordinated interactions, which represents a challenging problem to physics and social dynamics modeling. By combining two-scale dynamics model with empirical data analysis from a well-known Questions & Answers system Mathematics, we show that this process occurs as a collective phenomenon in an enlarged network (of actors and their artifacts) where the cognitive recognition interactions are properly encoded. The emergent behavior is quantified by the information divergence and innovation advancing of knowledge over time and the signatures of self-organization and knowledge sharing communities. These measures elucidate the impact of each cognitive element and the individual actor’s expertise in the collective dynamics. The results are relevant to stochastic processes involving smart components and to collaborative social endeavors, for instance, crowdsourcing scientific knowledge production with online games.

The dynamics of meaningful social interactions and the emergence of collective knowledge.

PubMed

Dankulov, Marija Mitrović; Melnik, Roderick; Tadić, Bosiljka

2015-07-15

Collective knowledge as a social value may arise in cooperation among actors whose individual expertise is limited. The process of knowledge creation requires meaningful, logically coordinated interactions, which represents a challenging problem to physics and social dynamics modeling. By combining two-scale dynamics model with empirical data analysis from a well-known Questions &Answers system Mathematics, we show that this process occurs as a collective phenomenon in an enlarged network (of actors and their artifacts) where the cognitive recognition interactions are properly encoded. The emergent behavior is quantified by the information divergence and innovation advancing of knowledge over time and the signatures of self-organization and knowledge sharing communities. These measures elucidate the impact of each cognitive element and the individual actor's expertise in the collective dynamics. The results are relevant to stochastic processes involving smart components and to collaborative social endeavors, for instance, crowdsourcing scientific knowledge production with online games.

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

Modelling fungal growth in heterogeneous soil: analyses of the effect of soil physical structure on fungal community dynamics

NASA Astrophysics Data System (ADS)

Falconer, R.; Radoslow, P.; Grinev, D.; Otten, W.

2009-04-01

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for community dynamics are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects fungal colony dynamics and also how fungal dynamics affect soil structure. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, fractal dimension, and the connectivity of the pore volume. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on microbial dynamics by qualifying biomass abundances and distributions. We demonstrate how soil structure can critically affect fungal species interactions with consequences for biological control and fungal biodiversity.

Coexistence and survival in conservative Lotka-Volterra networks.

PubMed

Knebel, Johannes; Krüger, Torben; Weber, Markus F; Frey, Erwin

2013-04-19

Analyzing coexistence and survival scenarios of Lotka-Volterra (LV) networks in which the total biomass is conserved is of vital importance for the characterization of long-term dynamics of ecological communities. Here, we introduce a classification scheme for coexistence scenarios in these conservative LV models and quantify the extinction process by employing the Pfaffian of the network's interaction matrix. We illustrate our findings on global stability properties for general systems of four and five species and find a generalized scaling law for the extinction time.

Coexistence and Survival in Conservative Lotka-Volterra Networks

NASA Astrophysics Data System (ADS)

Knebel, Johannes; Krüger, Torben; Weber, Markus F.; Frey, Erwin

2013-04-01

Analyzing coexistence and survival scenarios of Lotka-Volterra (LV) networks in which the total biomass is conserved is of vital importance for the characterization of long-term dynamics of ecological communities. Here, we introduce a classification scheme for coexistence scenarios in these conservative LV models and quantify the extinction process by employing the Pfaffian of the network’s interaction matrix. We illustrate our findings on global stability properties for general systems of four and five species and find a generalized scaling law for the extinction time.

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study.

PubMed

Gertler, Christoph; Näther, Daniela J; Cappello, Simone; Gerdts, Gunnar; Quilliam, Richard S; Yakimov, Michail M; Golyshin, Peter N

2012-09-01

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A. borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

PubMed Central

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

Hydroclimatic Controls over Global Variations in Phenology and Carbon Flux

NASA Technical Reports Server (NTRS)

Koster, Randal; Walker, G.; Thornton, Patti; Collatz, G. J.

2012-01-01

The connection between phenological and hydroclimatological variations are quantified through joint analyses of global NDVI, LAI, and precipitation datasets. The global distributions of both NDVI and LAI in the warm season are strongly controlled by three quantities: mean annual precipitation, the standard deviation of annual precipitation, and Budyko's index of dryness. Upon demonstrating that these same basic (if biased) relationships are produced by a dynamic vegetation model (the dynamic vegetation and carbon storage components of the NCAR Community Land Model version 4 combined with the water and energy balance framework of the Catchment Land Surface Model of the NASA Global Modeling and Assimilation Office), we use the model to perform a sensitivity study focusing on how phenology and carbon flux might respond to climatic change. The offline (decoupled from the atmosphere) simulations show us, for example, where on the globe a given small increment in precipitation mean or variability would have the greatest impact on carbon uptake. The analysis framework allows us in addition to quantify the degree to which climatic biases in a free-running GCM are manifested as biases in simulated phenology.

Hydroclimatic Controls over Global Variations in Phenology and Carbon Flux

NASA Astrophysics Data System (ADS)

Koster, R. D.; Walker, G.; Thornton, P. E.; Collatz, G. J.

2012-12-01

The connection between phenological and hydroclimatological variations are quantified through joint analyses of global NDVI, LAI, and precipitation datasets. The global distributions of both NDVI and LAI in the warm season are strongly controlled by three quantities: mean annual precipitation, the standard deviation of annual precipitation, and Budyko's index of dryness. Upon demonstrating that these same basic (if somewhat biased) relationships are produced by a dynamic vegetation model (the dynamic vegetation and carbon storage components of the NCAR Community Land Model version 4 combined with the water and energy balance framework of the Catchment Land Surface Model of the NASA Global Modeling and Assimilation Office), we use the model to perform a sensitivity study focusing on how phenology and carbon flux might respond to climatic change. The offline (decoupled from the atmosphere) simulations show us, for example, where on the globe a given small increment in precipitation mean or variability would have the greatest impact on carbon uptake. The analysis framework allows us in addition to quantify the degree to which climatic biases in a free-running GCM are manifested as biases in simulated phenology.

Effects of ENSO and Temporal Rainfall Variation on the Dynamics of Successional Communities in Old-Field Succession of a Tropical Dry Forest

PubMed Central

Maza-Villalobos, Susana; Poorter, Lourens; Martínez-Ramos, Miguel

2013-01-01

The effects of temporal variation of rainfall on secondary succession of tropical dry ecosystems are poorly understood. We studied effects of inter-seasonal and inter-year rainfall variation on the dynamics of regenerative successional communities of a tropical dry forest in Mexico. We emphasized the effects caused by the severe El Niño Southern Oscillation (ENSO) occurred in 2005. We established permanent plots in sites representing a chronosequence of Pasture (abandoned pastures, 0–1 years fallow age), Early (3–5), Intermediate (8–12), and Old-Growth Forest categories (n = 3 per category). In total, 8210 shrubs and trees 10 to 100-cm height were identified, measured, and monitored over four years. Rates of plant recruitment, growth and mortality, and gain and loss of species were quantified per season (dry vs. rainy), year, and successional category, considering whole communities and separating seedlings from sprouts and shrubs from trees. Community rates changed with rainfall variation without almost any effect of successional stage. Mortality and species loss rates peaked during the ENSO year and the following year; however, after two rainy years mortality peaked in the rainy season. Such changes could result from the severe drought in the ENSO year, and of the outbreak of biotic agents during the following rainy years. Growth, recruitment and species gain rates were higher in the rainy season but they were significantly reduced after the ENSO year. Seedlings exhibited higher recruitment and mortality rate than sprouts, and shrubs showed higher recruitment than trees. ENSO strongly impacted both the dynamics and trajectory of succession, creating transient fluctuations in the abundance and species richness of the communities. Overall, there was a net decline in plant and species density in most successional stages along the years. Therefore, strong drought events have critical consequences for regeneration dynamics, delaying the successional process and modifying the resilience of these systems. PMID:24349179

CSDMS2.0: Computational Infrastructure for Community Surface Dynamics Modeling

NASA Astrophysics Data System (ADS)

Syvitski, J. P.; Hutton, E.; Peckham, S. D.; Overeem, I.; Kettner, A.

2012-12-01

The Community Surface Dynamic Modeling System (CSDMS) is an NSF-supported, international and community-driven program that seeks to transform the science and practice of earth-surface dynamics modeling. CSDMS integrates a diverse community of more than 850 geoscientists representing 360 international institutions (academic, government, industry) from 60 countries and is supported by a CSDMS Interagency Committee (22 Federal agencies), and a CSDMS Industrial Consortia (18 companies). CSDMS presently distributes more 200 Open Source models and modeling tools, access to high performance computing clusters in support of developing and running models, and a suite of products for education and knowledge transfer. CSDMS software architecture employs frameworks and services that convert stand-alone models into flexible "plug-and-play" components to be assembled into larger applications. CSDMS2.0 will support model applications within a web browser, on a wider variety of computational platforms, and on other high performance computing clusters to ensure robustness and sustainability of the framework. Conversion of stand-alone models into "plug-and-play" components will employ automated wrapping tools. Methods for quantifying model uncertainty are being adapted as part of the modeling framework. Benchmarking data is being incorporated into the CSDMS modeling framework to support model inter-comparison. Finally, a robust mechanism for ingesting and utilizing semantic mediation databases is being developed within the Modeling Framework. Six new community initiatives are being pursued: 1) an earth - ecosystem modeling initiative to capture ecosystem dynamics and ensuing interactions with landscapes, 2) a geodynamics initiative to investigate the interplay among climate, geomorphology, and tectonic processes, 3) an Anthropocene modeling initiative, to incorporate mechanistic models of human influences, 4) a coastal vulnerability modeling initiative, with emphasis on deltas and their multiple threats and stressors, 5) a continental margin modeling initiative, to capture extreme oceanic and atmospheric events generating turbidity currents in the Gulf of Mexico, and 6) a CZO Focus Research Group, to develop compatibility between CSDMS architecture and protocols and Critical Zone Observatory-developed models and data.

Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics

PubMed Central

Friedman, Elliot S.; McPhillips, Lauren E.; Werner, Jeffrey J.; Poole, Angela C.; Ley, Ruth E.; Walter, M. Todd; Angenent, Largus T.

2016-01-01

Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of 6 weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ∼45% (when normalized to remove temporal effects). CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics. PMID:26793170

Perceptions of Empowerment Within and Across Partnerships in Community-Based Participatory Research: A Dyadic Interview Analysis.

PubMed

Paradiso de Sayu, Rebecca; Chanmugam, Amy

2016-01-01

Although the concept of empowerment is a key principle of community-based participatory research (CBPR), little is known about how academic and community partners perceive empowerment during a CBPR process. CBPR partners' perceptions of the process were explored using semi-structured interviews with both partners in 10 CBPR partnerships that had completed projects addressing social determinants of health. Dyadic interview analysis was employed to understand dynamics within and across partnerships. Five partnerships showed no differences in perceptions of empowerment. Four had minor discrepancies. Only one partnership varied considerably between partners, where the community partner perceived less empowerment regarding determining the study topic and overall control, influence, and respect throughout the process. This article discusses implications of findings for CBPR. Evaluating partners' perceived empowerment throughout a CBPR project might reveal areas to adjust, as not all projects with quantifiably successful outcomes involve processes that are successful in terms of empowerment. © The Author(s) 2015.

Dynamic energy budget approach to evaluate antibiotic effects on biofilms

NASA Astrophysics Data System (ADS)

Birnir, Bjorn; Carpio, Ana; Cebrián, Elena; Vidal, Perfecto

2018-01-01

Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix. Coupling a dynamic energy budget based description of cell metabolism to surrounding concentration fields, we are able to approximate survival curves measured for different antibiotics. We reproduce numerically stratified distributions of cell types within the biofilm and introduce ways to incorporate different resistance mechanisms. Qualitative predictions follow that are in agreement with experimental observations, such as higher survival rates of cells close to the substratum when employing antibiotics targeting active cells or enhanced polymer production when antibiotics are administered. The current computational model enables validation and hypothesis testing when developing therapies.

Fronto-Parietal Subnetworks Flexibility Compensates For Cognitive Decline Due To Mental Fatigue.

PubMed

Taya, Fumihiko; Dimitriadis, Stavros I; Dragomir, Andrei; Lim, Julian; Sun, Yu; Wong, Kian Foong; Thakor, Nitish V; Bezerianos, Anastasios

2018-04-24

Fronto-parietal subnetworks were revealed to compensate for cognitive decline due to mental fatigue by community structure analysis. Here, we investigate changes in topology of subnetworks of resting-state fMRI networks due to mental fatigue induced by prolonged performance of a cognitively demanding task, and their associations with cognitive decline. As it is well established that brain networks have modular organization, community structure analyses can provide valuable information about mesoscale network organization and serve as a bridge between standard fMRI approaches and brain connectomics that quantify the topology of whole brain networks. We developed inter- and intramodule network metrics to quantify topological characteristics of subnetworks, based on our hypothesis that mental fatigue would impact on functional relationships of subnetworks. Functional networks were constructed with wavelet correlation and a data-driven thresholding scheme based on orthogonal minimum spanning trees, which allowed detection of communities with weak connections. A change from pre- to posttask runs was found for the intermodule density between the frontal and the temporal subnetworks. Seven inter- or intramodule network metrics, mostly at the frontal or the parietal subnetworks, showed significant predictive power of individual cognitive decline, while the network metrics for the whole network were less effective in the predictions. Our results suggest that the control-type fronto-parietal networks have a flexible topological architecture to compensate for declining cognitive ability due to mental fatigue. This community structure analysis provides valuable insight into connectivity dynamics under different cognitive states including mental fatigue. © 2018 Wiley Periodicals, Inc.

The (ab)normal-social-personality catena: Exploring The Journal of Abnormal and Social Psychology during the interwar years.

PubMed

Davidson, Ian J

2018-05-01

This article is a cocitation network analysis of The Journal of Abnormal and Social Psychology ( JASP ) from 1925 to 1942. The analysis was conducted to help shed light on the historical roots of the intellectual and institutional relationships among social, personality, and abnormal psychology. JASP was a main venue for the boundary work of early- to mid-twentieth-century American psychologists. One of the main goals of these various research communities was to appropriate psychoanalytic and sociological concepts into preferred methods and approaches that favored an individualistic, quantifiable, and ultimately normal subject. Five major research communities are identified using the citations, and historically contextualized: Community #1, Measuring Social Aspects; Community #2, Psychometrics; Community #3, Operationalizing Psychoanalysis; Community #4, Introversion Studies; and Community #5, Experimental Social Psychology. This analysis demonstrates how disciplinary psychologists, at least within JASP , were united by the work of delimiting their research from closely aligned fields studying the same concepts-even while psychologists' methodological commitments to experimentalism or psychological testing might have ostensibly divided them. Possible future research incorporating post-World War II research and dynamic networking approaches is recommended. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Structural stability of nonlinear population dynamics.

PubMed

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Structural stability of nonlinear population dynamics

NASA Astrophysics Data System (ADS)

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Predicting community responses to perturbations in the face of imperfect knowledge and network complexity

USGS Publications Warehouse

Novak, Mark; Wootton, J. Timothy; Doak, Daniel F.; Emmerson, Mark; Estes, James A.; Tinker, M. Timothy

2011-01-01

How best to predict the effects of perturbations to ecological communities has been a long-standing goal for both applied and basic ecology. This quest has recently been revived by new empirical data, new analysis methods, and increased computing speed, with the promise that ecologically important insights may be obtainable from a limited knowledge of community interactions. We use empirically based and simulated networks of varying size and connectance to assess two limitations to predicting perturbation responses in multispecies communities: (1) the inaccuracy by which species interaction strengths are empirically quantified and (2) the indeterminacy of species responses due to indirect effects associated with network size and structure. We find that even modest levels of species richness and connectance (∼25 pairwise interactions) impose high requirements for interaction strength estimates because system indeterminacy rapidly overwhelms predictive insights. Nevertheless, even poorly estimated interaction strengths provide greater average predictive certainty than an approach that uses only the sign of each interaction. Our simulations provide guidance in dealing with the trade-offs involved in maximizing the utility of network approaches for predicting dynamics in multispecies communities.

Seasonal dynamics of extraradical mycelium and mycorrhizas in a black truffle (Tuber melanosporum) plantation.

PubMed

Queralt, Mikel; Parladé, Javier; Pera, Joan; DE Miguel, Ana María

2017-08-01

Seasonal dynamics of black truffle (Tuber melanosporum) extraradical mycelium as well as the associated mycorrhizal community have been evaluated in a 16-year-old plantation with productive and non-productive trees. Mycelium biomass was seasonally quantified by real-time PCR over two consecutive years and the correlation with environmental variables explored. Extraradical mycelium biomass varied seasonally and between the two consecutive years, being correlated with the precipitation that occurred 1 month before sampling. In addition, productive trees had more mycelium in the brûlé area than non-productive trees did. The ectomycorrhizal community composition inside the burnt areas was seasonally evaluated during a year. Ten mycorrhizal morphotypes were detected; T. melanosporum was the most abundant in productive and non-productive trees. Black truffle mycorrhizas were more abundant (mycorrhizal tips per unit of soil volume) in productive trees, and no seasonal variation was observed. The occurrence of black truffle mycorrhizas was significantly and positively correlated with the biomass of extraradical mycelium. The mycorrhizal community within the brûlé areas was significantly different between productive and non-productive trees, and no variation was detected between seasons. The assessment of the fungal vegetative structures in a mature plantation is of paramount importance to develop trufficulture methods based on the knowledge of the biological cycle of the fungus and its relationships with the associated ectomycorrhizal communities.

Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species

USGS Publications Warehouse

Ruiz-Gutierrez, Viviana; Zipkin, Elise F.; Dhondt, Andre A.

2010-01-01

1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6.Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal and inter-patch matrix habitats to identify which species within a community are likely to be impacted most by habitat loss and fragmentation. This model can be applied to other taxa (i.e. amphibians, mammals and insects) to estimate species and community occurrence dynamics in response to current environmental conditions and to make predictions in response to future changes in habitat configurations.

Dynamics of Legionella spp. and bacterial populations during the proliferation of L. pneumophila in a cooling tower facility.

PubMed

Wéry, Nathalie; Bru-Adan, Valérie; Minervini, Céline; Delgénes, Jean-Philippe; Garrelly, Laurent; Godon, Jean-Jacques

2008-05-01

The dynamics of Legionella spp. and of dominant bacteria were investigated in water from a cooling tower plant over a 9-month period which included several weeks when Legionella pneumophila proliferated. The structural diversity of both the bacteria and the Legionella spp. was monitored by a fingerprint technique, single-strand conformation polymorphism, and Legionella spp. and L. pneumophila were quantified by real-time quantitative PCR. The structure of the bacterial community did not change over time, but it was perturbed periodically by chemical treatment or biofilm detachment. In contrast, the structure of the Legionella sp. population changed in different periods, its dynamics at times showing stability but also a rapid major shift during the proliferation of L. pneumophila in July. The dynamics of the Legionella spp. and of dominant bacteria were not correlated. In particular, no change in the bacterial community structure was observed during the proliferation of L. pneumophila. Legionella spp. present in the cooling tower system were identified by cloning and sequencing of 16S rRNA genes. A high diversity of Legionella spp. was observed before proliferation, including L. lytica, L. fallonii, and other Legionella-like amoebal pathogen types, along with as-yet-undescribed species. During the proliferation of L. pneumophila, Legionella sp. diversity decreased significantly, L. fallonii and L. pneumophila being the main species recovered.

Dynamics of Legionella spp. and Bacterial Populations during the Proliferation of L. pneumophila in a Cooling Tower Facility▿

PubMed Central

Wéry, Nathalie; Bru-Adan, Valérie; Minervini, Céline; Delgénes, Jean-Philippe; Garrelly, Laurent; Godon, Jean-Jacques

2008-01-01

The dynamics of Legionella spp. and of dominant bacteria were investigated in water from a cooling tower plant over a 9-month period which included several weeks when Legionella pneumophila proliferated. The structural diversity of both the bacteria and the Legionella spp. was monitored by a fingerprint technique, single-strand conformation polymorphism, and Legionella spp. and L. pneumophila were quantified by real-time quantitative PCR. The structure of the bacterial community did not change over time, but it was perturbed periodically by chemical treatment or biofilm detachment. In contrast, the structure of the Legionella sp. population changed in different periods, its dynamics at times showing stability but also a rapid major shift during the proliferation of L. pneumophila in July. The dynamics of the Legionella spp. and of dominant bacteria were not correlated. In particular, no change in the bacterial community structure was observed during the proliferation of L. pneumophila. Legionella spp. present in the cooling tower system were identified by cloning and sequencing of 16S rRNA genes. A high diversity of Legionella spp. was observed before proliferation, including L. lytica, L. fallonii, and other Legionella-like amoebal pathogen types, along with as-yet-undescribed species. During the proliferation of L. pneumophila, Legionella sp. diversity decreased significantly, L. fallonii and L. pneumophila being the main species recovered. PMID:18390683

Forest fragmentation and bird community dynamics: inference at regional scales

USGS Publications Warehouse

Boulinier, T.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Flather, C.H.; Pollock, K.H.

2001-01-01

With increasing fragmentation of natural areas and a dramatic reduction of forest cover in several parts of the world, quantifying the impact of such changes on species richness and community dynamics has been a subject of much concern. Here, we tested whether in more fragmented landscapes there was a lower number of area-sensitive species and higher local extinction and turnover rates, which could explain higher temporal variability in species richness. To investigate such potential landscape effects at a regional scale, we merged two independent, large-scale monitoring efforts: the North American Breeding Bird Survey (BBS) and the Land Use and Land Cover Classification data from the U.S. Geological Survey. We used methods that accounted for heterogeneity in the probability of detecting species to estimate species richness and temporal changes in the bird communities for BBS routes in three mid-Atlantic U.S. states. Forest breeding bird species were grouped prior to the analyses into area-sensitive and non-area-sensitive species according to previous studies. We tested predictions relating measures of forest structure at one point in time (1974) to species richness at that time and to parameters of forest bird community change over the following 22-yr-period (1975-1996). We used the mean size of forest patches to characterize landscape structure, as high correlations among landscape variables did not allow us to disentangle the relative roles of habitat fragmentation per se and habitat loss. As predicted, together with lower species richness for area-sensitive species on routes surrounded by landscapes with lower mean forest-patch size, we found higher mean year-to-year rates of local extinction. Moreover, the mean year-to-year rates of local turnover (proportion of locally new species) for area-sensitive species were also higher in landscapes with lower mean forest-patch size. These associations were not observed for the non-area-sensitive species group. These results suggest that landscape structure may influence forest bird communities at regional scales through its effects on the total number of species but also on the temporal rates of change in community composition. Evidence for higher rates of local extinction and turnover in more fragmented landscapes suggests that bird communities function as metapopulations at a regional scale, and points out the importance of colonizations and recolonizations from surrounding landscapes to local community dynamics. Further, our results illustrate that the methods used to estimate the community parameters can be a powerful statistical tool in addressing questions relative to the dynamics of communities.

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

PubMed

Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

2015-08-03

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Associative nature of event participation dynamics: A network theory approach

PubMed Central

Smiljanić, Jelena; Mitrović Dankulov, Marija

2017-01-01

The affiliation with various social groups can be a critical factor when it comes to quality of life of each individual, making such groups an essential element of every society. The group dynamics, longevity and effectiveness strongly depend on group’s ability to attract new members and keep them engaged in group activities. It was shown that high heterogeneity of scientist’s engagement in conference activities of the specific scientific community depends on the balance between the numbers of previous attendances and non-attendances and is directly related to scientist’s association with that community. Here we show that the same holds for leisure groups of the Meetup website and further quantify individual members’ association with the group. We examine how structure of personal social networks is evolving with the event attendance. Our results show that member’s increasing engagement in the group activities is primarily associated with the strengthening of already existing ties and increase in the bonding social capital. We also show that Meetup social networks mostly grow trough big events, while small events contribute to the groups cohesiveness. PMID:28166305

Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

PubMed

Leibold, Mathew A; Loeuille, Nicolas

2015-12-01

Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models.

Demographic drivers of functional composition dynamics.

PubMed

Muscarella, Robert; Lohbeck, Madelon; Martínez-Ramos, Miguel; Poorter, Lourens; Rodríguez-Velázquez, Jorge Enrique; van Breugel, Michiel; Bongers, Frans

2017-11-01

Mechanisms of community assembly and ecosystem function are often analyzed using community-weighted mean trait values (CWMs). We present a novel conceptual framework to quantify the contribution of demographic processes (i.e., growth, recruitment, and mortality) to temporal changes in CWMs. We used this framework to analyze mechanisms of secondary succession in wet tropical forests in Mexico. Seed size increased over time, reflecting a trade-off between colonization by small seeds early in succession, to establishment by large seeds later in succession. Specific leaf area (SLA) and leaf phosphorus content decreased over time, reflecting a trade-off between fast growth early in succession vs. high survival late in succession. On average, CWM shifts were driven mainly (70%) by growth of surviving trees that comprise the bulk of standing biomass, then mortality (25%), and weakly by recruitment (5%). Trait shifts of growing and recruiting trees mirrored the CWM trait shifts, and traits of dying trees did not change during succession, indicating that these traits are important for recruitment and growth, but not for mortality, during the first 30 yr of succession. Identifying the demographic drivers of functional composition change links population dynamics to community change, and enhances insights into mechanisms of succession. © 2017 by the Ecological Society of America.

Dynamics of arbuscular mycorrhizal fungal community structure and functioning along a nitrogen enrichment gradient in an alpine meadow ecosystem.

PubMed

Jiang, Shengjing; Liu, Yongjun; Luo, Jiajia; Qin, Mingsen; Johnson, Nancy Collins; Öpik, Maarja; Vasar, Martti; Chai, Yuxing; Zhou, Xiaolong; Mao, Lin; Du, Guozhen; An, Lizhe; Feng, Huyuan

2018-03-30

Nitrogen (N) availability is increasing dramatically in many ecosystems, but the influence of elevated N on the functioning of arbuscular mycorrhizal (AM) fungi in natural ecosystems is not well understood. We measured AM fungal community structure and mycorrhizal function simultaneously across an experimental N addition gradient in an alpine meadow that is limited by N but not by phosphorus (P). AM fungal communities at both whole-plant-community (mixed roots) and single-plant-species (Elymus nutans roots) scales were described using pyro-sequencing, and the mycorrhizal functioning was quantified using a mycorrhizal-suppression treatment in the field (whole-plant-community scale) and a glasshouse inoculation experiment (single-plant-species scale). Nitrogen enrichment progressively reduced AM fungal abundance, changed AM fungal community composition, and shifted mycorrhizal functioning towards parasitism at both whole-plant-community and E. nutans scales. N-induced shifts in AM fungal community composition were tightly linked to soil N availability and/or plant species richness, whereas the shifts in mycorrhizal function were associated with the communities of specific AM fungal lineages. The observed changes in both AM fungal community structure and functioning across an N enrichment gradient highlight that N enrichment of ecosystems that are not P-limited can induce parasitic mycorrhizal functioning and influence plant community structure and ecosystem sustainability. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Annual changes in seasonal river water temperatures in the eastern and western United States

USGS Publications Warehouse

Wagner, Tyler; Midway, Stephen R.; Whittier, Joanna B.; DeWeber, Jefferson T.; Paukert, Craig P.

2017-01-01

Changes in river water temperatures are anticipated to have direct effects on thermal habitat and fish population vital rates, and therefore, understanding temporal trends in water temperatures may be necessary for predicting changes in thermal habitat and how species might respond to such changes. However, many investigations into trends in water temperatures use regression methods that assume long-term monotonic changes in temperature, when in fact changes are likely to be nonmonotonic. Therefore, our objective was to highlight the need and provide an example of an analytical method to better quantify the short-term, nonmonotonic temporal changes in thermal habitat that are likely necessary to determine the effects of changing thermal conditions on fish populations and communities. To achieve this objective, this study uses Bayesian dynamic linear models (DLMs) to examine seasonal trends in river water temperatures from sites located in the eastern and western United States, regions that have dramatically different riverine habitats and fish communities. We estimated the annual rate of change in water temperature and found little evidence of seasonal changes in water temperatures in the eastern U.S. We found more evidence of warming for river sites located in the western U.S., particularly during the fall and winter seasons. Use of DLMs provided a more detailed view of temporal dynamics in river thermal habitat compared to more traditional methods by quantifying year-to-year changes and associated uncertainty, providing managers with the information needed to adapt decision making to short-term changes in habitat conditions that may be necessary for conserving aquatic resources in the face of a changing climate.

Decay of interspecific avian flock networks along a disturbance gradient in Amazonia.

PubMed

Mokross, Karl; Ryder, Thomas B; Côrtes, Marina Corrêa; Wolfe, Jared D; Stouffer, Philip C

2014-02-07

Our understanding of how anthropogenic habitat change shapes species interactions is in its infancy. This is in large part because analytical approaches such as network theory have only recently been applied to characterize complex community dynamics. Network models are a powerful tool for quantifying how ecological interactions are affected by habitat modification because they provide metrics that quantify community structure and function. Here, we examine how large-scale habitat alteration has affected ecological interactions among mixed-species flocking birds in Amazonian rainforest. These flocks provide a model system for investigating how habitat heterogeneity influences non-trophic interactions and the subsequent social structure of forest-dependent mixed-species bird flocks. We analyse 21 flock interaction networks throughout a mosaic of primary forest, fragments of varying sizes and secondary forest (SF) at the Biological Dynamics of Forest Fragments Project in central Amazonian Brazil. Habitat type had a strong effect on network structure at the levels of both species and flock. Frequency of associations among species, as summarized by weighted degree, declined with increasing levels of forest fragmentation and SF. At the flock level, clustering coefficients and overall attendance positively correlated with mean vegetation height, indicating a strong effect of habitat structure on flock cohesion and stability. Prior research has shown that trophic interactions are often resilient to large-scale changes in habitat structure because species are ecologically redundant. By contrast, our results suggest that behavioural interactions and the structure of non-trophic networks are highly sensitive to environmental change. Thus, a more nuanced, system-by-system approach may be needed when thinking about the resiliency of ecological networks.

Analyzing complex networks evolution through Information Theory quantifiers

NASA Astrophysics Data System (ADS)

Carpi, Laura C.; Rosso, Osvaldo A.; Saco, Patricia M.; Ravetti, Martín Gómez

2011-01-01

A methodology to analyze dynamical changes in complex networks based on Information Theory quantifiers is proposed. The square root of the Jensen-Shannon divergence, a measure of dissimilarity between two probability distributions, and the MPR Statistical Complexity are used to quantify states in the network evolution process. Three cases are analyzed, the Watts-Strogatz model, a gene network during the progression of Alzheimer's disease and a climate network for the Tropical Pacific region to study the El Niño/Southern Oscillation (ENSO) dynamic. We find that the proposed quantifiers are able not only to capture changes in the dynamics of the processes but also to quantify and compare states in their evolution.

Quantification of brain macrostates using dynamical nonstationarity of physiological time series.

PubMed

Latchoumane, Charles-Francois Vincent; Jeong, Jaeseung

2011-04-01

The brain shows complex, nonstationarity temporal dynamics, with abrupt micro- and macrostate transitions during its information processing. Detecting and characterizing these transitions in dynamical states of the brain is a critical issue in the field of neuroscience and psychiatry. In the current study, a novel method is proposed to quantify brain macrostates (e.g., sleep stages or cognitive states) from shifts of dynamical microstates or dynamical nonstationarity. A ``dynamical microstate'' is a temporal unit of the information processing in the brain with fixed dynamical parameters and specific spatial distribution. In this proposed approach, a phase-space-based dynamical dissimilarity map (DDM) is used to detect transitions between dynamically stationary microstates in the time series, and Tsallis time-dependent entropy is applied to quantify dynamical patterns of transitions in the DDM. We demonstrate that the DDM successfully detects transitions between microstates of different temporal dynamics in the simulated physiological time series against high levels of noise. Based on the assumption of nonlinear, deterministic brain dynamics, we also demonstrate that dynamical nonstationarity analysis is useful to quantify brain macrostates (sleep stages I, II, III, IV, and rapid eye movement (REM) sleep) from sleep EEGs with an overall accuracy of 77%. We suggest that dynamical nonstationarity is a useful tool to quantify macroscopic mental states (statistical integration) of the brain using dynamical transitions at the microscopic scale in physiological data.

Ecosystem composition changes over the past millennium: model simulations and comparison with paleoecological observations

NASA Astrophysics Data System (ADS)

Liu, Y.; Rollinson, C.; Dietze, M.; McLachlan, J. S.; Poulter, B.; Quaife, T. L.; Raiho, A.; Ricciuto, D. M.; Schaefer, K. M.; Steinkamp, J.; Moore, D. J.

2015-12-01

Over multi-decadal to multi-centennial timescales, ecosystem function and carbon storage is largely influenced by vegetation composition. The predictability of ecosystem responses to climate change thus depends on the understanding of long-term community dynamics. Our study aims to quantify the influence of the most relevant ecological factors that control plant distribution and abundance, in contemporary terrestrial biosphere models and in paleo-records, and constrain the model processes and parameters with paleoecological data. We simulated vegetation changes at 6 sites in the northeastern United States over the past 1160 years using 7 terrestrial biosphere models and variations (CLM4.5-CN, ED2, ED2-LU, JULES-TRIFFID, LINKAGES, LPJ-GUESS, LPJ-wsl) driven by common paleoclimatic drivers. We examined plant growth, recruitment, and mortality (including other carbon turnover) of the plant functional types (PFTs) in the models, attributed the responses to three major factors (climate, competition, and disturbance), and estimated the relative effect of each factor. We assessed the model responses against plant-community theories (bioclimatic limits, niche difference, temporal variation and storage effect, and disturbance). We found that vegetation composition were sensitive to realized niche differences (e.g. differential growth response) among PFTs. Because many models assume unlimited dispersal and sometimes recruitment, the "storage effect" constantly affects community composition. Fire was important in determining the ecosystem composition, yet the vegetation to fire feedback was weak in the models. We also found that vegetation-composition changes in the simulations were driven to a much greater degree by growth as opposed to by turnover/mortality, when compared with those in paleoecological records. Our work suggest that 1) for forecasting slow changes in vegetation composition, we can use paleo-data to better quantify the realized niches of PFTs and associated uncertainties, and 2) for predicting abrupt changes in vegetation composition, we need to better implement processes of dynamic turnover and fire in current ecosystem models.

Evaluation of the effect of an additional fertilizer on the dynamics of microbial community and the decomposition of organic matter in soil

NASA Astrophysics Data System (ADS)

Fabiola, B.; Olivier, M.; Houdusse, F.; Fuentes, M.; Garcia, M. J. M.; Lévêque, J.; Yvin, J. C.; Maron, P. A.; Lemenager, D.

2012-04-01

Organic matter (OM) influences many of the soil functions and occupies a central position in the global carbon cycle. At the scale of the agro-ecosystem, primary productivity is dependent on the recycling of soil organic matter (SOM) by the action of decomposers (mainly bacteria and fungi), which mineralize organic compounds, releasing the nutrients needed for plant growth. At a global scale, the recycling of the SOM determines the carbon flux between soil and atmosphere, with major consequences in terms of environmental quality. In this context, the management of SOM stocks in agro-ecosystems is a major issue from which depend the maintenance of the productivity and sustainability of agricultural practices. The use of additional fertilizer appears to be a promising way to achieve such management. These products have been proven effectives in many field trials. However, their mode of action, particularly in terms of impact on soil microbial component, is still nearly unknown. In this context, this study aims to test the influence of an additional fertilizer on (i) soil microbial communities (total biomass, density of bacteria and fungi), and (ii) soil functioning in terms of dynamics of organic matter. It is based on experiments in soil microcosms which follow in parallel the kinetics of mineralization of different organic carbon compartments (endogenous compartment: soil organic matter; exogenous compartment: wheat residue provided) and the dynamics of microbial communities after the addition of wheat residues in soil. Two different soils were used to evaluate the influence of soil physicochemical characteristics on the effect induced by the addition in terms of fertilization. The first results show a significant effect of the input of additional fertilizer on the dynamics of soil organic matter. They also show that soil pH as well as the dose at which the additional fertilizer is applied are important for modulating the observed effect. Characterization of microbial communities by molecular tools (quantification of molecular biomass, quantitative PCR of 16S and 18S ribosomal genes to quantify bacteria and fungi, respectively) will allow linking the changes of the mineralization of carbon compartments with the response of the soil microbial communities.

Signatures of ecological processes in microbial community time series.

PubMed

Faust, Karoline; Bauchinger, Franziska; Laroche, Béatrice; de Buyl, Sophie; Lahti, Leo; Washburne, Alex D; Gonze, Didier; Widder, Stefanie

2018-06-28

Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection. We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model. We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.

Relative stability of core groups in pollination networks in a biodiversity hotspot over four years.

PubMed

Fang, Qiang; Huang, Shuang-Quan

2012-01-01

Plants and their pollinators form pollination networks integral to the evolution and persistence of species in communities. Previous studies suggest that pollination network structure remains nested while network composition is highly dynamic. However, little is known about temporal variation in the structure and function of plant-pollinator networks, especially in species-rich communities where the strength of pollinator competition is predicted to be high. Here we quantify temporal variation of pollination networks over four consecutive years in an alpine meadow in the Hengduan Mountains biodiversity hotspot in China. We found that ranked positions and idiosyncratic temperatures of both plants and pollinators were more conservative between consecutive years than in non-consecutive years. Although network compositions exhibited high turnover, generalized core groups--decomposed by a k-core algorithm--were much more stable than peripheral groups. Given the high rate of turnover observed, we suggest that identical plants and pollinators that persist for at least two successive years sustain pollination services at the community level. Our data do not support theoretical predictions of a high proportion of specialized links within species-rich communities. Plants were relatively specialized, exhibiting less variability in pollinator composition at pollinator functional group level than at the species level. Both specialized and generalized plants experienced narrow variation in functional pollinator groups. The dynamic nature of pollination networks in the alpine meadow demonstrates the potential for networks to mitigate the effects of fluctuations in species composition in a high biodiversity area.

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhou; Wang, Yingfeng; Yao, Qiuming

2014-01-01

Detailed characterization of posttranslational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further,more » Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.« less

Biophysical feedbacks mediate carbonate chemistry in coastal ecosystems across spatiotemporal gradients.

PubMed

Silbiger, Nyssa J; Sorte, Cascade J B

2018-01-15

Ocean acidification (OA) projections are primarily based on open ocean environments, despite the ecological importance of coastal systems in which carbonate dynamics are fundamentally different. Using temperate tide pools as a natural laboratory, we quantified the relative contribution of community composition, ecosystem metabolism, and physical attributes to spatiotemporal variability in carbonate chemistry. We found that biological processes were the primary drivers of local pH conditions. Specifically, non-encrusting producer-dominated systems had the highest and most variable pH environments and the highest production rates, patterns that were consistent across sites spanning 11° of latitude and encompassing multiple gradients of natural variability. Furthermore, we demonstrated a biophysical feedback loop in which net community production increased pH, leading to higher net ecosystem calcification. Extreme spatiotemporal variability in pH is, thus, both impacting and driven by biological processes, indicating that shifts in community composition and ecosystem metabolism are poised to locally buffer or intensify the effects of OA.

Immigrant community integration in world cities

PubMed Central

Lamanna, Fabio; Lenormand, Maxime; Salas-Olmedo, María Henar; Romanillos, Gustavo; Gonçalves, Bruno

2018-01-01

As a consequence of the accelerated globalization process, today major cities all over the world are characterized by an increasing multiculturalism. The integration of immigrant communities may be affected by social polarization and spatial segregation. How are these dynamics evolving over time? To what extent the different policies launched to tackle these problems are working? These are critical questions traditionally addressed by studies based on surveys and census data. Such sources are safe to avoid spurious biases, but the data collection becomes an intensive and rather expensive work. Here, we conduct a comprehensive study on immigrant integration in 53 world cities by introducing an innovative approach: an analysis of the spatio-temporal communication patterns of immigrant and local communities based on language detection in Twitter and on novel metrics of spatial integration. We quantify the Power of Integration of cities –their capacity to spatially integrate diverse cultures– and characterize the relations between different cultures when acting as hosts or immigrants. PMID:29538383

Functional trait differences influence neighbourhood interactions in a hyperdiverse Amazonian forest.

PubMed

Fortunel, Claire; Valencia, Renato; Wright, S Joseph; Garwood, Nancy C; Kraft, Nathan J B

2016-09-01

As distinct community assembly processes can produce similar community patterns, assessing the ecological mechanisms promoting coexistence in hyperdiverse rainforests remains a considerable challenge. We use spatially explicit neighbourhood models of tree growth to quantify how functional trait and phylogenetic similarities predict variation in growth and crowding effects for the 315 most abundant tree species in a 25-ha lowland rainforest plot in Ecuador. We find that functional trait differences reflect variation in (1) species maximum potential growth, (2) the intensity of interspecific interactions for some species, and (3) species sensitivity to neighbours. We find that neighbours influenced tree growth in 28% of the 315 focal tree species. Neighbourhood effects are not detected in the remaining 72%, which may reflect the low statistical power to model rare taxa and/or species insensitivity to neighbours. Our results highlight the spectrum of ways in which functional trait differences can shape community dynamics in highly diverse rainforests. © 2016 John Wiley & Sons Ltd/CNRS.

Factors Influencing Obstacle Crossing Performance in Patients with Parkinson's Disease

PubMed Central

Liao, Ying-Yi; Yang, Yea-Ru; Wu, Yih-Ru; Wang, Ray-Yau

2014-01-01

Background Tripping over obstacles is the major cause of falls in community-dwelling patients with Parkinson's disease (PD). Understanding the factors associated with the obstacle crossing behavior may help to develop possible training programs for crossing performance. This study aimed to identify the relationships and important factors determining obstacle crossing performance in patients with PD. Methods Forty-two idiopathic patients with PD (Hoehn and Yahr stages I to III) participated in this study. Obstacle crossing performance was recorded by the Liberty system, a three-dimensional motion capture device. Maximal isometric strength of the lower extremity was measured by a handheld dynamometer. Dynamic balance and sensory integration ability were assessed using the Balance Master system. Movement velocity (MV), maximal excursion (ME), and directional control (DC) were obtained during the limits of stability test to quantify dynamic balance. The sum of sensory organization test (SOT) scores was used to quantify sensory organization ability. Results Both crossing stride length and stride velocity correlated significantly with lower extremity muscle strength, dynamic balance control (forward and sideward), and sum of SOT scores. From the regression model, forward DC and ankle dorsiflexor strength were identified as two major determinants for crossing performance (R2 = .37 to.41 for the crossing stride length, R2 = .43 to.44 for the crossing stride velocity). Conclusions Lower extremity muscle strength, dynamic balance control and sensory integration ability significantly influence obstacle crossing performance. We suggest an emphasis on muscle strengthening exercises (especially ankle dorsiflexors), balance training (especially forward DC), and sensory integration training to improve obstacle crossing performance in patients with PD. PMID:24454723

Graph Theory Approach for Studying Food Webs

NASA Astrophysics Data System (ADS)

Longjas, A.; Tejedor, A.; Foufoula-Georgiou, E.

2017-12-01

Food webs are complex networks of feeding interactions among species in ecological communities. Metrics describing food web structure have been proposed to compare and classify food webs ranging from food chain length, connectance, degree distribution, centrality measures, to the presence of motifs (distinct compartments), among others. However, formal methodologies for studying both food web topology and the dynamic processes operating on them are still lacking. Here, we utilize a quantitative framework using graph theory within which a food web is represented by a directed graph, i.e., a collection of vertices (species or trophic species defined as sets of species sharing the same predators and prey) and directed edges (predation links). This framework allows us to identify apex (environmental "source" node) to outlet (top predators) subnetworks and compute the steady-state flux (e.g., carbon, nutrients, energy etc.) in the food web. We use this framework to (1) construct vulnerability maps that quantify the relative change of flux delivery to the top predators in response to perturbations in prey species (2) identify keystone species, whose loss would precipitate further species extinction, and (3) introduce a suite of graph-theoretic metrics to quantify the topologic (imposed by food web connectivity) and dynamic (dictated by the flux partitioning and distribution) components of a food web's complexity. By projecting food webs into a 2D Topodynamic Complexity Space whose coordinates are given by Number of alternative paths (topologic) and Leakage Index (dynamic), we show that this space provides a basis for food web comparison and provide physical insights into their dynamic behavior.

Mapping the Evolution of Scientific Fields

PubMed Central

Herrera, Mark; Roberts, David C.; Gulbahce, Natali

2010-01-01

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985–2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development. PMID:20463949

Mapping the evolution of scientific fields.

PubMed

Herrera, Mark; Roberts, David C; Gulbahce, Natali

2010-05-04

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985-2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development.

Predicting community responses to perturbations in the face of imperfect knowledge and network complexity

USGS Publications Warehouse

Novak, M.; Wootton, J.T.; Doak, D.F.; Emmerson, M.; Estes, J.A.; Tinker, M.T.

2011-01-01

How best to predict the effects of perturbations to ecological communities has been a long-standing goal for both applied and basic ecology. This quest has recently been revived by new empirical data, new analysis methods, and increased computing speed, with the promise that ecologically important insights may be obtainable from a limited knowledge of community interactions. We use empirically based and simulated networks of varying size and connectance to assess two limitations to predicting perturbation responses in multispecies communities: (1) the inaccuracy by which species interaction strengths are empirically quantified and (2) the indeterminacy of species responses due to indirect effects associated with network size and structure. We find that even modest levels of species richness and connectance (??25 pairwise interactions) impose high requirements for interaction strength estimates because system indeterminacy rapidly overwhelms predictive insights. Nevertheless, even poorly estimated interaction strengths provide greater average predictive certainty than an approach that uses only the sign of each interaction. Our simulations provide guidance in dealing with the trade-offs involved in maximizing the utility of network approaches for predicting dynamics in multispecies communities. ?? 2011 by the Ecological Society of America.

Quantifying the Dynamics of Bacterial Secondary Metabolites by Spectral Multi-Photon Microscopy

PubMed Central

Sullivan, Nora L.; Tzeranis, Dimitrios S.; Wang, Yun; So, Peter T.C.; Newman, Dianne

2011-01-01

Phenazines, a group of fluorescent small molecules produced by the bacterium Pseudomonas aeruginosa, play a role in maintaining cellular redox homeostasis. Phenazines have been challenging to study in vivo due to their redox activity, presence both intra- and extracellularly, and their diverse chemical properties. Here, we describe a non-invasive in vivo optical technique to monitor phenazine concentrations within bacterial cells using time-lapsed spectral multi-photon fluorescence microscopy. This technique enables simultaneous monitoring of multiple weakly-fluorescent molecules (phenazines, siderophores, NAD(P)H) expressed by bacteria in culture. This work provides the first in vivo measurements of reduced phenazine concentration as well as the first description of the temporal dynamics of the phenazine-NAD(P)H redox system in Pseudomonas aeruginosa, illuminating an unanticipated role for 1-hydroxyphenazine. Similar approaches could be used to study the abundance and redox dynamics of a wide range of small molecules within bacteria, both as single cells and in communities. PMID:21671613

Oman Drilling Project GT3 site survey: dynamics at the roof of an oceanic magma chamber

NASA Astrophysics Data System (ADS)

France, L.; Nicollet, C.; Debret, B.; Lombard, M.; Berthod, C.; Ildefonse, B.; Koepke, J.

2017-12-01

Oman Drilling Project (OmanDP) aims at bringing new constraints on oceanic crust accretion and evolution by drilling Holes in the whole ophiolite section (mantle and crust). Among those, operations at GT3 in the Sumail massif drilled 400 m to sample the dike - gabbro transition that corresponds to the top (gabbros) and roof (dikes) of the axial magma chamber, an interface where hydrothermal and magmatic system interacts. Previous studies based on oceanic crust formed at present day fast-spreading ridges and preserved in ophiolites have highlighted that this interface is a dynamic horizon where the axial melt lens that top the main magma chamber can intrude, reheat, and partially assimilate previously hydrothermally altered roof rocks. Here we present the preliminary results obtained in GT3 area that have allowed the community to choose the drilling site. We provide a geological and structural map of the area, together with new petrographic and chemical constraints on the dynamics of the dike - gabbro transition. Our new results allow us to quantify the dynamic processes, and to propose that 1/ the intrusive contact of the varitextured gabbro within the dikes highlights the intrusion of the melt lens top in the dike rooting zone, 2/ both dikes and previously crystallized gabbros are reheated, and recrystallized by underlying melt lens dynamics (up to 1050°C, largely above the hydrous solidus temperature of altered dikes and gabbros), 3/ the reheating range can be > 200°C, 4/ the melt lens depth variations for a given ridge position is > 200m, 5/ the reheating stage and associated recrystallization within the dikes occurred under hydrous conditions, 6/ the reheating stage is recorded at the root zone of the sheeted dike complex by one of the highest stable conductive thermal gradient ever recorded on Earth ( 3°C/m), 7/ local chemical variations in recrystallized dikes and gabbros are highlighted and used to quantify crystallization and anatectic processes, and the presence of trapped melt, 8/ melt lens cannibalism is attested by numerous assimilation figures close its roof. Besides providing a general context for future studies at OmanDP GT3 site, those new results allow us to quantify the dynamic processes that govern the layer 2 - layer 3 transition in ocean lithosphere.

Eco-evolutionary dynamics in urbanized landscapes: evolution, species sorting and the change in zooplankton body size along urbanization gradients.

PubMed

Brans, Kristien I; Govaert, Lynn; Engelen, Jessie M T; Gianuca, Andros T; Souffreau, Caroline; De Meester, Luc

2017-01-19

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50-3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Eco-evolutionary dynamics in urbanized landscapes: evolution, species sorting and the change in zooplankton body size along urbanization gradients

PubMed Central

Souffreau, Caroline

2017-01-01

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50–3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920375

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

PubMed

King, Andrew J; Preheim, Sarah P; Bailey, Kathryn L; Robeson, Michael S; Roy Chowdhury, Taniya; Crable, Bryan R; Hurt, Richard A; Mehlhorn, Tonia; Lowe, Kenneth A; Phelps, Tommy J; Palumbo, Anthony V; Brandt, Craig C; Brown, Steven D; Podar, Mircea; Zhang, Ping; Lancaster, W Andrew; Poole, Farris; Watson, David B; W Fields, Matthew; Chandonia, John-Marc; Alm, Eric J; Zhou, Jizhong; Adams, Michael W W; Hazen, Terry C; Arkin, Adam P; Elias, Dwayne A

2017-03-07

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

Can trait patterns along gradients predict plant community responses to climate change?

PubMed

Guittar, John; Goldberg, Deborah; Klanderud, Kari; Telford, Richard J; Vandvik, Vigdis

2016-10-01

Plant functional traits vary consistently along climate gradients and are therefore potential predictors of plant community response to climate change. We test this space-for-time assumption by combining a spatial gradient study with whole-community turf transplantation along temperature and precipitation gradients in a network of 12 grassland sites in Southern Norway. Using data on eight traits for 169 species and annual vegetation censuses of 235 turfs over 5 yr, we quantify trait-based responses to climate change by comparing observed community dynamics in transplanted turfs to field-parameterized null model simulations. Three traits related to species architecture (maximum height, number of dormant meristems, and ramet-ramet connection persistence) varied consistently along spatial temperature gradients and also correlated to changes in species abundances in turfs transplanted to warmer climates. Two traits associated with resource acquisition strategy (SLA, leaf area) increased along spatial temperature gradients but did not correlate to changes in species abundances following warming. No traits correlated consistently with precipitation. Our study supports the hypothesis that spatial associations between plant traits and broad-scale climate variables can be predictive of community response to climate change, but it also suggests that not all traits with clear patterns along climate gradients will necessarily influence community response to an equal degree. © 2016 by the Ecological Society of America.

The Role of Diverse Strategies in Sustainable Knowledge Production

PubMed Central

Wu, Lingfei; Baggio, Jacopo A.; Janssen, Marco A.

2016-01-01

Online communities are becoming increasingly important as platforms for large-scale human cooperation. These communities allow users seeking and sharing professional skills to solve problems collaboratively. To investigate how users cooperate to complete a large number of knowledge-producing tasks, we analyze Stack Exchange, one of the largest question and answer systems in the world. We construct attention networks to model the growth of 110 communities in the Stack Exchange system and quantify individual answering strategies using the linking dynamics on attention networks. We identify two answering strategies. Strategy A aims at performing maintenance by doing simple tasks, whereas strategy B aims at investing time in doing challenging tasks. Both strategies are important: empirical evidence shows that strategy A decreases the median waiting time for answers and strategy B increases the acceptance rate of answers. In investigating the strategic persistence of users, we find that users tends to stick on the same strategy over time in a community, but switch from one strategy to the other across communities. This finding reveals the different sets of knowledge and skills between users. A balance between the population of users taking A and B strategies that approximates 2:1, is found to be optimal to the sustainable growth of communities. PMID:26934733

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

DOE PAGES

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.; ...

2017-01-23

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

The Role of Diverse Strategies in Sustainable Knowledge Production.

PubMed

Wu, Lingfei; Baggio, Jacopo A; Janssen, Marco A

2016-01-01

Online communities are becoming increasingly important as platforms for large-scale human cooperation. These communities allow users seeking and sharing professional skills to solve problems collaboratively. To investigate how users cooperate to complete a large number of knowledge-producing tasks, we analyze Stack Exchange, one of the largest question and answer systems in the world. We construct attention networks to model the growth of 110 communities in the Stack Exchange system and quantify individual answering strategies using the linking dynamics on attention networks. We identify two answering strategies. Strategy A aims at performing maintenance by doing simple tasks, whereas strategy B aims at investing time in doing challenging tasks. Both strategies are important: empirical evidence shows that strategy A decreases the median waiting time for answers and strategy B increases the acceptance rate of answers. In investigating the strategic persistence of users, we find that users tends to stick on the same strategy over time in a community, but switch from one strategy to the other across communities. This finding reveals the different sets of knowledge and skills between users. A balance between the population of users taking A and B strategies that approximates 2:1, is found to be optimal to the sustainable growth of communities.

Cryptic herbivores mediate the strength and form of ungulate impacts on a long-lived savanna tree.

PubMed

Maclean, Janet E; Goheen, Jacob R; Doak, Daniel F; Palmer, Todd M; Young, Truman P

2011-08-01

Plant populations are regulated by a diverse array of herbivores that impose demographic filters throughout their life cycle. Few studies, however, simultaneously quantify the impacts of multiple herbivore guilds on the lifetime performance or population growth rate of plants. In African savannas, large ungulates (such as elephants) are widely regarded as important drivers of woody plant population dynamics, while the potential impacts of smaller, more cryptic herbivores (such as rodents) have largely been ignored. We combined a large-scale ungulate exclusion experiment with a five-year manipulation of rodent densities to quantify the impacts of three herbivore guilds (wild ungulates, domestic cattle, and rodents) on all life stages of a widespread savanna tree. We utilized demographic modeling to reveal the overall role of each guild in regulating tree population dynamics, and to elucidate the importance of different demographic hurdles in driving population growth under contrasting consumer communities. We found that wild ungulates dramatically reduced population growth, shifting the population trajectory from increase to decline, but that the mechanisms driving these effects were strongly mediated by rodents. The impact of wild ungulates on population growth was predominantly driven by their negative effect on tree reproduction when rodents were excluded, and on adult tree survival when rodents were present. By limiting seedling survival, rodents also reduced population growth; however, this effect was strongly dampened where wild ungulates were present. We suggest that these complex interactions between disparate consumer guilds can have important consequences for the population demography of long-lived species, and that the effects of a single consumer group are often likely to vary dramatically depending on the larger community in which interactions are embedded.

Effective time closures: quantifying the conservation benefits of input control for the Pacific chub mackerel fishery.

PubMed

Ichinokawa, Momoko; Okamura, Hiroshi; Watanabe, Chikako; Kawabata, Atsushi; Oozeki, Yoshioki

2015-09-01

Restricting human access to a specific wildlife species, community, or ecosystem, i.e., input control, is one of the most popular tools to control human impacts for natural resource management and wildlife conservation. However, quantitative evaluations of input control are generally difficult, because it is unclear how much human impacts can actually be reduced by the control. We present a model framework to quantify the effectiveness of input control using day closures to reduce actual fishing impact by considering the observed fishery dynamics. The model framework was applied to the management of the Pacific stock of the chub mackerel (Scomber japonicus) fishery, in which fishing was suspended for one day following any day when the total mackerel catch exceeded a threshold level. We evaluated the management measure according to the following steps: (1) we fitted the daily observed catch and fishing effort data to a generalized linear model (GLM) or generalized autoregressive state-space model (GASSM), (2) we conducted population dynamics simulations based on annual catches randomly generated from the parameters estimated in the first step, (3) we quantified the effectiveness of day closures by comparing the results of two simulation scenarios with and without day closures, and (4) we conducted additional simulations based on different sets of explanatory variables and statistical models (sensitivity analysis). In the first step, we found that the GASSM explained the observed data far better than the simple GLM. The model parameterized with the estimates from the GASSM demonstrated that the day closures implemented from 2004 to 2009 would have decreased exploitation fractions by ~10% every year and increased the 2009 stock biomass by 37-46% (median), relative to the values without day closures. The sensitivity analysis revealed that the effectiveness of day closures was particularly influenced by autoregressive processes in the fishery data and by positive relationships between fishing effort and total biomass. Those results indicated the importance of human behavioral dynamics under input control in quantifying the conservation benefit of natural resource management and the applicability of our model framework to the evaluation of the input controls that are actually implemented.

Simulating the impacts of disturbances on forest carbon cycling in North America: Processes, data, models, and challenges

USGS Publications Warehouse

Liu, Shuguang; Bond-Lamberty, Ben; Hicke, Jeffrey A.; Vargas, Rodrigo; Zhao, Shuqing; Chen, Jing; Edburg, Steven L.; Hu, Yueming; Liu, Jinxun; McGuire, A. David; Xiao, Jingfeng; Keane, Robert; Yuan, Wenping; Tang, Jianwu; Luo, Yiqi; Potter, Christopher; Oeding, Jennifer

2011-01-01

Forest disturbances greatly alter the carbon cycle at various spatial and temporal scales. It is critical to understand disturbance regimes and their impacts to better quantify regional and global carbon dynamics. This review of the status and major challenges in representing the impacts of disturbances in modeling the carbon dynamics across North America revealed some major advances and challenges. First, significant advances have been made in representation, scaling, and characterization of disturbances that should be included in regional modeling efforts. Second, there is a need to develop effective and comprehensive process‐based procedures and algorithms to quantify the immediate and long‐term impacts of disturbances on ecosystem succession, soils, microclimate, and cycles of carbon, water, and nutrients. Third, our capability to simulate the occurrences and severity of disturbances is very limited. Fourth, scaling issues have rarely been addressed in continental scale model applications. It is not fully understood which finer scale processes and properties need to be scaled to coarser spatial and temporal scales. Fifth, there are inadequate databases on disturbances at the continental scale to support the quantification of their effects on the carbon balance in North America. Finally, procedures are needed to quantify the uncertainty of model inputs, model parameters, and model structures, and thus to estimate their impacts on overall model uncertainty. Working together, the scientific community interested in disturbance and its impacts can identify the most uncertain issues surrounding the role of disturbance in the North American carbon budget and develop working hypotheses to reduce the uncertainty

Coral reef metabolism and carbon chemistry dynamics of a coral reef flat

NASA Astrophysics Data System (ADS)

Albright, Rebecca; Benthuysen, Jessica; Cantin, Neal; Caldeira, Ken; Anthony, Ken

2015-05-01

Global carbon emissions continue to acidify the oceans, motivating growing concern for the ability of coral reefs to maintain net positive calcification rates. Efforts to develop robust relationships between coral reef calcification and carbonate parameters such as aragonite saturation state (Ωarag) aim to facilitate meaningful predictions of how reef calcification will change in the face of ocean acidification. Here we investigate natural trends in carbonate chemistry of a coral reef flat over diel cycles and relate these trends to benthic carbon fluxes by quantifying net community calcification and net community production. We find that, despite an apparent dependence of calcification on Ωarag seen in a simple pairwise relationship, if the dependence of net calcification on net photosynthesis is accounted for, knowing Ωarag does not add substantial explanatory value. This suggests that, over short time scales, the control of Ωarag on net calcification is weak relative to factors governing net photosynthesis.

Pneumonic Plague in Johannesburg, South Africa, 1904

PubMed Central

Egan, Joseph R.; Hall, Ian

2018-01-01

Plague is a potentially dangerous reemerging disease. Because modern outbreaks are relatively infrequent, data for epidemiologic study are best found in historical accounts. In 1905, the Rand Plague Committee published a report describing an explosive outbreak of 113 cases of pneumonic plague that occurred in Johannesburg, South Africa, in 1904. Using these data, we investigated social, spatial, and temporal dynamics and quantified transmissibility as measured by the time-varying reproduction number. Risk for transmission was highest when friends, family members, and caregivers approached the sick. Reproduction numbers were 2–4. Transmission rates rapidly diminished after implementation of control measures, including isolation and safer burial practices. A contemporaneous smaller bubonic plague outbreak associated with a low-key epizootic of rats also occurred. Clusters of cases of pneumonic plague were mostly limited to the Indian community; cases of bubonic plague were mostly associated with white communities and their black African servants.

Ozone depleting substances: a key forcing of the Brewer-Dobson circulation

NASA Astrophysics Data System (ADS)

Abalos, M.; Polvani, L. M.; Garcia, R. R.; Kinnison, D. E.; Randel, W. J.

2017-12-01

In contrast with monotonically-increasing greenhouse gases (GHG), Ozone Depleting Substances (ODS) peak approximately on the year 2000 and decrease thereafter, thanks to the Montreal Protocol. We examine the influence of these anthropogenic emissions on the Brewer-Dobson circulation (BDC) using specifically designed runs of the Community Earth System Model - Whole Atmosphere Community Climate Model (CESM-WACCM). Consistent with previous works, we find a dominant role of ODSs on the observed BDC acceleration up to 2000 in the SH summer, through dynamical changes induced by the ozone hole. We extend the analyses to quantify the influence of ODSs on the BDC for different regions and seasons, and compare the model results to observational estimates. Finally, we show that ODSs will substantially reduce the GHG-induced BDC acceleration in the future. Specifically, the trends in stratospheric mean age of air will be 4 times smaller in the period 2000-2080 as compared to the period 1965-2000.

A simple mathematical model of society collapse applied to Easter Island

NASA Astrophysics Data System (ADS)

Bologna, M.; Flores, J. C.

2008-02-01

In this paper we consider a mathematical model for the evolution and collapse of the Easter Island society. Based on historical reports, the available primary resources consisted almost exclusively in the trees, then we describe the inhabitants and the resources as an isolated dynamical system. A mathematical, and numerical, analysis about the Easter Island community collapse is performed. In particular, we analyze the critical values of the fundamental parameters and a demographic curve is presented. The technological parameter, quantifying the exploitation of the resources, is calculated and applied to the case of another extinguished civilization (Copán Maya) confirming the consistency of the adopted model.

Functional enzyme-based modeling approach for dynamic simulation of denitrification process in hyporheic zone sediments: Genetically structured microbial community model

NASA Astrophysics Data System (ADS)

Song, H. S.; Li, M.; Qian, W.; Song, X.; Chen, X.; Scheibe, T. D.; Fredrickson, J.; Zachara, J. M.; Liu, C.

2016-12-01

Modeling environmental microbial communities at individual organism level is currently intractable due to overwhelming structural complexity. Functional guild-based approaches alleviate this problem by lumping microorganisms into fewer groups based on their functional similarities. This reduction may become ineffective, however, when individual species perform multiple functions as environmental conditions vary. In contrast, the functional enzyme-based modeling approach we present here describes microbial community dynamics based on identified functional enzymes (rather than individual species or their groups). Previous studies in the literature along this line used biomass or functional genes as surrogate measures of enzymes due to the lack of analytical methods for quantifying enzymes in environmental samples. Leveraging our recent development of a signature peptide-based technique enabling sensitive quantification of functional enzymes in environmental samples, we developed a genetically structured microbial community model (GSMCM) to incorporate enzyme concentrations and various other omics measurements (if available) as key modeling input. We formulated the GSMCM based on the cybernetic metabolic modeling framework to rationally account for cellular regulation without relying on empirical inhibition kinetics. In the case study of modeling denitrification process in Columbia River hyporheic zone sediments collected from the Hanford Reach, our GSMCM provided a quantitative fit to complex experimental data in denitrification, including the delayed response of enzyme activation to the change in substrate concentration. Our future goal is to extend the modeling scope to the prediction of carbon and nitrogen cycles and contaminant fate. Integration of a simpler version of the GSMCM with PFLOTRAN for multi-scale field simulations is in progress.

Biogeochemistry from Gliders at the Hawaii Ocean Times-Series

NASA Astrophysics Data System (ADS)

Nicholson, D. P.; Barone, B.; Karl, D. M.

2016-02-01

At the Hawaii Ocean Time-series (HOT) autonomous, underwater gliders equipped with biogeochemical sensors observe the oceans for months at a time, sampling spatiotemporal scales missed by the ship-based programs. Over the last decade, glider data augmented by a foundation of time-series observations have shed light on biogeochemical dynamics occuring spatially at meso- and submesoscales and temporally on scales from diel to annual. We present insights gained from the synergy between glider observations, time-series measurements and remote sensing in the subtropical North Pacific. We focus on diel variability observed in dissolved oxygen and bio-optics and approaches to autonomously quantify net community production and gross primary production (GPP) as developed during the 2012 Hawaii Ocean Experiment - DYnamics of Light And Nutrients (HOE-DYLAN). Glider-based GPP measurements were extended to explore the relationship between GPP and mesoscale context over multiple years of Seaglider deployments.

Diagnosis of middle atmosphere chemistry-dynamics interactions

NASA Astrophysics Data System (ADS)

Zhu, X.; Swartz, W. H.; Garcia, R. R.; Chartier, A.; Yee, J. H.; Yue, J.

2017-12-01

We apply the recently developed middle atmosphere climate feedback-response analysis method (MCFRAM) to diagnosing the temperature variations associated with chemistry-dynamics interactions in the middle atmosphere. By using output fields from the Whole Atmosphere Community Climate Model (WACCM) coupled with the measurements, we identify and isolate the distinctive characteristics of different components in the observed temperature variations. Both the temperature trends associated with the anthropogenic forcing and temperature changes associated with natural and internal feedback processes are quantified based on MCFRAM defined partial temperature changes corresponding to localized radiative heating, non-localized chemical heating, eddy transport, and transport by the mean meridional circulation of energy and chemical species. In addition, the temperature responses to variations of CO2, O3, and solar flux have distinctly different spatial structures that can be systematically categorized by the eigenmodes of the generalized damping matrix derived from MCFRAM.

Critical Watersheds: Climate Change, Tipping Points, and Energy-Water Impacts

NASA Astrophysics Data System (ADS)

Middleton, R. S.; Brown, M.; Coon, E.; Linn, R.; McDowell, N. G.; Painter, S. L.; Xu, C.

2014-12-01

Climate change, extreme climate events, and climate-induced disturbances will have a substantial and detrimental impact on terrestrial ecosystems. How ecosystems respond to these impacts will, in turn, have a significant effect on the quantity, quality, and timing of water supply for energy security, agriculture, industry, and municipal use. As a community, we lack sufficient quantitative and mechanistic understanding of the complex interplay between climate extremes (e.g., drought, floods), ecosystem dynamics (e.g., vegetation succession), and disruptive events (e.g., wildfire) to assess ecosystem vulnerabilities and to design mitigation strategies that minimize or prevent catastrophic ecosystem impacts. Through a combination of experimental and observational science and modeling, we are developing a unique multi-physics ecohydrologic framework for understanding and quantifying feedbacks between novel climate and extremes, surface and subsurface hydrology, ecosystem dynamics, and disruptive events in critical watersheds. The simulation capability integrates and advances coupled surface-subsurface hydrology from the Advanced Terrestrial Simulator (ATS), dynamic vegetation succession from the Ecosystem Demography (ED) model, and QUICFIRE, a novel wildfire behavior model developed from the FIRETEC platform. These advances are expected to make extensive contributions to the literature and to earth system modeling. The framework is designed to predict, quantify, and mitigate the impacts of climate change on vulnerable watersheds, with a focus on the US Mountain West and the energy-water nexus. This emerging capability is used to identify tipping points in watershed ecosystems, quantify impacts on downstream users, and formally evaluate mitigation efforts including forest (e.g., thinning, prescribed burns) and watershed (e.g., slope stabilization). The framework is being trained, validated, and demonstrated using field observations and remote data collections in the Valles Caldera National Preserve, including pre- and post-wildfire and infestation observations. Ultimately, the framework will be applied to the upper Colorado River basin. Here, we present an overview of the framework development strategy and latest field and modeling results.

Introducing a means of quantifying community reputation: the print media as a data source.

PubMed

McLaren, Lindsay; Perry, Rosemary; Carruthers, Lesley; Hawe, Penelope

2005-06-01

A community's reputation may have implications for self-esteem, morale, or other health outcomes of residents. In this study, we introduce a means of quantifying the reputation of communities in Calgary, Canada based on their portrayal in the daily citywide newspaper. Publication dates were selected from an 8.5-year period using constructed week sampling. For communities designated as high or low in well-being, sampled references were rated as positive, negative, or neutral in topic, by two independent raters who were blind to community identity. Findings suggest that the print media represent a convenient and discriminating data source for characterising some aspects of community reputation.

Plant-pollinator interactions in a biodiverse meadow are rather stable and tight for 3 consecutive years.

PubMed

Fang, Qiang; Huang, Shuangquan

2016-05-01

Plant-pollinator interactions can be highly variable across years in natural communities. Although variation in the species composition and its basic structure has been investigated to understand the dynamic nature of pollination networks, little is known about the temporal dynamic of interaction strength between the same plant and pollinator species in any natural community. Pollinator-mediated selection on the evolution of floral traits could be diminished if plant-pollinator interactions vary temporally. To quantify the temporal variation in plant-pollinator interactions and the interaction strength (observed visits), we compared weighted networks between plants and pollinators in a biodiverse alpine meadow in Shangri-La, southwest China for 3 consecutive years. Although plant-pollinator interactions were highly dynamic such that identical interactions only accounted for 10.7% of the total between pair years, the diversity of interactions was stable. These identical interactions contributed 41.2% of total visits and were similar in strength and weighted nestedness. For plant species, 72.6% of species were visited by identical pollinator species between pair years, accounting for over half of the total visits and three-quarters at the functional group level. More generalized pollinators contributed more connectiveness and were more central in networks across years. However, there was no similar or even opposite trend for plant species, which suggested that specialized plant species may also be central in pollinator networks. The variation in pollinator composition decreased as pollinator species numbers increased, suggesting that generalized plants experienced stable pollinator partition. The stable, tight interactions between generalized pollinators and specialized plants represent cornerstones of the studied community. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Trend and seasonality of community-acquired Escherichia coli antimicrobial resistance and its dynamic relationship with antimicrobial use assessed by ARIMA models.

PubMed

Asencio Egea, María Ángeles; Huertas Vaquero, María; Carranza González, Rafael; Herráez Carrera, Óscar; Redondo González, Olga; Arias Arias, Ángel

2017-12-04

We studied the trend and seasonality of community-acquired Escherichia coli resistance and quantified its correlation with the previous use of certain antibiotics. A time series study of resistant community-acquired E. coli isolates and their association with antibiotic use was conducted in a Primary Health Care Area from 2008 to 2012. A Poisson regression model was constructed to estimate the trend and seasonality of E. coli resistance. A significant increasing trend in mean E. coli resistance to cephalosporins, aminoglycosides and nitrofurantoin was observed. Seasonal resistance to ciprofloxacin and amoxicillin-clavulanic acid was significantly higher in autumn-winter. There was a delay of 7, 10 and 12 months between the use of cotrimoxazole (P<0.038), fosfomycin (P<0.024) and amoxicillin-clavulanic acid (P<0.015), respectively, and the occurrence of E. coli resistance. An average delay of 10 months between the previous use of amoxicillin-clavulanic acid, cotrimoxazole and fosfomycin and the appearance of resistant community-acquired E. coli strains was detected. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

How plants connect pollination and herbivory networks and their contribution to community stability.

PubMed

Sauve, Alix M C; Thébault, Elisa; Pocock, Michael J O; Fontaine, Colin

2016-04-01

Pollination and herbivory networks have mainly been studied separately, highlighting their distinct structural characteristics and the related processes and dynamics. However, most plants interact with both pollinators and herbivores, and there is evidence that both types of interaction affect each other. Here we investigated the way plants connect these mutualistic and antagonistic networks together, and the consequences for community stability. Using an empirical data set, we show that the way plants connect pollination and herbivory networks is not random and promotes community stability. Analyses of the structure of binary and quantitative networks show different results: the plants' generalism with regard to pollinators is positively correlated to their generalism with regard to herbivores when considering binary interactions, but not when considering quantitative interactions. We also show that plants that share the same pollinators do not share the same herbivores. However, the way plants connect pollination and herbivory networks promotes stability for both binary and quantitative networks. Our results highlight the relevance of considering the diversity of interaction types in ecological communities, and stress the need to better quantify the costs and benefits of interactions, as well as to develop new metrics characterizing the way different interaction types are combined within ecological networks.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

The Extended Community-Level Effects of Genetic Variation in Foliar Wax Chemistry in the Forest Tree Eucalyptus globulus.

PubMed

Gosney, Benjamin; O'Reilly-Wapstra, Julianne; Forster, Lynne; Whiteley, Carmen; Potts, Brad

2017-05-01

Genetic variation in foundation trees can influence dependent communities, but little is known about the mechanisms driving these extended genetic effects. We studied the potential chemical drivers of genetic variation in the dependent foliar community of the focal tree Eucalyptus globulus. We focus on the role of cuticular waxes and compare the effects to that of the terpenes, a well-studied group of secondary compounds known to be bioactive in eucalypts. The canopy community was quantified based on the abundance of thirty-nine distinctive arthropod and fungal symptoms on foliar samples collected from canopies of 246 progeny from 13 E. globulus sub-races grown in a common garden trial. Cuticular waxes and foliar terpenes were quantified using gas chromatography - mass spectrometry (GC-MC). A total of 4 of the 13 quantified waxes and 7 of the 16 quantified terpenes were significantly associated with the dependent foliar community. Variation in waxes explained 22.9% of the community variation among sub-races, which was equivalent to that explained by terpenes. In combination, waxes and terpenes explained 35% of the genetic variation among sub-races. Only a small proportion of wax and terpene compounds showing statistically significant differences among sub-races were implicated in community level effects. The few significant waxes have previously shown evidence of divergent selection in E. globulus, which signals that adaptive variation in phenotypic traits may have extended effects. While highlighting the role of the understudied cuticular waxes, this study demonstrates the complexity of factors likely to lead to community genetic effects in foundation trees.

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities

PubMed Central

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species’ ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics. PMID:23874815

Spatial structures of the environment and of dispersal impact species distribution in competitive metacommunities.

PubMed

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species' ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics.

The dynamics of emotions in online interaction

PubMed Central

Kappas, Arvid; Küster, Dennis

2016-01-01

We study the changes in emotional states induced by reading and participating in online discussions, empirically testing a computational model of online emotional interaction. Using principles of dynamical systems, we quantify changes in valence and arousal through subjective reports, as recorded in three independent studies including 207 participants (110 female). In the context of online discussions, the dynamics of valence and arousal is composed of two forces: an internal relaxation towards baseline values independent of the emotional charge of the discussion and a driving force of emotional states that depends on the content of the discussion. The dynamics of valence show the existence of positive and negative tendencies, while arousal increases when reading emotional content regardless of its polarity. The tendency of participants to take part in the discussion increases with positive arousal. When participating in an online discussion, the content of participants' expression depends on their valence, and their arousal significantly decreases afterwards as a regulation mechanism. We illustrate how these results allow the design of agent-based models to reproduce and analyse emotions in online communities. Our work empirically validates the microdynamics of a model of online collective emotions, bridging online data analysis with research in the laboratory. PMID:27853586

Effect of aging on dynamic postural stability and variability during a multi-directional lean and reach object transportation task.

PubMed

Huntley, Andrew H; Zettel, John L; Vallis, Lori Ann

2016-01-01

A "reach and transport object" task that represents common activities of daily living may provide improved insight into dynamic postural stability and movement variability deficits in older adults compared to previous lean to reach and functional reach tests. Healthy young and older, community dwelling adults performed three same elevation object transport tasks and two multiple elevation object transport tasks under two self-selected speeds, self-paced and fast-paced. Dynamic postural stability and movement variability was quantified by whole-body center of mass motion. Older adults demonstrated significant decrements in frontal plane stability during the multiple elevation tasks while exhibiting the same movement variability as their younger counterparts, regardless of task speed. Interestingly, older adults did not exhibit a tradeoff in maneuverability in favour of maintaining stability throughout the tasks, as has previously been reported. In conclusion, the multi-planar, ecologically relevant tasks employed in the current study were specific enough to elucidate decrements in dynamic stability, and thus may be useful for assessing fall risk in older adults with suspected postural instability. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

NASA Astrophysics Data System (ADS)

Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

2015-04-01

In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

Local Competition and Metapopulation Processes Drive Long-Term Seagrass-Epiphyte Population Dynamics

PubMed Central

Lobelle, Delphine; Kenyon, Emma J.; Cook, Kevan J.; Bull, James C.

2013-01-01

It is well known that ecological processes such as population regulation and natural enemy interactions potentially occur over a range of spatial scales, and there is a substantial body of literature developing theoretical understanding of the interplay between these processes. However, there are comparatively few studies quantifying the long-term effects of spatial scaling in natural ecosystems. A key challenge is that trophic complexity in real-world biological communities quickly obscures the signal from a focal process. Seagrass meadows provide an excellent opportunity in this respect: in many instances, seagrasses effectively form extensive natural monocultures, in which hypotheses about endogenous dynamics can be formulated and tested. We present amongst the longest unbroken, spatially explict time series of seagrass abundance published to date. Data include annual measures of shoot density, total above-ground abundance, and associated epiphyte cover from five Zostera marina meadows distributed around the Isles of Scilly, UK, from 1996 to 2011. We explore empirical patterns at the local and metapopulation scale using standard time series analysis and develop a simple population dynamic model, testing the hypothesis that both local and metapopulation scale feedback processes are important. We find little evidence of an interaction between scales in seagrass dynamics but that both scales contribute approximately equally to observed local epiphyte abundance. By quantifying the long-term dynamics of seagrass-epiphyte interactions we show how measures of density and extent are both important in establishing baseline information relevant to predicting responses to environmental change and developing management plans. We hope that this study complements existing mechanistic studies of physiology, genetics and productivity in seagrass, whilst highlighting the potential of seagrass as a model ecosystem. More generally, this study provides a rare opportunity to test some of the predictions of ecological theory in a natural ecosystem of global conservation and economic value. PMID:23437313

Local competition and metapopulation processes drive long-term seagrass-epiphyte population dynamics.

PubMed

Lobelle, Delphine; Kenyon, Emma J; Cook, Kevan J; Bull, James C

2013-01-01

It is well known that ecological processes such as population regulation and natural enemy interactions potentially occur over a range of spatial scales, and there is a substantial body of literature developing theoretical understanding of the interplay between these processes. However, there are comparatively few studies quantifying the long-term effects of spatial scaling in natural ecosystems. A key challenge is that trophic complexity in real-world biological communities quickly obscures the signal from a focal process. Seagrass meadows provide an excellent opportunity in this respect: in many instances, seagrasses effectively form extensive natural monocultures, in which hypotheses about endogenous dynamics can be formulated and tested. We present amongst the longest unbroken, spatially explict time series of seagrass abundance published to date. Data include annual measures of shoot density, total above-ground abundance, and associated epiphyte cover from five Zostera marina meadows distributed around the Isles of Scilly, UK, from 1996 to 2011. We explore empirical patterns at the local and metapopulation scale using standard time series analysis and develop a simple population dynamic model, testing the hypothesis that both local and metapopulation scale feedback processes are important. We find little evidence of an interaction between scales in seagrass dynamics but that both scales contribute approximately equally to observed local epiphyte abundance. By quantifying the long-term dynamics of seagrass-epiphyte interactions we show how measures of density and extent are both important in establishing baseline information relevant to predicting responses to environmental change and developing management plans. We hope that this study complements existing mechanistic studies of physiology, genetics and productivity in seagrass, whilst highlighting the potential of seagrass as a model ecosystem. More generally, this study provides a rare opportunity to test some of the predictions of ecological theory in a natural ecosystem of global conservation and economic value.

Comparison of heaving buoy and oscillating flap wave energy converters

NASA Astrophysics Data System (ADS)

Abu Bakar, Mohd Aftar; Green, David A.; Metcalfe, Andrew V.; Najafian, G.

2013-04-01

Waves offer an attractive source of renewable energy, with relatively low environmental impact, for communities reasonably close to the sea. Two types of simple wave energy converters (WEC), the heaving buoy WEC and the oscillating flap WEC, are studied. Both WECs are considered as simple energy converters because they can be modelled, to a first approximation, as single degree of freedom linear dynamic systems. In this study, we estimate the response of both WECs to typical wave inputs; wave height for the buoy and corresponding wave surge for the flap, using spectral methods. A nonlinear model of the oscillating flap WEC that includes the drag force, modelled by the Morison equation is also considered. The response to a surge input is estimated by discrete time simulation (DTS), using central difference approximations to derivatives. This is compared with the response of the linear model obtained by DTS and also validated using the spectral method. Bendat's nonlinear system identification (BNLSI) technique was used to analyze the nonlinear dynamic system since the spectral analysis was only suitable for linear dynamic system. The effects of including the nonlinear term are quantified.

Strong Spatial Influence on Colonization Rates in a Pioneer Zooplankton Metacommunity

PubMed Central

Frisch, Dagmar; Cottenie, Karl; Badosa, Anna; Green, Andy J.

2012-01-01

The magnitude of community-wide dispersal is central to metacommunity models, yet dispersal is notoriously difficult to quantify in passive and cryptic dispersers such as many freshwater invertebrates. By overcoming the problem of quantifying dispersal rates, colonization rates into new habitats can provide a useful estimate of the magnitude of effective dispersal. Here we study the influence of spatial and local processes on colonization rates into new ponds that indicate differential dispersal limitation of major zooplankton taxa, with important implications for metacommunity dynamics. We identify regional and local factors that affect zooplankton colonization rates and spatial patterns in a large-scale experimental system. Our study differs from others in the unique setup of the experimental pond area by which we were able to test spatial and environmental variables at a large spatial scale. We quantified colonization rates separately for the Copepoda, Cladocera and Rotifera from samples collected over a period of 21 months in 48 newly constructed temporary ponds of 0.18–2.95 ha distributed in a restored wetland area of 2,700 ha in Doñana National Park, Southern Spain. Species richness upon initial sampling of new ponds was about one third of that in reference ponds, although the rate of detection of new species from thereon were not significantly different, probably owing to high turnover in the dynamic, temporary reference ponds. Environmental heterogeneity had no detectable effect on colonization rates in new ponds. In contrast, connectivity, space (based on latitude and longitude) and surface area were key determinants of colonization rates for copepods and cladocerans. This suggests dispersal limitation in cladocerans and copepods, but not in rotifers, possibly due to differences in propagule size and abundance. PMID:22792241

Strong spatial influence on colonization rates in a pioneer zooplankton metacommunity.

PubMed

Frisch, Dagmar; Cottenie, Karl; Badosa, Anna; Green, Andy J

2012-01-01

The magnitude of community-wide dispersal is central to metacommunity models, yet dispersal is notoriously difficult to quantify in passive and cryptic dispersers such as many freshwater invertebrates. By overcoming the problem of quantifying dispersal rates, colonization rates into new habitats can provide a useful estimate of the magnitude of effective dispersal. Here we study the influence of spatial and local processes on colonization rates into new ponds that indicate differential dispersal limitation of major zooplankton taxa, with important implications for metacommunity dynamics. We identify regional and local factors that affect zooplankton colonization rates and spatial patterns in a large-scale experimental system. Our study differs from others in the unique setup of the experimental pond area by which we were able to test spatial and environmental variables at a large spatial scale. We quantified colonization rates separately for the Copepoda, Cladocera and Rotifera from samples collected over a period of 21 months in 48 newly constructed temporary ponds of 0.18-2.95 ha distributed in a restored wetland area of 2,700 ha in Doñana National Park, Southern Spain. Species richness upon initial sampling of new ponds was about one third of that in reference ponds, although the rate of detection of new species from thereon were not significantly different, probably owing to high turnover in the dynamic, temporary reference ponds. Environmental heterogeneity had no detectable effect on colonization rates in new ponds. In contrast, connectivity, space (based on latitude and longitude) and surface area were key determinants of colonization rates for copepods and cladocerans. This suggests dispersal limitation in cladocerans and copepods, but not in rotifers, possibly due to differences in propagule size and abundance.

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

PubMed Central

Li, Song; Avera, Bethany N.; Strahm, Brian D.; Badgley, Brian D.

2017-01-01

ABSTRACT Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages. PMID:28476769

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration.

PubMed

Sun, Shan; Li, Song; Avera, Bethany N; Strahm, Brian D; Badgley, Brian D

2017-07-15

Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages. Copyright © 2017 American Society for Microbiology.

Constraining the variability of optical properties in the Santa Barbara Channel, CA: A phytoplankton story

NASA Astrophysics Data System (ADS)

Barron, Rebecca Katherine

The research presented in this dissertation evaluates the direct relationships of phytoplankton community composition and inherent optical properties (IOP); that is, the absorption and scattering of light in the ocean. Phytoplankton community composition affect IOPs in both direct and indirect ways, thus creating challenges for optical measurements of biological and biogeochemical properties in aquatic systems. Studies were performed in the Santa Barbara Channel (SBC), CA where an array of optical and biogeochemical measurements were made. Phytoplankton community structure was characterized by an empirical orthogonal functional analysis (EOF) using phytoplankton accessory pigments. The results showed that phytoplankton community significantly correlated to all IOPs, e.g. phytoplankton specific absorption, detrital absorption, CDOM absorption and particle backscattering coefficients. Furthermore, the EOF analysis was unique in splitting the microphytoplankton size class into separate diatom and dinoflagellate regimes allowing for assessment optical property differences within the same size class, a technique previously not systematically achievable. The phytoplankton functional group dinoflagellates were particularly influential to IOPs in surprising ways. Dinoflagellates showed higher backscattering efficiencies than would be predicted based on Mie theory, and significantly influenced CDOM absorption via direct association with dissolved mycosproine-like amino acid absorption (MAA) peaks in CDOM spectra. A new index was developed in this work to quantify MAA absorption peaks in CDOM spectra, and was named the MAA Index. Prior to this research dissolved MAA absorption in natural waters was never quantified, and CDOM data containing these peaks were often disregarded and discarded from analysis. CDOM dynamics in the SBC were assessed for a 15-year study period, and this work shows that significantly large MAA Index values, e.g. MAA Index > 1, were present in approximately 16% of surface water data. Variability in CDOM spectral shape was quantified using the EOF technique, and regression analysis with EOF outputs showed that CDOM absorption intensity and spectral shape were well correlated dinoflagellate presence. Furthermore, results showed that phytoplankton biomass played a secondary role in relation to CDOM absorption, and that variability in CDOM absorption coefficients were primarily driven by community composition. CDOM quality in the SBC was also assessed using CDOM fluorescence properties via excitation emission matrix spectroscopy (EEMS). The EEMS data was analyzed using a multivariate statistical procedure, again, an EOF analysis, to identify three dominant CDOM source regimes: the surface pelagic regime, deep-water (up to 300 m) regime and kelp forest pelagic regime. This work also found that while CDOM absorption coefficient was strongly influence by which phytoplankton groups were present, DOM quality was characterized more so by the amount of phytoplankton biomass, hence indicating strong microbial component to DOM production. Lastly, with the use of the EEMS data, and characterization of CDOM absorption properties, e.g. spectral slope, S, slope ratio, SR, specific UV-absorbance, SUVA and MAA Index, we found that terrestrial sources of CDOM were very limited in the SBC. Based on this research, mineral particle concentrations that significantly correlated with IOPs were thought to be associated with suspended sediments from shoaling of the continental shelf rather than from stream/river influence. Thus, the SBC is a unique, optically complex ocean system where IOP dynamics, thus remote sensing reflectance, are strongly influenced by shifts in phytoplankton community structure.

BELOWGROUND NITROGEN UPTAKE AND ALLOCATION ...

EPA Pesticide Factsheets

Anthropogenic nitrogen inputs coupled with rising sea level complicate predictions of marsh stability. As marsh stability is a function of its vegetation, it is important to understand the mechanisms that drive community dynamics. Many studies have examined aboveground dynamics and nutrient cycling, but few have studied the belowground uptake and allocation of nitrogen. Literature suggests that D. spicata may dominate the marsh platform in nutrient-rich conditions, though the mechanism driving the vegetation shift is unclear. Our study examines belowground nutrient uptake and allocation underlying these patterns. To determine whether D. spicata is a more efficient scavenger of nutrients than S. alterniflora we performed a 15N pulse-chase experiment. Tracer was added to mesocosms growing D. spicata and S. alterniflora in monoculture. After the initial pulse, a subset of pots were sacrificed weekly and partitioned into detailed depth intervals for 15N analysis of several belowground pools: live coarse and fine roots, live rhizomes, dead organic matter, and bulk sediment. Comparisons between D. spicata and S. alterniflora uptake and allocation can explain mechanisms of competitive advantage and predictions of D. spicata dominance. Additionally, we used denitrification enzyme assays (DEA) and greenhouse gas slurries to quantify denitrification rates and potentials. Initial results suggest that the vegetation types support similar N-relevant microbial communities. Th

Landscape variation of seasonal pool plant communities in forests of northern Minnesota, USA

Treesearch

Brian Palik; Dwight Streblow; Leanne Egeland; Richard Buech

2007-01-01

Seasonal forest pools are abundant in the northern Great Lakes forest landscape, but the range of variation in their plant communities and the relationship of this variation to multi-scale landscape features remains poorly quantified. We examined seasonal pools in forests of northern Minnesota USA with the objective of quantifying the range of variation in plant...

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

DOE PAGES

Kim, Young-Mo; Nowack, Shane; Olsen, Millie; ...

2015-04-17

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Young-Mo; Nowack, Shane; Olsen, Millie

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

PubMed Central

Kim, Young-Mo; Nowack, Shane; Olsen, Millie T.; Becraft, Eric D.; Wood, Jason M.; Thiel, Vera; Klapper, Isaac; Kühl, Michael; Fredrickson, James K.; Bryant, Donald A.; Ward, David M.; Metz, Thomas O.

2015-01-01

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches. PMID:25941514

Localised Effects of a Mega-Disturbance: Spatiotemporal Responses of Intertidal Sandy Shore Communities to the 2010 Chilean Earthquake.

PubMed

Sepúlveda, Roger D; Valdivia, Nelson

2016-01-01

Determining the effects of unpredictable disturbances on dynamic ecological systems is challenged by the paucity of appropriate temporal and spatial coverage of data. On 27 February 2010, an 8.8 Mw mega-earthquake and tsunami struck central Chile and caused coastal land-level changes, massive damage to coastal infrastructure, and widespread mortality of coastal organisms. Wave-exposed sandy beaches showed significant changes of species abundances from before to after the earthquake, but the highly dynamic biotic and abiotic conditions of these habitats make difficult to draw clear-cut conclusions from these patterns. Here, we analysed a beyond-BACI (Before-After Control-Impact) sampling design to test whether the effects of the Maule earthquake on sandy-shore species diversity, abundance, and structure were heterogeneous along the shore. Invertebrate species abundances were quantified before (i.e. February 2010) and after (i.e. March 2010, September 2010, and March 2011) the earthquake at three sandy shores randomly located within the earthquake rupture area and three sites within a "control" area located >400 km southward from epicentre. Immediately after the earthquake took place, the three sites located in the rupture area showed anomalous beach-profile uplifts that did not comply with the erosion (i.e. "negative" uplifts) that regularly occurs during late summer in the region. Species richness, abundance, and community structure significantly varied from before to after the strike, but these patterns of change varied among sites within both areas. Only the site with the strongest and persistent beach-profile uplift within the rupture area showed significant concomitant changes in species richness and community structure; after 13 months, this community showed a similar multivariate structure to the before-disturbance state. This site, in particular, was located in the section of the rupture area that received most of the impact of the after-earthquake tsunami. Therefore, our results suggest that the effects of the Maule mega-earthquake on the ecological communities were spatially heterogeneous and highly localised. We suggest that high mobility and other species' adaptations to the dynamic environmental conditions of sandy beaches might explain the comparatively high resilience of these assemblages. With this work we hope to motivate further experimental research on the role of individual- and population-level properties in the response of sandy-beach communities to interacting sources of disturbances.

Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes

PubMed Central

Scherer, Pia I.; Millard, Andrew D.; Miller, Andreas; Schoen, Renate; Raeder, Uta; Geist, Juergen; Zwirglmaier, Katrin

2017-01-01

Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the correlation of a genetic marker with microcystin concentration and aimed to identify the main microcystin producer. We used Illumina MiSeq sequencing to study the bacterioplankton in two recreational lakes in South Germany. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of microcystin biosynthesis genes. Bloom toxicity did not alter the bacterial community composition, which was highly dynamic at the lowest taxonomic level for some phyla such as Cyanobacteria. At the OTU level, we found distinctly different degrees of temporal variation between major bacteria phyla. Cyanobacteria and Bacteroidetes showed drastic temporal changes in their community compositions, while the composition of Actinobacteria remained rather stable in both lakes. The bacterial community composition of Alpha- and Beta-proteobacteria remained stable over time in Lake Klostersee, but it showed temporal variations in Lake Bergknappweiher. The presence of potential microcystin degraders and potential algicidal bacteria amongst prevalent Bacteroidetes and Alphaproteobacteria implied a role of those co-occurring heterotrophic bacteria in cyanobacterial bloom dynamics. Comparison of both lakes studied revealed a large shared microbiome, which was shaped toward the lake specific community composition by environmental factors. Microcystin variants detected were microcystin-LR, -RR, and -YR. The maximum microcystin concentrations measured was 6.7 μg/L, a value still acceptable for recreational waters but not drinking water. Microcystin concentration correlated positively with total phosphorus and mcyB copy number. We identified low abundant Microcystis sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that non-dominant species may cause toxicity of the blooms observed. PMID:29255452

Localised Effects of a Mega-Disturbance: Spatiotemporal Responses of Intertidal Sandy Shore Communities to the 2010 Chilean Earthquake

PubMed Central

Sepúlveda, Roger D.; Valdivia, Nelson

2016-01-01

Determining the effects of unpredictable disturbances on dynamic ecological systems is challenged by the paucity of appropriate temporal and spatial coverage of data. On 27 February 2010, an 8.8 Mw mega-earthquake and tsunami struck central Chile and caused coastal land-level changes, massive damage to coastal infrastructure, and widespread mortality of coastal organisms. Wave-exposed sandy beaches showed significant changes of species abundances from before to after the earthquake, but the highly dynamic biotic and abiotic conditions of these habitats make difficult to draw clear-cut conclusions from these patterns. Here, we analysed a beyond-BACI (Before-After Control-Impact) sampling design to test whether the effects of the Maule earthquake on sandy-shore species diversity, abundance, and structure were heterogeneous along the shore. Invertebrate species abundances were quantified before (i.e. February 2010) and after (i.e. March 2010, September 2010, and March 2011) the earthquake at three sandy shores randomly located within the earthquake rupture area and three sites within a “control” area located >400 km southward from epicentre. Immediately after the earthquake took place, the three sites located in the rupture area showed anomalous beach-profile uplifts that did not comply with the erosion (i.e. “negative” uplifts) that regularly occurs during late summer in the region. Species richness, abundance, and community structure significantly varied from before to after the strike, but these patterns of change varied among sites within both areas. Only the site with the strongest and persistent beach-profile uplift within the rupture area showed significant concomitant changes in species richness and community structure; after 13 months, this community showed a similar multivariate structure to the before-disturbance state. This site, in particular, was located in the section of the rupture area that received most of the impact of the after-earthquake tsunami. Therefore, our results suggest that the effects of the Maule mega-earthquake on the ecological communities were spatially heterogeneous and highly localised. We suggest that high mobility and other species’ adaptations to the dynamic environmental conditions of sandy beaches might explain the comparatively high resilience of these assemblages. With this work we hope to motivate further experimental research on the role of individual- and population-level properties in the response of sandy-beach communities to interacting sources of disturbances. PMID:27383744

Spatial variation and seasonal dynamics of leaf-area index in the arctic tundra-implications for linking ground observations and satellite images

NASA Astrophysics Data System (ADS)

Juutinen, Sari; Virtanen, Tarmo; Kondratyev, Vladimir; Laurila, Tuomas; Linkosalmi, Maiju; Mikola, Juha; Nyman, Johanna; Räsänen, Aleksi; Tuovinen, Juha-Pekka; Aurela, Mika

2017-09-01

Vegetation in the arctic tundra typically consists of a small-scale mosaic of plant communities, with species differing in growth forms, seasonality, and biogeochemical properties. Characterization of this variation is essential for understanding and modeling the functioning of the arctic tundra in global carbon cycling, as well as for evaluating the resolution requirements for remote sensing. Our objective was to quantify the seasonal development of the leaf-area index (LAI) and its variation among plant communities in the arctic tundra near Tiksi, coastal Siberia, consisting of graminoid, dwarf shrub, moss, and lichen vegetation. We measured the LAI in the field and used two very-high-spatial resolution multispectral satellite images (QuickBird and WorldView-2), acquired at different phenological stages, to predict landscape-scale patterns. We used the empirical relationships between the plant community-specific LAI and degree-day accumulation (0 °C threshold) and quantified the relationship between the LAI and satellite NDVI (normalized difference vegetation index). Due to the temporal difference between the field data and satellite images, the LAI was approximated for the imagery dates, using the empirical model. LAI explained variation in the NDVI values well (R 2 adj. 0.42-0.92). Of the plant functional types, the graminoid LAI showed the largest seasonal amplitudes and was the main cause of the varying spatial patterns of the NDVI and the related LAI between the two images. Our results illustrate how the short growing season, rapid development of the LAI, yearly climatic variation, and timing of the satellite data should be accounted for in matching imagery and field verification data in the Arctic region.

Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates

PubMed Central

Khan, Munawwar A.; Patel, Poojabahen G.; Ganesh, Arpitha G.; Rais, Naushad; Faheem, Sultan M.; Khan, Shams T.

2018-01-01

Introduction: Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique. Methods & Materials: Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies. Results and Discussion: In general, the aceticlastic organisms (Methanosarcinaceae & Methanosaetaceae) were more abundant than the hydrogenotrophic organisms (Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that family Methanosaetaceae was the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters. Conclusion: Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters. PMID:29785219

Interspecific variation in the phenology of advertisement calling in a temperate Australian frog community.

PubMed

Heard, Geoffrey W; Canessa, Stefano; Parris, Kirsten M

2015-09-01

Spatial and temporal partitioning of resources underlies the coexistence of species with similar niches. In communities of frogs and toads, the phenology of advertisement calling provides insights into temporal partitioning of reproductive effort and its implications for community dynamics. This study assessed the phenology of advertisement calling in an anuran community from Melbourne, in southern Australia. We collated data from 1432 surveys of 253 sites and used logistic regression to quantify seasonality in the nightly probability of calling and the influence of meteorological variables on this probability for six species of frogs. We found limited overlap in the predicted seasonal peaks of calling among these species. Those shown to have overlapping calling peaks are unlikely to be in direct competition, due to differences in larval ecology (Crinia signifera and Litoria ewingii) or differences in calling behavior and acoustics (Limnodynastes dumerilii and Litoria raniformis). In contrast, closely related and ecologically similar species (Crinia signfera and Crinia parinsignifera;Litoria ewingii and Litoria verreauxii) appear to have staggered seasonal peaks of calling. In combination with interspecific variation in the meteorological correlates of calling, these results may be indicative of temporal partitioning of reproductive activity to facilitate coexistence, as has been reported for tropical and temperate anurans from other parts of the globe.

Bioremediation of PAH-contamined soils: Consequences on formation and degradation of polar-polycyclic aromatic compounds and microbial community abundance.

PubMed

Biache, Coralie; Ouali, Salma; Cébron, Aurélie; Lorgeoux, Catherine; Colombano, Stéfan; Faure, Pierre

2017-05-05

A bioslurry batch experiment was carried out over five months on three polycyclic aromatic compound (PAC) contaminated soils to study the PAC (PAH and polar-PAC) behavior during soil incubation and to evaluate the impact of PAC contamination on the abundance of microbial communities and functional PAH-degrading populations. Organic matter characteristics and reactivity, assessed through solvent extractable organic matter and PAC contents, and soil organic matter mineralization were monitored during 5 months. Total bacteria and fungi, and PAH-ring hydroxylating dioxygenase genes were quantified. Results showed that PAHs and polar-PACs were degraded with different degradation dynamics. Differences in degradation rates were observed among the three soils depending on PAH distribution and availability. Overall, low molecular weight compounds were preferentially degraded. Degradation selectivity between isomers and structurally similar compounds was observed which could be used to check the efficiency of bioremediation processes. Bacterial communities were dominant over fungi and were most likely responsible for PAC degradation. Abundance of PAH-degrading bacteria increased during incubations, but their proportion in the bacterial communities tended to decrease. The accumulation of some oxygenated-PACs during the bioslurry experiment underlines the necessity to monitor these compounds during application of remediation treatment on PAH contaminated soils. Copyright © 2017 Elsevier B.V. All rights reserved.

Species selection under long-term experimental warming and drought explained by climatic distributions.

PubMed

Liu, Daijun; Peñuelas, Josep; Ogaya, Romà; Estiarte, Marc; Tielbörger, Katja; Slowik, Fabian; Yang, Xiaohong; Bilton, Mark C

2018-03-01

Global warming and reduced precipitation may trigger large-scale species losses and vegetation shifts in ecosystems around the world. However, currently lacking are practical ways to quantify the sensitivity of species and community composition to these often-confounded climatic forces. Here we conducted long-term (16 yr) nocturnal-warming (+0.6°C) and reduced precipitation (-20% soil moisture) experiments in a Mediterranean shrubland. Climatic niche groups (CNGs) - species ranked or classified by similar temperature or precipitation distributions - informatively described community responses under experimental manipulations. Under warming, CNGs revealed that only those species distributed in cooler regions decreased. Correspondingly, under reduced precipitation, a U-shaped treatment effect observed in the total community was the result of an abrupt decrease in wet-distributed species, followed by a delayed increase in dry-distributed species. Notably, while partially correlated, CNG explanations of community response were stronger for their respective climate parameter, suggesting some species possess specific adaptations to either warming or drought that may lead to independent selection to the two climatic variables. Our findings indicate that when climatic distributions are combined with experiments, the resulting incorporation of local plant evolutionary strategies and their changing dynamics over time leads to predictable and informative shifts in community structure under independent climate change scenarios. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Poissonian steady states: from stationary densities to stationary intensities.

PubMed

Eliazar, Iddo

2012-10-01

Markov dynamics are the most elemental and omnipresent form of stochastic dynamics in the sciences, with applications ranging from physics to chemistry, from biology to evolution, and from economics to finance. Markov dynamics can be either stationary or nonstationary. Stationary Markov dynamics represent statistical steady states and are quantified by stationary densities. In this paper, we generalize the notion of steady state to the case of general Markov dynamics. Considering an ensemble of independent motions governed by common Markov dynamics, we establish that the entire ensemble attains Poissonian steady states which are quantified by stationary Poissonian intensities and which hold valid also in the case of nonstationary Markov dynamics. The methodology is applied to a host of Markov dynamics, including Brownian motion, birth-death processes, random walks, geometric random walks, renewal processes, growth-collapse dynamics, decay-surge dynamics, Ito diffusions, and Langevin dynamics.

Poissonian steady states: From stationary densities to stationary intensities

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2012-10-01

Markov dynamics are the most elemental and omnipresent form of stochastic dynamics in the sciences, with applications ranging from physics to chemistry, from biology to evolution, and from economics to finance. Markov dynamics can be either stationary or nonstationary. Stationary Markov dynamics represent statistical steady states and are quantified by stationary densities. In this paper, we generalize the notion of steady state to the case of general Markov dynamics. Considering an ensemble of independent motions governed by common Markov dynamics, we establish that the entire ensemble attains Poissonian steady states which are quantified by stationary Poissonian intensities and which hold valid also in the case of nonstationary Markov dynamics. The methodology is applied to a host of Markov dynamics, including Brownian motion, birth-death processes, random walks, geometric random walks, renewal processes, growth-collapse dynamics, decay-surge dynamics, Ito diffusions, and Langevin dynamics.

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Green, K.; Murphy, M. A.; Shepard, C.; Chorover, J.; Rich, V. I.; Gallery, R. E.

2015-12-01

Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more reducing conditions typically occur in convergent zones and at depth. These results highlight the significance of fluctuating oxygen-depleted zones in aerobic soils on microbial community activity and structure, linking community response to larger scale ecosystem processes.

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.

2012-01-01

Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

Entropy of dynamical social networks

NASA Astrophysics Data System (ADS)

Zhao, Kun; Karsai, Marton; Bianconi, Ginestra

2012-02-01

Dynamical social networks are evolving rapidly and are highly adaptive. Characterizing the information encoded in social networks is essential to gain insight into the structure, evolution, adaptability and dynamics. Recently entropy measures have been used to quantify the information in email correspondence, static networks and mobility patterns. Nevertheless, we still lack methods to quantify the information encoded in time-varying dynamical social networks. In this talk we present a model to quantify the entropy of dynamical social networks and use this model to analyze the data of phone-call communication. We show evidence that the entropy of the phone-call interaction network changes according to circadian rhythms. Moreover we show that social networks are extremely adaptive and are modified by the use of technologies such as mobile phone communication. Indeed the statistics of duration of phone-call is described by a Weibull distribution and is significantly different from the distribution of duration of face-to-face interactions in a conference. Finally we investigate how much the entropy of dynamical social networks changes in realistic models of phone-call or face-to face interactions characterizing in this way different type human social behavior.

Nitrogen-limitation and invasive sweetclover impacts vary between two Great Plains plant communities

USGS Publications Warehouse

Van Riper, Laura C.; Larson, Diane L.; Larson, Jennifer L.

2010-01-01

Yellow sweetclover is an exotic herbaceous legume common in the Great Plains of the US. Although woody legumes have been shown to affect ecosystem processes through nitrogen (N) fixation (i.e., they can be considered "transformers" sensu Richardson et al. (2000)), the same has not been shown for short-lived herbaceous species. The objectives of this study were to (1) quantify the effects of yellow sweetclover on N mineralization and nitrification and (2) assess the effects of N fertilization on two plant communities, badlands sparse vegetation and western wheatgrass prairie. We used in situ (in wheatgrass prairie) and laboratory incubations (for both plant communities) to assess N dynamics at sites with high and low sweetclover cover in the two plant communities. We found that both N mineralization and nitrification were higher in the high sweetclover plots in the sparse plant community, but not in the wheatgrass prairie. To assess fertilization effects and determine if nutrients or water were limiting at our sites, we conducted a field experiment with five resource addition treatments, (1) N, (2) N + water, (3) water, (4) phosphorus, and (5) no addition. Water was limiting in the wheatgrass prairie but contrary to expectation, N was not. In contrast, N was limiting in the sparse community, where a fertilization effect was seen in exotic forbs, especially the toxic invader Halogeton glomeratus. Our results emphasize the contingent nature of plant invasion in which effects are largely dependent on attributes of the recipient vegetation.

Microbial Communities Are Well Adapted to Disturbances in Energy Input

PubMed Central

Vallino, Joseph J.

2016-01-01

ABSTRACT Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic “unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems. PMID:27822558

Determining the resilience of carbon dynamics in semi-arid biomes of the Southwestern US to severe drought and altered rainfall patterns

NASA Astrophysics Data System (ADS)

Litvak, M. E.; Krofcheck, D. J.; Hilton, T. W.; Fox, A. M.; Osuna, J. L.

2011-12-01

Water is critically important for biotic processes in semi-arid ecosystems and 2011 is developing as one of the most severe drought years on record for many parts of the Southwestern US. To quantify the impact of this severe drought on regional carbon and energy balance, we need a more detailed understanding of how water limitation alters ecosystem processes across a range of semi-arid biomes. We quantified the impact of severe drought and changes in both the quantity and distribution of precipitation on ecosystem biotic structure and function across the range of biomes represented in the NM elevation gradient network (desert grassland, creosote shrubland, juniper savanna, piñon-juniper woodland, ponderosa pine forest and subalpine mixed conifer forest). We compared how daily, seasonal and annual carbon and energy balance and their components in each of these biomes respond to changes in rainfall patterns using continuous measurements of carbon, water and energy exchange and associated measurements in each of these biomes during a 5 year period (2006-2011) that included a severe drought, and large variability in both winter precipitation and the timing and intensity of the monsoon. To understand the underlying mechanisms, we used time series of radiation absorbed by vegetation, surface albedo, soil moisture storage, phenology, gross primary productivity (GPP), ecosystem respiration (Re), and WorldView-2 images acquired pre- and post-monsoon in each of these biomes. In all of the biomes except the desert grassland site, the strength and timing of both winter and monsoon precipitation are important controls over carbon and energy dynamics in this region, though we see site-specific sensitivities across the elevation gradient. Over the past 5 years, carbon dynamics in the desert grassland site appears to be decoupled from winter precipitation. In addition, carbon dynamics in disturbed grassland and pinon-juniper ecosystems were more sensitive to severe drought than their undisturbed counterparts. We use the results to extend theory related to the vulnerability of semi-arid ecosystems to climate change and to understand biotic feedbacks within these biomes that may help to maintain resilience against structural and functional change. We also used the NCAR Community Land Model (CLM) parameterized for each biome and run in point mode to quantify the implications these changes in rainfall patterns have on ecosystem physiology, and regional carbon balance.

Development of negative feedback during successive growth cycles of black cherry.

PubMed Central

Packer, Alissa; Clay, Keith

2004-01-01

Negative feedback between plant and soil microbial communities can be a key determinant of vegetation structure and dynamics. Previous research has shown that negative feedback between black cherry (Prunus serotina) and soil pathogens is strongly distance dependent. Here, we investigate the temporal dynamics of negative feedback. To examine short-term changes, we planted successive cycles of seedlings in the same soil. We found that seedling mortality increased steadily with growth cycle when sterile background soil was inoculated with living field soil but not in controls inoculated with sterilized field soil. To examine long-term changes, we quantified negative feedback across successive growth cycles in soil inoculated with living field soil from a mature forest system (more than 70 years old) versus a younger successional site (ca. 25 years old). In both cases negative feedback developed similarly. Our results suggest that negative feedback can develop very quickly in forest systems, at the spatial scale of a single seedling. PMID:15058444

Interaction rewiring and the rapid turnover of plant-pollinator networks.

PubMed

CaraDonna, Paul J; Petry, William K; Brennan, Ross M; Cunningham, James L; Bronstein, Judith L; Waser, Nickolas M; Sanders, Nathan J

2017-03-01

Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant-pollinator interactions from weekly censuses across 3 years in a subalpine ecosystem. Week-to-week turnover of interactions (1) was high, (2) followed a consistent seasonal progression in all years of study and (3) was dominated by interaction rewiring (the reassembly of interactions among species). Simulation models revealed that species' phenologies and relative abundances constrained both total interaction turnover and rewiring. Our findings reveal the diversity of species interactions that may be missed when the temporal dynamics of networks are ignored. © 2017 John Wiley & Sons Ltd/CNRS.

Stability measures in arid ecosystems

NASA Astrophysics Data System (ADS)

Nosshi, M. I.; Brunsell, N. A.; Koerner, S.

2015-12-01

Stability, the capacity of ecosystems to persist in the face of change, has proven its relevance as a fundamental component of ecological theory. Here, we would like to explore meaningful and quantifiable metrics to define stability, with a focus on highly variable arid and semi-arid savanna ecosystems. Recognizing the importance of a characteristic timescale to any definition of stability, our metrics will be focused scales from annual to multi-annual, capturing different aspects of stability. Our three measures of stability, in increasing order of temporal scale, are: (1) Ecosystem resistance, quantified as the degree to which the system maintains its mean state in response to a perturbation (drought), based on inter-annual variability in Normalized Difference Vegetation Index (NDVI). (2) An optimization approach, relevant to arid systems with pulse dynamics, that models vegetation structure and function based on a trade off between the ability to respond to resource availability and avoid stress. (3) Community resilience, measured as species turnover rate (β diversity). Understanding the nature of stability in structurally-diverse arid ecosystems, which are highly variable, yields theoretical insight which has practical implications.

Coral–algal phase shifts alter fish communities and reduce fisheries production

PubMed Central

Ainsworth, Cameron H; Mumby, Peter J

2015-01-01

Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One set of simulations represents extreme scenarios, including 100% loss of coral. In this experiment, ecosystem changes are driven by coral loss itself and a degree of habitat dependency by reef fish is assumed. An alternative simulation is presented without assumed habitat dependency, where changes to the ecosystem are driven by historical observations of reef fish communities when coral is lost. The coral–algal phase shift results in reduced biodiversity and ecosystem maturity. Relative increases in the biomass of small-bodied fish species mean higher productivity on reefs overall, but much reduced landings of traditionally targeted species. PMID:24953835

Mangroves enhance the biomass of coral reef fish communities in the Caribbean.

PubMed

Mumby, Peter J; Edwards, Alasdair J; Arias-González, J Ernesto; Lindeman, Kenyon C; Blackwell, Paul G; Gall, Angela; Gorczynska, Malgosia I; Harborne, Alastair R; Pescod, Claire L; Renken, Henk; Wabnitz, Colette C C; Llewellyn, Ghislane

2004-02-05

Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs.

Mangroves enhance the biomass of coral reef fish communities in the Caribbean

NASA Astrophysics Data System (ADS)

Mumby, Peter J.; Edwards, Alasdair J.; Ernesto Arias-González, J.; Lindeman, Kenyon C.; Blackwell, Paul G.; Gall, Angela; Gorczynska, Malgosia I.; Harborne, Alastair R.; Pescod, Claire L.; Renken, Henk; C. C. Wabnitz, Colette; Llewellyn, Ghislane

2004-02-01

Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs.

Leaf and fine root carbon stocks and turnover are coupled across Arctic ecosystems.

PubMed

Sloan, Victoria L; Fletcher, Benjamin J; Press, Malcolm C; Williams, Mathew; Phoenix, Gareth K

2013-12-01

Estimates of vegetation carbon pools and their turnover rates are central to understanding and modelling ecosystem responses to climate change and their feedbacks to climate. In the Arctic, a region containing globally important stores of soil carbon, and where the most rapid climate change is expected over the coming century, plant communities have on average sixfold more biomass below ground than above ground, but knowledge of the root carbon pool sizes and turnover rates is limited. Here, we show that across eight plant communities, there is a significant positive relationship between leaf and fine root turnover rates (r(2) = 0.68, P < 0.05), and that the turnover rates of both leaf (r(2) = 0.63, P < 0.05) and fine root (r(2) = 0.55, P < 0.05) pools are strongly correlated with leaf area index (LAI, leaf area per unit ground area). This coupling of root and leaf dynamics supports the theory of a whole-plant economics spectrum. We also show that the size of the fine root carbon pool initially increases linearly with increasing LAI, and then levels off at LAI = 1 m(2) m(-2), suggesting a functional balance between investment in leaves and fine roots at the whole community scale. These ecological relationships not only demonstrate close links between above and below-ground plant carbon dynamics but also allow plant carbon pool sizes and their turnover rates to be predicted from the single readily quantifiable (and remotely sensed) parameter of LAI, including the possibility of estimating root data from satellites. © 2013 John Wiley & Sons Ltd.

Oil spills and their impacts on sand beach invertebrate communities: A literature review.

PubMed

Bejarano, Adriana C; Michel, Jacqueline

2016-11-01

Sand beaches are highly dynamic habitats that can experience considerable impacts from oil spills. This review provides a synthesis of the scientific literature on major oil spills and their impacts on sand beaches, with emphasis on studies documenting effects and recoveries of intertidal invertebrate communities. One of the key observations arising from this review is that more attention has generally been given to studying the impacts of oil spills on invertebrates (mostly macrobenthos), and not to documenting their biological recovery. Biological recovery of sand beach invertebrates is highly dynamic, depending on several factors including site-specific physical properties and processes (e.g., sand grain size, beach exposure), the degree of oiling, depth of oil burial, and biological factors (e.g., species-specific life-history traits). Recovery of affected communities ranges from several weeks to several years, with longer recoveries generally associated with physical factors that facilitate oil persistence, or when cleanup activities are absent on heavily oiled beaches. There are considerable challenges in quantifying impacts from spills on sand beach invertebrates because of insufficient baseline information (e.g., distribution, abundance and composition), knowledge gaps in their natural variability (spatial and temporal), and inadequate sampling and replication during and after oil spills. Thus, environment assessments of impacts and recovery require a rigorous experimental design that controls for confounding sources of variability. General recommendations on sampling strategies and toxicity testing, and a preliminary framework for incorporating species-specific life history traits into future assessments are also provided. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ecosystem and Community Responses to Rainfall Manipulations in Shrublands Depends on Dominant Vegetation Cover

NASA Astrophysics Data System (ADS)

Esch, E. H.; Lipson, D.; Kim, J. B.; Cleland, E. E.

2014-12-01

Southern California is predicted to face decreasing precipitation with increased interannual variability in the coming century. Native shrublands in this area are increasingly invaded by exotic annual grasses, though invasion dynamics can vary by rainfall scenario, with wet years generally associated with high invasion pressure. Interplay between rainfall and invasion scenarios can influence carbon stocks and community composition. Here we asked how invasion alters ecosystem and community responses in drought versus high rainfall scenarios, as quantified by community identity, biomass production, and the normalized difference vegetation index (NDVI). To do this, we performed a rainfall manipulation experiment with paired plots dominated either by native shrubs or exotic herbaceous species, subjected to treatments of 50%, 100%, or 150% of ambient rainfall. The study site was located in a coastal sage scrub ecosystem, with patches dominated by native shrubs and exotic grasses located in San Diego County, USA. During two growing seasons, we found that native, herbaceous biomass production was significantly affected by rainfall treatment (p<0.05 for both years), though was not affected by dominant community composition. Photosynthetic biomass production of shrub species also varied by treatment (p=0.035). Exotic biomass production showed a significant interaction between dominant community composition and rainfall treatment, and both individual effects (p<0.001 for all). NDVI showed similar results, but also indicated the importance of rainfall timing on overall biomass production between years. Community composition data showed certain species, of both native and exotic identities, segregating by treatment. These results indicate that exotic species are more sensitive to rainfall, and that increased rainfall may promote greater carbon storage in annual dominated communities when compared to shrub dominated communities in high rainfall years, but with drought, this trend is reversed.

Who acquires infection from whom and how? Disentangling multi-host and multi-mode transmission dynamics in the ‘elimination’ era

PubMed Central

Borlase, Anna; Rudge, James W.

2017-01-01

Multi-host infectious agents challenge our abilities to understand, predict and manage disease dynamics. Within this, many infectious agents are also able to use, simultaneously or sequentially, multiple modes of transmission. Furthermore, the relative importance of different host species and modes can itself be dynamic, with potential for switches and shifts in host range and/or transmission mode in response to changing selective pressures, such as those imposed by disease control interventions. The epidemiology of such multi-host, multi-mode infectious agents thereby can involve a multi-faceted community of definitive and intermediate/secondary hosts or vectors, often together with infectious stages in the environment, all of which may represent potential targets, as well as specific challenges, particularly where disease elimination is proposed. Here, we explore, focusing on examples from both human and animal pathogen systems, why and how we should aim to disentangle and quantify the relative importance of multi-host multi-mode infectious agent transmission dynamics under contrasting conditions, and ultimately, how this can be used to help achieve efficient and effective disease control. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289259

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

PubMed Central

Emerson, Brent C.; Cicconardi, Francesco; Fanciulli, Pietro P.; Shaw, Peter J. A.

2011-01-01

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages. PMID:21768154

From the Last Interglacial to the Anthropocene: Modelling a Complete Glacial Cycle (PalMod)

NASA Astrophysics Data System (ADS)

Brücher, Tim; Latif, Mojib

2017-04-01

We will give a short overview and update on the current status of the national climate modelling initiative PalMod (Paleo Modelling, www.palmod.de). PalMod focuses on the understanding of the climate system dynamics and its variability during the last glacial cycle. The initiative is funded by the German Federal Ministry of Education and Research (BMBF) and its specific topics are: (i) to identify and quantify the relative contributions of the fundamental processes which determined the Earth's climate trajectory and variability during the last glacial cycle, (ii) to simulate with comprehensive Earth System Models (ESMs) the climate from the peak of the last interglacial - the Eemian warm period - up to the present, including the changes in the spectrum of variability, and (iii) to assess possible future climate trajectories beyond this century during the next millennia with sophisticated ESMs tested in such a way. The research is intended to be conducted over a period of 10 years, but with shorter funding cycles. PalMod kicked off in February 2016. The first phase focuses on the last deglaciation (app. the last 23.000 years). From the ESM perspective PalMod pushes forward model development by coupling ESM with dynamical ice sheet models. Computer scientists work on speeding up climate models using different concepts (like parallelisation in time) and one working group is dedicated to perform a comprehensive data synthesis to validate model performance. The envisioned approach is innovative in three respects. First, the consortium aims at simulating a full glacial cycle in transient mode and with comprehensive ESMs which allow full interactions between the physical and biogeochemical components of the Earth system, including ice sheets. Second, we shall address climate variability during the last glacial cycle on a large range of time scales, from interannual to multi-millennial, and attempt to quantify the relative contributions of external forcing and processes internal to the Earth system to climate variability at different time scales. Third, in order to achieve a higher level of understanding of natural climate variability at time scales of millennia, its governing processes and implications for the future climate, we bring together three different research communities: the Earth system modeling community, the proxy data community and the computational science community. The consortium consists of 18 partners including all major modelling centers within Germany. The funding comprises approximately 65 PostDoc positions and more than 120 scientists are involved. PalMod is coordinated at the Helmholtz Centre for Ocean Research Kiel (GEOMAR).

Climate change-driven treeline advances in the Urals alter soil microbial communities

NASA Astrophysics Data System (ADS)

Djukic, Ika; Moiseev, Pavel; Hagedorn, Frank

2016-04-01

Climatic warming may affect microbial communities and their functions either directly through increased temperatures or indirectly by changes in vegetation. Treelines are temperature-limited vegetation boundaries from tundra to forests. In unmanaged regions of the Ural mountains, there is evidence that the forest-tundra ecotone has shifted upward in response to climate warming during the 20th century. Little is known about the effects of the treeline advances on the microbial structure and function and hence they feedbacks on the belowground carbon and nitrogen cycling In our study, we aimed to estimate how ongoing upward shifts of the treeline ecotone might affect soil biodiversity and its function and hence soil carbon (C) and nitrogen (N) dynamics in the Southern and Polar Ural mountains. Along altitudinal gradients reaching from the tundra to forests, we determined the soil microbial community composition (using Phospholipid Fatty Acids method) and quantified the activity of several extracellular enzymes involved in the C and nutrient cycling. In addition, we measured C pools in biomass and soils and quantified C and N mineralization. The results for the top soils, both in South Urals and in the Polar Ural, indicate a close link between climate change driven vegetation changes and soil microbial communities. The observed changes in microbial structure are induced through the resulting more favorable conditions than due to a shift in litter quality. The activities of chitinase were significantly higher under trees than under herbaceous plants, while activities of cellulase and protease declined with altitude from the tundra to the closed forest. In contrast to enzymatic activities, soil carbon stocks did not change significantly with altitude very likely as a result of a balancing out of increased C inputs from vegetation by an enhanced C output through mineralization with forest expansion. The accelerated organic matter turnover in the forest than in the tundra leads to higher contents of mineral N and net nitrification rates. In turn, the increasing N availability may stimulate plant growth and hence, induce a positive feedback between treeline advances and soil nitrogen cycling through soil microbial communities.

Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.

PubMed

Tsigkinopoulou, Areti; Baker, Syed Murtuza; Breitling, Rainer

2017-06-01

Although there is still some skepticism in the biological community regarding the value and significance of quantitative computational modeling, important steps are continually being taken to enhance its accessibility and predictive power. We view these developments as essential components of an emerging 'respectful modeling' framework which has two key aims: (i) respecting the models themselves and facilitating the reproduction and update of modeling results by other scientists, and (ii) respecting the predictions of the models and rigorously quantifying the confidence associated with the modeling results. This respectful attitude will guide the design of higher-quality models and facilitate the use of models in modern applications such as engineering and manipulating microbial metabolism by synthetic biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Consumption dynamics of the adult piscivorous fish community in Spirit Lake, Iowa

USGS Publications Warehouse

Liao, H.; Pierce, C.L.; Larscheid, J.G.

2004-01-01

At Spirit Lake, one of Iowa's most important fisheries, walleye Sander vitreus (formerly Stizostedion vitreum) is one of the most popular species with anglers. Despite a century of walleye stocking and management in Spirit Lake, walleye growth rate, size structure, and angler harvest continue to decline. Our purpose was to determine the magnitude and dynamics of walleye population consumption relative to those of other piscivorous species in Spirit Lake, which would allow managers to judge the feasibility of increasing the abundance, growth rate, and size structure of the walleye population. We quantified food consumption by the adult piscivorous fish community in Spirit Lake over a 3-year period. Data on population dynamics, diet, energy density, and water temperature from 1995 to 1997 were used in bioenergetics models to estimate total consumption by walleye, yellow perch Perca flavescens, smallmouth bass Micropterus dolomieu, largemouth bass Micropterus salmoides, black crappie Pomoxis nigromaculatus, and northern pike Esox lucius. Estimated annual consumption by the piscivorous community varied roughly fourfold, ranging from 154,752 kg in 1995 to 662,776 kg in 1997. Walleyes dominated total consumption, accounting for 68, 73, and 90% (1995-1997, respectively) of total food consumption. Walleyes were also the dominant consumers of fish, accounting for 76, 86, and 97% of piscivorous consumption; yellow perch followed, accounting for 16% of piscivorous consumption in 1995 and 12% in 1996. Yellow perch were the predominant fish prey species in all 3 years, accounting for 68, 52, and 36% of the total prey consumed. Natural reproduction is weak, so high walleye densities are maintained by intensive stocking. Walleye stocking drives piscivorous consumption in Spirit Lake, and yearly variation in the cannibalism of stocked walleye fry may be an important determinant of walleye year-class strength and angler success. Reducing walleye stocking intensity, varying stocking intensity from year to year, and attempting to match stocking intensity with the abundance of prey species other than walleye may improve the walleye fishery in Spirit Lake.

Large-scale modeling on the fate and transport of polycyclic aromatic hydrocarbons (PAHs) in multimedia over China

NASA Astrophysics Data System (ADS)

Huang, Y.; Liu, M.; Wada, Y.; He, X.; Sun, X.

2017-12-01

In recent decades, with rapid economic growth, industrial development and urbanization, expanding pollution of polycyclic aromatic hydrocarbons (PAHs) has become a diversified and complicated phenomenon in China. However, the availability of sufficient monitoring activities for PAHs in multi-compartment and the corresponding multi-interface migration processes are still limited, especially at a large geographic area. In this study, we couple the Multimedia Fate Model (MFM) to the Community Multi-Scale Air Quality (CMAQ) model in order to consider the fugacity and the transient contamination processes. This coupled dynamic contaminant model can evaluate the detailed local variations and mass fluxes of PAHs in different environmental media (e.g., air, surface film, soil, sediment, water and vegetation) across different spatial (a county to country) and temporal (days to years) scales. This model has been applied to a large geographical domain of China at a 36 km by 36 km grid resolution. The model considers response characteristics of typical environmental medium to complex underlying surface. Results suggest that direct emission is the main input pathway of PAHs entering the atmosphere, while advection is the main outward flow of pollutants from the environment. In addition, both soil and sediment act as the main sink of PAHs and have the longest retention time. Importantly, the highest PAHs loadings are found in urbanized and densely populated regions of China, such as Yangtze River Delta and Pearl River Delta. This model can provide a good scientific basis towards a better understanding of the large-scale dynamics of environmental pollutants for land conservation and sustainable development. In a next step, the dynamic contaminant model will be integrated with the continental-scale hydrological and water resources model (i.e., Community Water Model, CWatM) to quantify a more accurate representation and feedbacks between the hydrological cycle and water quality at even larger geographical domains. Keywords: PAHs; Community multi-scale air quality model; Multimedia fate model; Land use

Fluctuating interaction network and time-varying stability of a natural fish community

NASA Astrophysics Data System (ADS)

Ushio, Masayuki; Hsieh, Chih-Hao; Masuda, Reiji; Deyle, Ethan R.; Ye, Hao; Chang, Chun-Wei; Sugihara, George; Kondoh, Michio

2018-02-01

Ecological theory suggests that large-scale patterns such as community stability can be influenced by changes in interspecific interactions that arise from the behavioural and/or physiological responses of individual species varying over time. Although this theory has experimental support, evidence from natural ecosystems is lacking owing to the challenges of tracking rapid changes in interspecific interactions (known to occur on timescales much shorter than a generation time) and then identifying the effect of such changes on large-scale community dynamics. Here, using tools for analysing nonlinear time series and a 12-year-long dataset of fortnightly collected observations on a natural marine fish community in Maizuru Bay, Japan, we show that short-term changes in interaction networks influence overall community dynamics. Among the 15 dominant species, we identify 14 interspecific interactions to construct a dynamic interaction network. We show that the strengths, and even types, of interactions change with time; we also develop a time-varying stability measure based on local Lyapunov stability for attractor dynamics in non-equilibrium nonlinear systems. We use this dynamic stability measure to examine the link between the time-varying interaction network and community stability. We find seasonal patterns in dynamic stability for this fish community that broadly support expectations of current ecological theory. Specifically, the dominance of weak interactions and higher species diversity during summer months are associated with higher dynamic stability and smaller population fluctuations. We suggest that interspecific interactions, community network structure and community stability are dynamic properties, and that linking fluctuating interaction networks to community-level dynamic properties is key to understanding the maintenance of ecological communities in nature.

Quantification of the microphytobenthic primary production in european intertidal mudflats - A modelling approach

USGS Publications Warehouse

Guarini, J.-M.; Blanchard, G.F.; Gros, P.

2000-01-01

A deterministic model quantifying the dynamics of the microphytobenthic biomass in the first centimeter of the mud was formulated as part of the MAST-III/INTRMUD project. The main modelled processes are production by photosynthesis, active vertical migration of the microphytobenthos and global biomass losses, encompassing grazing, mortality and resuspension during immersion periods. The model emphasizes the role of the interface between mud and air, which is crucial for the production. The microalgal biofilm present at the mud surface during day-time emersion periods induces most of the differences between microphytobenthos and phytoplankton communities dynamics. The study of the mathematical properties of the system, under some simplifying assumptions, shows the convergence of the solutions to a stable cyclic equilibrium, in the whole observed range of the frequencies of the physical synchronizers of the production. Resilience time estimates suggest that microphytobenthic biomass attains an equilibrium rapidly, even after a strong perturbation. Around the equilibrium, the local model solutions agree fairly with the in situ observed dynamics of the total biomass. The sensitivity analysis suggests investigating the processes governing biomass losses, which are so far uncertain, and may further vary in space and time. (C) 2000 Elsevier Science Ltd.

Ten Years of Observatory Science from Saanich Inlet on the VENUS Cabled Ocean Observatory

NASA Astrophysics Data System (ADS)

Dewey, R. K.; Tunnicliffe, V.; Macoun, P.; Round, A.

2016-02-01

The Saanich Inlet array of the VENUS cabled ocean observatory, maintained and operated by Ocean Networks Canada, was installed in February 2006, and in 2016 will have supported ten years of comprehensive interactive science. Representing the first in the present generation of cabled observing technologies, this coastal array has provided continuous high power and broadband communications to a variety of instrument platforms, hundreds of sensors, and enabled dozens of short, medium, and long-term studies. Saanich Inlet is a protected fjord with limited tidal action, resulting in an extremely productive environment, with strong seasonal chemical variations driven by episodic deep water renewal events and oxygen reduction processes. The breadth of the research has included microbial and benthic community dynamics, biogeochemical cycles, forensics, quantifying inter-annual variations, benthic-pelagic coupling, sensor testing, plankton dynamics, and bio-turbulence. Observatory measurements include core water properties (CTD & O2) and water-column echo-sounder records, as well as experiment-oriented deployments utilizing cameras, Gliders, Dopplers, hydrophones, and a variety of biogeochemical sensors. With a recently installed Buoy Profiler System for monitoring the entire water column, community plans continue with a dedicated Redox experiment through the 2016-17 seasons. Highlights from the dozens of research papers and theses will be presented to demonstrate the achievements enabled by a comprehensive coastal cabled observing system.

Perspectives of Community Co-Researchers About Group Dynamics and Equitable Partnership Within a Community-Academic Research Team.

PubMed

Vaughn, Lisa M; Jacquez, Farrah; Zhen-Duan, Jenny

2018-04-01

Equitable partnership processes and group dynamics, including individual, relational, and structural factors, have been identified as key ingredients to successful community-based participatory research partnerships. The purpose of this qualitative study was to investigate the key aspects of group dynamics and partnership from the perspectives of community members serving as co-researchers. Semistructured, in-depth interviews were conducted with 15 Latino immigrant co-researchers from an intervention project with Latinos Unidos por la Salud (LU-Salud), a community research team composed of Latino immigrant community members and academic investigators working in a health research partnership. A deductive framework approach guided the interview process and qualitative data analysis. The LU-Salud co-researchers described relationships, personal growth, beliefs/identity motivation (individual dynamics), coexistence (relational dynamics), diversity, and power/resource sharing (structural dynamics) as key foundational aspects of the community-academic partnership. Building on existing CBPR and team science frameworks, these findings demonstrate that group dynamics and partnership processes are fundamental drivers of individual-level motivation and meaning making, which ultimately sustain efforts of community partners to engage with the research team and also contribute to the achievement of intended research outcomes.

Interactions among vegetation, climate, and herbivory control greenhouse gas fluxes in a subarctic coastal wetland

USGS Publications Warehouse

Kelsey, K.C.; Leffler, A.J.; Beard, K.H.; Schmutz, Joel A.; Choi, R.T.; Welker, J.M.

2016-01-01

High-latitude ecosystems are experiencing the most rapid climate changes globally, and in many areas these changes are concurrent with shifts in patterns of herbivory. Individually, climate and herbivory are known to influence biosphere-atmosphere greenhouse gas (GHG) exchange; however, the interactive effects of climate and herbivory in driving GHG fluxes have been poorly quantified, especially in coastal systems that support large populations of migratory waterfowl. We investigated the magnitude and the climatic and physical controls of GHG exchange within the Yukon-Kuskokwim Delta in western Alaska across four distinct vegetation communities formed by herbivory and local microtopography. Net CO2 flux was greatest in the ungrazed Carex meadow community (3.97 ± 0.58 [SE] µmol CO2 m−2 s−1), but CH4 flux was greatest in the grazed community (14.00 ± 6.56 nmol CH4 m−2 s−1). The grazed community is also the only vegetation type where CH4 was a larger contributor than CO2 to overall GHG forcing. We found that vegetation community was an important predictor of CO2 and CH4 exchange, demonstrating that variation in regional gas exchange is best explained when the effect of grazing, determined by the difference between grazed and ungrazed communities, is included. Further, we identified an interaction between temperature and vegetation community, indicating that grazed regions could experience the greatest increases in CH4 emissions with warming. These results suggest that future GHG fluxes could be influenced by both climate and by changes in herbivore population dynamics that expand or contract the vegetation community most responsive to future temperature change.

Belowground Plant Dynamics Across an Arctic Landscape

NASA Astrophysics Data System (ADS)

Salmon, V. G.; Iversen, C. M.; Breen, A. L.; Thornton, P. E.; Wullschleger, S.

2017-12-01

High-latitude ecosystems are made up of a mosaic of different plant communities, all of which are exposed to warming at a rate double that observed in ecosystems at lower latitudes. Arctic regions are an important component of global Earth system models due to the large amounts of soil carbon (C) currently stored in permafrost as well their potential for increased plant C sequestration under warmer conditions. Losses of C from thawing and decomposing permafrost may be offset by increased plant productivity, but plant allocation to belowground structures and acquisition of limiting nutrients remain key sources of uncertainty in these ecosystems. The relationship between belowground plant traits and environmental conditions is not well understood, nor are tradeoffs between above- and belowground plant traits. To address these knowledge gaps, we sampled above- and belowground plant tissues along the Kougarok Hillslope on the Seward Peninsula, Alaska. The vegetation communities sampled included Alder shrubland, willow birch tundra, tussock tundra, dwarf shrub lichen tundra, and non-acidic mountain complex. Within each plant community, aboveground biomass was quantified and specific leaf area, leaf chemistry (%C, %N, %P and δ15N), and wood density were measured. Belowground fine-root biomass and rooting depth distribution were also determined at the community level. Fine roots from shrubs and graminoids were separated so that specific root area, diameter, and chemistry (%C, %N, %P and δ15N) could be assessed for these contrasting plant functional types. Initial findings indicate fine root biomass pools across the widely varying plant communities are constrained by soil depth, regardless of whether the rooting zone is restricted by permafrost or rock. The presence of Alnus viridis subspp. fruticosa, a deciduous shrub that facilitates nitrogen (N) fixation within its root nodules by Frankia bacteria, in Alder shrubland and willow birch tundra communities was associated with increased soil N availability and altered chemistry in neighboring plants. This research aims to identify sources of variation in belowground plant traits and provide insight into how incorporating belowground plant dynamics into Earth system models may improve our ability to predict the fate of these rapidly warming ecosystems.

Developments in dynamic MR elastography for in vitro biomechanical assessment of hyaline cartilage under high-frequency cyclical shear.

PubMed

Lopez, Orlando; Amrami, Kimberly K; Manduca, Armando; Rossman, Phillip J; Ehman, Richard L

2007-02-01

The design, construction, and evaluation of a customized dynamic magnetic resonance elastography (MRE) technique for biomechanical assessment of hyaline cartilage in vitro are described. For quantification of the dynamic shear properties of hyaline cartilage by dynamic MRE, mechanical excitation and motion sensitization were performed at frequencies in the kilohertz range. A custom electromechanical actuator and a z-axis gradient coil were used to generate and image shear waves throughout cartilage at 1000-10,000 Hz. A radiofrequency (RF) coil was also constructed for high-resolution imaging. The technique was validated at 4000 and 6000 Hz by quantifying differences in shear stiffness between soft ( approximately 200 kPa) and stiff ( approximately 300 kPa) layers of 5-mm-thick bilayered phantoms. The technique was then used to quantify the dynamic shear properties of bovine and shark hyaline cartilage samples at frequencies up to 9000 Hz. The results demonstrate that one can obtain high-resolution shear stiffness measurements of hyaline cartilage and small, stiff, multilayered phantoms at high frequencies by generating robust mechanical excitations and using large magnetic field gradients. Dynamic MRE can potentially be used to directly quantify the dynamic shear properties of hyaline and articular cartilage, as well as other cartilaginous materials and engineered constructs. (c) 2007 Wiley-Liss, Inc.

Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut.

PubMed

Jemielita, Matthew; Taormina, Michael J; Burns, Adam R; Hampton, Jennifer S; Rolig, Annah S; Guillemin, Karen; Parthasarathy, Raghuveer

2014-12-16

The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging. Copyright © 2014 Jemielita et al.

Observation and quantification of the quantum dynamics of a strong-field excited multi-level system.

PubMed

Liu, Zuoye; Wang, Quanjun; Ding, Jingjie; Cavaletto, Stefano M; Pfeifer, Thomas; Hu, Bitao

2017-01-04

The quantum dynamics of a V-type three-level system, whose two resonances are first excited by a weak probe pulse and subsequently modified by another strong one, is studied. The quantum dynamics of the multi-level system is closely related to the absorption spectrum of the transmitted probe pulse and its modification manifests itself as a modulation of the absorption line shape. Applying the dipole-control model, the modulation induced by the second strong pulse to the system's dynamics is quantified by eight intensity-dependent parameters, describing the self and inter-state contributions. The present study opens the route to control the quantum dynamics of multi-level systems and to quantify the quantum-control process.

Enhancing quantitative approaches for assessing community resilience

USGS Publications Warehouse

Chuang, W. C.; Garmestani, A.S.; Eason, T. N.; Spanbauer, T. L.; Fried-Peterson, H. B.; Roberts, C.P.; Sundstrom, Shana M.; Burnett, J.L.; Angeler, David G.; Chaffin, Brian C.; Gunderson, L.; Twidwell, Dirac; Allen, Craig R.

2018-01-01

Scholars from many different intellectual disciplines have attempted to measure, estimate, or quantify resilience. However, there is growing concern that lack of clarity on the operationalization of the concept will limit its application. In this paper, we discuss the theory, research development and quantitative approaches in ecological and community resilience. Upon noting the lack of methods that quantify the complexities of the linked human and natural aspects of community resilience, we identify several promising approaches within the ecological resilience tradition that may be useful in filling these gaps. Further, we discuss the challenges for consolidating these approaches into a more integrated perspective for managing social-ecological systems.

Enhancing quantitative approaches for assessing community resilience.

PubMed

Chuang, W C; Garmestani, A; Eason, T N; Spanbauer, T L; Fried-Petersen, H B; Roberts, C P; Sundstrom, S M; Burnett, J L; Angeler, D G; Chaffin, B C; Gunderson, L; Twidwell, D; Allen, C R

2018-05-01

Scholars from many different intellectual disciplines have attempted to measure, estimate, or quantify resilience. However, there is growing concern that lack of clarity on the operationalization of the concept will limit its application. In this paper, we discuss the theory, research development and quantitative approaches in ecological and community resilience. Upon noting the lack of methods that quantify the complexities of the linked human and natural aspects of community resilience, we identify several promising approaches within the ecological resilience tradition that may be useful in filling these gaps. Further, we discuss the challenges for consolidating these approaches into a more integrated perspective for managing social-ecological systems. Published by Elsevier Ltd.

Invasive lionfish had no measurable effect on prey fish community structure across the Belizean Barrier Reef

PubMed Central

Valdivia, Abel; Cox, Courtney E.; Silbiger, Nyssa J.; Bruno, John F.

2017-01-01

Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0–10 cm total length) at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations. PMID:28560093

Invasive lionfish had no measurable effect on prey fish community structure across the Belizean Barrier Reef.

PubMed

Hackerott, Serena; Valdivia, Abel; Cox, Courtney E; Silbiger, Nyssa J; Bruno, John F

2017-01-01

Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0-10 cm total length) at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations.

Unconventional Tools for an Unconventional Resource: Community and Landscape Planning for Shale in the Marcellus Region

NASA Astrophysics Data System (ADS)

Murtha, T., Jr.; Orland, B.; Goldberg, L.; Hammond, R.

2014-12-01

Deep shale natural gas deposits made accessible by new technologies are quickly becoming a considerable share of North America's energy portfolio. Unlike traditional deposits and extraction footprints, shale gas offers dispersed and complex landscape and community challenges. These challenges are both cultural and environmental. This paper describes the development and application of creative geospatial tools as a means to engage communities along the northern tier counties of Pennsylvania, experiencing Marcellus shale drilling in design and planning. Uniquely combining physical landscape models with predictive models of exploration activities, including drilling, pipeline construction and road reconstruction, the tools quantify the potential impacts of drilling activities for communities and landscapes in the commonwealth of Pennsylvania. Dividing the state into 9836 watershed sub-basins, we first describe the current state of Marcellus related activities through 2014. We then describe and report the results of three scaled predictive models designed to investigate probable sub-basins where future activities will be focused. Finally, the core of the paper reports on the second level of tools we have now developed to engage communities in planning for unconventional gas extraction in Pennsylvania. Using a geodesign approach we are working with communities to transfer information for comprehensive landscape planning and informed decision making. These tools not only quantify physical landscape impacts, but also quantify potential visual, aesthetic and cultural resource implications.

The activated sludge ecosystem contains a core community of abundant organisms

PubMed Central

Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

2016-01-01

Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

Impact of Soil Texture on Soil Ciliate Communities

NASA Astrophysics Data System (ADS)

Chau, J. F.; Brown, S.; Habtom, E.; Brinson, F.; Epps, M.; Scott, R.

2014-12-01

Soil water content and connectivity strongly influence microbial activities in soil, controlling access to nutrients and electron acceptors, and mediating interactions between microbes within and between trophic levels. These interactions occur at or below the pore scale, and are influenced by soil texture and structure, which determine the microscale architecture of soil pores. Soil protozoa are relatively understudied, especially given the strong control they exert on bacterial communities through predation. Here, ciliate communities in soils of contrasting textures were investigated. Two ciliate-specific primer sets targeting the 18S rRNA gene were used to amplify DNA extracted from eight soil samples collected from Sumter National Forest in western South Carolina. Primer sets 121F-384F-1147R (semi-nested) and 315F-959R were used to amplify soil ciliate DNA via polymerase chain reaction (PCR), and the resulting PCR products were analyzed by gel electrophoresis to obtain quantity and band size. Approximately two hundred ciliate 18S rRNA sequences were obtained were obtained from each of two contrasting soils. Sequences were aligned against the NCBI GenBank database for identification, and the taxonomic classification of best-matched sequences was determined. The ultimate goal of the work is to quantify changes in the ciliate community under short-timescale changes in hydrologic conditions for varying soil textures, elucidating dynamic responses to desiccation stress in major soil ciliate taxa.

Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.

2014-04-07

Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retainedmore » in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.« less

Opinion diversity and community formation in adaptive networks

NASA Astrophysics Data System (ADS)

Yu, Y.; Xiao, G.; Li, G.; Tay, W. P.; Teoh, H. F.

2017-10-01

It is interesting and of significant importance to investigate how network structures co-evolve with opinions. In this article, we show that, a simple model integrating consensus formation, link rewiring, and opinion change allows complex system dynamics to emerge, driving the system into a dynamic equilibrium with the co-existence of diversified opinions. Specifically, similar opinion holders may form into communities yet with no strict community consensus; and rather than being separated into disconnected communities, different communities are connected by a non-trivial proportion of inter-community links. More importantly, we show that the complex dynamics may lead to different numbers of communities at the steady state with a given tolerance between different opinion holders. We construct a framework for theoretically analyzing the co-evolution process. Theoretical analysis and extensive simulation results reveal some useful insights into the complex co-evolution process, including the formation of dynamic equilibrium, the transition between different steady states with different numbers of communities, and the dynamics between opinion distribution and network modularity.

A computer analysis of reflex eyelid motion in normal subjects and in facial neuropathy.

PubMed

Somia, N N; Rash, G S; Epstein, E E; Wachowiak, M; Sundine, M J; Stremel, R W; Barker, J H; Gossman, D

2000-12-01

To demonstrate how computerized eyelid motion analysis can quantify the human reflex blink. Seventeen normal subjects and 10 patients with unilateral facial nerve paralysis were analyzed. Eyelid closure is currently evaluated by systems primarily designed to assess lower/midfacial movements. The methods are subjective, difficult to reproduce, and measure only volitional closure. Reflex closure is responsible for eye hydration, and its evaluation demands dynamic analysis. A 60Hz video camera incorporated into a helmet was used to analyze blinking. Reflective markers on the forehead and eyelids allowed for the dynamic measurement of the reflex blink. Eyelid displacement, velocity and acceleration were calculated. The degree of synchrony between bilateral blinks was also determined. This study demonstrates that video motion analysis can describe normal and altered eyelid motions in a quantifiable manner. To our knowledge, this is the first study to measure dynamic reflex blinks. Eyelid closure may now be evaluated in kinematic terms. This technique could increase understanding of eyelid motion and permit more accurate evaluation of eyelid function. Dynamic eyelid evaluation has immediate applications in the treatment of facial palsy affecting the reflex blink. Relevance No method has been developed that objectively quantifies dynamic eyelid closure. Methods currently in use evaluate only volitional eyelid closure, and are based on direct and indirect observer assessments. These methods are subjective and are incapable of analyzing dynamic eyelid movements, which are critical to maintenance of corneal hydration and comfort. A system that quantifies eyelid kinematics can provide a functional analysis of blink disorders and an objective evaluation of their treatment(s).

Quantifying Transmission of Clostridium difficile within and outside Healthcare Settings

PubMed Central

Olsen, Margaret A.; Dubberke, Erik R.; Galvani, Alison P.; Townsend, Jeffrey P.

2016-01-01

To quantify the effect of hospital and community-based transmission and control measures on Clostridium difficile infection (CDI), we constructed a transmission model within and between hospital, community, and long-term care-facility settings. By parameterizing the model from national databases and calibrating it to C. difficile prevalence and CDI incidence, we found that hospitalized patients with CDI transmit C. difficile at a rate 15 (95% CI 7.2–32) times that of asymptomatic patients. Long-term care facility residents transmit at a rate of 27% (95% CI 13%–51%) that of hospitalized patients, and persons in the community at a rate of 0.1% (95% CI 0.062%–0.2%) that of hospitalized patients. Despite lower transmission rates for asymptomatic carriers and community sources, these transmission routes have a substantial effect on hospital-onset CDI because of the larger reservoir of hospitalized carriers and persons in the community. Asymptomatic carriers and community sources should be accounted for when designing and evaluating control interventions. PMID:26982504

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

The benthoneuston of the Black Sea: Composition and environmental factors influencing its nocturnal dynamic

NASA Astrophysics Data System (ADS)

Vereshchaka, Alexander L.; Anokhina, Ludmila L.

2017-05-01

Plankton fauna nocturnally migrating from the sea-floor or near-bottom layer to the uppermost surface layer (benthoneuston) links benthic, benthopelagic, pelagic, and neustonic realms. We conducted five intervals of sampling (every 1-2 h during five nights) synchronously in the neustal (surface to 10-cm depth layer) and in the water column below to examine which taxa concentrate in the neustal, and under which circumstances they do so. We tested the following environmental factors: sea-floor biotope type, temperature, time after sunset, time to midnight, moon phase, and moon altitude. Of the 77 taxa recorded, about half (41) were found in the neustal. Among these, less than half (16) of the taxa showed a quantified attraction (by L-index) to the neustal and may be called the true benthoneuston. In contrast to the benthopelagic zone, where the contribution of the characteristic benthopelagic fauna exceeded 50%, the neustal was not dominated by a specific benthoneuston fauna. Nocturnal dynamics of the benthoneuston was mainly controlled by the proximity of the twilight time, then by the sea-floor biotope type and time to midnight. Neustonic taxa were more affected by moon illumination (moon phase and moon altitude) than those in the water column below. The benthoneuston in the studied area was represented by either juveniles or reproducing adults. This component of plankton communities is thus temporary and seasonal, at least in the temperate Black Sea. In the "high" summer-autumn season, contribution of benthoneuston to the coastal plankton communities is significant, whilst in winter this contribution may be negligible. The next step in the understanding of the role of benthoneuston should be associated with tropical areas where seasonal changes in reproduction are less distinctive and this group may represent an important permanent component of coastal communities.

Global Climate Impacts of Fixing the Southern Ocean Shortwave Radiation Bias in the Community Earth System Model (CESM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kay, Jennifer E.; Wall, Casey; Yettella, Vineel

Here, a large, long-standing, and pervasive climate model bias is excessive absorbed shortwave radiation (ASR) over the midlatitude oceans, especially the Southern Ocean. This study investigates both the underlying mechanisms for and climate impacts of this bias within the Community Earth System Model, version 1, with the Community Atmosphere Model, version 5 [CESM1(CAM5)]. Excessive Southern Ocean ASR in CESM1(CAM5) results in part because low-level clouds contain insufficient amounts of supercooled liquid. In a present-day atmosphere-only run, an observationally motivated modification to the shallow convection detrainment increases supercooled cloud liquid, brightens low-level clouds, and substantially reduces the Southern Ocean ASR bias.more » Tuning to maintain global energy balance enables reduction of a compensating tropical ASR bias. In the resulting preindustrial fully coupled run with a brighter Southern Ocean and dimmer tropics, the Southern Ocean cools and the tropics warm. As a result of the enhanced meridional temperature gradient, poleward heat transport increases in both hemispheres (especially the Southern Hemisphere), and the Southern Hemisphere atmospheric jet strengthens. Because northward cross-equatorial heat transport reductions occur primarily in the ocean (80%), not the atmosphere (20%), a proposed atmospheric teleconnection linking Southern Ocean ASR bias reduction and cooling with northward shifts in tropical precipitation has little impact. In summary, observationally motivated supercooled liquid water increases in shallow convective clouds enable large reductions in long-standing climate model shortwave radiation biases. Of relevance to both model bias reduction and climate dynamics, quantifying the influence of Southern Ocean cooling on tropical precipitation requires a model with dynamic ocean heat transport.« less

Global Climate Impacts of Fixing the Southern Ocean Shortwave Radiation Bias in the Community Earth System Model (CESM)

DOE PAGES

Kay, Jennifer E.; Wall, Casey; Yettella, Vineel; ...

2016-06-10

Here, a large, long-standing, and pervasive climate model bias is excessive absorbed shortwave radiation (ASR) over the midlatitude oceans, especially the Southern Ocean. This study investigates both the underlying mechanisms for and climate impacts of this bias within the Community Earth System Model, version 1, with the Community Atmosphere Model, version 5 [CESM1(CAM5)]. Excessive Southern Ocean ASR in CESM1(CAM5) results in part because low-level clouds contain insufficient amounts of supercooled liquid. In a present-day atmosphere-only run, an observationally motivated modification to the shallow convection detrainment increases supercooled cloud liquid, brightens low-level clouds, and substantially reduces the Southern Ocean ASR bias.more » Tuning to maintain global energy balance enables reduction of a compensating tropical ASR bias. In the resulting preindustrial fully coupled run with a brighter Southern Ocean and dimmer tropics, the Southern Ocean cools and the tropics warm. As a result of the enhanced meridional temperature gradient, poleward heat transport increases in both hemispheres (especially the Southern Hemisphere), and the Southern Hemisphere atmospheric jet strengthens. Because northward cross-equatorial heat transport reductions occur primarily in the ocean (80%), not the atmosphere (20%), a proposed atmospheric teleconnection linking Southern Ocean ASR bias reduction and cooling with northward shifts in tropical precipitation has little impact. In summary, observationally motivated supercooled liquid water increases in shallow convective clouds enable large reductions in long-standing climate model shortwave radiation biases. Of relevance to both model bias reduction and climate dynamics, quantifying the influence of Southern Ocean cooling on tropical precipitation requires a model with dynamic ocean heat transport.« less

Circumpolar arctic tundra biomass and productivity dynamics in response to projected climate change and herbivory.

PubMed

Yu, Qin; Epstein, Howard; Engstrom, Ryan; Walker, Donald

2017-09-01

Satellite remote sensing data have indicated a general 'greening' trend in the arctic tundra biome. However, the observed changes based on remote sensing are the result of multiple environmental drivers, and the effects of individual controls such as warming, herbivory, and other disturbances on changes in vegetation biomass, community structure, and ecosystem function remain unclear. We apply ArcVeg, an arctic tundra vegetation dynamics model, to estimate potential changes in vegetation biomass and net primary production (NPP) at the plant community and functional type levels. ArcVeg is driven by soil nitrogen output from the Terrestrial Ecosystem Model, existing densities of Rangifer populations, and projected summer temperature changes by the NCAR CCSM4.0 general circulation model across the Arctic. We quantified the changes in aboveground biomass and NPP resulting from (i) observed herbivory only; (ii) projected climate change only; and (iii) coupled effects of projected climate change and herbivory. We evaluated model outputs of the absolute and relative differences in biomass and NPP by country, bioclimate subzone, and floristic province. Estimated potential biomass increases resulting from temperature increase only are approximately 5% greater than the biomass modeled due to coupled warming and herbivory. Such potential increases are greater in areas currently occupied by large or dense Rangifer herds such as the Nenets-occupied regions in Russia (27% greater vegetation increase without herbivores). In addition, herbivory modulates shifts in plant community structure caused by warming. Plant functional types such as shrubs and mosses were affected to a greater degree than other functional types by either warming or herbivory or coupled effects of the two. © 2017 John Wiley & Sons Ltd.

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales.

PubMed

Bautista-de Los Santos, Quyen Melina; Schroeder, Joanna L; Blakemore, Oliver; Moses, Jonathan; Haffey, Mark; Sloan, William; Pinto, Ameet J

2016-03-01

High-throughput and deep DNA sequencing, particularly amplicon sequencing, is being increasingly utilized to reveal spatial and temporal dynamics of bacterial communities in drinking water systems. Whilst the sampling and methodological biases associated with PCR and sequencing have been studied in other environments, they have not been quantified for drinking water. These biases are likely to have the greatest effect on the ability to characterize subtle spatio-temporal patterns influenced by process/environmental conditions. In such cases, intra-sample variability may swamp any underlying small, systematic variation. To evaluate this, we undertook a study with replication at multiple levels including sampling sites, sample collection, PCR amplification, and high throughput sequencing of 16S rRNA amplicons. The variability inherent to the PCR amplification and sequencing steps is significant enough to mask differences between bacterial communities from replicate samples. This was largely driven by greater variability in detection of rare bacteria (relative abundance <0.01%) across PCR/sequencing replicates as compared to replicate samples. Despite this, we captured significant changes in bacterial community over diurnal time-scales and find that the extent and pattern of diurnal changes is specific to each sampling location. Further, we find diurnal changes in bacterial community arise due to differences in the presence/absence of the low abundance bacteria and changes in the relative abundance of dominant bacteria. Finally, we show that bacterial community composition is significantly different across sampling sites for time-periods during which there are typically rapid changes in water use. This suggests hydraulic changes (driven by changes in water demand) contribute to shaping the bacterial community in bulk drinking water over diurnal time-scales. Copyright © 2015 Elsevier Ltd. All rights reserved.

Overlapping community detection based on link graph using distance dynamics

NASA Astrophysics Data System (ADS)

Chen, Lei; Zhang, Jing; Cai, Li-Jun

2018-01-01

The distance dynamics model was recently proposed to detect the disjoint community of a complex network. To identify the overlapping structure of a network using the distance dynamics model, an overlapping community detection algorithm, called L-Attractor, is proposed in this paper. The process of L-Attractor mainly consists of three phases. In the first phase, L-Attractor transforms the original graph to a link graph (a new edge graph) to assure that one node has multiple distances. In the second phase, using the improved distance dynamics model, a dynamic interaction process is introduced to simulate the distance dynamics (shrink or stretch). Through the dynamic interaction process, all distances converge, and the disjoint community structure of the link graph naturally manifests itself. In the third phase, a recovery method is designed to convert the disjoint community structure of the link graph to the overlapping community structure of the original graph. Extensive experiments are conducted on the LFR benchmark networks as well as real-world networks. Based on the results, our algorithm demonstrates higher accuracy and quality than other state-of-the-art algorithms.

Supporting statement for community study of human response to aircraft noise

NASA Technical Reports Server (NTRS)

Dempsey, T. K.; Deloach, R.; Stephens, D. G.

1980-01-01

A study plan for quantifying the relationship between human annoyance and the noise level of individual aircraft events is studied. The validity of various noise descriptors or noise metrics for quantifying aircraft noise levels are assessed.

Quantifying stochasticity in the dynamics of delay-coupled semiconductor lasers via forbidden patterns.

PubMed

Tiana-Alsina, Jordi; Buldú, Javier M; Torrent, M C; García-Ojalvo, Jordi

2010-01-28

We quantify the level of stochasticity in the dynamics of two mutually coupled semiconductor lasers. Specifically, we concentrate on a regime in which the lasers synchronize their dynamics with a non-zero lag time, and the leader and laggard roles alternate irregularly between the lasers. We analyse this switching dynamics in terms of the number of forbidden patterns of the alternate time series. The results reveal that the system operates in a stochastic regime, with the level of stochasticity decreasing as the lasers are pumped further away from their lasing threshold. This behaviour is similar to that exhibited by a single semiconductor laser subject to external optical feedback, as its dynamics shifts from the regime of low-frequency fluctuations to coherence collapse. This journal is © 2010 The Royal Society

Improving assessment and modelling of climate change impacts on global terrestrial biodiversity.

PubMed

McMahon, Sean M; Harrison, Sandy P; Armbruster, W Scott; Bartlein, Patrick J; Beale, Colin M; Edwards, Mary E; Kattge, Jens; Midgley, Guy; Morin, Xavier; Prentice, I Colin

2011-05-01

Understanding how species and ecosystems respond to climate change has become a major focus of ecology and conservation biology. Modelling approaches provide important tools for making future projections, but current models of the climate-biosphere interface remain overly simplistic, undermining the credibility of projections. We identify five ways in which substantial advances could be made in the next few years: (i) improving the accessibility and efficiency of biodiversity monitoring data, (ii) quantifying the main determinants of the sensitivity of species to climate change, (iii) incorporating community dynamics into projections of biodiversity responses, (iv) accounting for the influence of evolutionary processes on the response of species to climate change, and (v) improving the biophysical rule sets that define functional groupings of species in global models. Published by Elsevier Ltd.

Biotic interactions at hydrothermal vents: Recruitment inhibition by the mussel Bathymodiolus thermophilus

NASA Astrophysics Data System (ADS)

Lenihan, H. S.; Mills, S. W.; Mullineaux, L. S.; Peterson, C. H.; Fisher, C. R.; Micheli, F.

2008-12-01

The structure and dynamics of marine communities are regulated in part by variation in recruitment. As in other ecosystems, recruitment at deep-sea hydrothermal vents is controlled by the interplay of propagule supply and behavior, gradients in physical-chemical conditions, and biotic interactions during pre- and post-settlement periods. Recent research along the East Pacific Rise indicates that inhibition of recently settled larvae by mobile predators (mainly limpets) influences patterns of recruitment and subsequent community succession. We conducted a manipulative experiment at the same sites (˜2510 m water depth) to test whether high-density assemblages of the mussel Bathymodiolus thermophilus also inhibit recruitment. In a preliminary study, recruitment of vent invertebrates within the faunal zone dominated by B. thermophilus was strikingly different at two sites, East Wall and Worm Hole. East Wall had high densities of mussels but very low total recruitment. In contrast, Worm Hole had few mussels but high recruitment. Using the submersible Alvin, we transplanted a large number of mussels from East Wall to Worm Hole and quantified recruitment on basalt blocks placed in three treatments: (1) naturally high densities of mussels at East Wall; (2) naturally low densities of mussels at Worm Hole; and (3) high densities of transplanted mussels at Worm Hole. After 11 months, a total of 24 taxa had recruited to the basalt blocks. Recruitment was 44-60% lower in the transplanted high-density mussel patch at Worm Hole and the natural high-density patch at East Wall than within the natural low-density patch at Worm Hole. Biotic processes that may have caused the pattern of recruitment observed included predation of larvae via water filtration by mussels, larval avoidance of superior competitors, interference competition, and enhanced predation by species within the mussel-bed community. Our results indicate that biotic interactions affecting recruitment must be understood to explain patterns of invertebrate community organization and dynamics at hydrothermal vents.

Quantifying an Integral Ecology Framework: A Case Study of the Riverina, Australia

NASA Astrophysics Data System (ADS)

Wheeler, Sarah A.; Haensch, Juliane; Edwards, Jane; Schirmer, Jackie; Zuo, Alec

2018-02-01

Communities in Australia's Murray-Darling Basin face the challenge of trying to achieve social, economic, and environmental sustainability; but experience entrenched conflict about the best way to achieve a sustainable future, especially for small rural communities. Integral ecology is a philosophical concept that seeks to address community, economic, social, and environmental sustainability simultaneously. Its inclusive processes are designed to reduce stakeholder conflict. However, to date the application of the integral ecology concept has been largely qualitative in nature. This study developed a quantitative integral ecology framework, and applied this framework to a case study of the Riverina, in the Murray-Darling Basin. Seventy-seven community-focused initiatives were assessed, ranked, and quantified. The majority of the community-focused ranked initiatives did not exhibit all aspects of integral ecology. Initiatives typically prioritized either (1) economic and community development or (2) environmental health; rarely both together. The integral ecology framework developed here enables recommendations on future community initiatives and may provide a pathway for community leaders and other policy-makers to more readily apply integral ecology objectives. Further research refining the framework's operationalization, application and implementation to a wider-scale may enhance communities' capacity to develop and grow sustainably.

Astute, Assertive, and Alpha-1: Quantifying Empowerment in a Rare Genetic Community

ERIC Educational Resources Information Center

Finn, Symma

2008-01-01

We investigated empowerment in the Alpha-1 Antitrypsin Deficiency (Alpha-1) community, a rare, genetic disease network in the United States. The research was motivated by nine years of observations in the community. After observing what seemed to be a heightened amount of activism among Alpha-1 community members, I had hypothesized that this…

Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes.

PubMed

Roguet, Adélaïde; Therial, Claire; Catherine, Arnaud; Bressy, Adèle; Varrault, Gilles; Bouhdamane, Lila; Tran, Viet; Lemaire, Bruno J; Vincon-Leite, Brigitte; Saad, Mohamed; Moulin, Laurent; Lucas, Françoise S

2018-05-01

Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 10 3 to 1.9 × 10 8 genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.

Phosphorous bioavailability along a soil chronosequence

NASA Astrophysics Data System (ADS)

Roberts, K.; Vokhshoori, N. L.; Rosenthanl, A.; Turner, B. L.; Condron, L.; Paytan, A.

2011-12-01

In humid environments, as soils age nutrient loss through leaching and chemical trasformations affect the succession and composition of the biological communities. In particular phosphorus (P), often a limiting nutrient in terrestrial systems, tends to evolve into less bio-available forms over time, compounding loss through leaching. Thus P availability has the potential to strongly affect community productivity and structure. Low standing stock of P may not necessarily imply P limitation as the bio-available P pool is continuously recycled and re-utilized. Thus extensive recycling can reduce to varying extents the effect of P limitation. The bio-availability and recycling rates of P are difficult to measure; multiple sequential extraction processes have been developed to try to define and quantify the bio-availability of both inorganic and organic forms of P. In this preliminary study, we will present results of P concentrations in different soil fractions and oxygen isotopes in phosphate. These data together increase our understanding of P dynamics as soils age. The work is being done with a well characterized and dated chronosequence from the west coast of the South Island of New Zealand near the Haast River.

Climate Change Impacts on Natural Sulfur Production: Ocean Acidification and Community Shifts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menzo, Zachary; Elliott, Scott; Hartin, Corinne

Utilizing the reduced-complexity model Hector, a regional scale analysis was conducted quantifying the possible effects climate change may have on dimethyl sulfide (DMS) emissions within the oceans. The investigation began with a review of the sulfur cycle in modern Earth system models. We then expanded the biogeochemical representation within Hector to include a natural ocean component while accounting for acidification and planktonic community shifts. The report presents results from both a latitudinal and a global perspective. This new approach highlights disparate outcomes which have been inadequately characterized via planetary averages in past publications. Our findings suggest that natural sulfur emissionsmore » (ESN) may exert a forcing up to 4 times that of the CO2 marine feedback, 0.62 and 0.15 Wm-2, respectively, and reverse the radiative forcing sign in low latitudes. Additionally, sensitivity tests were conducted to demonstrate the need for further examination of the DMS loop. Ultimately, the present work attempts to include dynamic ESN within reduced-complexity simulations of the sulfur cycle, illustrating its impact on the global radiative budget« less

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soner Yorgun, M.; Rood, Richard B.

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

DOE PAGES

Soner Yorgun, M.; Rood, Richard B.

2016-11-11

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

Quantifying and comparing dynamic predictive accuracy of joint models for longitudinal marker and time-to-event in presence of censoring and competing risks.

PubMed

Blanche, Paul; Proust-Lima, Cécile; Loubère, Lucie; Berr, Claudine; Dartigues, Jean-François; Jacqmin-Gadda, Hélène

2015-03-01

Thanks to the growing interest in personalized medicine, joint modeling of longitudinal marker and time-to-event data has recently started to be used to derive dynamic individual risk predictions. Individual predictions are called dynamic because they are updated when information on the subject's health profile grows with time. We focus in this work on statistical methods for quantifying and comparing dynamic predictive accuracy of this kind of prognostic models, accounting for right censoring and possibly competing events. Dynamic area under the ROC curve (AUC) and Brier Score (BS) are used to quantify predictive accuracy. Nonparametric inverse probability of censoring weighting is used to estimate dynamic curves of AUC and BS as functions of the time at which predictions are made. Asymptotic results are established and both pointwise confidence intervals and simultaneous confidence bands are derived. Tests are also proposed to compare the dynamic prediction accuracy curves of two prognostic models. The finite sample behavior of the inference procedures is assessed via simulations. We apply the proposed methodology to compare various prediction models using repeated measures of two psychometric tests to predict dementia in the elderly, accounting for the competing risk of death. Models are estimated on the French Paquid cohort and predictive accuracies are evaluated and compared on the French Three-City cohort. © 2014, The International Biometric Society.

Evolution properties of the community members for dynamic networks

NASA Astrophysics Data System (ADS)

Yang, Kai; Guo, Qiang; Li, Sheng-Nan; Han, Jing-Ti; Liu, Jian-Guo

2017-03-01

The collective behaviors of community members for dynamic social networks are significant for understanding evolution features of communities. In this Letter, we empirically investigate the evolution properties of the new community members for dynamic networks. Firstly, we separate data sets into different slices, and analyze the statistical properties of new members as well as communities they joined in for these data sets. Then we introduce a parameter φ to describe community evolution between different slices and investigate the dynamic community properties of the new community members. The empirical analyses for the Facebook, APS, Enron and Wiki data sets indicate that both the number of new members and joint communities increase, the ratio declines rapidly and then becomes stable over time, and most of the new members will join in the small size communities that is s ≤ 10. Furthermore, the proportion of new members in existed communities decreases firstly and then becomes stable and relatively small for these data sets. Our work may be helpful for deeply understanding the evolution properties of community members for social networks.

Ecology of duckweed ponds used for nutrient recovery from wastewater.

PubMed

Teles, C C; Mohedano, R A; Tonon, G; Filho, P Belli; Costa, R H R

2017-06-01

The microorganism community that grows under duckweed shelter can play an important role on treatment processes. Therefore, the present study aimed to assess the zooplankton dynamic and microbial community in duckweed ponds (DPs) applied for domestic wastewater treatment under open field conditions. A pilot system comprised of two DPs in series (DP1 and DP2), with 10 m 2 each, received domestic wastewater through a flow rate of 200 L·day -1 . Thus, the system was monitored during 314 days through samples collected and analysed weekly. Also, the zooplankton organisms were identified and quantified. DNA sequencing was performed in order to identify the bacterial populations. The findings showed a high efficiency of nutrient removal with 93% and 91% of total phosphorus and total nitrogen, respectively. A high density of microcrustaceans was observed in DP1 reaching 4,700 org.100 mL -1 and rotifers (over than 32,000 org.100 mL -1 ) in DP2, that could be related to the low suspended solids concentration (<30 mg·L -1 ) and turbidity (<10 NTU). The bacterial community showed a strong heterogeneity between samples collected along the seasons. Through these findings, it is possible to realise that the understanding of ecology could help to enhance the operation and designs of DPs.

Parasite transmission in a natural multihost–multiparasite community

PubMed Central

2017-01-01

Understanding the transmission and dynamics of infectious diseases in natural communities requires understanding the extent to which the ecology, evolution and epidemiology of those diseases are shaped by alternative hosts. We performed laboratory experiments to test how parasite spillover affected traits associated with transmission in two co-occurring parasites: the bacterium Pasteuria ramosa and the fungus Metschnikowia bicuspidata. Both parasites were capable of transmission from the reservoir host (Daphnia dentifera) to the spillover host (Ceriodaphnia dubia), but this occurred at a much higher rate for the fungus than the bacterium. We quantified transmission potential by combining information on parasite transmission and growth rate, and used this to compare parasite fitness in the two host species. For both parasites, transmission potential was lower in the spillover host. For the bacterium, virulence was higher in the spillover host. Transmission back to the original host was high for both parasites, with spillover influencing transmission rate of the fungus but not the bacterium. Thus, while inferior, the spillover host is not a dead-end for either parasite. Overall, our results demonstrate that the presence of multiple hosts in a community can have important consequences for disease transmission, and host and parasite fitness. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289264

Carcasses of invasive species are predominantly utilized by invasive scavengers in an island ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abernethy, Erin F.; Turner, Kelsey L.; Beasley, James C.

Invasive species have significantly affected ecosystems, particularly islands, and species invasions continue with increasing globalization. Largely unstudied, the influence of invasive species on island ecosystem functions, especially scavenging and decomposition, could be substantive. Quantifying carcass utilization by different scavengers and shifts in community dynamics in the presence of invasive animals is of particular interest for understanding impacts on nutrient recycling. Invasive species could benefit greatly from carcass resources within highly invaded island ecosystems, through increased invasion success and population growth, subsequently exacerbating their impacts on native species. Here, we quantified how experimentally placed invasive amphibian, reptile, small mammal, and birdmore » carcasses were utilized by vertebrate and invertebrate scavengers on the Big Island of Hawai’i in three island habitats: a barren lava field, a vegetated lava field, and a rainforest. We used camera traps to record vertebrate scavengers removing carcasses and elapsed time until removal. We evaluated differences in cavenging between vertebrates and invertebrates and within the vertebrate community across different habitats and carcass types. Despite the small carcass sizes (<1 kg) used in this study, 55% of carcasses were removed by vertebrate scavengers, all invasive: mongoose, rodents, cats, pigs, and a common myna. Our data indicate that invasive vertebrate scavengers in this island ecosystem are highly efficient at assimilating a range of carrion resources across a variety of habitats. Carcasses of invasive animals could contribute substantially to energy budgets of other invasive vertebrate species. Finally, this may be a critical component contributing to successful invasions especially on islands and subsequent impacts on ecosystem function.« less

Carcasses of invasive species are predominantly utilized by invasive scavengers in an island ecosystem

DOE PAGES

Abernethy, Erin F.; Turner, Kelsey L.; Beasley, James C.; ...

2016-10-01

Invasive species have significantly affected ecosystems, particularly islands, and species invasions continue with increasing globalization. Largely unstudied, the influence of invasive species on island ecosystem functions, especially scavenging and decomposition, could be substantive. Quantifying carcass utilization by different scavengers and shifts in community dynamics in the presence of invasive animals is of particular interest for understanding impacts on nutrient recycling. Invasive species could benefit greatly from carcass resources within highly invaded island ecosystems, through increased invasion success and population growth, subsequently exacerbating their impacts on native species. Here, we quantified how experimentally placed invasive amphibian, reptile, small mammal, and birdmore » carcasses were utilized by vertebrate and invertebrate scavengers on the Big Island of Hawai’i in three island habitats: a barren lava field, a vegetated lava field, and a rainforest. We used camera traps to record vertebrate scavengers removing carcasses and elapsed time until removal. We evaluated differences in cavenging between vertebrates and invertebrates and within the vertebrate community across different habitats and carcass types. Despite the small carcass sizes (<1 kg) used in this study, 55% of carcasses were removed by vertebrate scavengers, all invasive: mongoose, rodents, cats, pigs, and a common myna. Our data indicate that invasive vertebrate scavengers in this island ecosystem are highly efficient at assimilating a range of carrion resources across a variety of habitats. Carcasses of invasive animals could contribute substantially to energy budgets of other invasive vertebrate species. Finally, this may be a critical component contributing to successful invasions especially on islands and subsequent impacts on ecosystem function.« less

A multi-scale comparison of trait linkages to environmental and spatial variables in fish communities across a large freshwater lake.

PubMed

Strecker, Angela L; Casselman, John M; Fortin, Marie-Josée; Jackson, Donald A; Ridgway, Mark S; Abrams, Peter A; Shuter, Brian J

2011-07-01

Species present in communities are affected by the prevailing environmental conditions, and the traits that these species display may be sensitive indicators of community responses to environmental change. However, interpretation of community responses may be confounded by environmental variation at different spatial scales. Using a hierarchical approach, we assessed the spatial and temporal variation of traits in coastal fish communities in Lake Huron over a 5-year time period (2001-2005) in response to biotic and abiotic environmental factors. The association of environmental and spatial variables with trophic, life-history, and thermal traits at two spatial scales (regional basin-scale, local site-scale) was quantified using multivariate statistics and variation partitioning. We defined these two scales (regional, local) on which to measure variation and then applied this measurement framework identically in all 5 study years. With this framework, we found that there was no change in the spatial scales of fish community traits over the course of the study, although there were small inter-annual shifts in the importance of regional basin- and local site-scale variables in determining community trait composition (e.g., life-history, trophic, and thermal). The overriding effects of regional-scale variables may be related to inter-annual variation in average summer temperature. Additionally, drivers of fish community traits were highly variable among study years, with some years dominated by environmental variation and others dominated by spatially structured variation. The influence of spatial factors on trait composition was dynamic, which suggests that spatial patterns in fish communities over large landscapes are transient. Air temperature and vegetation were significant variables in most years, underscoring the importance of future climate change and shoreline development as drivers of fish community structure. Overall, a trait-based hierarchical framework may be a useful conservation tool, as it highlights the multi-scaled interactive effect of variables over a large landscape.

Assessment of snow modeling decisions in the extra-tropical Andes Cordillera

NASA Astrophysics Data System (ADS)

Mendoza, P. A.; Musselman, K. N.; Raleigh, M. S.; Clark, M. P.; McPhee, J. P.

2017-12-01

Improving model realism is an ongoing challenge for the cryosphere research community, not only to advance process understanding, but also to quantify and reduce uncertainty under global warming conditions. This work attempts to characterize the interplay and impact of user decisions about snow model structure and parameter specification on model uncertainty. Snow simulations were conducted in the extra-tropical Andes - a mountainous region that acts as a natural reservoir for Central Chile and Western Argentina. To address this topic, we apply the Structure for Unifying Multiple Modeling Alternatives (SUMMA) to simulate seasonal snowpack dynamics at three sites with different hydroclimatic regimes (semi-arid, Mediterranean, and temperate humid). Results are verified against extensive ground-based observations. Site elevations decrease from north to south, whereas precipitation amounts increase with latitude. Results highlight the impact of different windflow and snow transport decisions on model skill during the accumulation period, and different parameterizations (e.g., albedo decay) on spring simulations. We anticipate that the outcomes from this study will have important implications on current and future research, in particular on the configuration of snow models used to quantify the availability of water resources in this region.

Game theory and extremal optimization for community detection in complex dynamic networks.

PubMed

Lung, Rodica Ioana; Chira, Camelia; Andreica, Anca

2014-01-01

The detection of evolving communities in dynamic complex networks is a challenging problem that recently received attention from the research community. Dynamics clearly add another complexity dimension to the difficult task of community detection. Methods should be able to detect changes in the network structure and produce a set of community structures corresponding to different timestamps and reflecting the evolution in time of network data. We propose a novel approach based on game theory elements and extremal optimization to address dynamic communities detection. Thus, the problem is formulated as a mathematical game in which nodes take the role of players that seek to choose a community that maximizes their profit viewed as a fitness function. Numerical results obtained for both synthetic and real-world networks illustrate the competitive performance of this game theoretical approach.

Quantifying the impacts of land surface schemes and dynamic vegetation on the model dependency of projected changes in surface energy and water budgets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Miao; Wang, Guiling; Chen, Haishan

Assessing and quantifying the uncertainties in projected future changes of energy and water budgets over land surface are important steps toward improving our confidence in climate change projections. In our study, the contribution of land surface models to the inter-GCM variation of projected future changes in land surface energy and water fluxes are assessed based on output from 19 global climate models (GCMs) and offline Community Land Model version 4 (CLM4) simulations driven by meteorological forcing from the 19 GCMs. Similar offline simulations using CLM4 with its dynamic vegetation submodel are also conducted to investigate how dynamic vegetation feedback, amore » process that is being added to more earth system models, may amplify or moderate the intermodel variations of projected future changes. Projected changes are quantified as the difference between the 2081–2100 period from the Representative Concentration Pathway 8.5 (RCP8.5) future experiment and the 1981–2000 period from the historical simulation. Under RCP8.5, projected changes in surface water and heat fluxes show a high degree of model dependency across the globe. Although precipitation is very likely to increase in the high latitudes of the Northern Hemisphere, a high degree of model-related uncertainty exists for evapotranspiration, soil water content, and surface runoff, suggesting discrepancy among land surface models (LSMs) in simulating the surface hydrological processes and snow-related processes. Large model-related uncertainties for the surface water budget also exist in the Tropics including southeastern South America and Central Africa. Moreover, these uncertainties would be reduced in the hypothetical scenario of a single near-perfect land surface model being used across all GCMs, suggesting the potential to reduce uncertainties through the use of more consistent approaches toward land surface model development. Under such a scenario, the most significant reduction is likely to be seen in the Northern Hemisphere high latitudes. Including representation of vegetation dynamics is expected to further amplify the model-related uncertainties in projected future changes in surface water and heat fluxes as well as soil moisture content. This is especially the case in the high latitudes of the Northern Hemisphere (e.g., northwestern North America and central North Asia) where the projected vegetation changes are uncertain and in the Tropics (e.g., the Amazon and Congo Basins) where dense vegetation exists. Finally, findings from this study highlight the importance of improving land surface model parameterizations related to soil and snow processes, as well as the importance of improving the accuracy of dynamic vegetation models.« less

Quantifying the impacts of land surface schemes and dynamic vegetation on the model dependency of projected changes in surface energy and water budgets

DOE PAGES

Yu, Miao; Wang, Guiling; Chen, Haishan

2016-03-01

Assessing and quantifying the uncertainties in projected future changes of energy and water budgets over land surface are important steps toward improving our confidence in climate change projections. In our study, the contribution of land surface models to the inter-GCM variation of projected future changes in land surface energy and water fluxes are assessed based on output from 19 global climate models (GCMs) and offline Community Land Model version 4 (CLM4) simulations driven by meteorological forcing from the 19 GCMs. Similar offline simulations using CLM4 with its dynamic vegetation submodel are also conducted to investigate how dynamic vegetation feedback, amore » process that is being added to more earth system models, may amplify or moderate the intermodel variations of projected future changes. Projected changes are quantified as the difference between the 2081–2100 period from the Representative Concentration Pathway 8.5 (RCP8.5) future experiment and the 1981–2000 period from the historical simulation. Under RCP8.5, projected changes in surface water and heat fluxes show a high degree of model dependency across the globe. Although precipitation is very likely to increase in the high latitudes of the Northern Hemisphere, a high degree of model-related uncertainty exists for evapotranspiration, soil water content, and surface runoff, suggesting discrepancy among land surface models (LSMs) in simulating the surface hydrological processes and snow-related processes. Large model-related uncertainties for the surface water budget also exist in the Tropics including southeastern South America and Central Africa. Moreover, these uncertainties would be reduced in the hypothetical scenario of a single near-perfect land surface model being used across all GCMs, suggesting the potential to reduce uncertainties through the use of more consistent approaches toward land surface model development. Under such a scenario, the most significant reduction is likely to be seen in the Northern Hemisphere high latitudes. Including representation of vegetation dynamics is expected to further amplify the model-related uncertainties in projected future changes in surface water and heat fluxes as well as soil moisture content. This is especially the case in the high latitudes of the Northern Hemisphere (e.g., northwestern North America and central North Asia) where the projected vegetation changes are uncertain and in the Tropics (e.g., the Amazon and Congo Basins) where dense vegetation exists. Finally, findings from this study highlight the importance of improving land surface model parameterizations related to soil and snow processes, as well as the importance of improving the accuracy of dynamic vegetation models.« less

ESTUARINE AND SCALAR PATTERNS OF INVASION IN THE SOFT-BOTTOM BENTHIC COMMUNITIES OF THE SAN FRANCISCO ESTUARY

EPA Science Inventory

The spatial patterns of nonindigenous species in seven subtidal soft-bottom communities in the San Francisco Estuary were quantified. Sixty nonindigenous species were found out of the 533 taxa enumerated (11%). Patterns of invasion across the communities were evaluated using a ...

Biomimetic measurement of allelochemical dynamics in the rhizosphere.

PubMed

Weidenhamer, Jeffrey D

2005-02-01

Polydimethylsiloxane (PDMS) materials were used to quantify levels of the photosynthesis inhibitor sorgoleone in the undisturbed rhizosphere of sorghum plants. The materials used included stir bars coated with PDMS (stir bar sorptive extraction), technical grade optical fiber coated with a thin film of PDMS (matrix-solid phase microextraction), and PDMS tubing. PDMS tubing retained the most sorgoleone. As analyzed by high performance liquid chromatography, amounts of sorgoleone retained on the PDMS materials increased with time. Other materials tested (polyurethane foam plugs, C18 and Tenax disks, and resin capsules) proved less suitable, as they were subject to sometimes extensive penetration by fine root hairs. These results demonstrate the potential for PDMS-based materials to monitor the release of allelochemicals in the undisturbed rhizosphere of allelopathic plants. Unlike extraction procedures that recover all available compounds present in the soil, PDMS functions in a manner more analogous to plant roots in sorbing compounds from soil solution or root exudates. Information on chemical dynamics in the rhizosphere is crucial for evaluating specific hypotheses of allelopathic effects, understanding allelopathic mechanisms, and assessing the importance of allelopathic processes in plant communities.

Building community research capacity: process evaluation of community training and education in a community-based participatory research program serving a predominantly Puerto Rican community.

PubMed

Tumiel-Berhalter, Laurene M; McLaughlin-Diaz, Victoria; Vena, John; Crespo, Carlos J

2007-01-01

Education and training build community research capacity and have impact on improvements of health outcomes. This manuscript describes the training and educational approaches to building research capacity that were utilized in a community-based participatory research program serving a Puerto Rican population and identifies barriers and strategies for overcoming them. A process evaluation identified a multitiered approach to training and education that was critical to reaching the broad community. This approach included four major categories providing a continuum of education and training opportunities: networking, methods training, on-the-job experience, and community education. Participation in these opportunities supported the development of a registry, the implementation of a survey, and two published manuscripts. Barriers included the lack of a formal evaluation of the education and training components, language challenges that limited involvement of ethnic groups other than Puerto Ricans, and potential biases associated with the familiarity of the data collector and the participant. The CBPR process facilitated relationship development between the university and the community and incorporated the richness of the community experience into research design. Strategies for improvement include incorporating evaluation into every training and educational opportunity and developing measures to quantify research capacity at the individual and community levels. Evaluating training and education in the community allows researchers to quantify the impact of CBPR on building community research capacity.

Quantifying chaotic dynamics from integrate-and-fire processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavlov, A. N.; Saratov State Technical University, Politehnicheskaya Str. 77, 410054 Saratov; Pavlova, O. N.

2015-01-15

Characterizing chaotic dynamics from integrate-and-fire (IF) interspike intervals (ISIs) is relatively easy performed at high firing rates. When the firing rate is low, a correct estimation of Lyapunov exponents (LEs) describing dynamical features of complex oscillations reflected in the IF ISI sequences becomes more complicated. In this work we discuss peculiarities and limitations of quantifying chaotic dynamics from IF point processes. We consider main factors leading to underestimated LEs and demonstrate a way of improving numerical determining of LEs from IF ISI sequences. We show that estimations of the two largest LEs can be performed using around 400 mean periodsmore » of chaotic oscillations in the regime of phase-coherent chaos. Application to real data is discussed.« less

An efficient approach to the analysis of rail surface irregularities accounting for dynamic train-track interaction and inelastic deformations

NASA Astrophysics Data System (ADS)

Andersson, Robin; Torstensson, Peter T.; Kabo, Elena; Larsson, Fredrik

2015-11-01

A two-dimensional computational model for assessment of rolling contact fatigue induced by discrete rail surface irregularities, especially in the context of so-called squats, is presented. Dynamic excitation in a wide frequency range is considered in computationally efficient time-domain simulations of high-frequency dynamic vehicle-track interaction accounting for transient non-Hertzian wheel-rail contact. Results from dynamic simulations are mapped onto a finite element model to resolve the cyclic, elastoplastic stress response in the rail. Ratcheting under multiple wheel passages is quantified. In addition, low cycle fatigue impact is quantified using the Jiang-Sehitoglu fatigue parameter. The functionality of the model is demonstrated by numerical examples.

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

A Statistical Comparison of Coupled Thermosphere-Ionosphere Models

NASA Astrophysics Data System (ADS)

Liuzzo, L. R.

2014-12-01

The thermosphere-ionosphere system is a highly dynamic, non-linearly coupled interaction that fluctuates on a daily basis. Many models exist to attempt to quantify the relationship between the two atmospheric layers, and each approaches the problem differently. Because these models differ in the implementation of the equations that govern the dynamics of the thermosphere-ionosphere system, it is important to understand under which conditions each model performs best, and under which conditions each model may have limitations in accuracy. With this in consideration, this study examines the ability of two of the leading coupled thermosphere-ionosphere models in the community, TIE-GCM and GITM, to reproduce thermospheric and ionospheric quantities observed by the CHAMP satellite during times of differing geomagnetic activity. Neutral and electron densities are studied for three geomagnetic activity levels, ranging form high to minimal activity. Metrics used to quantify differences between the two models include root-mean-square error and prediction efficiency, and qualitative differences between a model and observed data is also considered. The metrics are separated into the high- mid- and low-latitude region to depict any latitudinal dependencies of the models during the various events. Despite solving for the same parameters, the models are shown to be highly dependent on the amount of activity level that occurs and can be significantly different from each other. In addition, in comparing previous statistical studies that use the models, a clear improvement is observed in the evolution of each model as thermospheric and ionosphericconstituents during the differing levels of activity are solved.

EcoPAD, an interactive platform for near real-time ecological forecasting by assimilating data into model

NASA Astrophysics Data System (ADS)

MA, S.; Huang, Y.; Stacy, M.; Jiang, J.; Sundi, N.; Ricciuto, D. M.; Hanson, P. J.; Luo, Y.; Saruta, V.

2017-12-01

Ecological forecasting is critical in various aspects of our coupled human-nature systems, such as disaster risk reduction, natural resource management and climate change mitigation. Novel advancements are in urgent need to deepen our understandings of ecosystem dynamics, boost the predictive capacity of ecology, and provide timely and effective information for decision-makers in a rapidly changing world. Our study presents a smart system - Ecological Platform for Assimilation of Data (EcoPAD) - which streamlines web request-response, data management, model execution, result storage and visualization. EcoPAD allows users to (i) estimate model parameters or state variables, (ii) quantify uncertainty of estimated parameters and projected states of ecosystems, (iii) evaluate model structures, (iv) assess sampling strategies, (v) conduct ecological forecasting, and (vi) detect ecosystem acclimation to climate change. One of the key innovations of the web-based EcoPAD is the automated near- or real-time forecasting of ecosystem dynamics with uncertainty fully quantified. The user friendly webpage enables non-modelers to explore their data for simulation and data assimilation. As a case study, we applied EcoPAD to the Spruce and Peatland Responses Under Climatic and Environmental Change Experiment (SPRUCE), a whole ecosystem warming and CO2 enrichment treatment project in the northern peatland, assimilated multiple data streams into a process based ecosystem model, enhanced timely feedback between modelers and experimenters, ultimately improved ecosystem forecasting and made better use of current knowledge. Built in a framework with flexible API, EcoPAD is easily portable and will benefit scientific communities, policy makers as well as the general public.

Phosphorus and Defoliation Interact and Improve the Growth and Composition of the Plant Community and Soil Properties in an Alpine Pasture of Qinghai-Tibet Plateau.

PubMed

Qi, Juan; Nie, Zhongnan; Jiao, Ting; Zhang, Degang

2015-01-01

Pasture degradation caused by overgrazing and inappropriate fertiliser management is a major production and environmental threat in Qinghai-Tibet Plateau. Previous research has focused on the effects of mixed nitrogen (N) and phosphorus (P) fertiliser and reduced grazing pressure on the plant community of the grassland; however, the role of P and how it interacts with various defoliation (the process of the complete or partial removal of the above-ground parts of plants by grazing or cutting) intensities on the plant and soil of the grassland ecosystem have not been quantified. A field experiment was conducted to quantify how P application in combination of defoliation pressure could impact the dynamic change of the plant and soil in a native alpine grassland ecosystem of the Qinghai-Tibet Plateau, China, from May 2012 to September 2014. A split-plot design with 4 replicates and repeated measures was used to determine the growth and composition of plant community and soil physical and chemical properties under various levels of P fertiliser and defoliation intensity. The results showed that applying 20 kg P/ha increased the herbage yield of Melissitus ruthenica by 68% and total pasture yield by 25%. Close defoliation favoured the growth and plant frequency of the shorter species, whereas lax defoliation favoured that of the taller plant species. Medium P rate and cutting to 3 cm above ground gave an overall best outcome in pasture yield, quality and frequency and soil moisture and nutrient concentration. Application of P fertiliser with a moderate defoliation pressure to promote legume growth and N fixation has the potential to achieve multiple benefits in increasing pasture and livestock production and improving environmental sustainability in the alpine pasture of Qinghai-Tibet Plateau, a fragile and P-deficient ecosystem zone in China and its western neighbouring countries.

Phosphorus and Defoliation Interact and Improve the Growth and Composition of the Plant Community and Soil Properties in an Alpine Pasture of Qinghai-Tibet Plateau

PubMed Central

Qi, Juan; Nie, Zhongnan; Jiao, Ting; Zhang, Degang

2015-01-01

Pasture degradation caused by overgrazing and inappropriate fertiliser management is a major production and environmental threat in Qinghai-Tibet Plateau. Previous research has focused on the effects of mixed nitrogen (N) and phosphorus (P) fertiliser and reduced grazing pressure on the plant community of the grassland; however, the role of P and how it interacts with various defoliation (the process of the complete or partial removal of the above-ground parts of plants by grazing or cutting) intensities on the plant and soil of the grassland ecosystem have not been quantified. A field experiment was conducted to quantify how P application in combination of defoliation pressure could impact the dynamic change of the plant and soil in a native alpine grassland ecosystem of the Qinghai-Tibet Plateau, China, from May 2012 to September 2014. A split-plot design with 4 replicates and repeated measures was used to determine the growth and composition of plant community and soil physical and chemical properties under various levels of P fertiliser and defoliation intensity. The results showed that applying 20 kg P/ha increased the herbage yield of Melissitus ruthenica by 68% and total pasture yield by 25%. Close defoliation favoured the growth and plant frequency of the shorter species, whereas lax defoliation favoured that of the taller plant species. Medium P rate and cutting to 3 cm above ground gave an overall best outcome in pasture yield, quality and frequency and soil moisture and nutrient concentration. Application of P fertiliser with a moderate defoliation pressure to promote legume growth and N fixation has the potential to achieve multiple benefits in increasing pasture and livestock production and improving environmental sustainability in the alpine pasture of Qinghai-Tibet Plateau, a fragile and P-deficient ecosystem zone in China and its western neighbouring countries. PMID:26513363

Methodology for Uncertainty Analysis of Dynamic Computational Toxicology Models

EPA Science Inventory

The task of quantifying the uncertainty in both parameter estimates and model predictions has become more important with the increased use of dynamic computational toxicology models by the EPA. Dynamic toxicological models include physiologically-based pharmacokinetic (PBPK) mode...

Dynamics of phytoplankton community composition in the western Gulf of Maine

NASA Astrophysics Data System (ADS)

Moore, Timothy S.

This dissertation is founded on the importance of phytoplankton community composition to marine biogeochemistry and ecosystem processes and motivated by the need to understand their distributions on regional to global scales. The ultimate goal was to predict surface phytoplankton communities using satellite remote sensing by relating marine habitats--defined through a statistical description of environmental properties--to different phytoplankton communities. While phytoplankton community composition is governed by the interplay of abiotic and biotic interactions, the strategy adopted here was to focus on the physical abiotic factors. This allowed for the detection of habitats from ocean satellites based on abiotic factors that were linked to associated phytoplankton communities. The research entailed three studies that addressed different aspects of the main goal using a dataset collected in the western Gulf of Maine over a 3-year period. The first study evaluated a chemotaxonomic method that quantified phytoplankton composition from pigment data. This enabled the characterization of three phytoplankton communities, which were defined by the relative abundance of diatoms and flagellates. The second study examined the cycles of these communities along with environmental variables, and the results revealed that the three phytoplankton communities exhibited an affinity to different hydrographic regimes. The third study focused on the implementation of a classifier that predicted phytoplankton communities from environmental variables. Its ability to differentiate communities dominated by diatoms versus flagellates was shown to be high. However, the increase in data imprecision when using satellite data led to lowered performance and favored an approach that incorporated fuzzy logic. The fuzzy method is well suited to characterize the uncertainties in phytoplankton community prediction, and provides a measure of confidence on predicted communities. The final product of the overall dissertation was a time series of maps generated from satellite observations depicting the likelihood of three phytoplankton communities. This dissertation reached the main goal and, moreover, demonstrated that improvements in the predictive power of the method can be achieved with increased precision and more advanced satellite-derived products. The results of this research can benefit present bio-optical and primary productivity models, and ecosystem-based models of the marine environment.

Complex responses of spring alpine vegetation phenology to snow cover dynamics over the Tibetan Plateau, China.

PubMed

Wang, Siyuan; Wang, Xiaoyue; Chen, Guangsheng; Yang, Qichun; Wang, Bin; Ma, Yuanxu; Shen, Ming

2017-09-01

Snow cover dynamics are considered to play a key role on spring phenological shifts in the high-latitude, so investigating responses of spring phenology to snow cover dynamics is becoming an increasingly important way to identify and predict global ecosystem dynamics. In this study, we quantified the temporal trends and spatial variations of spring phenology and snow cover across the Tibetan Plateau by calibrating and analyzing time series of the NOAA AVHRR-derived normalized difference vegetation index (NDVI) during 1983-2012. We also examined how snow cover dynamics affect the spatio-temporal pattern of spring alpine vegetation phenology over the plateau. Our results indicated that 52.21% of the plateau experienced a significant advancing trend in the beginning of vegetation growing season (BGS) and 34.30% exhibited a delaying trend. Accordingly, the snow cover duration days (SCD) and snow cover melt date (SCM) showed similar patterns with a decreasing trend in the west and an increasing trend in the southeast, but the start date of snow cover (SCS) showed an opposite pattern. Meanwhile, the spatial patterns of the BGS, SCD, SCS and SCM varied in accordance with the gradients of temperature, precipitation and topography across the plateau. The response relationship of spring phenology to snow cover dynamics varied within different climate, terrain and alpine plant community zones, and the spatio-temporal response patterns were primarily controlled by the long-term local heat-water conditions and topographic conditions. Moreover, temperature and precipitation played a profound impact on diverse responses of spring phenology to snow cover dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

Emergent Phototactic Responses of Cyanobacteria under Complex Light Regimes

PubMed Central

Chau, Rosanna Man Wah

2017-01-01

ABSTRACT Environmental cues can stimulate a variety of single-cell responses, as well as collective behaviors that emerge within a bacterial community. These responses require signal integration and transduction, which can occur on a variety of time scales and often involve feedback between processes, for example, between growth and motility. Here, we investigate the dynamics of responses of the phototactic, unicellular cyanobacterium Synechocystis sp. PCC6803 to complex light inputs that simulate the natural environments that cells typically encounter. We quantified single-cell motility characteristics in response to light of different wavelengths and intensities. We found that red and green light primarily affected motility bias rather than speed, while blue light inhibited motility altogether. When light signals were simultaneously presented from different directions, cells exhibited phototaxis along the vector sum of the light directions, indicating that cells can sense and combine multiple signals into an integrated motility response. Under a combination of antagonistic light signal regimes (phototaxis-promoting green light and phototaxis-inhibiting blue light), the ensuing bias was continuously tuned by competition between the wavelengths, and the community response was dependent on both bias and cell growth. The phototactic dynamics upon a rapid light shift revealed a wavelength dependence on the time scales of photoreceptor activation/deactivation. Thus, Synechocystis cells achieve exquisite integration of light inputs at the cellular scale through continuous tuning of motility, and the pattern of collective behavior depends on single-cell motility and population growth. PMID:28270586

Dynamics in microbial communities: Unraveling mechanisms to identify principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan; Lindemann, Stephen R.; Fredrickson, Jim K.

2015-07-01

Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richermore » network of community interactions, and it is this “system” that is the basis for higher order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.« less

Estimating planktonic diversity through spatial dominance patterns in a model ocean.

PubMed

Soccodato, Alice; d'Ovidio, Francesco; Lévy, Marina; Jahn, Oliver; Follows, Michael J; De Monte, Silvia

2016-10-01

In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantifying full phenological event distributions reveals simultaneous advances, temporal stability and delays in spring and autumn migration timing in long-distance migratory birds.

PubMed

Miles, Will T S; Bolton, Mark; Davis, Peter; Dennis, Roy; Broad, Roger; Robertson, Iain; Riddiford, Nick J; Harvey, Paul V; Riddington, Roger; Shaw, Deryk N; Parnaby, David; Reid, Jane M

2017-04-01

Phenological changes in key seasonally expressed life-history traits occurring across periods of climatic and environmental change can cause temporal mismatches between interacting species, and thereby impact population and community dynamics. However, studies quantifying long-term phenological changes have commonly only measured variation occurring in spring, measured as the first or mean dates on which focal traits or events were observed. Few studies have considered seasonally paired events spanning spring and autumn or tested the key assumption that single convenient metrics accurately capture entire event distributions. We used 60 years (1955-2014) of daily bird migration census data from Fair Isle, Scotland, to comprehensively quantify the degree to which the full distributions of spring and autumn migration timing of 13 species of long-distance migratory bird changed across a period of substantial climatic and environmental change. In most species, mean spring and autumn migration dates changed little. However, the early migration phase (≤10th percentile date) commonly got earlier, while the late migration phase (≥90th percentile date) commonly got later. Consequently, species' total migration durations typically lengthened across years. Spring and autumn migration phenologies were not consistently correlated within or between years within species and hence were not tightly coupled. Furthermore, different metrics quantifying different aspects of migration phenology within seasons were not strongly cross-correlated, meaning that no single metric adequately described the full pattern of phenological change. These analyses therefore reveal complex patterns of simultaneous advancement, temporal stability and delay in spring and autumn migration phenologies, altering species' life-history structures. Additionally, they demonstrate that this complexity is only revealed if multiple metrics encompassing entire seasonal event distributions, rather than single metrics, are used to quantify phenological change. Existing evidence of long-term phenological changes detected using only one or two metrics should consequently be interpreted cautiously because divergent changes occurring simultaneously could potentially have remained undetected. © 2016 John Wiley & Sons Ltd.

Modeling the Effects of Trait Diversity on Short-term Adaptive Capacity and Long-term Productivity of Phytoplankton Communities

NASA Astrophysics Data System (ADS)

Smith, S. L.; Vallina, S. M.; Merico, A.

2016-02-01

We examine Biodiversity and Ecosystem Function (BEF) in a model phytoplankton community, using two recently developed mechanisms for sustaining diversity. The Trait Diffusion (TD) formulation represents the maintenance of diversity via endogenous mechanisms, such as inter-generational trait plasticity and rapid evolution. The 'Kill-the-Winner' (KTW) formulation for grazing sustains prey biodiversity via the exogenous mechanism of active prey switching. We implement both TD and KTW in a continuous trait-distribution model using simplified size-scalings to define a gleaner-opportunist trade-off for a phytoplankton community. By simulating semi-continuous culture experiments with periodic external dilutions, we test the dynamic response of the phytoplankton community to different scenarios of pulsed nutrient supply. We quantify the short-term Adaptive Capacity (AC) of the community by the specific growth rate averaged over the first 3 days of perturbations, and the Long-term Productivity (LP) by its average over the entire 120 day period of perturbations. When either the frequency or intensity of pulses is low, both AC and LP tend to decrease with diversity (and vice versa). Trait diversity has more impact on AC, particularly for pulses of high frequency or intensity, for which it tends to increase gradually at first, then steeply, and then to saturate with increasing diversity. For pulses of moderate intensity and frequency, increasing trait diversity from low to moderate levels leads to a trade-off between enhancing AC while slightly decreasing LP. Ultimately, we find that sustaining diversity increases the speed at which the phytoplankton community changes its composition in terms of size and hence nutrient acquisition traits, which may have implications for the transfer of productivity through the foodweb.

A Modelling Approach on Fine Particle Spatial Distribution for Street Canyons in Asian Residential Community

NASA Astrophysics Data System (ADS)

Ling, Hong; Lung, Shih-Chun Candice; Uhrner, Ulrich

2016-04-01

Rapidly increasing urban pollution poses severe health risks.Especially fine particles pollution is considered to be closely related to respiratory and cardiovascular disease. In this work, ambient fine particles are studied in street canyons of a typical Asian residential community using a computational fluid dynamics (CFD) dispersion modelling approach. The community is characterised by an artery road with a busy traffic flow of about 4000 light vehicles (mainly cars and motorcycles) per hour at rush hours, three streets with hundreds light vehicles per hour at rush hours and several small lanes with less traffic. The objective is to study the spatial distribution of the ambient fine particle concentrations within micro-environments, in order to assess fine particle exposure of the people living in the community. The GRAL modelling system is used to simulate and assess the emission and dispersion of the traffic-related fine particles within the community. Traffic emission factors and traffic situation is assigned using both field observation and local emissions inventory data. High resolution digital elevation data (DEM) and building height data are used to resolve the topographical features. Air quality monitoring and mobile monitoring within the community is used to validate the simulation results. By using this modelling approach, the dispersion of fine particles in street canyons is simulated; the impact of wind condition and street orientation are investigated; the contributions of car and motorcycle emissions are quantified respectively; the residents' exposure level of fine particles is assessed. The study is funded by "Taiwan Megacity Environmental Research (II)-chemistry and environmental impacts of boundary layer aerosols (Year 2-3) (103-2111-M-001-001-); Spatial variability and organic markers of aerosols (Year 3)(104-2111-M-001 -005 -)"

Biomass-C specific temperature responses of microbial C transformations reveal consistency regardless of microbial community structure across diverse timescales of inquiry

NASA Astrophysics Data System (ADS)

Min, K.; Buckeridge, K. M.; Ziegler, S. E.; Edwards, K. A.; Bagchi, S.; Billings, S. A.

2016-12-01

The responses of heterotrophic microbial process rates to temperature in soils are often investigated in the short-term (hours to months), making it difficult to predict longer-term temperature responses. Here, we integrate the temperature sensitivity obtained from the Arrhenius model with the concepts of microbial resistance, resilience, and susceptibility to assess temporal dynamics of microbial temperature responses. We collected soils along a boreal forest climate gradient (long-term effect), and quantified exo-enzyme activities and CO2 respiration at 5, 15, and 25°C for 84 days (relatively short-term effect). Microbial process rates were examined at two levels (per g microbial biomass-C; and per g dry soil) along with community structure, to characterize driving mechanisms for temporal patterns (e.g., size of biomass, physiological plasticity, community composition). Although temperature sensitivity of exo-enzyme activities on a per g dry soil basis showed both resistance and resilience depending on the types of exo-enzyme, biomass -C-specific responses always exhibited resistance regardless of distinct community composition. Temperature sensitivity of CO2 respiration was constant across time and different communities at both units. This study advances our knowledge in two ways. First, resistant temperature sensitivity of exo-enzymes and respiration at biomass-C specific level across distinct communities and diverse timescales indicates a common relationship between microbial physiology and temperature at a fundamental level, a useful feature allowing microbial process models to be reasonably simplified. Second, different temporal responses of exo-enzymes depending on the unit selected provide a cautionary tale for those projecting future microbial behaviors, because interpretation of ecosystem process rates may vary with the unit of observation.

Modeling the effects of environmental disturbance on wildlife communities: avian responses to prescribed fire.

PubMed

Russell, Robin E; Royle, J Andrew; Saab, Victoria A; Lehmkuhl, John F; Block, William M; Sauer, John R

2009-07-01

Prescribed fire is a management tool used to reduce fuel loads on public lands in forested areas in the western United States. Identifying the impacts of prescribed fire on bird communities in ponderosa pine (Pinus ponderosa) forests is necessary for providing land management agencies with information regarding the effects of fuel reduction on sensitive, threatened, and migratory bird species. Recent developments in occupancy modeling have established a framework for quantifying the impacts of management practices on wildlife community dynamics. We describe a Bayesian hierarchical model of multi-species occupancy accounting for detection probability, and we demonstrate the model's usefulness for identifying effects of habitat disturbances on wildlife communities. Advantages to using the model include the ability to estimate the effects of environmental impacts on rare or elusive species, the intuitive nature of the modeling, the incorporation of detection probability, the estimation of parameter uncertainty, the flexibility of the model to suit a variety of experimental designs, and the composite estimate of the response that applies to the collection of observed species as opposed to merely a small subset of common species. Our modeling of the impacts of prescribed fire on avian communities in a ponderosa pine forest in Washington indicate that prescribed fire treatments result in increased occupancy rates for several bark-insectivore, cavity-nesting species including a management species of interest, Black-backed Woodpeckers (Picoides arcticus). Three aerial insectivore species, and the ground insectivore, American Robin (Turdus migratorius), also responded positively to prescribed fire, whereas three foliage insectivores and two seed specialists, Clark's Nutcracker (Nucifraga columbiana) and the Pine Siskin (Carduelis pinus), declined following treatments. Land management agencies interested in determining the effects of habitat manipulations on wildlife communities can use these methods to provide guidance for future management activities.

The Community Surface Dynamics Modeling System: Experiences on Building a Collaborative Modeling Platform

NASA Astrophysics Data System (ADS)

Overeem, I.; Hutton, E.; Kettner, A.; Peckham, S. D.; Syvitski, J. P.

2012-12-01

The Community Surface Dynamics Modeling System - CSDMS- develops a software platform with shared and coupled modules for modeling earth surface processes as a community resource. The framework allows prediction of water, sediment and nutrient transport through the landscape and seacape. The underlying paradigm is that the Earth surface we live on is a dynamic system; topography changes with seasons, with landslides and earthquakes, with erosion and deposition. The Earth Surface changes due to storms and floods, and important boundaries, like the coast, are ever-moving features. CSDMS sets out to make better predictions of these changes. Earth surface process modeling bridges the terrestrial, coastal and marine domains and requires understanding of the system over a range of time scales, which inherently needs interdisciplinarity. Members of CSDMS (~830 in July 2012) are largely from academic institutions (˜75%), followed by federal agencies (˜17%), and oil and gas companies (˜5%). Members and governmental bodies meet once annually and rely additionally on web-based information for communication. As an organization that relies on volunteer participation, CSDMS faces challenges to scientific collaboration. Encouraging volunteerism among its members to provide and adapt metadata and model code to be sufficiently standardized for coupling is crucial to building an integrated community modeling system. We here present CSDMS strategies aimed at providing the appropriate technical tools and cyberinfrastructure to support a variety of user types, ranging from advanced to novice modelers. Application of these advances in science is key, both into the educational realm and for managers and decision-makers. We discuss some of the implemented ideas to further organizational transparency and user engagement in small-scale governance, such as advanced trackers and voting systems for model development prioritization through the CSDMS wiki. We analyzed data on community contributions and novice user engagement and evaluate the effectiveness of CSDMS' strategies toward these two challenges over the first 5 years based on member and user data, surveys, computing logs and web log analysis. Analysis shows that sponsored member participation in annual meetings (˜30%) is relatively high. Direct CSDMS governance relies on ˜4% of members. About 15% of members contributed code and metadata, and 18% use the common supercomputing resources. Technological development and documentation lie predominantly in hands of funded members, and a small number of others (˜3% together). Potential new users are trained in clinics and courses, and on a one-to-one basis with quantified positive effects on self-efficacy and recruitment of new advanced developers.

The Rise of China in the International Trade Network: A Community Core Detection Approach

PubMed Central

Zhu, Zhen; Cerina, Federica; Chessa, Alessandro; Caldarelli, Guido; Riccaboni, Massimo

2014-01-01

Theory of complex networks proved successful in the description of a variety of complex systems ranging from biology to computer science and to economics and finance. Here we use network models to describe the evolution of a particular economic system, namely the International Trade Network (ITN). Previous studies often assume that globalization and regionalization in international trade are contradictory to each other. We re-examine the relationship between globalization and regionalization by viewing the international trade system as an interdependent complex network. We use the modularity optimization method to detect communities and community cores in the ITN during the years 1995–2011. We find rich dynamics over time both inter- and intra-communities. In particular, the Asia-Oceania community disappeared and reemerged over time along with a switch in leadership from Japan to China. We provide a multilevel description of the evolution of the network where the global dynamics (i.e., communities disappear or reemerge) and the regional dynamics (i.e., community core changes between community members) are related. Moreover, simulation results show that the global dynamics can be generated by a simple dynamic-edge-weight mechanism. PMID:25136895

The rise of China in the International Trade Network: a community core detection approach.

PubMed

Zhu, Zhen; Cerina, Federica; Chessa, Alessandro; Caldarelli, Guido; Riccaboni, Massimo

2014-01-01

Theory of complex networks proved successful in the description of a variety of complex systems ranging from biology to computer science and to economics and finance. Here we use network models to describe the evolution of a particular economic system, namely the International Trade Network (ITN). Previous studies often assume that globalization and regionalization in international trade are contradictory to each other. We re-examine the relationship between globalization and regionalization by viewing the international trade system as an interdependent complex network. We use the modularity optimization method to detect communities and community cores in the ITN during the years 1995-2011. We find rich dynamics over time both inter- and intra-communities. In particular, the Asia-Oceania community disappeared and reemerged over time along with a switch in leadership from Japan to China. We provide a multilevel description of the evolution of the network where the global dynamics (i.e., communities disappear or reemerge) and the regional dynamics (i.e., community core changes between community members) are related. Moreover, simulation results show that the global dynamics can be generated by a simple dynamic-edge-weight mechanism.

How Visualizing Ecosystem Land Management Assessments (VELMA) modeling quantifies co-benefits and tradeoffs in Community Forest management

EPA Science Inventory

The Northwest Community Forest Coalition invited EPA-WED Research Scientist Bob McKane to present the Keynote Address for the 2018 Northwest Community Forest Forum on May 9‐11 in Astoria, OR. His address will describe "How Visualizing Ecosystem Land Management Assessme...

Assessing self-organization of plant communities--A thermodynamic approach

NASA Astrophysics Data System (ADS)

Lin, H.; Cao, M.; Stoy, P.; Zhang, Y.

2013-12-01

Thermodynamics is a powerful tool for the study of system development and has the potential to be applied to studies of ecological complexity. Here, we develop a set of thermodynamic indicators including energy capture and energy dissipation to quantify plant community self-organization. The study ecosystems included a tropical seasonal rainforest, an artificial tropical rainforest, a rubber plantation, and two Chromolaena odorata (L.) R.M. King & H. Robinson communities aged 13 years and 1 year. The communities represent a complexity transect from primary vegetation, to transitional community, economic plantation, and fallows and are typical for Xishuangbanna, southwestern China. The indicators of ecosystem self-organization are sensitive to plant community type and seasonality, and demonstrate that the tropical seasonal rainforest is highly self-organized and plays an important role in local environmental stability via the land surface thermal regulation. The rubber plantation is at a very low level of self-organization as quantified by the thermodynamic indicators, especially during the dry season. The expansion of the area of rubber plantation and shrinkage of tropical seasonal rainforest would likely induce local surface warming and a larger daily temperature range.

Gaining perspective on the water-energy nexus at the community scale.

PubMed

Perrone, Debra; Murphy, Jennifer; Hornberger, George M

2011-05-15

Water and energy resources are interrelated but their influence on each other is rarely considered. To quantify the water and energy portfolios associated with a community's water-energy nexus (WEN) and the influence of geographic location on resources, we present the WEN tool. The WEN tool quantifies a community's transport (consumed for or lost before delivery) and nexus (energy for water and water for energy) resources so communities can assess their resource flows. In addition, to provide insight into the full range of impacts of water and energy resource acquisition and to frame the influence of geography on resources, we coin the term "urban resource islands". The concept of urban resource islands provides a framework for considering the implication of geography on a community's water and energy resource acquisition and use. The WEN tool and the concept of resource islands can promote communities to think about their hidden resources and integrate such concepts into their sustainability trade-off analyses and policy decisions. In this paper, we use Tucson, Arizona, United States as a case study.

Investigating student communities with network analysis of interactions in a physics learning center

NASA Astrophysics Data System (ADS)

Brewe, Eric; Kramer, Laird; Sawtelle, Vashti

2012-06-01

Developing a sense of community among students is one of the three pillars of an overall reform effort to increase participation in physics, and the sciences more broadly, at Florida International University. The emergence of a research and learning community, embedded within a course reform effort, has contributed to increased recruitment and retention of physics majors. We utilize social network analysis to quantify interactions in Florida International University’s Physics Learning Center (PLC) that support the development of academic and social integration. The tools of social network analysis allow us to visualize and quantify student interactions and characterize the roles of students within a social network. After providing a brief introduction to social network analysis, we use sequential multiple regression modeling to evaluate factors that contribute to participation in the learning community. Results of the sequential multiple regression indicate that the PLC learning community is an equitable environment as we find that gender and ethnicity are not significant predictors of participation in the PLC. We find that providing students space for collaboration provides a vital element in the formation of a supportive learning community.

Dynamics of sustained use and abandonment of clean cooking systems: study protocol for community-based system dynamics modeling.

PubMed

Kumar, Praveen; Chalise, Nishesh; Yadama, Gautam N

2016-04-26

More than 3 billion of the world's population are affected by household air pollution from relying on unprocessed solid fuels for heating and cooking. Household air pollution is harmful to human health, climate, and environment. Sustained uptake and use of cleaner cooking technologies and fuels are proposed as solutions to this problem. In this paper, we present our study protocol aimed at understanding multiple interacting feedback mechanisms involved in the dynamic behavior between social, ecological, and technological systems driving sustained use or abandonment of cleaner cooking technologies among the rural poor in India. This study uses a comparative case study design to understand the dynamics of sustained use or abandonment of cleaner cooking technologies and fuels in four rural communities of Rajasthan, India. The study adopts a community based system dynamics modeling approach. We describe our approach of using community based system dynamics with rural communities to delineate the feedback mechanisms involved in the uptake and sustainment of clean cooking technologies. We develop a reference mode with communities showing the trend over time of use or abandonment of cleaner cooking technologies and fuels in these communities. Subsequently, the study develops a system dynamics model with communities to understand the complex sub-systems driving the behavior in these communities as reflected in the reference mode. We use group model building techniques to facilitate participation of relevant stakeholders in the four communities and elicit a narrative describing the feedback mechanisms underlying sustained adoption or abandonment of cleaner cooking technologies. In understanding the dynamics of feedback mechanisms in the uptake and exclusive use of cleaner cooking systems, we increase the likelihood of dissemination and implementation of efficacious interventions into everyday settings to improve the health and wellbeing of women and children most affected by household air pollution. The challenge is not confined to developing robust technical solutions to reduce household air pollution and exposure to improve respiratory health, and prevent associated diseases. The bigger challenge is to disseminate and implement cleaner cooking technologies and fuels in the context of various social, behavioral, and economic constraints faced by poor households and communities. The Institutional Review Board of Washington University in St. Louis has exempted community based system dynamics modeling from review.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

PubMed Central

Hannigan, Geoffrey D.; Duhaime, Melissa B.; Koutra, Danai

2018-01-01

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. PMID:29668682

Assessing Effects of Climate Change on Access to Ecosystem Services in Rural Alaska: Enhancing the Science through Community Engagement

NASA Astrophysics Data System (ADS)

Brinkman, T. J.; Cold, H.; Brown, D. N.; Brown, C.; Hollingsworth, T. N.; Verbyla, D.

2017-12-01

In Arctic-Boreal regions, studies quantifying the characteristics and prevalence of environmental disruptions to access to ecosystem services are lacking. Empirical investigations are needed to assess the vulnerability of rural communities to climate change. We integrated community-based local observation (9 Interior Alaska Communities), field-based ground measurements, and remote sensing data to: 1) identify and prioritize the relative importance of different environmental changes affecting access, 2) characterize the biophysical causes and mechanisms related to access, and 3) evaluate long-term (30 year) trends in the environment that are challenging access. Dynamic winter ice and snow conditions (e.g., dangerous ice travel; n =147) were the most commonly reported cause of disturbance to access, followed by changes in summer hydrology (e.g., river navigability; n = 77) and seasonal shifts in freeze/thaw cycles (n = 31). Supporting local observations, our remote-sensing analysis indicated a trend toward environmental conditions that hinder or disrupt traditional uses of ecosystem services. For example, we found that the window of safe travel on ice has narrowed by approximately 2 weeks since the 1980s. Shifts in travel have implications on the effectiveness of subsistence activities, such as winter trapping and spring waterfowl hunting. From a methods perspective, we implemented a study design that generated novel science while also addressing locally relevant issues. Our approach and findings highlight opportunities for connecting biophysical science with societal concerns.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.

PubMed

Hannigan, Geoffrey D; Duhaime, Melissa B; Koutra, Danai; Schloss, Patrick D

2018-04-01

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.

Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes.

PubMed

Kravchenko, Alexandra; Falconer, Ruth E; Grinev, Dmitri; Otten, Wilfred

2011-06-01

Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed-soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native-species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was > or =110 microm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long-term no-till, while large connected pores in soils under native vegetation or in tilled agriculture promoted the invasion.

Post-fire reconstructions of fire intensity from fire severity data: quantifying the role of spatial variability of fire intensity on forest dynamics

NASA Astrophysics Data System (ADS)

Baker, Patrick; Oborne, Lisa

2015-04-01

Large, high-intensity fires have direct and long-lasting effects on forest ecosystems and present a serious threat to human life and property. However, even within the most catastrophic fires there is important variability in local-scale intensity that has important ramifications for forest mortality and regeneration. Quantifying this variability is difficult due to the rarity of catastrophic fire events, the extreme conditions at the time of the fires, and their large spatial extent. Instead fire severity is typically measured or estimated from observed patterns of vegetation mortality; however, differences in species- and size-specific responses to fires often makes fire severity a poor proxy for fire intensity. We developed a statistical method using simple, plot-based measurements of individual tree mortality to simultaneously estimate plot-level fire intensity and species-specific mortality patterns as a function of tree size. We applied our approach to an area of forest burned in the catastrophic Black Saturday fires that occurred near Melbourne, Australia, in February 2009. Despite being the most devastating fire in the past 70 years and our plots being located in the area that experienced some of the most intense fires in the 350,000 ha fire complex, we found that the estimated fire intensity was highly variable at multiple spatial scales. All eight tree species in our study differed in their susceptibility to fire-induced mortality, particularly among the largest size classes. We also found that seedling height and species richness of the post-fire seedling communities were both positively correlated with fire intensity. Spatial variability in disturbance intensity has important, but poorly understood, consequences for the short- and long-term dynamics of forests in the wake of catastrophic wildfires. Our study provides a tool to estimate fire intensity after a fire has passed, allowing new opportunities for linking spatial variability in fire intensity to forest ecosystem dynamics.

Predictability in community dynamics.

PubMed

Blonder, Benjamin; Moulton, Derek E; Blois, Jessica; Enquist, Brian J; Graae, Bente J; Macias-Fauria, Marc; McGill, Brian; Nogué, Sandra; Ordonez, Alejandro; Sandel, Brody; Svenning, Jens-Christian

2017-03-01

The coupling between community composition and climate change spans a gradient from no lags to strong lags. The no-lag hypothesis is the foundation of many ecophysiological models, correlative species distribution modelling and climate reconstruction approaches. Simple lag hypotheses have become prominent in disequilibrium ecology, proposing that communities track climate change following a fixed function or with a time delay. However, more complex dynamics are possible and may lead to memory effects and alternate unstable states. We develop graphical and analytic methods for assessing these scenarios and show that these dynamics can appear in even simple models. The overall implications are that (1) complex community dynamics may be common and (2) detailed knowledge of past climate change and community states will often be necessary yet sometimes insufficient to make predictions of a community's future state. © 2017 John Wiley & Sons Ltd/CNRS.

Ecological communities with Lotka-Volterra dynamics

NASA Astrophysics Data System (ADS)

Bunin, Guy

2017-04-01

Ecological communities in heterogeneous environments assemble through the combined effect of species interaction and migration. Understanding the effect of these processes on the community properties is central to ecology. Here we study these processes for a single community subject to migration from a pool of species, with population dynamics described by the generalized Lotka-Volterra equations. We derive exact results for the phase diagram describing the dynamical behaviors, and for the diversity and species abundance distributions. A phase transition is found from a phase where a unique globally attractive fixed point exists to a phase where multiple dynamical attractors exist, leading to history-dependent community properties. The model is shown to possess a symmetry that also establishes a connection with other well-known models.

Ecological communities with Lotka-Volterra dynamics.

PubMed

Bunin, Guy

2017-04-01

Ecological communities in heterogeneous environments assemble through the combined effect of species interaction and migration. Understanding the effect of these processes on the community properties is central to ecology. Here we study these processes for a single community subject to migration from a pool of species, with population dynamics described by the generalized Lotka-Volterra equations. We derive exact results for the phase diagram describing the dynamical behaviors, and for the diversity and species abundance distributions. A phase transition is found from a phase where a unique globally attractive fixed point exists to a phase where multiple dynamical attractors exist, leading to history-dependent community properties. The model is shown to possess a symmetry that also establishes a connection with other well-known models.

Quantifying dynamic characteristics of human walking for comprehensive gait cycle.

PubMed

Mummolo, Carlotta; Mangialardi, Luigi; Kim, Joo H

2013-09-01

Normal human walking typically consists of phases during which the body is statically unbalanced while maintaining dynamic stability. Quantifying the dynamic characteristics of human walking can provide better understanding of gait principles. We introduce a novel quantitative index, the dynamic gait measure (DGM), for comprehensive gait cycle. The DGM quantifies the effects of inertia and the static balance instability in terms of zero-moment point and ground projection of center of mass and incorporates the time-varying foot support region (FSR) and the threshold between static and dynamic walking. Also, a framework of determining the DGM from experimental data is introduced, in which the gait cycle segmentation is further refined. A multisegmental foot model is integrated into a biped system to reconstruct the walking motion from experiments, which demonstrates the time-varying FSR for different subphases. The proof-of-concept results of the DGM from a gait experiment are demonstrated. The DGM results are analyzed along with other established features and indices of normal human walking. The DGM provides a measure of static balance instability of biped walking during each (sub)phase as well as the entire gait cycle. The DGM of normal human walking has the potential to provide some scientific insights in understanding biped walking principles, which can also be useful for their engineering and clinical applications.

Community helping services: dynamic of formation and expressiveness of the cultural care.

PubMed

Landim, Fátima Luna Pinheiro

2006-01-01

Community helping services is an expression used by the social movements to designate families that live in shacks installed in a public area intended for building of own house at a community helping system. Studies in ethnonursing that aimed: in order to detail dynamic configuration in a community helping service. It took place in an community helping area located in the outskirts of Fortaleza, Ceará. The community members acting as general informants from the local culture, while eight (8) women heads-of-families, working as key informers. The data collect used the Observation-Participation-Reflection Model. The analyses were processing by the time that the dates were collected, considering the categories: inserting in the community helping culture to obtain their history; community helping is not a slum -describing the formation dynamic. Established that the formation dynamic of the community helping go on the own house representation as a symbol of " a better life". To assimilate such expression introducing in own cultural universe is a challenge for the nursing to assist a care culture congruent.

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions.

PubMed

Gebremikael, Mesfin T; Steel, Hanne; Buchan, David; Bert, Wim; De Neve, Stefaan

2016-09-08

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

PubMed Central

Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

2016-01-01

We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions

NASA Astrophysics Data System (ADS)

Gebremikael, Mesfin T.; Steel, Hanne; Buchan, David; Bert, Wim; de Neve, Stefaan

2016-09-01

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Impact of a regional distributed medical education program on an underserved community: perceptions of community leaders.

PubMed

Toomey, Patricia; Lovato, Chris Y; Hanlon, Neil; Poole, Gary; Bates, Joanna

2013-06-01

To describe community leaders' perceptions regarding the impact of a fully distributed undergraduate medical education program on a small, medically underserved host community. The authors conducted semistructured interviews in 2007 with 23 community leaders representing, collectively, the education, health, economic, media, and political sectors. They reinterviewed six participants from a pilot study (2005) and recruited new participants using purposeful and snowball sampling. The authors employed analytic induction to organize content thematically, using the sectors as a framework, and they used open coding to identify new themes. The authors reanalyzed transcripts to identify program outcomes (e.g., increased research capacity) and construct a list of quantifiable indicators (e.g., number of grants and publications). Participants reported their perspectives on the current and anticipated impact of the program on education, health services, the economy, media, and politics. Perceptions of impact were overwhelmingly positive (e.g., increased physician recruitment), though some were negative (e.g., strains on health resources). The authors identified new outcomes and confirmed outcomes described in 2005. They identified 16 quantifiable indicators of impact, which they judged to be plausible and measureable. Participants perceive that the regional undergraduate medical education program in their community has broad, local impacts. Findings suggest that early observed outcomes have been maintained and may be expanding. Results may be applicable to medical education programs with distributed or regional sites in similar rural, remote, and/or underserved regions. The areas of impact, outcomes, and quantifiable indicators identified will be of interest to future researchers and evaluators.

Modern perspectives on measuring and interpreting seafloor heat flux

USGS Publications Warehouse

Harris, Reid N.; Fisher, A.; Ruppel, C.; Martinez, F.

2008-01-01

There has been a resurgence of interest in marine heat flow in the past 10–15 years, coinciding with fundamental achievements in understanding the Earth's thermal state and quantifying the dynamics and impacts of material and energy fluxes within and between the lithosphere and hydrosphere. At the same time, technical capabilities have dwindled to the point that no U.S. academic institution currently operates a seagoing heat flow capacity.In September 2007, a workshop was convened in Salt Lake City with sponsorship from the U.S. National Science Foundation (NSF) and participation by scientists and engineers from North America, Europe, and Asia. The primary goals of the workshop were to (1) assess high-priority scientific and technical needs and (2) to evaluate options for developing and maintaining essential capabilities in marine heat flow for the U.S. scientific community.

Fishermen Follow Fine-scaled Physical Ocean Features For Finance

NASA Astrophysics Data System (ADS)

Fuller, E.; Watson, J. R.; Samhouri, J.; Castruccio, F. S.

2016-12-01

The seascapes on which many millions of people make their living and secure food have complex and dynamic spatial features - the figurative hills and valleys - that control where and how people work at sea. Here, we quantify the physical mosaic of the surface ocean by identifying Lagrangian Coherent Structures for a whole seascape - the California Current - and assess their impact on the spatial distribution of fishing. We show that there is a mixed response: some fisheries track these physical features, and others avoid them. This spatial behavior maps to economic impacts: we find that tuna fishermen can expect to make three times more revenue per trip if fishing occurs on strong coherent structures. These results highlight a connection between the physical state of the oceans, the spatial patterns of human activity and ultimately the economic prosperity of coastal communities.

Mineral Control of Soil Carbon Dynamics in Forest Soils: A Lithosequence Under Ponderosa Pine

NASA Astrophysics Data System (ADS)

Heckman, K. A.; Welty-Bernard, A.; Rasmussen, C.; Schwartz, E.; Chorover, J.

2008-12-01

The role of soil organic carbon in regulating atmospheric CO2 concentration has spurred interest in both quantifying existing soil C stocks and modeling the behavior of soil C under climate change scenarios. Soil parent material exerts direct control over soil organic carbon content through its influence on soil pH and mineral composition. Soil acidity and mineral composition also influence soil microbial community composition and activity, thereby controlling soil respiration rates and microbial biomass size. We sampled a lithosequence of four parent materials (rhyolite, granite, basalt, limestone) under Pinus ponderosa to examine the effects of soil mineralogy and acidity on soil organic carbon content and soil microbial community. Three soil profiles were examined on each parent material and analyzed by X-ray diffraction, pH, selective dissolution, C and N content, and 13C signature. Soils from each of the four parent materials were incubated for 40 days, and microbial communities were compared on the basis of community composition (as determined through T-RFLP analysis), specific metabolic activity, biomass, δ13C of respired CO2, and cumulative amount of C mineralized over the course of the incubation. Soil C content varied significantly among soils of different parent material, and was strongly and positively associated with the abundance of Al-humus complexes r2 = 0.71; P < 0.0001, Fe-humus complexes r2 = 0.74; P = 0.0003, and crystalline Fe-oxide content r2 = 0.63; P = 0.0023. Microbial community composition varied significantly among soils and showed strong associations with soil pH 1:1 in KCl; r2 = 0.87; P < 0.0001, concentration of exchangeable Al r2 = 0.81; P < 0.0001, amorphous Fe oxide content r2 = 0.59; P < 0.004, and Al-humus content r2 = 0.35; P < 0.04. Mineralization rates, biomass and δ13C of respired CO2 differed among parent materials, and also varied with incubation time as substrate quality and N availability changed. The results demonstrate that within a specific ecosystem type, soil parent material exerts significant control over the lability and bioavailability of soil C and soil microbial community composition. We suggest that soil parent material and mineralogy are critical parameters for predicting soil C dynamics and recalcitrance of soil C stocks.

Air and Water Quality Impacts of Brownfields Redevelopment: A Study of Five Communities

EPA Pesticide Factsheets

This Study of Five Communities tests an analytical approach to quantifying the environmental impacts of multiple redevelopment projects in a given municipal area in a manner that can be replicated in other regions.

Tools to Assess Community-Based Cumulative Risk and Exposures

EPA Science Inventory

Multiple agents and stressors can interact in a given community to adversely affect human and ecological conditions. A cumulative risk assessment (CRA) analyzes, characterizes, and potentially quantifies the effects from multiple stressors, which include chemical agents (for exam...

Community and individual effects on SOD intensification in California redwood forests: implications for tanoak persistence

Treesearch

Richard C. Cobb; Joao A. N. Filipe; Ross K. Meentemeyer; Chris A. Gilligan; Shannon C. Lynch; David M. Rizzo

2010-01-01

Processes operating across different spatial scales (for example, individual, community, landscape) influence disease dynamics. Understanding these processes and their interactions can yield general insights into disease control, disease dynamics within communities, and community response to disease. For Phytophthora ramorum, pathogen establishment...

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities.

PubMed

Frelat, Romain; Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs.

Species composition, community and population dynamics of two gallery forests from the Brazilian Cerrado domain

PubMed Central

Almado, Roosevelt P; Miazaki, Angela S; Diniz, Écio S; Moreira, Luis C B; Meira-Neto, João A.A.

2016-01-01

Abstract Background To understand the impacts of global changes on future community compositions, knowledge of community dynamics is of crucial importance. To improve our knowledge of community composition, biomass stock and maintenance of gallery forests in the Brazilian Cerrado, we provide two datasets from the 0.5 ha Corrego Fazendinha Gallery Forest Dynamics Plot and the Corrego Fundo Gallery Forest Dynamics Plot situated in the Bom Despacho region, Minas Gerais, Southeastern Brazil. New information We report diameter at breast height, basal area and height measurements of 3417 trees and treelets identified during three censuses in both areas. PMID:27660529

Approaches for evaluating the effects of bivalve filter feeding on nutrient dynamics in Puget Sound, Washington

USGS Publications Warehouse

Konrad, Christopher P.

2014-01-01

Marine bivalves such as clams, mussels, and oysters are an important component of the food web, which influence nutrient dynamics and water quality in many estuaries. The role of bivalves in nutrient dynamics and, particularly, the contribution of commercial shellfish activities, are not well understood in Puget Sound, Washington. Numerous approaches have been used in other estuaries to quantify the effects of bivalves on nutrient dynamics, ranging from simple nutrient budgeting to sophisticated numerical models that account for tidal circulation, bioenergetic fluxes through food webs, and biochemical transformations in the water column and sediment. For nutrient management in Puget Sound, it might be possible to integrate basic biophysical indicators (residence time, phytoplankton growth rates, and clearance rates of filter feeders) as a screening tool to identify places where nutrient dynamics and water quality are likely to be sensitive to shellfish density and, then, apply more sophisticated methods involving in-situ measurements and simulation models to quantify those dynamics.

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

PubMed Central

Zhen, Zhen; Liu, Haitao; Wang, Na; Guo, Liyue; Meng, Jie; Ding, Na; Wu, Guanglei; Jiang, Gaoming

2014-01-01

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils. PMID:25302996

Landscape fragmentation affects responses of avian communities to climate change.

PubMed

Jarzyna, Marta A; Porter, William F; Maurer, Brian A; Zuckerberg, Benjamin; Finley, Andrew O

2015-08-01

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats. © 2015 John Wiley & Sons Ltd.

Toward understanding the ecological impact of transportation corridors

Treesearch

Victoria J. Bennett; Winston P. Smith; Matthew G. Betts

2011-01-01

Transportation corridors (notably roads) affect wildlife habitat, populations, and entire ecosystems. Considerable effort has been expended to quantify direct effects of roads on wildlife populations and ecological communities and processes. Much less effort has been expended toward quantifying indirect effects. In this report, we provide a comprehensive review of road...

Regional gradient analysis and spatial pattern of woody plant communities in Oregon forests.

Treesearch

J.L. Ohmann; T.A. Spies

1998-01-01

Knowledge of regional-scale patterns of ecological community structure, and of factors that control them, is largely conceptual. Regional- and local-scale factors associated with regional variation in community composition have not been quantified. We analyzed data on woody plant species abundance from 2443 field plots across natural and seminatural forests and...

Rapid Assessment of Tree Debris Following Urban Forest Ice Storms

Treesearch

Richard J. Hauer; Angela J. Hauer; Dudley R. Hartel; Jill R. Johnson

2011-01-01

This paper presents a rapid assessment method to estimate urban tree debris following an ice storm. Data were collected from 60 communities to quantify tree debris volumes, mostly from public rights-of-way, following ice storms based on community infrastructure, weather parameters, and urban forest structure. Ice thickness, area of a community, and street distance are...

Fractional Stability of Trunk Acceleration Dynamics of Daily-Life Walking: Toward a Unified Concept of Gait Stability

PubMed Central

Ihlen, Espen A. F.; van Schooten, Kimberley S.; Bruijn, Sjoerd M.; Pijnappels, Mirjam; van Dieën, Jaap H.

2017-01-01

Over the last decades, various measures have been introduced to assess stability during walking. All of these measures assume that gait stability may be equated with exponential stability, where dynamic stability is quantified by a Floquet multiplier or Lyapunov exponent. These specific constructs of dynamic stability assume that the gait dynamics are time independent and without phase transitions. In this case the temporal change in distance, d(t), between neighboring trajectories in state space is assumed to be an exponential function of time. However, results from walking models and empirical studies show that the assumptions of exponential stability break down in the vicinity of phase transitions that are present in each step cycle. Here we apply a general non-exponential construct of gait stability, called fractional stability, which can define dynamic stability in the presence of phase transitions. Fractional stability employs the fractional indices, α and β, of differential operator which allow modeling of singularities in d(t) that cannot be captured by exponential stability. The fractional stability provided an improved fit of d(t) compared to exponential stability when applied to trunk accelerations during daily-life walking in community-dwelling older adults. Moreover, using multivariate empirical mode decomposition surrogates, we found that the singularities in d(t), which were well modeled by fractional stability, are created by phase-dependent modulation of gait. The new construct of fractional stability may represent a physiologically more valid concept of stability in vicinity of phase transitions and may thus pave the way for a more unified concept of gait stability. PMID:28900400

Coastal oceanography sets the pace of rocky intertidal community dynamics.

PubMed

Menge, B A; Lubchenco, J; Bracken, M E S; Chan, F; Foley, M M; Freidenburg, T L; Gaines, S D; Hudson, G; Krenz, C; Leslie, H; Menge, D N L; Russell, R; Webster, M S

2003-10-14

The structure of ecological communities reflects a tension among forces that alter populations. Marine ecologists previously emphasized control by locally operating forces (predation, competition, and disturbance), but newer studies suggest that inputs from large-scale oceanographically modulated subsidies (nutrients, particulates, and propagules) can strongly influence community structure and dynamics. On New Zealand rocky shores, the magnitude of such subsidies differs profoundly between contrasting oceanographic regimes. Community structure, and particularly the pace of community dynamics, differ dramatically between intermittent upwelling regimes compared with relatively persistent down-welling regimes. We suggest that subsidy rates are a key determinant of the intensity of species interactions, and thus of structure in marine systems, and perhaps also nonmarine communities.

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

DOE PAGES

Sippel, Sebastian; Lange, Holger; Mahecha, Miguel D.; ...

2016-10-20

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observedmore » and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. Here we demonstrate that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics.« less

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sippel, Sebastian; Lange, Holger; Mahecha, Miguel D.

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observedmore » and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. Here we demonstrate that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics.« less

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers

PubMed Central

Sippel, Sebastian; Mahecha, Miguel D.; Hauhs, Michael; Bodesheim, Paul; Kaminski, Thomas; Gans, Fabian; Rosso, Osvaldo A.

2016-01-01

Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observed and simulated time series of Gross Primary Productivity (GPP), a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. We demonstrate here that information content and complexity, or Information Theory Quantifiers (ITQ) for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective ecological time series. At global scale, our understanding of C fluxes relies on the use of consistently applied land models. Here, we use ITQ to evaluate model structure: The measures are largely insensitive to climatic scenarios, land use and atmospheric gas concentrations used to drive them, but clearly separate the structure of 13 different land models taken from the CMIP5 archive and an observations-based product. In conclusion, diagnostic measures of this kind provide data-analytical tools that distinguish different types of natural processes based solely on their dynamics, and are thus highly suitable for environmental science applications such as model structural diagnostics. PMID:27764187

Recurrence quantity analysis based on matrix eigenvalues

NASA Astrophysics Data System (ADS)

Yang, Pengbo; Shang, Pengjian

2018-06-01

Recurrence plots is a powerful tool for visualization and analysis of dynamical systems. Recurrence quantification analysis (RQA), based on point density and diagonal and vertical line structures in the recurrence plots, is considered to be alternative measures to quantify the complexity of dynamical systems. In this paper, we present a new measure based on recurrence matrix to quantify the dynamical properties of a given system. Matrix eigenvalues can reflect the basic characteristics of the complex systems, so we show the properties of the system by exploring the eigenvalues of the recurrence matrix. Considering that Shannon entropy has been defined as a complexity measure, we propose the definition of entropy of matrix eigenvalues (EOME) as a new RQA measure. We confirm that EOME can be used as a metric to quantify the behavior changes of the system. As a given dynamical system changes from a non-chaotic to a chaotic regime, the EOME will increase as well. The bigger EOME values imply higher complexity and lower predictability. We also study the effect of some factors on EOME,including data length, recurrence threshold, the embedding dimension, and additional noise. Finally, we demonstrate an application in physiology. The advantage of this measure lies in a high sensitivity and simple computation.

Quantification of causal couplings via dynamical effects: A unifying perspective

NASA Astrophysics Data System (ADS)

Smirnov, Dmitry A.

2014-12-01

Quantitative characterization of causal couplings from time series is crucial in studies of complex systems of different origin. Various statistical tools for that exist and new ones are still being developed with a tendency to creating a single, universal, model-free quantifier of coupling strength. However, a clear and generally applicable way of interpreting such universal characteristics is lacking. This work suggests a general conceptual framework for causal coupling quantification, which is based on state space models and extends the concepts of virtual interventions and dynamical causal effects. Namely, two basic kinds of interventions (state space and parametric) and effects (orbital or transient and stationary or limit) are introduced, giving four families of coupling characteristics. The framework provides a unifying view of apparently different well-established measures and allows us to introduce new characteristics, always with a definite "intervention-effect" interpretation. It is shown that diverse characteristics cannot be reduced to any single coupling strength quantifier and their interpretation is inevitably model based. The proposed set of dynamical causal effect measures quantifies different aspects of "how the coupling manifests itself in the dynamics," reformulating the very question about the "causal coupling strength."

Plant reproduction is altered by simulated herbicide drift to constructed plant communities

EPA Science Inventory

Herbicide drift may have unintended impacts on native vegetation, adversely affecting structure and function of plant communities. However, these potential effects have been rarely studied or quantified. To determine potential ecological effects of herbicide drift, we construct...

Navigating the Power Dynamics between Institutions and Their Communities

ERIC Educational Resources Information Center

White, Byron P.

2009-01-01

The author's career experiences--as an impartial observer of community building, as an advocate working from within urban communities, and as a catalyst working from the outside--have given him a unique perspective into the dynamics of institutional/community engagement. "Basically, they have left me with three overriding convictions. First,…

Supportive-Expressive Dynamic Psychotherapy in the Community Mental Health System: A Pilot Effectiveness Trial for the Treatment of Depression

PubMed Central

Connolly Gibbons, Mary Beth; Thompson, Sarah M.; Scott, Kelli; Schauble, Lindsay A.; Mooney, Tessa; Thompson, Donald; Green, Patricia; MacArthur, Mary Jo; Crits-Christoph, Paul

2013-01-01

The goal of the current article is to present the results of a randomized pilot investigation of a brief dynamic psychotherapy compared with treatment-as-usual (TAU) in the treatment of moderate-to-severe depression in the community mental health system. Forty patients seeking services for moderate-to-severe depression in the community mental health system were randomized to 12 weeks of psychotherapy, with either a community therapist trained in brief dynamic psychotherapy or a TAU therapist. Results indicated that blind judges could discriminate the dynamic sessions from the TAU sessions on adherence to dynamic interventions. The results indicate moderate-to-large effect sizes in favor of the dynamic psychotherapy over the TAU therapy in the treatment of depression. The Behavior and Symptom Identification Scale-24 showed that 50% of patients treated with dynamic therapy moved into a normative range compared with only 29% of patients treated with TAU. PMID:22962971

Estimating Cyanobacteria Community Dynamics and its Relationship with Environmental Factors

PubMed Central

Luo, Wenhuai; Chen, Huirong; Lei, Anping; Lu, Jun; Hu, Zhangli

2014-01-01

The cyanobacteria community dynamics in two eutrophic freshwater bodies (Tiegang Reservoir and Shiyan Reservoir) was studied with both a traditional microscopic counting method and a PCR-DGGE genotyping method. Results showed that cyanobacterium Phormidium tenue was the predominant species; twenty-six cyanobacteria species were identified in water samples collected from the two reservoirs, among which fourteen were identified with the morphological method and sixteen with the PCR-DGGE method. The cyanobacteria community composition analysis showed a seasonal fluctuation from July to December. The cyanobacteria population peaked in August in both reservoirs, with cell abundances of 3.78 × 108 cells L-1 and 1.92 × 108 cells L-1 in the Tiegang and Shiyan reservoirs, respectively. Canonical Correspondence Analysis (CCA) was applied to further investigate the correlation between cyanobacteria community dynamics and environmental factors. The result indicated that the cyanobacteria community dynamics was mostly correlated with pH, temperature and total nitrogen. This study demonstrated that data obtained from PCR-DGGE combined with a traditional morphological method could reflect cyanobacteria community dynamics and its correlation with environmental factors in eutrophic freshwater bodies. PMID:24448632

Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models.

PubMed

Li, Wenlin; Schaeffer, R Dustin; Otwinowski, Zbyszek; Grishin, Nick V

2016-01-01

The Critical Assessment of techniques for protein Structure Prediction (or CASP) is a community-wide blind test experiment to reveal the best accomplishments of structure modeling. Assessors have been using the Global Distance Test (GDT_TS) measure to quantify prediction performance since CASP3 in 1998. However, identifying significant score differences between close models is difficult because of the lack of uncertainty estimations for this measure. Here, we utilized the atomic fluctuations caused by structure flexibility to estimate the uncertainty of GDT_TS scores. Structures determined by nuclear magnetic resonance are deposited as ensembles of alternative conformers that reflect the structural flexibility, whereas standard X-ray refinement produces the static structure averaged over time and space for the dynamic ensembles. To recapitulate the structural heterogeneous ensemble in the crystal lattice, we performed time-averaged refinement for X-ray datasets to generate structural ensembles for our GDT_TS uncertainty analysis. Using those generated ensembles, our study demonstrates that the time-averaged refinements produced structure ensembles with better agreement with the experimental datasets than the averaged X-ray structures with B-factors. The uncertainty of the GDT_TS scores, quantified by their standard deviations (SDs), increases for scores lower than 50 and 70, with maximum SDs of 0.3 and 1.23 for X-ray and NMR structures, respectively. We also applied our procedure to the high accuracy version of GDT-based score and produced similar results with slightly higher SDs. To facilitate score comparisons by the community, we developed a user-friendly web server that produces structure ensembles for NMR and X-ray structures and is accessible at http://prodata.swmed.edu/SEnCS. Our work helps to identify the significance of GDT_TS score differences, as well as to provide structure ensembles for estimating SDs of any scores.

An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae

PubMed Central

Lehtinen, Sonja; Fraser, Christophe

2017-01-01

The frequency of resistance to antibiotics in Streptococcus pneumoniae has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates in phase with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance. PMID:28566489

Analysis of in situ manganese(II) oxidation in the Columbia River and offshore plume: Linking microbial community structure to active biogeochemical cycles

PubMed Central

Anderson, C. R.; Davis, R. E.; Bandolin, N. S.; Baptista, A. M.; Tebo, B. M.

2017-01-01

The Columbia River is a major source of dissolved nutrients and trace metals for the west coast of North America. A large proportion of these nutrients are sourced from the Columbia River Estuary where coastal and terrestrial waters mix and resuspend particulate matter within the water column. As estuarine water is discharged off the coast it transports the particulate matter, dissolved nutrients and microorganisms forming nutrient rich and metabolically dynamic plumes. In this study, bacterial manganese oxidation within the plume and estuary was investigated during spring and neap tides. The microbial community proteome was fractionated and assayed for Mn oxidation activity. Proteins from the outer membrane and the loosely bound outer membrane fractions were separated using size exclusion chromatography and Mn(II)-oxidizing eluates were analyzed with tandem mass spectrometry to identify potential Mn oxidase protein targets. Multi-copper oxidase (MCO) and heme-peroxidase enzymes were identified in active fractions. T-RFLP cluster analysis indicates that the organisms oxidizing the most Mn(II) were sourced from the Columbia River estuary and nearshore coastal ocean. These organisms are producing up to 10 fM MnO2 cell−1 day−1. Evidence for the presence of Mn(II)-oxidizing bacterial isolates from the genera Aurantimonas, Rhodobacter, Bacillus, and Shewanella was found in T-RFLP profiles. Q-PCR was used to quantify the gene copies of the heme-peroxidase, Aurantimonas SSU rRNA and total bacterial SSU rRNA gene copies. The probes used suggested that Aurantimonas could only account for 1.7% of heme-peroxidase genes quantified suggesting that peroxidase driven manganese oxidation capabilities are widespread throughout other organisms in this environment. PMID:21418498

Moving alcohol prevention research forward-Part II: new directions grounded in community-based system dynamics modeling.

PubMed

Apostolopoulos, Yorghos; Lemke, Michael K; Barry, Adam E; Lich, Kristen Hassmiller

2018-02-01

Given the complexity of factors contributing to alcohol misuse, appropriate epistemologies and methodologies are needed to understand and intervene meaningfully. We aimed to (1) provide an overview of computational modeling methodologies, with an emphasis on system dynamics modeling; (2) explain how community-based system dynamics modeling can forge new directions in alcohol prevention research; and (3) present a primer on how to build alcohol misuse simulation models using system dynamics modeling, with an emphasis on stakeholder involvement, data sources and model validation. Throughout, we use alcohol misuse among college students in the United States as a heuristic example for demonstrating these methodologies. System dynamics modeling employs a top-down aggregate approach to understanding dynamically complex problems. Its three foundational properties-stocks, flows and feedbacks-capture non-linearity, time-delayed effects and other system characteristics. As a methodological choice, system dynamics modeling is amenable to participatory approaches; in particular, community-based system dynamics modeling has been used to build impactful models for addressing dynamically complex problems. The process of community-based system dynamics modeling consists of numerous stages: (1) creating model boundary charts, behavior-over-time-graphs and preliminary system dynamics models using group model-building techniques; (2) model formulation; (3) model calibration; (4) model testing and validation; and (5) model simulation using learning-laboratory techniques. Community-based system dynamics modeling can provide powerful tools for policy and intervention decisions that can result ultimately in sustainable changes in research and action in alcohol misuse prevention. © 2017 Society for the Study of Addiction.

Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

PubMed Central

Lindegren, Martin; Denker, Tim Spaanheden; Floeter, Jens; Fock, Heino O.; Sguotti, Camilla; Stäbler, Moritz; Otto, Saskia A.; Möllmann, Christian

2017-01-01

Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e.g. Principal Component Analysis) but extends it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low frequency temperature variability inherent in the Atlantic Multidecadal Oscillation. Finally, we identified six major sub-communities composed of species sharing similar spatial distribution patterns and temporal dynamics. Our case study demonstrates the application and benefits of using tensor decomposition for studying complex community data sets usually derived from large-scale monitoring programs. PMID:29136658

Parasite transmission in a natural multihost-multiparasite community.

PubMed

Auld, Stuart K J R; Searle, Catherine L; Duffy, Meghan A

2017-05-05

Understanding the transmission and dynamics of infectious diseases in natural communities requires understanding the extent to which the ecology, evolution and epidemiology of those diseases are shaped by alternative hosts. We performed laboratory experiments to test how parasite spillover affected traits associated with transmission in two co-occurring parasites: the bacterium Pasteuria ramosa and the fungus Metschnikowia bicuspidata Both parasites were capable of transmission from the reservoir host ( Daphnia dentifera ) to the spillover host ( Ceriodaphnia dubia ), but this occurred at a much higher rate for the fungus than the bacterium. We quantified transmission potential by combining information on parasite transmission and growth rate, and used this to compare parasite fitness in the two host species. For both parasites, transmission potential was lower in the spillover host. For the bacterium, virulence was higher in the spillover host. Transmission back to the original host was high for both parasites, with spillover influencing transmission rate of the fungus but not the bacterium. Thus, while inferior, the spillover host is not a dead-end for either parasite. Overall, our results demonstrate that the presence of multiple hosts in a community can have important consequences for disease transmission, and host and parasite fitness.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Author(s).

NEP-ORD Collaborations on Quantifying the Ecosystem Goods and Services of Estuaries

EPA Science Inventory

Nature’s goods and services provided by estuarine ecosystems are integral to the economies and well-being of coastal communities. However, many valuable ecosystem goods and services (EGS), including their benefits to surrounding communities, are not explicitly considered i...

Distinct soil bacterial communities revealed under a diversely managed agroecosystem

USDA-ARS?s Scientific Manuscript database

Land-use change and management are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, soil microbial community complexity after manipulations is still difficult to quantify. In this study, replicate soil samples we...

Behavior of plywood and fiberglass steel composite tube structures subjected to impact loading

NASA Astrophysics Data System (ADS)

Armaghani, Seyamend Bilind

Paratransit buses are custom built as the major vehicle manufacturer produces the custom built passenger cage installed on the chassis for the Paratransit bus. In order for these Paratransit bus members to be sufficient, they have to be evaluated for crashworthiness and energy absorption. This has prompted Florida Department of Transportation (FDOT) to fund research for the safety evaluation of Paratransit busses consisting of crash and safety analysis. There has been a large body of research done on steel subjected to static loads, but more research is needed for steel applied under dynamic loading and high speeds in order to improve crashworthiness in events such as rollovers and side impacts. Bare steel Hollow Structural Section (HSS) tubing are used a lot as structural members of Paratransit buses because of their lightness and progressive buckling under loading. The research will be conducted on quantifying the tubing's behavior under bending by conducting static three point bending and impact loading tests. In addition to the bare tubing, plywood and fiberglass composites are investigated because they are both strong and lightweight and their behavior under dynamic loading hasn't been quantified. As a result, the main purpose of this research is to quantify the differences between the dynamic and static behavior of plywood steel composite and fiberglass steel composite tubing and compare these findings with those of bare steel tubing. The differences will be quantified using detailed and thorough experiments that will examine the composites behavior under both static and dynamic loading. These tests will determine if there are any advantages of using the composite materials and thus allow for recommendations to be made to the FDOT with the goal of improving the safety of Paratransit busses. Tensile tests were conducted to determine the material properties of the tested specimens. Before the static and dynamic experiments are run to investigate the differences between static and dynamic behavior, Preliminary three point bending testing was conducted to determine the parameters for the final experiments. Static bending testing was conducted on the bare, plywood composite, and fiberglass composite steel tubing. The point of these experiments was to produce a Moment vs. Rotation plot to determine the specimens' maximum moments and their associated rotation, as that is when the steel buckles and fails. The dynamic three point bending experiments were conducted using the impact loading apparatus and had the same purpose as the static experiments. For both static and dynamic experiments, the performances of the different types of specimens were compared based upon their Moment vs. Rotation plots. This will determine the effect that the composite has on the rotation and maximum moment at which the tubing fails. After conducting these experiments, amplification factors were established for each specimen by comparing the maximum moment and their associated rotation between static and dynamic testing. lambda was calculated to quantify the ratio between the static and dynamic maximum moments. beta was used to quantify the ratio between the rotation needed to produce the maximum moment between static and dynamic events. A small amplification factor denotes that material performs well under impact loading and the material doesn't experience dramatic change in behavior during dynamic events. Amplification factors were compared between the bare, plywood, and fiberglass composite steel tubing in order to evaluate the performance of the composites. After comparing the amplification factors of the different types of tubing, recommendations can be made. Fiberglass and plywood composite were shown to be valuable because it decreased the effect of dynamic forces as beta was reduced by a factor of 2 in comparison to bare tubing. Based upon the amplification factors, it was recommended to use 14 gauge fiberglass composite tubing as Paratransit bus structural members because it was affected the least by dynamic loading.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity.

PubMed

Frickel, Jens; Theodosiou, Loukas; Becks, Lutz

2017-10-17

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host-virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host-virus coevolution in the complex system and that the virus' effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

Modeling responses of large-river fish populations to global climate change through downscaling and incorporation of predictive uncertainty

USGS Publications Warehouse

Wildhaber, Mark L.; Wikle, Christopher K.; Anderson, Christopher J.; Franz, Kristie J.; Moran, Edward H.; Dey, Rima; Mader, Helmut; Kraml, Julia

2012-01-01

Climate change operates over a broad range of spatial and temporal scales. Understanding its effects on ecosystems requires multi-scale models. For understanding effects on fish populations of riverine ecosystems, climate predicted by coarse-resolution Global Climate Models must be downscaled to Regional Climate Models to watersheds to river hydrology to population response. An additional challenge is quantifying sources of uncertainty given the highly nonlinear nature of interactions between climate variables and community level processes. We present a modeling approach for understanding and accomodating uncertainty by applying multi-scale climate models and a hierarchical Bayesian modeling framework to Midwest fish population dynamics and by linking models for system components together by formal rules of probability. The proposed hierarchical modeling approach will account for sources of uncertainty in forecasts of community or population response. The goal is to evaluate the potential distributional changes in an ecological system, given distributional changes implied by a series of linked climate and system models under various emissions/use scenarios. This understanding will aid evaluation of management options for coping with global climate change. In our initial analyses, we found that predicted pallid sturgeon population responses were dependent on the climate scenario considered.

Predator–prey interactions mediated by prey personality and predator hunting mode

PubMed Central

Belgrad, Benjamin A.; Griffen, Blaine D.

2016-01-01

Predator–prey interactions are important drivers in structuring ecological communities. However, despite widespread acknowledgement that individual behaviours and predator species regulate ecological processes, studies have yet to incorporate individual behavioural variations in a multipredator system. We quantified a prevalent predator avoidance behaviour to examine the simultaneous roles of prey personality and predator hunting mode in governing predator–prey interactions. Mud crabs, Panopeus herbstii, reduce their activity levels and increase their refuge use in the presence of predator cues. We measured mud crab mortality and consistent individual variations in the strength of this predator avoidance behaviour in the presence of predatory blue crabs, Callinectes sapidus, and toadfish, Opsanus tau. We found that prey personality and predator species significantly interacted to affect mortality with blue crabs primarily consuming bold mud crabs and toadfish preferentially selecting shy crabs. Additionally, the strength of the predator avoidance behaviour depended upon the predation risk from the predator species. Consequently, the personality composition of populations and predator hunting mode may be valuable predictors of both direct and indirect predator–prey interaction strength. These findings support theories postulating mechanisms for maintaining intraspecies diversity and have broad implications for community dynamics. PMID:27075257

Assessing the Effect of Marine Reserves on Household Food Security in Kenyan Coral Reef Fishing Communities

PubMed Central

Darling, Emily S.

2014-01-01

Measuring the success or failure of natural resource management is a key challenge to evaluate the impact of conservation for ecological, economic and social outcomes. Marine reserves are a popular tool for managing coastal ecosystems and resources yet surprisingly few studies have quantified the social-economic impacts of marine reserves on food security despite the critical importance of this outcome for fisheries management in developing countries. Here, I conducted semi-structured household surveys with 113 women heads-of-households to investigate the influence of two old, well-enforced, no-take marine reserves on food security in four coastal fishing communities in Kenya, East Africa. Multi-model information-theoretic inference and matching methods found that marine reserves did not influence household food security, as measured by protein consumption, diet diversity and food coping strategies. Instead, food security was strongly influenced by fishing livelihoods and household wealth: fishing families and wealthier households were more food secure than non-fishing and poorer households. These findings highlight the importance of complex social and economic landscapes of livelihoods, urbanization, power and gender dynamics that can drive the outcomes of marine conservation and management. PMID:25422888

Desert Dust and Health: A Central Asian Review and Steppe Case Study.

PubMed

Sternberg, Troy; Edwards, Mona

2017-11-03

In Asian deserts environmental and anthropomorphic dust is a significant health risk to rural populations. Natural sources in dry landscapes are exacerbated by human activities that increase the vulnerability to dust and dust-borne disease vectors. Today in Central and Inner Asian drylands, agriculture, mining, and rapid development contribute to dust generation and community exposure. Thorough review of limited dust investigation in the region implies but does not quantify health risks. Anthropogenic sources, such as the drying of the Aral Sea, highlight the shifting dust dynamics across the Central EurAsian steppe. In the Gobi Desert, our case study in Khanbogd, Mongolia addressed large-scale mining's potential dust risk to the health of the local population. Dust traps showed variable exposure to particulates among herder households and town residents; dust density distribution indicated that sources beyond the mine need to be considered when identifying particulate sources. Research suggests that atmospheric dust from multiple causes may enhance human particulate exposure. Greater awareness of dust in greater Central Asia reflects community concern about related health implications. Future human well-being in the region will require more thorough information on dust emissions in the changing environment.

Predator-prey interactions mediated by prey personality and predator hunting mode.

PubMed

Belgrad, Benjamin A; Griffen, Blaine D

2016-04-13

Predator-prey interactions are important drivers in structuring ecological communities. However, despite widespread acknowledgement that individual behaviours and predator species regulate ecological processes, studies have yet to incorporate individual behavioural variations in a multipredator system. We quantified a prevalent predator avoidance behaviour to examine the simultaneous roles of prey personality and predator hunting mode in governing predator-prey interactions. Mud crabs, Panopeus herbstii, reduce their activity levels and increase their refuge use in the presence of predator cues. We measured mud crab mortality and consistent individual variations in the strength of this predator avoidance behaviour in the presence of predatory blue crabs, Callinectes sapidus, and toadfish, Opsanus tau We found that prey personality and predator species significantly interacted to affect mortality with blue crabs primarily consuming bold mud crabs and toadfish preferentially selecting shy crabs. Additionally, the strength of the predator avoidance behaviour depended upon the predation risk from the predator species. Consequently, the personality composition of populations and predator hunting mode may be valuable predictors of both direct and indirect predator-prey interaction strength. These findings support theories postulating mechanisms for maintaining intraspecies diversity and have broad implications for community dynamics. © 2016 The Author(s).

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae

PubMed Central

Giatsis, Christos; Sipkema, Detmer; Smidt, Hauke; Verreth, Johan; Verdegem, Marc

2014-01-01

The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable. PMID:25072852

Desert Dust and Health: A Central Asian Review and Steppe Case Study

PubMed Central

Sternberg, Troy; Edwards, Mona

2017-01-01

In Asian deserts environmental and anthropomorphic dust is a significant health risk to rural populations. Natural sources in dry landscapes are exacerbated by human activities that increase the vulnerability to dust and dust-borne disease vectors. Today in Central and Inner Asian drylands, agriculture, mining, and rapid development contribute to dust generation and community exposure. Thorough review of limited dust investigation in the region implies but does not quantify health risks. Anthropogenic sources, such as the drying of the Aral Sea, highlight the shifting dust dynamics across the Central EurAsian steppe. In the Gobi Desert, our case study in Khanbogd, Mongolia addressed large-scale mining’s potential dust risk to the health of the local population. Dust traps showed variable exposure to particulates among herder households and town residents; dust density distribution indicated that sources beyond the mine need to be considered when identifying particulate sources. Research suggests that atmospheric dust from multiple causes may enhance human particulate exposure. Greater awareness of dust in greater Central Asia reflects community concern about related health implications. Future human well-being in the region will require more thorough information on dust emissions in the changing environment. PMID:29099792

Assessing the effect of marine reserves on household food security in Kenyan coral reef fishing communities.

PubMed

Darling, Emily S

2014-01-01

Measuring the success or failure of natural resource management is a key challenge to evaluate the impact of conservation for ecological, economic and social outcomes. Marine reserves are a popular tool for managing coastal ecosystems and resources yet surprisingly few studies have quantified the social-economic impacts of marine reserves on food security despite the critical importance of this outcome for fisheries management in developing countries. Here, I conducted semi-structured household surveys with 113 women heads-of-households to investigate the influence of two old, well-enforced, no-take marine reserves on food security in four coastal fishing communities in Kenya, East Africa. Multi-model information-theoretic inference and matching methods found that marine reserves did not influence household food security, as measured by protein consumption, diet diversity and food coping strategies. Instead, food security was strongly influenced by fishing livelihoods and household wealth: fishing families and wealthier households were more food secure than non-fishing and poorer households. These findings highlight the importance of complex social and economic landscapes of livelihoods, urbanization, power and gender dynamics that can drive the outcomes of marine conservation and management.

Predators, environment and host characteristics influence the probability of infection by an invasive castrating parasite.

PubMed

Gehman, Alyssa-Lois M; Grabowski, Jonathan H; Hughes, A Randall; Kimbro, David L; Piehler, Michael F; Byers, James E

2017-01-01

Not all hosts, communities or environments are equally hospitable for parasites. Direct and indirect interactions between parasites and their predators, competitors and the environment can influence variability in host exposure, susceptibility and subsequent infection, and these influences may vary across spatial scales. To determine the relative influences of abiotic, biotic and host characteristics on probability of infection across both local and estuary scales, we surveyed the oyster reef-dwelling mud crab Eurypanopeus depressus and its parasite Loxothylacus panopaei, an invasive castrating rhizocephalan, in a hierarchical design across >900 km of the southeastern USA. We quantified the density of hosts, predators of the parasite and host, the host's oyster reef habitat, and environmental variables that might affect the parasite either directly or indirectly on oyster reefs within 10 estuaries throughout this biogeographic range. Our analyses revealed that both between and within estuary-scale variation and host characteristics influenced L. panopaei prevalence. Several additional biotic and abiotic factors were positive predictors of infection, including predator abundance and the depth of water inundation over reefs at high tide. We demonstrate that in addition to host characteristics, biotic and abiotic community-level variables both serve as large-scale indicators of parasite dynamics.

Assessing net carbon sequestration on urban and community forests of northern New England, USA

Treesearch

Daolan Zheng; Mark J. Ducey; Linda S. Heath

2013-01-01

Urban and community forests play an important role in the overall carbon budget of the USA. Accurately quantifying carbon sequestration by these forests can provide insight for strategic planning to mitigate greenhouse gas effects on climate change. This study provides a new methodology to estimate net forest carbon sequestration (FCS) in urban and community lands of...

Quantifying ecosystem service tradeoffs in response to alternative land use and climate scenarios: Pacific Northwest applications of the VELMA ecohydrological model

EPA Science Inventory

Scientists, policymakers, community planners and others have discussed ecosystem services for decades, however, society is still in the early stages of developing methodologies to quantify and value the goods and services that ecosystems provide. Essential to this goal are highl...

Quantifying the effect of a community-based injury prevention program in Queensland using a generalized estimating equation approach.

PubMed

Yorkston, Emily; Turner, Catherine; Schluter, Philip J; McClure, Rod

2007-06-01

To develop a generalized estimating equation (GEE) model of childhood injury rates to quantify the effectiveness of a community-based injury prevention program implemented in 2 communities in Australia, in order to contribute to the discussion of community-based injury prevention program evaluation. An ecological study was conducted comparing injury rates in two intervention communities in rural and remote Queensland, Australia, with those of 16 control regions. A model of childhood injury was built using hospitalization injury rate data from 1 July 1991 to 30 June 2005 and 16 social variables. The model was built using GEE analysis and was used to estimate parameters and to test the effectiveness of the intervention. When social variables were controlled for, the intervention was associated with a decrease of 0.09 injuries/10,000 children aged 0-4 years (95% CI -0.29 to 0.11) in logarithmically transformed injury rates; however, this decrease was not significant (p = 0.36). The evaluation methods proposed in this study provide a way of determining the effectiveness of a community-based injury prevention program while considering the effect of baseline differences and secular changes in social variables.

Variance in composition of inquiline communities in leaves of Sarracenia purpurea L. on multiple spatial scales.

PubMed

Harvey, E; Miller, T E

1996-11-01

A survey of the abundances of species that inhabit the water-bearing leaves of the pitcher plant Sarracenia purpurea was conducted at several different spatial scales in northern Florida. Individual leaves are hosts to communities of inquiline species, including mosquitoes, midges, mites, copepods, cladocerans, and a diverse bacterial assemblage. Inquiline communities were quantified from four pitchers per plant, three plants per subpopulation, two subpopulations per population, and three populations. Species varied in abundance at different spatial scales. Variation in the abundances of mosquitoes and copepods was not significantly associated with any spatial scale. Midges varied in abundance at the level of populations; one population contained significantly more midges than the other two. Cladocerans varied at the level of the subpopulation, whereas mites varied at the level of the individual plants. Bacterial communities were described by means of Biolog plates, which quantify the types of carbon media used by the bacteria in each pitcher. Bacterial communities were found to vary significantly in composition among individual plants but not among populations or subpopulations. These results suggest that independent factors determining the abundances of individual species are important in determining community patterns in pitcher-plant inquilines.

Multimodel inference to quantify the relative importance of abiotic factors in the population dynamics of marine zooplankton

NASA Astrophysics Data System (ADS)

Everaert, Gert; Deschutter, Yana; De Troch, Marleen; Janssen, Colin R.; De Schamphelaere, Karel

2018-05-01

The effect of multiple stressors on marine ecosystems remains poorly understood and most of the knowledge available is related to phytoplankton. To partly address this knowledge gap, we tested if combining multimodel inference with generalized additive modelling could quantify the relative contribution of environmental variables on the population dynamics of a zooplankton species in the Belgian part of the North Sea. Hence, we have quantified the relative contribution of oceanographic variables (e.g. water temperature, salinity, nutrient concentrations, and chlorophyll a concentrations) and anthropogenic chemicals (i.e. polychlorinated biphenyls) to the density of Acartia clausi. We found that models with water temperature and chlorophyll a concentration explained ca. 73% of the population density of the marine copepod. Multimodel inference in combination with regression-based models are a generic way to disentangle and quantify multiple stressor-induced changes in marine ecosystems. Future-oriented simulations of copepod densities suggested increased copepod densities under predicted environmental changes.

Extracting Plant Phenology Metrics in a Great Basin Watershed: Methods and Considerations for Quantifying Phenophases in a Cold Desert.

PubMed

Snyder, Keirith A; Wehan, Bryce L; Filippa, Gianluca; Huntington, Justin L; Stringham, Tamzen K; Snyder, Devon K

2016-11-18

Plant phenology is recognized as important for ecological dynamics. There has been a recent advent of phenology and camera networks worldwide. The established PhenoCam Network has sites in the United States, including the western states. However, there is a paucity of published research from semi-arid regions. In this study, we demonstrate the utility of camera-based repeat digital imagery and use of R statistical phenopix package to quantify plant phenology and phenophases in four plant communities in the semi-arid cold desert region of the Great Basin. We developed an automated variable snow/night filter for removing ephemeral snow events, which allowed fitting of phenophases with a double logistic algorithm. We were able to detect low amplitude seasonal variation in pinyon and juniper canopies and sagebrush steppe, and characterize wet and mesic meadows in area-averaged analyses. We used individual pixel-based spatial analyses to separate sagebrush shrub canopy pixels from interspace by determining differences in phenophases of sagebrush relative to interspace. The ability to monitor plant phenology with camera-based images fills spatial and temporal gaps in remotely sensed data and field based surveys, allowing species level relationships between environmental variables and phenology to be developed on a fine time scale thus providing powerful new tools for land management.

Temporal Dynamics of the Human Vaginal Microbiota

PubMed Central

Gajer, Pawel; Brotman, Rebecca M.; Bai, Guoyun; Sakamoto, Joyce; Schütte, Ursel M.E.; Zhong, Xue; Koenig, Sara S.K.; Fu, Li; Ma, Zhanshan; Zhou, Xia; Abdo, Zaid; Forney, Larry J.; Ravel, Jacques

2012-01-01

Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk of diseases that affect women’s health. Here, we describe the temporal dynamics of the composition of vaginal bacterial communities in 32 reproductive age women over a 16-week period. The analysis revealed the dynamics of five major classes of bacterial communities and showed that some communities change markedly over short time periods, whereas others are relatively stable. Modeling community stability using new quantitative measures indicates that deviation from stability correlates with time in the menstrual cycle, bacterial community composition and sexual activity. The women studied are healthy, thus it appears that neither variation in community composition per se, nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis, in which there is microbial imbalance accompanied by symptoms. PMID:22553250

Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

USDA-ARS?s Scientific Manuscript database

Changing environmental conditions result in substantial shifts in the composition of communities. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, most studies on environmental change quantify the biotic responses at single spat...

Comparisons of benthic filter feeder communities before and after a large-scale capital dredging program.

PubMed

Abdul Wahab, Muhammad Azmi; Fromont, Jane; Gomez, Oliver; Fisher, Rebecca; Jones, Ross

2017-09-15

Changes in turbidity, sedimentation and light over a two year large scale capital dredging program at Onslow, northwestern Australia, were quantified to assess their effects on filter feeder communities, in particular sponges. Community functional morphological composition was quantified using towed video surveys, while dive surveys allowed for assessments of species composition and chlorophyll content. Onslow is relatively diverse recording 150 sponge species. The area was naturally turbid (1.1 mean P 80 NTU), with inshore sites recording 6.5× higher turbidity than offshore localities, likely influenced by the Ashburton River discharge. Turbidity and sedimentation increased by up to 146% and 240% through dredging respectively, with corresponding decreases in light levels. The effects of dredging was variable, and despite existing caveats (i.e. bleaching event and passing of a cyclone), the persistence of sponges and the absence of a pronounced response post-dredging suggest environmental filtering or passive adaptation acquired pre-dredging may have benefited these communities. Copyright © 2017. Published by Elsevier Ltd.

Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

USGS Publications Warehouse

Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

2003-01-01

We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

PubMed Central

Smithwick, Erica A. H.; Naithani, Kusum J.; Balser, Teri C.; Romme, William H.; Turner, Monica G.

2012-01-01

Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R2<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21st Century. PMID:23226324

Impacts of exotic mangrove forests and mangrove deforestation on carbon remineralization and ecosystem functioning in marine sediments

USGS Publications Warehouse

Sweetman, A.K.; Middelburg, J.J.; Berle, A.M.; Bernardino, A.F.; Schander, C.; Demopoulos, A.W.J.; Smith, C.R.

2010-01-01

To evaluate how mangrove invasion and removal can modify benthic carbon cycling processes and ecosystem functioning, we used stable-isotopically labelled algae as a deliberate tracer to quantify benthic respiration and C-flow through macrofauna and bacteria in sediments collected from (1) an invasive mangrove forest, (2) deforested mangrove sites 2 and 6 years after removal of above-sediment mangrove biomass, and (3) two mangrove-free, control sites in the Hawaiian coastal zone. Sediment oxygen consumption (SOC) rates were significantly greater in the mangrove and mangrove removal site experiments than in controls and were significantly correlated with total benthic (macrofauna and bacteria) biomass and sedimentary mangrove biomass (SMB). Bacteria dominated short-term C-processing of added microalgal-C and benthic biomass in sediments from the invasive mangrove forest habitat. In contrast, macrofauna were the most important agents in the short-term processing of microalgal-C in sediments from the mangrove removal and control sites. Mean faunal abundance and short term C-uptake rates in sediments from both removal sites were significantly higher than in control cores, which collectively suggest that community structure and short-term C-cycling dynamics in habitats where mangroves have been cleared can remain fundamentally different from un-invaded mudflat sediments for at least 6-yrs following above-sediment mangrove removal. In summary, invasion by mangroves can lead to large shifts in benthic ecosystem function, with sediment metabolism, benthic community structure and short-term C-remineralization dynamics being affected for years following invader removal. ?? 2010 Author(s).

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

PubMed Central

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation. PMID:26067226

Collaborative Research: Quantifying the Uncertainties of Aerosol Indirect Effects and Impacts on Decadal-Scale Climate Variability in NCAR CAM5 and CESM1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nenes, Athanasios

The goal of this proposed project is to assess the climatic importance and sensitivity of aerosol indirect effect (AIE) to cloud and aerosol processes and feedbacks, which include organic aerosol hygroscopicity, cloud condensation nuclei (CCN) activation kinetics, Giant CCN, cloud-scale entrainment, ice nucleation in mixed-phase and cirrus clouds, and treatment of subgrid variability of vertical velocity. A key objective was to link aerosol, cloud microphysics and dynamics feedbacks in CAM5 with a suite of internally consistent and integrated parameterizations that provide the appropriate degrees of freedom to capture the various aspects of the aerosol indirect effect. The proposal integrated newmore » parameterization elements into the cloud microphysics, moist turbulence and aerosol modules used by the NCAR Community Atmospheric Model version 5 (CAM5). The CAM5 model was then used to systematically quantify the uncertainties of aerosol indirect effects through a series of sensitivity tests with present-day and preindustrial aerosol emissions. New parameterization elements were developed as a result of these efforts, and new diagnostic tools & methodologies were also developed to quantify the impacts of aerosols on clouds and climate within fully coupled models. Observations were used to constrain key uncertainties in the aerosol-cloud links. Advanced sensitivity tools were developed and implements to probe the drivers of cloud microphysical variability with unprecedented temporal and spatial scale. All these results have been published in top and high impact journals (or are in the final stages of publication). This proposal has also supported a number of outstanding graduate students.« less

Rapid contemporary evolution and clonal food web dynamics

PubMed Central

Jones, Laura E.; Becks, Lutz; Ellner, Stephen P.; Hairston, Nelson G.; Yoshida, Takehito; Fussmann, Gregor F.

2009-01-01

Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most readily explored in systems with short generations and simple genetics. Asexual and cyclically parthenogenetic organisms such as microalgae, cladocerans and rotifers, which frequently dominate freshwater plankton communities, meet these requirements. Multiple clonal lines can coexist within each species over extended periods, until either fixation occurs or a sexual phase reshuffles the genetic material. When clones differ in traits affecting interspecific interactions, within-species clonal dynamics can have major effects on the population dynamics. We first consider a simple predator–prey system with two prey genotypes, parametrized with data from a well-studied experimental system, and explore how the extent of differences in defence against predation within the prey population determine dynamic stability versus instability of the system. We then explore how increased potential for evolution affects the community dynamics in a more general community model with multiple predator and multiple prey genotypes. These examples illustrate how microevolutionary ‘details’ that enhance or limit the potential for heritable phenotypic change can have significant effects on contemporaneous community-level dynamics and the persistence and coexistence of species. PMID:19414472

Computational Aeroelastic Analysis of Ares Crew Launch Vehicle Bi-Modal Loading

NASA Technical Reports Server (NTRS)

Massey, Steven J.; Chwalowski, Pawel

2010-01-01

A Reynolds averaged Navier-Stokes analysis, with and without dynamic aeroelastic effects, is presented for the Ares I-X launch vehicle at transonic Mach numbers and flight Reynolds numbers for two grid resolutions and two angles of attack. The purpose of the study is to quantify the force and moment increment imparted by the sudden transition from fully separated flow around the crew module - service module junction to that of the bi-modal flow state in which only part of the flow reattaches. The bi-modal flow phenomenon is of interest to the guidance, navigation and control community because it causes a discontinuous jump in forces and moments. Computations with a rigid structure at zero zero angle of attack indicate significant increases in normal force and pitching moment. Dynamic aeroelastic computations indicate the bi-modal flow state is insensitive to vehicle flexibility due to the resulting deflections imparting only very small changes in local angle of attack. At an angle of attack of 2.5deg, the magnitude of the pitching moment increment resulting from the bi-modal state nearly triples, while occurring at a slightly lower Mach number. Significant grid induced variations between the solutions indicate that further grid refinement is warranted.

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kylasa, S.B., E-mail: skylasa@purdue.edu; Aktulga, H.M., E-mail: hmaktulga@lbl.gov; Grama, A.Y., E-mail: ayg@cs.purdue.edu

2014-09-01

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques wemore » developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.« less

Stereo Refractive Imaging of Breaking Free-Surface Waves in the Surf Zone

NASA Astrophysics Data System (ADS)

Mandel, Tracy; Weitzman, Joel; Koseff, Jeffrey; Environmental Fluid Mechanics Laboratory Team

2014-11-01

Ocean waves drive the evolution of coastlines across the globe. Wave breaking suspends sediments, while wave run-up, run-down, and the undertow transport this sediment across the shore. Complex bathymetric features and natural biotic communities can influence all of these dynamics, and provide protection against erosion and flooding. However, our knowledge of the exact mechanisms by which this occurs, and how they can be modeled and parameterized, is limited. We have conducted a series of controlled laboratory experiments with the goal of elucidating these details. These have focused on quantifying the spatially-varying characteristics of breaking waves and developing more accurate techniques for measuring and predicting wave setup, setdown, and run-up. Using dynamic refraction stereo imaging, data on free-surface slope and height can be obtained over an entire plane. Wave evolution is thus obtained with high spatial precision. These surface features are compared with measures of instantaneous turbulence and mean currents within the water column. We then use this newly-developed ability to resolve three-dimensional surface features over a canopy of seagrass mimics, in order to validate theoretical formulations of wave-vegetation interactions in the surf zone.

Impacts of Climate Change and Vegetation Dynamics on Runoff in the Mountainous Region of the Haihe River Basin in the Past Five Decades

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Huimin; Yang, Dawen; Huang, Maoyi

2014-04-16

Climate and atmospheric CO2 concentration have changed significantly in the mountainous region of the Haihe River basin over the past five decades. In the study, a process-based terrestrial model, version 4 of the Community Land Model (CLM4), was used to quantify the spatiotemporal changes in runoff over the region, driven by the varying climate factors and CO2 concentration. Overall, our simulations suggest that climate-induced change in runoff in this region show a decreasing trend since 1960. Changes in precipitation, solar radiation, air temperature, and wind speed accounts for 56%, -14%, 13%, -5% of the overall decrease in annual runoff, respectively,more » but their relative contributions vary across the study area. Rising atmospheric CO2 concentration was found to have limited impacts on runoff. Significant decrease in runoff over the southern and northeastern portion of the region is primarily attributed to decreasing precipitation, while decreasing solar radiation and increasing air temperature are the main causes of slight runoff increase in the northern portion. Our results also suggest that the magnitude of decreasing trend could be greatly underestimated if the dynamical interactions of vegetation phenology with the environmental factors are not considered in the modeling, highlighting the importance of including dynamic vegetation phenology in the prediction of runoff in this region.« less

Influence of hip and knee osteoarthritis on dynamic postural control parameters among older fallers.

PubMed

Mat, Sumaiyah; Ng, Chin Teck; Tan, Maw Pin

2017-03-06

To compare the relationship between postural control and knee and hip osteoarthritis in older adults with and without a history of falls. Fallers were those with ≥ 2 falls or 1 injurious fall over 12 months. Non-fallers were volunteers with no falls in the past year. Radiological evidence of osteoarthritis with no reported symptoms was considered "asymptomatic osteoarthritis", while "symptomatic osteoarthritis" was defined as radiographic osteoarthritis with pain or stiffness. Dynamic postural control was quantified with the limits of stability test measured on a balance platform (Neurocom® Balancemaster, California, USA). Parameters assessed were end-point excursion, maximal excursion, and directional control. A total of 102 older individuals, mean age 73 years (standard deviation 5.7) years were included. The association between falls and poor performance in maximal excursion and directional control was confounded by age and comorbidities. In the same linear equation model with falls, symptomatic osteoarthritis remained independently associated with poor end-point excursion (β-coefficient (95% confidence interval) -6.80 (-12.14 to -1.42)). Poor performance in dynamic postural control (maximal excursion and directional control) among fallers was not accounted for by hip/knee osteoarthritis, but was confounded by old age and comorbidities. Loss of postural control due to hip/knee osteoarthritis is not a risk factor for falls among community-dwelling older adults.

Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife (Lythrum salicaria L.).

PubMed

David, Aaron S; Quiram, Gina L; Sirota, Jennie I; Seabloom, Eric W

2016-01-01

Fungal endophytes are one of several groups of heterotrophic organisms that associate with living plants. The net effects of these groups of organisms on each other and ultimately on their host plants depend in part on how they facilitate or antagonize one another. In this study we quantified the associations between endophyte communities and herbivory induced by a biological control in the invasive Lythrum salicaria at various spatial scales using a culture-based approach. We found positive associations between herbivory damage and endophyte isolation frequency and richness at the site level and weak, positive associations at the leaf level. Herbivory damage was more strongly influenced by processes at the site level than were endophyte isolation frequency and community structure, which were influenced by processes at the plant and leaf levels. Furthermore, endophytic taxa found in low herbivory sites were nested subsets of those taxa found at high herbivory sites. Our findings suggest that endophyte communities of L. salicaria are associated with, and potentially facilitated by, biocontrol-induced herbivory. Quantifying the associations between heterotrophic groups ultimately may lead to a clearer understanding of their complex interactions with plants. © 2016 by The Mycological Society of America.

POPULATION DYNAMICS OF HISPID COTTON RATS (SIGMODON HISPIDUS) ACROSS A NITROGEN AMENDED LANDSCAPE

EPA Science Inventory

Population dynamics of some small-mammal species appear to be regulated by plant-community structure, vegetative cover, plant diversity, and food quality. Thus, plant community changes associated with nitrogen additions would likely impact dynamics and structure of small-mammal ...

77 FR 13607 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-07

... Transformation Grants: Use of System Dynamic Modeling and Economic Analysis in Select Communities--New--National... community interventions. Using a system dynamics approach, CDC also plans to conduct simulation modeling... the development of analytic tools for system dynamics modeling under more limited conditions. The...

How Well Has Global Ocean Heat Content Variability Been Measured?

NASA Astrophysics Data System (ADS)

Nelson, A.; Weiss, J.; Fox-Kemper, B.; Fabienne, G.

2016-12-01

We introduce a new strategy that uses synthetic observations of an ensemble of model simulations to test the fidelity of an observational strategy, quantifying how well it captures the statistics of variability. We apply this test to the 0-700m global ocean heat content anomaly (OHCA) as observed with in-situ measurements by the Coriolis Dataset for Reanalysis (CORA), using the Community Climate System Model (CCSM) version 3.5. One-year running mean OHCAs for the years 2005 onward are found to faithfully capture the variability. During these years, synthetic observations of the model are strongly correlated at 0.94±0.06 with the actual state of the model. Overall, sub-annual variability and data before 2005 are significantly affected by the variability of the observing system. In contrast, the sometimes-used weighted integral of observations is not a good indicator of OHCA as variability in the observing system contaminates dynamical variability.

Absolute quantification of microbial taxon abundances.

PubMed

Props, Ruben; Kerckhof, Frederiek-Maarten; Rubbens, Peter; De Vrieze, Jo; Hernandez Sanabria, Emma; Waegeman, Willem; Monsieurs, Pieter; Hammes, Frederik; Boon, Nico

2017-02-01

High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys.

Parkinsonian Balance Deficits Quantified Using a Game Industry Board and a Specific Battery of Four Paradigms.

PubMed

Darbin, Olivier; Gubler, Coral; Naritoku, Dean; Dees, Daniel; Martino, Anthony; Adams, Elizabeth

2016-01-01

This study describes a cost-effective screening protocol for parkinsonism based on combined objective and subjective monitoring of balance function. Objective evaluation of balance function was performed using a game industry balance board and an automated analyses of the dynamic of the center of pressure in time, frequency, and non-linear domains collected during short series of stand up tests with different modalities and severity of sensorial deprivation. The subjective measurement of balance function was performed using the Dizziness Handicap Inventory questionnaire. Principal component analyses on both objective and subjective measurements of balance function allowed to obtained a specificity and selectivity for parkinsonian patients (vs. healthy subjects) of 0.67 and 0.71 respectively. The findings are discussed regarding the relevance of cost-effective balance-based screening system as strategy to meet the needs of broader and earlier screening for parkinsonism in communities with limited access to healthcare.

Native arbuscular mycorrhizal fungi in the Yungas forests, Argentina.

PubMed

Becerra, Alejandra G; Cabello, Marta N; Bartoloni, Norberto J

2011-01-01

The arbuscular mycorrhizal fungal (AMF) communities from the Yungas forests of Argentina were studied. The AMF species present in the rhizosphere of some dominant native plants (one tree: Alnus acuminata; three herbaceous species: Duchesnea indica, Oxalis conorrhiza, Trifolium aff. repens; and one shrub: Sambucus peruviana) from two sites (Quebrada del Portugués and Narváez Range) of the Yungas forests were isolated, identified and quantified during the four seasons of the year. Twenty-two AMF morphotaxa were found. Spore density of some AMF species at each site varied among seasons. The genera that most contributed to the biodiversity index were Acaulospora for Quebrada del Portugués and Glomus for Narváez Range. High diversity values were observed in the Yungas forests, particularly in the spring (rainy season). We concluded AMF differed in species composition and seasonal sporulation dynamics in the Yungas forests.

Dynamic modeling of environmental risk associated with drilling discharges to marine sediments.

PubMed

Durgut, İsmail; Rye, Henrik; Reed, Mark; Smit, Mathijs G D; Ditlevsen, May Kristin

2015-10-15

Drilling discharges are complex mixtures of base-fluids, chemicals and particulates, and may, after discharge to the marine environment, result in adverse effects on benthic communities. A numerical model was developed to estimate the fate of drilling discharges in the marine environment, and associated environmental risks. Environmental risk from deposited drilling waste in marine sediments is generally caused by four types of stressors: oxygen depletion, toxicity, burial and change of grain size. In order to properly model these stressors, natural burial, biodegradation and bioturbation processes were also included. Diagenetic equations provide the basis for quantifying environmental risk. These equations are solved numerically by an implicit-central differencing scheme. The sediment model described here is, together with a fate and risk model focusing on the water column, implemented in the DREAM and OSCAR models, both available within the Marine Environmental Modeling Workbench (MEMW) at SINTEF in Trondheim, Norway. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Sun-Earth saddle point: characterization and opportunities to test general relativity

NASA Astrophysics Data System (ADS)

Topputo, Francesco; Dei Tos, Diogene A.; Rasotto, Mirco; Nakamiya, Masaki

2018-04-01

The saddle points are locations where the net gravitational accelerations balance. These regions are gathering more attention within the astrophysics community. Regions about the saddle points present clean, close-to-zero background acceleration environments where possible deviations from General Relativity can be tested and quantified. Their location suggests that flying through a saddle point can be accomplished by leveraging highly nonlinear orbits. In this paper, the geometrical and dynamical properties of the Sun-Earth saddle point are characterized. A systematic approach is devised to find ballistic orbits that experience one or multiple passages through this point. A parametric analysis is performed to consider spacecraft initially on L_{1,2} Lagrange point orbits. Sun-Earth saddle point ballistic fly-through trajectories are evaluated and classified for potential use. Results indicate an abundance of short-duration, regular solutions with a variety of characteristics.

Workshop held to discuss population connectivity in marine systems

NASA Astrophysics Data System (ADS)

Cowen, Robert K.; Thorrold, Simon; Pineda, Jesus; Gawarkiewicz, Glen

A central goal of marine ecology is to achieve a mechanistic understanding of the factors regulating the abundance and distribution of marine populations. One critical component of the above goal is to quantify rates of exchange, or connectivity among sub-populations of marine organisms via larval dispersal. Theoretical studies suggest that these linkages play a fundamental role in local and meta-population dynamics, community structure, genetic diversity, and the resiliency of populations to human exploitation [Fogarty, 1998].Understanding population connectivity is also key in efforts to develop spatial management methods for marine-capture fisheries, including the design of networks of marine reserves [Sala et al., 2002]. We have made considerable advances in our understanding of the biology of juvenile and adult life history stages through experimental marine ecology However, there has been no concomitant increase in our knowledge of the biological and physical processes that determine the extent to which marine populations are connected via larval dispersal.

A review of genomic data warehousing systems.

PubMed

Triplet, Thomas; Butler, Gregory

2014-07-01

To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. We provide a comprehensive and quantitative review of those genomic data warehousing frameworks in the context of large-scale systems biology. We reviewed in detail four genomic data warehouses (BioMart, BioXRT, InterMine and PathwayTools) freely available to the academic community. We quantified 20 aspects of the warehouses, covering the accuracy of their responses, their computational requirements and development efforts. Performance of the warehouses was evaluated under various hardware configurations to help laboratories optimize hardware expenses. Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW (http://warehousebenchmark.fungalgenomics.ca/benchmark/) to build custom warehouse profiles and tailor our results to their specific needs.

Culturally Relevant Physical Education in Urban Schools: Reflecting Cultural Knowledge

ERIC Educational Resources Information Center

Flory, Sara B.; McCaughtry, Nate

2011-01-01

Using a three-part theoretical framework, the cultural relevance cycle--which consists of (a) knowing community dynamics, (b) knowing how community dynamics influence educational processes, and (c) implementing strategies that reflect cultural knowledge of the community--we examined teachers' and students' perspectives on culturally relevant…

Dynamics of primary and secondary microbubbles created by laser-induced breakdown of an optically trapped nanoparticle

PubMed Central

Arita, Y.; Antkowiak, M.; Venugopalan, V.; Gunn-Moore, F. J.; Dholakia, K.

2012-01-01

Laser-induced breakdown of an optically trapped nanoparticle is a unique system for studying cavitation dynamics. It offers additional degrees of freedom, namely the nanoparticle material, its size, and the relative position between the laser focus and the center of the optically trapped nanoparticle. We quantify the spatial and temporal dynamics of the cavitation and secondary bubbles created in this system and use hydrodynamic modeling to quantify the observed dynamic shear stress of the expanding bubble. In the final stage of bubble collapse, we visualize the formation of multiple submicrometer secondary bubbles around the toroidal bubble on the substrate. We show that the pattern of the secondary bubbles typically has its circular symmetry broken along an axis whose unique angle rotates over time. This is a result of vorticity along the jet towards the boundary upon bubble collapse near solid boundaries. PMID:22400669

A combinatorial framework to quantify peak/pit asymmetries in complex dynamics.

PubMed

Hasson, Uri; Iacovacci, Jacopo; Davis, Ben; Flanagan, Ryan; Tagliazucchi, Enzo; Laufs, Helmut; Lacasa, Lucas

2018-02-23

We explore a combinatorial framework which efficiently quantifies the asymmetries between minima and maxima in local fluctuations of time series. We first showcase its performance by applying it to a battery of synthetic cases. We find rigorous results on some canonical dynamical models (stochastic processes with and without correlations, chaotic processes) complemented by extensive numerical simulations for a range of processes which indicate that the methodology correctly distinguishes different complex dynamics and outperforms state of the art metrics in several cases. Subsequently, we apply this methodology to real-world problems emerging across several disciplines including cases in neurobiology, finance and climate science. We conclude that differences between the statistics of local maxima and local minima in time series are highly informative of the complex underlying dynamics and a graph-theoretic extraction procedure allows to use these features for statistical learning purposes.

Assessment of Walking Stability of Elderly by Means of Nonlinear Time-Series Analysis and Simple Accelerometry

NASA Astrophysics Data System (ADS)

Ohtaki, Yasuaki; Arif, Muhammad; Suzuki, Akihiro; Fujita, Kazuki; Inooka, Hikaru; Nagatomi, Ryoichi; Tsuji, Ichiro

This study presents an assessment of walking stability in elderly people, focusing on local dynamic stability of walking. Its main objectives were to propose a technique to quantify local dynamic stability using nonlinear time-series analyses and a portable instrument, and to investigate their reliability in revealing the efficacy of an exercise training intervention for elderly people for improvement of walking stability. The method measured three-dimensional acceleration of the upper body, and computation of Lyapunov exponents, thereby directly quantifying the local stability of the dynamic system. Straight level walking of young and elderly subjects was investigated in the experimental study. We compared Lyapunov exponents of young and the elderly subjects, and of groups before and after the exercise intervention. Experimental results demonstrated that the exercise intervention improved local dynamic stability of walking. The proposed method was useful in revealing effects and efficacies of the exercise intervention for elderly people.

A 15 Year Ecological Comparison for the Market Dynamics of Minnesota Community Pharmacies from 2002 to 2017.

PubMed

Olson, Anthony W; Schommer, Jon C; Hadsall, Ronald S

2018-06-02

Background: Understanding the factors that influence the market entry, exit, and stability of community pharmacies (i.e., market dynamics) is important for stakeholders ranging from patients to health policymakers and small business owners to large corporate institutions. Objective: The study's first objective was to describe the market dynamics of community pharmacies for Minnesota counties in 2002, 2007, 2012, and 2017 by associating county (a) population density and (b) metropolitan designation with the change in the number of 'All community pharmacies,' 'Chain community pharmacies', and 'Independent community pharmacies'. The study's second objective was to describe the number and proportion of community pharmacies for Minnesota counties in 2002, 2007, 2012, and 2017 by (1) 'Business Organization Structure' and (2) 'Pharmacy Type.' Methods: County-level data were obtained from the Minnesota Board of Pharmacy, US Census Bureau, and Minnesota State Demographic Center for 2002, 2007, 2012, and 2017. Findings were summarized and the associations between study variables described using descriptive statistics. Results: The ratio of 'Independent community pharmacies' to 'Chain community pharmacies' was about 1:1 (466:530) in 2002, 1:2 (352:718) in 2007, 1:2 (387:707) in 2012, and 1:3 (256:807) in 2017. There was not a consistent relationship that carried through the 15 year analysis between county population density and metropolitan designation and the market dynamic patterns of community pharmacies. The types of pharmacy in Minnesota changed significantly over the study with increases in state, regional, and national chains and declines in single entity and small chain independents. There were also notable declines in mass merchandiser community pharmacies and increases in clinic and medical center community pharmacies. Discussion: The findings suggest that different or additional factors beyond traditional market dynamic predictors of population density and metropolitan designation were at play in each five year interval of this study. We propose that the traditional dichotomy of independent and chain community pharmacy groupings no longer provide an optimal characterization for the market dynamics of pharmacies today. Instead, community pharmacies may be better organized by their capacity to operate as healthcare access points that provide and are reimbursed for patient care and public health services like medication therapy management, immunizations, and more. Conclusions: The findings showed that community pharmacy distribution in Minnesota's 87 counties has shifted between 2002 and 2017 from traditional retail models to emerging healthcare models based on population health needs. This signals the need for not only a new approach for tracking community pharmacy market dynamics but also adjustments by community pharmacies to remain relevant in a new environment of patient care services.

Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil.

PubMed

Santalahti, Minna; Sun, Hui; Jumpponen, Ari; Pennanen, Taina; Heinonsalo, Jussi

2016-11-01

Fungal communities are important for carbon (C) transformations in boreal forests that are one of the largest C pools in terrestrial ecosystems, warranting thus further investigation of fungal community dynamics in time and space. We investigated fungal diversity and community composition seasonally and across defined soil horizons in boreal Scots pine forest in Finland using 454 pyrosequencing. We collected a total of 120 samples from five vertical soil horizons monthly from March to October; in March, under snow. Boreal forest soil generally harbored diverse fungal communities across soil horizons. The communities shifted drastically and rapidly over time. In late winter, saprotrophs dominated the community and were replaced by ectomycorrhizal fungi during the growing season. Our studies are among the first to dissect the spatial and temporal dynamics in boreal forest ecosystems and highlights the ecological importance of vertically distinct communities and their rapid seasonal dynamics. As climate change is predicted to result in warmer and longer snow-free winter seasons, as well as increase the rooting depth of trees in boreal forest, the seasonal and vertical distribution of fungal communities may change. These changes are likely to affect the organic matter decomposition by the soil-inhabiting fungi and thus alter organic C pools. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Dynamics of Different Bacterial Communities Are Capable of Generating Sustainable Electricity from Microbial Fuel Cells with Organic Waste

PubMed Central

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m−2. Polarization curve analyses revealed that the maximum power density was 7.4 W m−3 with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste. PMID:24789988

Dynamics of different bacterial communities are capable of generating sustainable electricity from microbial fuel cells with organic waste.

PubMed

Yamamoto, Shuji; Suzuki, Kei; Araki, Yoko; Mochihara, Hiroki; Hosokawa, Tetsuya; Kubota, Hiroko; Chiba, Yusuke; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki

2014-01-01

The relationship between the bacterial communities in anolyte and anode biofilms and the electrochemical properties of microbial fuel cells (MFCs) was investigated when a complex organic waste-decomposing solution was continuously supplied to MFCs as an electron donor. The current density increased gradually and was maintained at approximately 100 to 150 mA m(-2). Polarization curve analyses revealed that the maximum power density was 7.4 W m(-3) with an internal resistance of 110 Ω. Bacterial community structures in the organic waste-decomposing solution and MFCs differed from each other. Clonal analyses targeting 16S rRNA genes indicated that bacterial communities in the biofilms on MFCs developed to specific communities dominated by novel Geobacter. Multidimensional scaling analyses based on DGGE profiles revealed that bacterial communities in the organic waste-decomposing solution fluctuated and had no dynamic equilibrium. Bacterial communities on the anolyte in MFCs had a dynamic equilibrium with fluctuations, while those of the biofilm converged to the Geobacter-dominated structure. These bacterial community dynamics of MFCs differed from those of control-MFCs under open circuit conditions. These results suggested that bacterial communities in the anolyte and biofilm have a gentle symbiotic system through electron flow, which resulted in the advance of current density from complex organic waste.

COPEWELL: A Conceptual Framework and System Dynamics Model for Predicting Community Functioning and Resilience After Disasters.

PubMed

Links, Jonathan M; Schwartz, Brian S; Lin, Sen; Kanarek, Norma; Mitrani-Reiser, Judith; Sell, Tara Kirk; Watson, Crystal R; Ward, Doug; Slemp, Cathy; Burhans, Robert; Gill, Kimberly; Igusa, Tak; Zhao, Xilei; Aguirre, Benigno; Trainor, Joseph; Nigg, Joanne; Inglesby, Thomas; Carbone, Eric; Kendra, James M

2018-02-01

Policy-makers and practitioners have a need to assess community resilience in disasters. Prior efforts conflated resilience with community functioning, combined resistance and recovery (the components of resilience), and relied on a static model for what is inherently a dynamic process. We sought to develop linked conceptual and computational models of community functioning and resilience after a disaster. We developed a system dynamics computational model that predicts community functioning after a disaster. The computational model outputted the time course of community functioning before, during, and after a disaster, which was used to calculate resistance, recovery, and resilience for all US counties. The conceptual model explicitly separated resilience from community functioning and identified all key components for each, which were translated into a system dynamics computational model with connections and feedbacks. The components were represented by publicly available measures at the county level. Baseline community functioning, resistance, recovery, and resilience evidenced a range of values and geographic clustering, consistent with hypotheses based on the disaster literature. The work is transparent, motivates ongoing refinements, and identifies areas for improved measurements. After validation, such a model can be used to identify effective investments to enhance community resilience. (Disaster Med Public Health Preparedness. 2018;12:127-137).

Impact of storm events on the structure of a stream microbiome

EPA Science Inventory

The microbial structural and/or functional state in a stream community is assumed to be in relative stasis until a perturbation (e.g., runoff event with entrained pollutants) affects the community structure and its functional state. Quantifying these changes and resolving the spe...

The Level of Decision Making, Perceived Influence and Perceived Satisfaction of Faculty and Their Impact on Student Retention in Community Colleges

ERIC Educational Resources Information Center

Miller, Lisa M.

2017-01-01

Community colleges have been important open access entry points into education and employment. In order to improve the community college average retention rate of 60%, this study began looking at other areas that may have been impacting student retention without having been previously quantified. To evaluate the impact of faculty inclusion in…

Thermal and Hydrodynamic Environments Mediate Individual and Aggregative Feeding of a Functionally Important Omnivore in Reef Communities

PubMed Central

Frey, Desta L.; Gagnon, Patrick

2015-01-01

In eastern Canada, the destruction of kelp beds by dense aggregations (fronts) of the omnivorous green sea urchin, Strongylocentrotus droebachiensis, is a key determinant of the structure and dynamics of shallow reef communities. Recent studies suggest that hydrodynamic forces, but not sea temperature, determine the strength of urchin-kelp interactions, which deviates from the tenets of the metabolic theory of ecology (MTE). We tested the hypothesis that water temperature can predict short-term kelp bed destruction by S. droebachiensis in calm hydrodynamic environments. Specifically, we experimentally determined relationships among water temperature, body size, and individual feeding in the absence of waves, as well as among wave velocity, season, and aggregative feeding. We quantified variation in kelp-bed boundary dynamics, sea temperature, and wave height over three months at one subtidal site in Newfoundland to test the validity of thermal tipping ranges and regression equations derived from laboratory results. Consistent with the MTE, individual feeding during early summer (June-July) obeyed a non-linear, size- and temperature-dependent relationship: feeding in large urchins was consistently highest and positively correlated with temperature <12°C and dropped within and above the 12–15°C tipping range. This relationship was more apparent in large than small urchins. Observed and expected rates of kelp loss based on sea temperature and urchin density and size structure at the front were highly correlated and differed by one order of magnitude. The present study speaks to the importance of considering body size and natural variation in sea temperature in studies of urchin-kelp interactions. It provides the first compelling evidence that sea temperature, and not only hydrodynamic forces, can predict kelp bed destruction by urchin fronts in shallow reef communities. Studying urchin-seaweed-predator interactions within the conceptual foundations of the MTE holds high potential for improving capacity to predict and manage shifts in marine food web structure and productivity. PMID:25774674

Thermal and hydrodynamic environments mediate individual and aggregative feeding of a functionally important omnivore in reef communities.

PubMed

Frey, Desta L; Gagnon, Patrick

2015-01-01

In eastern Canada, the destruction of kelp beds by dense aggregations (fronts) of the omnivorous green sea urchin, Strongylocentrotus droebachiensis, is a key determinant of the structure and dynamics of shallow reef communities. Recent studies suggest that hydrodynamic forces, but not sea temperature, determine the strength of urchin-kelp interactions, which deviates from the tenets of the metabolic theory of ecology (MTE). We tested the hypothesis that water temperature can predict short-term kelp bed destruction by S. droebachiensis in calm hydrodynamic environments. Specifically, we experimentally determined relationships among water temperature, body size, and individual feeding in the absence of waves, as well as among wave velocity, season, and aggregative feeding. We quantified variation in kelp-bed boundary dynamics, sea temperature, and wave height over three months at one subtidal site in Newfoundland to test the validity of thermal tipping ranges and regression equations derived from laboratory results. Consistent with the MTE, individual feeding during early summer (June-July) obeyed a non-linear, size- and temperature-dependent relationship: feeding in large urchins was consistently highest and positively correlated with temperature <12°C and dropped within and above the 12-15°C tipping range. This relationship was more apparent in large than small urchins. Observed and expected rates of kelp loss based on sea temperature and urchin density and size structure at the front were highly correlated and differed by one order of magnitude. The present study speaks to the importance of considering body size and natural variation in sea temperature in studies of urchin-kelp interactions. It provides the first compelling evidence that sea temperature, and not only hydrodynamic forces, can predict kelp bed destruction by urchin fronts in shallow reef communities. Studying urchin-seaweed-predator interactions within the conceptual foundations of the MTE holds high potential for improving capacity to predict and manage shifts in marine food web structure and productivity.

Impacts on Coralligenous Outcrop Biodiversity of a Dramatic Coastal Storm

PubMed Central

Teixidó, Núria; Casas, Edgar; Cebrián, Emma; Linares, Cristina; Garrabou, Joaquim

2013-01-01

Extreme events are rare, stochastic perturbations that can cause abrupt and dramatic ecological change within a short period of time relative to the lifespan of organisms. Studies over time provide exceptional opportunities to detect the effects of extreme climatic events and to measure their impacts by quantifying rates of change at population and community levels. In this study, we show how an extreme storm event affected the dynamics of benthic coralligenous outcrops in the NW Mediterranean Sea using data acquired before (2006–2008) and after the impact (2009–2010) at four different sites. Storms of comparable severity have been documented to occur occasionally within periods of 50 years in the Mediterranean Sea. We assessed the effects derived from the storm comparing changes in benthic community composition at sites exposed to and sheltered from this extreme event. The sites analyzed showed different damage from severe to negligible. The most exposed and impacted site experienced a major shift immediately after the storm, represented by changes in the species richness and beta diversity of benthic species. This site also showed higher compositional variability immediately after the storm and over the following year. The loss of cover of benthic species resulted between 22% and 58%. The damage across these species (e.g. calcareous algae, sponges, anthozoans, bryozoans, tunicates) was uneven, and those with fragile forms were the most impacted, showing cover losses up to 50 to 100%. Interestingly, small patches survived after the storm and began to grow slightly during the following year. In contrast, sheltered sites showed no significant changes in all the studied parameters, indicating no variations due to the storm. This study provides new insights into the responses to large and rare extreme events of Mediterranean communities with low dynamics and long-lived species, which are among the most threatened by the effects of global change. PMID:23326496

A comparative analysis of alternative approaches for quantifying nonlinear dynamics in cardiovascular system.

PubMed

Chen, Yun; Yang, Hui

2013-01-01

Heart rate variability (HRV) analysis has emerged as an important research topic to evaluate autonomic cardiac function. However, traditional time and frequency-domain analysis characterizes and quantify only linear and stationary phenomena. In the present investigation, we made a comparative analysis of three alternative approaches (i.e., wavelet multifractal analysis, Lyapunov exponents and multiscale entropy analysis) for quantifying nonlinear dynamics in heart rate time series. Note that these extracted nonlinear features provide information about nonlinear scaling behaviors and the complexity of cardiac systems. To evaluate the performance, we used 24-hour HRV recordings from 54 healthy subjects and 29 heart failure patients, available in PhysioNet. Three nonlinear methods are evaluated not only individually but also in combination using three classification algorithms, i.e., linear discriminate analysis, quadratic discriminate analysis and k-nearest neighbors. Experimental results show that three nonlinear methods capture nonlinear dynamics from different perspectives and the combined feature set achieves the best performance, i.e., sensitivity 97.7% and specificity 91.5%. Collectively, nonlinear HRV features are shown to have the promise to identify the disorders in autonomic cardiovascular function.

Loschmidt echo as a robust decoherence quantifier for many-body systems

NASA Astrophysics Data System (ADS)

Zangara, Pablo R.; Dente, Axel D.; Levstein, Patricia R.; Pastawski, Horacio M.

2012-07-01

We employ the Loschmidt echo, i.e., the signal recovered after the reversal of an evolution, to identify and quantify the processes contributing to decoherence. This procedure, which has been extensively used in single-particle physics, is employed here in a spin ladder. The isolated chains have 1/2 spins with XY interaction and their excitations would sustain a one-body-like propagation. One of them constitutes the controlled system S whose reversible dynamics is degraded by the weak coupling with the uncontrolled second chain, i.e., the environment E. The perturbative SE coupling is swept through arbitrary combinations of XY and Ising-like interactions, that contain the standard Heisenberg and dipolar ones. Different time regimes are identified for the Loschmidt echo dynamics in this perturbative configuration. In particular, the exponential decay scales as a Fermi golden rule, where the contributions of the different SE terms are individually evaluated and analyzed. Comparisons with previous analytical and numerical evaluations of decoherence based on the attenuation of specific interferences show that the Loschmidt echo is an advantageous decoherence quantifier at any time, regardless of the S internal dynamics.

Glacier retreat and associated sediment dynamics in proglacial areas: a case study from the Silvretta Alps, Austria

NASA Astrophysics Data System (ADS)

Felbauer, Lucia; Pöppl, Ronald

2016-04-01

Global warming results in an ongoing retreat of glaciers in the Alps, leaving behind large amounts of easily erodible sediments. In addition, the debuttressing of rock-walls and the decay of permafrost in the high mountain regions facilitates mass movements of potential disastrous consequences, such as rock falls, landslides and debris flows. Therefore, it is highly important to quantify the amount of sediments that are supplied from the different compartments and to investigate how glacial retreat influences sediment dynamics in proglacial areas. In the presented work glacier retreat and associated sediment dynamics were investigated in the Kromer valley (Silvretta Alps, Austria) by analyzing remote sensing data. Glacial retreat from the period of 1950 to 2012 was documented by interpreting aerial photographs. By digitizing the different stages of the glaciers for six time frames, changes in glacier area and length were mapped and quantified. In order to identify, characterize and quantify sediment dynamics in the proglacial areas a high resolution DEM of difference (DoD) between 2007 and 2012 was created and analyzed, further differentiating between different zones (e.g. valley bottom, hillslope) and types of geomorphic processes (e.g. fluvial, gravitational). First results will be presented at the EGU General Assembly 2016.

Spatio-temporal dynamics in phytobenthos structural properties reveal insights into agricultural catchment dynamics and nutrient fluxes

NASA Astrophysics Data System (ADS)

Reaney, S. M.; Snell, M. A.; Barker, P. A.; Aftab, A.; Barber, N. J.; Benskin, C.; Burke, S.; Cleasby, W.; Haygarth, P.; Jonczyk, J. C.; Owen, G. J.; Perks, M. T.; Quinn, P. F.; Surridge, B.

2016-12-01

Low order streams are spatially extensive, temporally dynamic, systems within the agricultural landscape. This dynamism extends to the aquatic communities within these streams, including the phytobentos, which demonstrates considerable resilience to diffuse anthropogenic nutrient pressures and changing climate dynamics. The phytobenthos community can substantially contribute to the food web, in particular diatoms, which dominate photo-autotrophic assemblages in low order streams. Diatoms are widely used in ecological monitoring because of their high sensitivity to environmental condition, but knowledge is limited on the ecological effects of winter disturbances and variance introduced by multiple and interacting pressures (N, P, sediment), introducing bias in understanding temporal dynamics in benthic diatom communities. Using the environmental time series data from long term monitoring within the River Eden Demonstration Test Catchment programme, we assess the impact of multiple hydro-chemical stressors on phytobenthic community resilience, and synthesize the impact of an extreme winter event. Monthly data from diatom communities collected in the Eden DTC from March 2011 to present show that river flow, strongly coupled to precipitation, is a key driver of these communities. Discharge has a direct effect on communities through scouring, but is also tightly correlated to nutrient delivery, such that 80% of the annual TP load arrives in 10% of the time. Trophic Diatom Index (TDI) values demonstrated considerable resilience by the stability of inter-monthly TDI scores over 5 seasonal cycles against the characterised highly variable hydrological regime. This research demonstrates that well characterised winter disturbances are critical to understanding drivers of aquatic dynamics. This has implications for catchment diffuse pollution policy, farm management and economics, given the climate projections of increases in frequency and intensity of extreme winter events, which may alter instream nutrient fluxes.

Quantifying a Total Non-Methane Hydrocarbon Signal using Low-Cost VOC Sensors in an Effort to Help Communities Learn More About their Air Quality

NASA Astrophysics Data System (ADS)

Collier, A. M.; Hannigan, M.; Piedrahita, R.; Casey, J. G.; Johnston, J.; Chiang, S.

2016-12-01

The growing accessibility of low-cost air quality monitoring technologies has led to their increased usage among community-based organizations, particularly for the monitoring of pollutants dangerous to human health (e.g., hazardous air pollutants or HAPS). However, often these low-cost sensors are `off-the-shelf' and are being utilized in a manner that differs from their intended purpose - necessitating high quality calibrations. For example, VOC sensors intended for the detection of high levels of a particular compound in an industrial setting may instead be used for ambient monitoring of a group of VOCs. Academic/community partnerships can be an ideal way to improve this type of sensor quantification while providing a community with not only the opportunity to use these technologies with additional support around data quality, but also the opportunity for education around the abilities and applications of low-cost sensors. In the spring of 2016, our lab at the University of Colorado, Boulder partnered with communities in Los Angeles and Kern County to deploy low-cost air quality monitors for the purpose of quantifying methane and non-methane hydrocarbon signals in an effort to learn more about potential impacts from local sources (e.g., nearby highways and oil & gas development). The monitoring platform was developed in our lab and is capable of logging multiple gas phase species as well as some environmental parameters. The monitors include two different metal oxide VOC sensors - each with slightly different sensing capabilities. Calibration was achieved using a pre- and post-deployment field normalization to reference monitoring equipment maintained by the South Coast Air Quality Management District. Monitors were then deployed at locations throughout the community. We will present results on our efforts to quantify a total non-methane hydrocarbon signal, observations from the field data, and recommendations for academic/community partnerships formed around air quality monitoring.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity

PubMed Central

Frickel, Jens; Theodosiou, Loukas

2017-01-01

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species. PMID:28973943

Context and group dynamics in a CBPR-developed HIV prevention intervention

PubMed Central

Dickson-Gomez, Julia; Corbett, A. Michelle; Bodnar, Gloria; Zuniga, Maria Ofelia; Guevara, Carmen Eugenia; Rodriguez, Karla; Navas, Verónica

2016-01-01

This paper will explore in detail the effects of context and group dynamics on the development of a multi-level community-based HIV prevention intervention for crack cocaine users in the San Salvador Metropolitan Area, El Salvador. Community partners included residents from marginal communities, service providers from the historic center of San Salvador and research staff from a non-profit organization. The community contexts from which partners came varied considerably and affected structural group dynamics, i.e. who was identified as community partners, their research and organizational capacity, and their ability to represent their communities, with participants from marginal communities most likely to hold community leadership positions and be residents, and those from the center of San Salvador most likely to work in religious organizations dedicated to HIV prevention or feeding indigent drug users. These differences also affected the intervention priorities of different partners. The context of communities changed over time, particularly levels of violence, and affected group dynamics and the intervention developed. Finally, strategies were needed to elicit input from stakeholders under-represented in the community advisory board, in particular active crack users, in order to check the feasibility of the proposed intervention and revise it as necessary. Because El Salvador is a very different context than that in which most CBPR studies have been conducted, our results reveal important contextual factors and their effects on partnerships not often considered in the literature. PMID:25070835

Regulation of C:N:P stoichiometry of microbes and soil organic matter by optimizing enzyme allocation: an omics-informed model study

NASA Astrophysics Data System (ADS)

Song, Y.; Yao, Q.; Wang, G.; Yang, X.; Mayes, M. A.

2017-12-01

Increasing evidences is indicating that soil organic matter (SOM) decomposition and stabilization process is a continuum process and controlled by both microbial functions and their interaction with minerals (known as the microbial efficiency-matrix stabilization theory (MEMS)). Our metagenomics analysis of soil samples from both P-deficit and P-fertilization sites in Panama has demonstrated that community-level enzyme functions could adapt to maximize the acquisition of limiting nutrients and minimize energy demand for foraging (known as the optimal foraging theory). This optimization scheme can mitigate the imbalance of C/P ratio between soil substrate and microbial community and relieve the P limitation on microbial carbon use efficiency over the time. Dynamic allocation of multiple enzyme groups and their interaction with microbial/substrate stoichiometry has rarely been considered in biogeochemical models due to the difficulties in identifying microbial functional groups and quantifying the change in enzyme expression in response to soil nutrient availability. This study aims to represent the omics-informed optimal foraging theory in the Continuum Microbial ENzyme Decomposition model (CoMEND), which was developed to represent the continuum SOM decomposition process following the MEMS theory. The SOM pools in the model are classified based on soil chemical composition (i.e. Carbohydrates, lignin, N-rich SOM and P-rich SOM) and the degree of SOM depolymerization. The enzyme functional groups for decomposition of each SOM pool and N/P mineralization are identified by the relative composition of gene copy numbers. The responses of microbial activities and SOM decomposition to nutrient availability are simulated by optimizing the allocation of enzyme functional groups following the optimal foraging theory. The modeled dynamic enzyme allocation in response to P availability is evaluated by the metagenomics data measured from P addition and P-deficit soil samples in Panama sites.The implementation of dynamic enzyme allocation in response to nutrient availability in the CoMEND model enables us to capture the varying microbial C/P ratio and soil carbon dynamics in response to shifting nutrient constraints over time in tropical soils.

Detrimental effects of a novel flow regime on the functional trajectory of an aquatic invertebrate metacommunity.

PubMed

Ruhi, Albert; Dong, Xiaoli; McDaniel, Courtney H; Batzer, Darold P; Sabo, John L

2018-04-17

Novel flow regimes resulting from dam operations and overallocation of freshwater resources are an emerging consequence of global change. Yet, anticipating how freshwater biodiversity will respond to surging flow regime alteration requires overcoming two challenges in environmental flow science: shifting from local to riverscape-level understanding of biodiversity dynamics, and from static to time-varying characterizations of the flow regime. Here, we used time-series methods (wavelets and multivariate autoregressive models) to quantify flow-regime alteration and to link time-varying flow regimes to the dynamics of multiple local communities potentially connected by dispersal (i.e., a metacommunity). We studied the Chattahoochee River below Buford dam (Georgia, U.S.A.), and asked how flow regime alteration by a large hydropower dam may control the long-term functional trajectory of the downstream invertebrate metacommunity. We found that seasonal variation in hydropeaking synchronized temporal fluctuations in trait abundance among the flow-altered sites. Three biological trait states describing adaptation to fast flows benefitted from flow management for hydropower, but did not compensate for declines in 16 "loser" traits. Accordingly, metacommunity-wide functional diversity responded negatively to hydropeaking intensity, and stochastic simulations showed that the risk of functional diversity collapse within the next 4 years would decrease by 17% if hydropeaking was ameliorated, or by 9% if it was applied every other season. Finally, an analysis of 97 reference and 23 dam-affected river sites across the U.S. Southeast suggested that flow variation at extraneous, human-relevant scales (12-hr, 24-hr, 1-week) is relatively common in rivers affected by hydropower dams. This study advances the notion that novel flow regimes are widespread, and simplify the functional structure of riverine communities by filtering out taxa with nonadaptive traits and by spatially synchronizing their dynamics. This is relevant in the light of ongoing and future hydrologic alteration due to climate non-stationarity and the new wave of dams planned globally. © 2018 John Wiley & Sons Ltd.

Building-Resolved CFD Simulations for Greenhouse Gas Transport and Dispersion over Washington DC / Baltimore

NASA Astrophysics Data System (ADS)

Prasad, K.; Lopez-Coto, I.; Ghosh, S.; Mueller, K.; Whetstone, J. R.

2015-12-01

The North-East Corridor project aims to use a top-down inversion methodology to quantify sources of Greenhouse Gas (GHG) emissions over urban domains such as Washington DC / Baltimore with high spatial and temporal resolution. Atmospheric transport of tracer gases from an emission source to a tower mounted receptor are usually conducted using the Weather Research and Forecasting (WRF) model. For such simulations, WRF employs a parameterized turbulence model and does not resolve the fine scale dynamics generated by the flow around buildings and communities comprising a large city. The NIST Fire Dynamics Simulator (FDS) is a computational fluid dynamics model that utilizes large eddy simulation methods to model flow around buildings at length scales much smaller than is practical with WRF. FDS has the potential to evaluate the impact of complex urban topography on near-field dispersion and mixing difficult to simulate with a mesoscale atmospheric model. Such capabilities may be important in determining urban GHG emissions using atmospheric measurements. A methodology has been developed to run FDS as a sub-grid scale model within a WRF simulation. The coupling is based on nudging the FDS flow field towards that computed by WRF, and is currently limited to one way coupling performed in an off-line mode. Using the coupled WRF / FDS model, NIST will investigate the effects of the urban canopy at horizontal resolutions of 10-20 m in a domain of 12 x 12 km. The coupled WRF-FDS simulations will be used to calculate the dispersion of tracer gases in the North-East Corridor and to evaluate the upwind areas that contribute to tower observations, referred to in the inversion community as influence functions. Results of this study will provide guidance regarding the importance of explicit simulations of urban atmospheric turbulence in obtaining accurate estimates of greenhouse gas emissions and transport.

Constraining the dynamics of the water budget at high spatial resolution in the world's water towers using models and remote sensing data; Snake River Basin, USA

NASA Astrophysics Data System (ADS)

Watson, K. A.; Masarik, M. T.; Flores, A. N.

2016-12-01

Mountainous, snow-dominated basins are often referred to as the water towers of the world because they store precipitation in seasonal snowpacks, which gradually melt and provide water supplies to downstream communities. Yet significant uncertainties remain in terms of quantifying the stores and fluxes of water in these regions as well as the associated energy exchanges. Constraining these stores and fluxes is crucial for advancing process understanding and managing these water resources in a changing climate. Remote sensing data are particularly important to these efforts due to the remoteness of these landscapes and high spatial variability in water budget components. We have developed a high resolution regional climate dataset extending from 1986 to the present for the Snake River Basin in the northwestern USA. The Snake River Basin is the largest tributary of the Columbia River by volume and a critically important basin for regional economies and communities. The core of the dataset was developed using a regional climate model, forced by reanalysis data. Specifically the Weather Research and Forecasting (WRF) model was used to dynamically downscale the North American Regional Reanalysis (NARR) over the region at 3 km horizontal resolution for the period of interest. A suite of satellite remote sensing products provide independent, albeit uncertain, constraint on a number of components of the water and energy budgets for the region across a range of spatial and temporal scales. For example, GRACE data are used to constrain basinwide terrestrial water storage and MODIS products are used to constrain the spatial and temporal evolution of evapotranspiration and snow cover. The joint use of both models and remote sensing products allows for both better understanding of water cycle dynamics and associated hydrometeorologic processes, and identification of limitations in both the remote sensing products and regional climate simulations.

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

PubMed

Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

2014-12-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo

Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic andmore » mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S{sub in} in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.« less

Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

PubMed Central

Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

2014-01-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. PMID:25237788

Determination of Dynamic Fracture Toughness Properties of Rail Steels

DOT National Transportation Integrated Search

1987-11-01

Motivated by the occurrence of a long-running rail web fracture in service, dynamic fracture mechanics research was undertaken to (1) quantify the crack driving force due to the residual stresses induced by roller straightening operations, (2) determ...

Quantifying the dynamics of emotional expressions in family therapy of patients with anorexia nervosa.

PubMed

Pezard, Laurent; Doba, Karyn; Lesne, Annick; Nandrino, Jean-Louis

2017-07-01

Emotional interactions have been considered dynamical processes involved in the affective life of humans and their disturbances may induce mental disorders. Most studies of emotional interactions have focused on dyadic behaviors or self-reports of emotional states but neglected the dynamical processes involved in family therapy. The main objective of this study is to quantify the dynamics of emotional expressions and their changes using the family therapy of patients with anorexia nervosa as an example. Nonlinear methods characterize the variability of the dynamics at the level of the whole therapeutic system and reciprocal influence between the participants during family therapy. Results show that the variability of the dynamics is higher at the end of the therapy than at the beginning. The reciprocal influences between therapist and each member of the family and between mother and patient decrease with the course of family therapy. Our results support the development of new interpersonal strategies of emotion regulation during family therapy. The quantification of emotional dynamics can help understanding the emotional processes underlying psychopathology and evaluating quantitatively the changes achieved by the therapeutic intervention. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

The Bird Community Resilience Index: a novel remote sensing-based biodiversity variable for quantifying ecological integrity

NASA Astrophysics Data System (ADS)

Michel, N. L.; Wilsey, C.; Burkhalter, C.; Trusty, B.; Langham, G.

2017-12-01

Scalable indicators of biodiversity change are critical to reporting overall progress towards national and global targets for biodiversity conservation (e.g. Aichi Targets) and sustainable development (SDGs). These essential biodiversity variables capitalize on new remote sensing technologies and growth of community science participation. Here we present a novel biodiversity metric quantifying resilience of bird communities and, by extension, of their associated ecological communities. This metric adds breadth to the community composition class of essential biodiversity variables that track trends in condition and vulnerability of ecological communities. We developed this index for use with North American grassland birds, a guild that has experienced stronger population declines than any other avian guild, in order to evaluate gains from the implementation of best management practices on private lands. The Bird Community Resilience Index was designed to incorporate the full suite of species-specific responses to management actions, and be flexible enough to work across broad climatic, land cover, and bird community gradients (i.e., grasslands from northern Mexico through Canada). The Bird Community Resilience Index consists of four components: density estimates of grassland and arid land birds; weighting based on conservation need; a functional diversity metric to incorporate resiliency of bird communities and their ecosystems; and a standardized scoring system to control for interannual variation caused by extrinsic factors (e.g., climate). We present an analysis of bird community resilience across ranches in the Northern Great Plains region of the United States. As predicted, Bird Community Resilience was higher in lands implementing best management practices than elsewhere. While developed for grassland birds, this metric holds great potential for use as an Essential Biodiversity Variable for community composition in a variety of habitat.

Foraminifera Record the Good Years More than the Bad

NASA Astrophysics Data System (ADS)

Hull, P. M.

2014-12-01

Past ocean conditions are primarily discerned from geochemical and community-based analyses of fossilized taxa, each of which have unique environmental niches and dynamics. A key requirement of such paleoceanographic studies is that some unbiased or well-constrained record of the living ecosystem and climate is deposited on the sea floor and preserved through the post-depositional processes that act to distort them. It is widely known that foraminiferal species exhibit varying seasonal preferences and that seasonality is a key variable to account for in paleoceanographic reconstructions. However, on longer time scales (> year), it is generally assumed that species record the 'average' environmental conditions or typical variance (e.g., El Nino intensity) that existed in a given, time-averaged sediment sample. Here I examine planktonic foraminiferal population dynamics on yearly and longer time scales, in order to quantify their effect on paleoceanographic reconstructions. Using a previously published record of >250 years of population dynamics in the Santa Barbara Basin sediments, I find that the majority of individuals in a given species lived during a small subset of the total years (~15- 37% of years depending on the species). Populations of shallow, mixed layer species primarily represent the warmest, youngest years, while thermocline species primarily represent the cooler, older years. Importantly, the seasonality of species does not always predict their interannual dynamics. The general importance of long time-scale population dynamics on paleoceanographic reconstructions will also be considered in a theoretical model parameterized with temporally explicit species co-variances and temperature variability. Such modeling is needed to constrain the relative impact that a very good year can have on our interpretation of the 'average' of hundreds to thousands of years.

Rangeland resilience and resistance: annual and perennial grass stable states

USDA-ARS?s Scientific Manuscript database

The concept of resilience, the ability to resist a shift to an alternative vegetation state, has become an important topic in range management. To quantify the degree to which a plant community is resilient, we experimentally manipulated communities dominated by either the invasive annual grass chea...

Multistage, Multiband and sequential imagery to identify and quantify non-forest vegetation resources

NASA Technical Reports Server (NTRS)

Driscoll, R. S.

1971-01-01

Analysis and recognition processing of multispectral scanner imagery for plant community classification and interpretations of various film-filter-scale aerial photographs are reported. Data analyses and manuscript preparation of research on microdensitometry for plant community and component identification and remote estimates of biomass are included.

Medusahead: Available soil N and microbial communities in native and invasive soils

Treesearch

Robert R. Blank; Rene Sforza; Tye Morgan

2008-01-01

To better understand why medusahead (Taeniatherum caput-medusae) is invasive, we quantified soil N availability and characterized soil microbial communities between native and invasive populations. No consistent differences in soil N mineralization potentials were noted between native medusahead sites in Spain, Turkey, France, and Greece and two...

The herb community of a tropical forest in central Panamá: dynamics and impact of mammalian herbivores.

PubMed

Royo, Alejandro A; Carson, Walter P

2005-08-01

Mammals are hypothesized to either promote plant diversity by preventing competitive exclusion or limit diversity by reducing the abundance of sensitive plant species through their activities as browsers or disturbance agents. Previous studies of herbivore impacts in plant communities have focused on tree species and ignored the herbaceous community. In an experiment in mature-phase, tropical moist forest sites in central Panamá, we studied the impact of excluding ground-dwelling mammals on the richness and abundance of herbs in 16, 30x45-m plots. Within each plot, we censused the herbaceous community in 28, 2x2-m subplots (1,792 m2 total area sampled). We identified over 54 species of herbs averaging 1.21 ramets m-2 and covering approximately 4.25% of the forest floor. Excluding mammals for 5 years had no impact on overall species richness. Within exclosures, however, there was a significant two-fold increase in the density of rare species. Overall herbaceous density and percent cover did not differ between exclosures and adjacent control plots, although cover did increase over time. Mammalian exclusion significantly increased the total cover of three-dominant herb species, Pharus latifolius, Calathea inocephala, and Adiantum lucidum, but did not affect their density. This study represents one of the most extensive herbaceous community censuses conducted in tropical forests and is among a few that quantify herbaceous distribution and abundance in terms of both density and cover. Additionally, this work represents the first community level test of mammalian impacts on the herbaceous community in a tropical forest to date. Our results suggest that ground dwelling mammals do not play a key role in altering the relative abundance patterns of tropical herbs in the short term. Furthermore, our results contrast sharply with prior studies on similar temporal and spatial scales that demonstrate mammals strongly alter tree seedling composition and reduce seedling density. Thus, we question the pervasiveness of top-down control on tropical plant communities and the paradigm that defaunation will inexorably lead to widespread, catastrophic shifts in plant communities.

Epiphytic lichen community dynamics in deciduous forests around a phosphorus fertiliser factory in Central Lithuania.

PubMed

Motiejūnaite, Jurga

2007-03-01

The detailed dynamics of epiphytic lichen communities were observed while studying permanent quadrats in the zone of influence of a phosphorus fertiliser factory in central Lithuania. The most significant changes were induced by several factors: changes in macroenvironment (increase of illumination), bark scaling, succession processes, individual growth characteristics of the community members, and influence of fungal infection and invertebrate grazing. None of these changes could be directly linked with air pollution. These observations have shown that in conditions of more or less stable pollution, epiphytic community dynamics should be evaluated with care, the best indicators of the characteristics of the communities being species richness and presence/absence and abundance of indicator (nitrophilous or acidophilous) species.

Dynamics and control of diseases in networks with community structure.

PubMed

Salathé, Marcel; Jones, James H

2010-04-08

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jurburg, Stephanie D.; Nunes, Inês; Stegen, James C.

The response of bacterial communities to environmental change may affect local to global nutrient cycles; however the dynamics of these communities following disturbance are poorly understood, and are generally attributed to abiotic factors. Here, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days of recovery. Phylogenetic turnover patterns indicated that biotic interactions shaped the community during recovery, and that the disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response (1-4more » days after disturbance) in which surviving taxa increased in abundance; a secondary response phase (10-29 days), during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macroecological systems and exhibit path-dependent, autogenic dynamics during secondary succession.« less

Long-term dynamics of winter and summer annual communities in the Chihuahuan Desert

USGS Publications Warehouse

Guo, Q.; Brown, J.H.; Valone, T.J.

2002-01-01

Using 15 years of census data from permanent quadrats, this paper compared the characteristics and temporal dynamics of these two distinct, spatially coexistent but temporally segregated communities. Although the total number of summer annual species recorded during our 15 years observation was higher than winter annuals, the average number of species observed each year was higher in the winter community. The winter community exhibited lower temporal variation in total plant abundance and populations of individual species, lower species turnover rate and higher evenness than the summer community. The higher seasonal species diversity (i.e., number of species observed in each season) in winters rather than the overall special pool (over 15 yrs) may be responsible for the greater community stability of winter annuals. The difference in long-term community dynamics between the two communities of annuals plants are likely due to the differences in total species pool, life history traits (e.g., seed size), and seasonal climatic regimes.

Planning, implementing, and evaluating a program to address the oral health needs of aboriginal children in port augusta, australia.

PubMed

Parker, E J; Misan, G; Shearer, M; Richards, L; Russell, A; Mills, H; Jamieson, L M

2012-01-01

Aboriginal Australian children experience profound oral health disparities relative to their non-Aboriginal counterparts. In response to community concerns regarding Aboriginal child oral health in the regional town of Port Augusta, South Australia, a child dental health service was established within a Community Controlled Aboriginal Health Service. A partnership approach was employed with the key aims of (1) quantifying rates of dental service utilisation, (2) identifying factors influencing participation, and (3) planning and establishing a program for delivery of Aboriginal children's dental services that would increase participation and adapt to community needs. In planning the program, levels of participation were quantified and key issues identified through semistructured interviews. After 3.5 years, the participation rate for dental care among the target population increased from 53 to 70 percent. Key areas were identified to encourage further improvements and ensure sustainability in Aboriginal child oral health in this regional location.

Quantifying sleep architecture dynamics and individual differences using big data and Bayesian networks

PubMed Central

Shelton, Christian; Mednick, Sara C.

2018-01-01

The pattern of sleep stages across a night (sleep architecture) is influenced by biological, behavioral, and clinical variables. However, traditional measures of sleep architecture such as stage proportions, fail to capture sleep dynamics. Here we quantify the impact of individual differences on the dynamics of sleep architecture and determine which factors or set of factors best predict the next sleep stage from current stage information. We investigated the influence of age, sex, body mass index, time of day, and sleep time on static (e.g. minutes in stage, sleep efficiency) and dynamic measures of sleep architecture (e.g. transition probabilities and stage duration distributions) using a large dataset of 3202 nights from a non-clinical population. Multi-level regressions show that sex effects duration of all Non-Rapid Eye Movement (NREM) stages, and age has a curvilinear relationship for Wake After Sleep Onset (WASO) and slow wave sleep (SWS) minutes. Bayesian network modeling reveals sleep architecture depends on time of day, total sleep time, age and sex, but not BMI. Older adults, and particularly males, have shorter bouts (more fragmentation) of Stage 2, SWS, and they transition less frequently to these stages. Additionally, we showed that the next sleep stage and its duration can be optimally predicted by the prior 2 stages and age. Our results demonstrate the potential benefit of big data and Bayesian network approaches in quantifying static and dynamic architecture of normal sleep. PMID:29641599

Quantifying sleep architecture dynamics and individual differences using big data and Bayesian networks.

PubMed

Yetton, Benjamin D; McDevitt, Elizabeth A; Cellini, Nicola; Shelton, Christian; Mednick, Sara C

2018-01-01

The pattern of sleep stages across a night (sleep architecture) is influenced by biological, behavioral, and clinical variables. However, traditional measures of sleep architecture such as stage proportions, fail to capture sleep dynamics. Here we quantify the impact of individual differences on the dynamics of sleep architecture and determine which factors or set of factors best predict the next sleep stage from current stage information. We investigated the influence of age, sex, body mass index, time of day, and sleep time on static (e.g. minutes in stage, sleep efficiency) and dynamic measures of sleep architecture (e.g. transition probabilities and stage duration distributions) using a large dataset of 3202 nights from a non-clinical population. Multi-level regressions show that sex effects duration of all Non-Rapid Eye Movement (NREM) stages, and age has a curvilinear relationship for Wake After Sleep Onset (WASO) and slow wave sleep (SWS) minutes. Bayesian network modeling reveals sleep architecture depends on time of day, total sleep time, age and sex, but not BMI. Older adults, and particularly males, have shorter bouts (more fragmentation) of Stage 2, SWS, and they transition less frequently to these stages. Additionally, we showed that the next sleep stage and its duration can be optimally predicted by the prior 2 stages and age. Our results demonstrate the potential benefit of big data and Bayesian network approaches in quantifying static and dynamic architecture of normal sleep.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cotton, T. E. Anne; Fitter, Alastair H.; Miller, R. Michael

Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to global environmental change is essential for the prediction of future plant growth and ecosystem functions. We investigated the long-term temporal dynamics and effect of elevated atmospheric carbon dioxide (CO 2) and ozone (O 3) concentrations on AM fungal communities. Molecular methods were used to characterize the AM fungal communities of soybean ( Glycine max) grown under elevated and ambient atmospheric concentrations of both CO 2 and O 3 within a free air concentration enrichment experiment in three growing seasons over 5 yr. Elevated CO 2 altered themore » community composition of AM fungi, increasing the ratio of Glomeraceae to Gigasporaceae. By contrast, no effect of elevated O 3 on AM fungal communities was detected. However, the greatest compositional differences detected were between years, suggesting that, at least in the short term, large-scale interannual temporal dynamics are stronger mediators than atmospheric CO 2 concentrations of AM fungal communities. We conclude that, although atmospheric change may significantly alter AM fungal communities, this effect may be masked by the influences of natural changes and successional patterns through time. We suggest that changes in carbon availability are important determinants of the community dynamics of AM fungi.« less

Community Identity and User Engagement in a Multi-Community Landscape.

PubMed

Zhang, Justine; Hamilton, William L; Danescu-Niculescu-Mizil, Cristian; Jurafsky, Dan; Leskovec, Jure

2017-05-01

A community's identity defines and shapes its internal dynamics. Our current understanding of this interplay is mostly limited to glimpses gathered from isolated studies of individual communities. In this work we provide a systematic exploration of the nature of this relation across a wide variety of online communities. To this end we introduce a quantitative, language-based typology reflecting two key aspects of a community's identity: how distinctive , and how temporally dynamic it is. By mapping almost 300 Reddit communities into the landscape induced by this typology, we reveal regularities in how patterns of user engagement vary with the characteristics of a community. Our results suggest that the way new and existing users engage with a community depends strongly and systematically on the nature of the collective identity it fosters, in ways that are highly consequential to community maintainers. For example, communities with distinctive and highly dynamic identities are more likely to retain their users. However, such niche communities also exhibit much larger acculturation gaps between existing users and newcomers, which potentially hinder the integration of the latter. More generally, our methodology reveals differences in how various social phenomena manifest across communities, and shows that structuring the multi-community landscape can lead to a better understanding of the systematic nature of this diversity.

Fungi in the future: Interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities

DOE PAGES

Cotton, T. E. Anne; Fitter, Alastair H.; Miller, R. Michael; ...

2015-01-05

Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to global environmental change is essential for the prediction of future plant growth and ecosystem functions. We investigated the long-term temporal dynamics and effect of elevated atmospheric carbon dioxide (CO 2) and ozone (O 3) concentrations on AM fungal communities. Molecular methods were used to characterize the AM fungal communities of soybean ( Glycine max) grown under elevated and ambient atmospheric concentrations of both CO 2 and O 3 within a free air concentration enrichment experiment in three growing seasons over 5 yr. Elevated CO 2 altered themore » community composition of AM fungi, increasing the ratio of Glomeraceae to Gigasporaceae. By contrast, no effect of elevated O 3 on AM fungal communities was detected. However, the greatest compositional differences detected were between years, suggesting that, at least in the short term, large-scale interannual temporal dynamics are stronger mediators than atmospheric CO 2 concentrations of AM fungal communities. We conclude that, although atmospheric change may significantly alter AM fungal communities, this effect may be masked by the influences of natural changes and successional patterns through time. We suggest that changes in carbon availability are important determinants of the community dynamics of AM fungi.« less

Sound Links: Exploring the Social, Cultural and Educational Dynamics of Musical Communities in Australia

ERIC Educational Resources Information Center

Bartleet, Brydie-Leigh

2009-01-01

"Sound Links" examines the dynamics of community music in Australia, and the models it represents for informal music learning and teaching. This involves researching a selection of vibrant musical communities across the country, exploring their potential for complementarity and synergy with music in schools. This article focuses on the…

Design criteria for portable timber bridge systems : static versus dynamic loads

Treesearch

John M. Franklin; S. E. Taylor; Paul A. Morgan; M. A. Ritter

1999-01-01

Design criteria are needed specifically for portable bridges to insure that they are safe and cost effective. This paper discusses different portable bridge categories and their general design criteria. Specific emphasis is given to quantifying the effects of dynamic live loads on portable bridge design. Results from static and dynamic load tests of two portable timber...

The influence of floral traits on specialization and modularity of plant–pollinator networks in a biodiversity hotspot in the Peruvian Andes

PubMed Central

Watts, Stella; Dormann, Carsten F.; Martín González, Ana M.; Ollerton, Jeff

2016-01-01

Background and Aims Modularity is a ubiquitous and important structural property of ecological networks which describes the relative strengths of sets of interacting species and gives insights into the dynamics of ecological communities. However, this has rarely been studied in species-rich, tropical plant–pollinator networks. Working in a biodiversity hotspot in the Peruvian Andes we assessed the structure of quantitative plant–pollinator networks in nine valleys, quantifying modularity among networks, defining the topological roles of species and the influence of floral traits on specialization. Methods A total of 90 transects were surveyed for plants and pollinators at different altitudes and across different life zones. Quantitative modularity (QuanBiMo) was used to detect modularity and six indices were used to quantify specialization. Key Results All networks were highly structured, moderately specialized and significantly modular regardless of size. The strongest hubs were Baccharis plants, Apis mellifera, Bombus funebris and Diptera spp., which were the most ubiquitous and abundant species with the longest phenologies. Species strength showed a strong association with the modular structure of plant–pollinator networks. Hubs and connectors were the most centralized participants in the networks and were ranked highest (high generalization) when quantifying specialization with most indices. However, complementary specialization d' quantified hubs and connectors as moderately specialized. Specialization and topological roles of species were remarkably constant across some sites, but highly variable in others. Networks were dominated by ecologically and functionally generalist plant species with open access flowers which are closely related taxonomically with similar morphology and rewards. Plants associated with hummingbirds had the highest level of complementary specialization and exclusivity in modules (functional specialists) and the longest corollas. Conclusions We have demonstrated that the topology of networks in this tropical montane environment was non-random and highly organized. Our findings underline that specialization indices convey different concepts of specialization and hence quantify different aspects, and that measuring specialization requires careful consideration of what defines a specialist. PMID:27562649

The influence of floral traits on specialization and modularity of plant-pollinator networks in a biodiversity hotspot in the Peruvian Andes.

PubMed

Watts, Stella; Dormann, Carsten F; Martín González, Ana M; Ollerton, Jeff

2016-09-01

Modularity is a ubiquitous and important structural property of ecological networks which describes the relative strengths of sets of interacting species and gives insights into the dynamics of ecological communities. However, this has rarely been studied in species-rich, tropical plant-pollinator networks. Working in a biodiversity hotspot in the Peruvian Andes we assessed the structure of quantitative plant-pollinator networks in nine valleys, quantifying modularity among networks, defining the topological roles of species and the influence of floral traits on specialization. A total of 90 transects were surveyed for plants and pollinators at different altitudes and across different life zones. Quantitative modularity (QuanBiMo) was used to detect modularity and six indices were used to quantify specialization. All networks were highly structured, moderately specialized and significantly modular regardless of size. The strongest hubs were Baccharis plants, Apis mellifera, Bombus funebris and Diptera spp., which were the most ubiquitous and abundant species with the longest phenologies. Species strength showed a strong association with the modular structure of plant-pollinator networks. Hubs and connectors were the most centralized participants in the networks and were ranked highest (high generalization) when quantifying specialization with most indices. However, complementary specialization d' quantified hubs and connectors as moderately specialized. Specialization and topological roles of species were remarkably constant across some sites, but highly variable in others. Networks were dominated by ecologically and functionally generalist plant species with open access flowers which are closely related taxonomically with similar morphology and rewards. Plants associated with hummingbirds had the highest level of complementary specialization and exclusivity in modules (functional specialists) and the longest corollas. We have demonstrated that the topology of networks in this tropical montane environment was non-random and highly organized. Our findings underline that specialization indices convey different concepts of specialization and hence quantify different aspects, and that measuring specialization requires careful consideration of what defines a specialist. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Experimental investigation of the formaldehyde removal mechanisms in a dynamic botanical filtration system for indoor air purification.

PubMed

Wang, Zhiqiang; Pei, Jingjing; Zhang, Jensen S

2014-09-15

Botanical filtration has been proved to be effective for indoor gas pollutant removal. To understand the roles of different transport, storage and removal mechanism by a dynamic botanical air filter, a series of experimental investigations were designed and conducted in this paper. Golden Pothos (Epipremnum aureum) plants was selected for test, and its original soil or activated/pebbles root bed was used in different test cases. It was found that flowing air through the root bed with microbes dynamically was essential to obtain meaningful formaldehyde removal efficiency. For static potted plant as normally place in rooms, the clean air delivery rate (CADR), which is often used to quantify the air cleaning ability of portable air cleaners, was only ∼ 5.1m(3)/h per m(2) bed, while when dynamically with air flow through the bed, the CADR increased to ∼ 233 m(3)/h per m(2) bed. The calculated CADR due to microbial activity is ∼ 108 m(3)/h per m(2) bed. Moisture in the root bed also played an important role, both for maintaining a favorable living condition for microbes and for absorbing water-soluble compounds such as formaldehyde. The role of the plant was to introduce and maintain a favorable microbe community which effectively degraded the volatile organic compounds adsorbed or absorbed by the root bed. The presence of the plant increased the removal efficiency by a factor of two based on the results from the bench-scale root bed experiments. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantifying the Human Impacts on Papua New Guinea Reef Fish Communities across Space and Time.

PubMed

Drew, Joshua A; Amatangelo, Kathryn L; Hufbauer, Ruth A

2015-01-01

Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing and environmental perturbation. Using data from published species lists we categorize the reef fishes as either fished or non-fished based on their body size and reports from the published literature. Species diversity for both fished and non-fished groups decreases as the size of the local human population increases, and this relationship is stronger in species that are fished. Additionally, comparison of modern and museum collections show that modern reef communities have proportionally fewer fished species relative to 19th century ones. Together these findings show that the reef fish communities of Papua New Guinea experience multiple anthropogenic stressors and that even at low human population levels targeted species experience population declines across both time and space.

Growth and element flux at fine taxonomic resolution in natural microbial communities

NASA Astrophysics Data System (ADS)

Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

2015-04-01

Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

Temporal changes in randomness of bird communities across Central Europe.

PubMed

Renner, Swen C; Gossner, Martin M; Kahl, Tiemo; Kalko, Elisabeth K V; Weisser, Wolfgang W; Fischer, Markus; Allan, Eric

2014-01-01

Many studies have examined whether communities are structured by random or deterministic processes, and both are likely to play a role, but relatively few studies have attempted to quantify the degree of randomness in species composition. We quantified, for the first time, the degree of randomness in forest bird communities based on an analysis of spatial autocorrelation in three regions of Germany. The compositional dissimilarity between pairs of forest patches was regressed against the distance between them. We then calculated the y-intercept of the curve, i.e. the 'nugget', which represents the compositional dissimilarity at zero spatial distance. We therefore assume, following similar work on plant communities, that this represents the degree of randomness in species composition. We then analysed how the degree of randomness in community composition varied over time and with forest management intensity, which we expected to reduce the importance of random processes by increasing the strength of environmental drivers. We found that a high portion of the bird community composition could be explained by chance (overall mean of 0.63), implying that most of the variation in local bird community composition is driven by stochastic processes. Forest management intensity did not consistently affect the mean degree of randomness in community composition, perhaps because the bird communities were relatively insensitive to management intensity. We found a high temporal variation in the degree of randomness, which may indicate temporal variation in assembly processes and in the importance of key environmental drivers. We conclude that the degree of randomness in community composition should be considered in bird community studies, and the high values we find may indicate that bird community composition is relatively hard to predict at the regional scale.

Long-term dynamics of winter and summer annual communities in the Chihuahuan Desert

USGS Publications Warehouse

Guo, Q.; Brown, J.H.; Valone, T.J.

2002-01-01

Winter and summer annuals in the Chihuahuan Desert have been intensively studied in recent years but little is known about the similarities and differences in the dynamics between these two communities. Using 15 yr of census data from permanent quadrats, this paper compared the characteristics and temporal dynamics of these two distinct, spatially co-existent but temporally segregated communities. Although the total number of summer annual species recorded during our 15 yr of observation was higher than winter annuals, the mean number of species observed each year was higher in the winter community. The winter community exhibited lower temporal variation in total plant abundance and populations of individual species, lower species turnover rate and higher evenness than the summer community. The rank abundances of species in winter were significantly positively correlated for a period of up to 7 yr while in summer significant positive correlations in rank abundance disappeared after 2 to 3 yr. The higher seasonal species diversity (i.e. number of species observed in each season) in winter rather than the overall special pool (over 15 yr) may be responsible for the greater community stability of winter annuals. The difference in long-term community dynamics between the two communities of annual plants are likely due to the differences in total species pool, life history traits (e.g. seed size), and seasonal climatic regimes.

Quantifying "apparent" impact and distinguishing impact from invasiveness in multispecies plant invasions

Treesearch

Dean E. Pearson; Yvette K. Ortega; Ozkan Eren; Jose L. Hierro

2015-01-01

The quantification of invader impacts remains a major hurdle to understanding and managing invasions. Here, we demonstrate a method for quantifying the community-level impact of multiple plant invaders by applying Parker et al.'s (1999) equation (impact = range x local abundance x per capita effect or per unit effect) using data from 620 survey plots from 31...

Building a Community of Research Practice: Intragroup Team Social Dynamics in Interdisciplinary Mixed Methods

ERIC Educational Resources Information Center

Hemmings, Annette; Beckett, Gulbahar; Kennerly, Susan; Yap, Tracey

2013-01-01

This article explicates the intragroup social dynamics and work of a nursing and education research team as a community of research practice interested in organizational cultures and occupational subcultures. Dynamics were characterized by processes of socialization through reeducation and group social identity formation that enabled members to…

Nonlinear time series analysis of normal and pathological human walking

NASA Astrophysics Data System (ADS)

Dingwell, Jonathan B.; Cusumano, Joseph P.

2000-12-01

Characterizing locomotor dynamics is essential for understanding the neuromuscular control of locomotion. In particular, quantifying dynamic stability during walking is important for assessing people who have a greater risk of falling. However, traditional biomechanical methods of defining stability have not quantified the resistance of the neuromuscular system to perturbations, suggesting that more precise definitions are required. For the present study, average maximum finite-time Lyapunov exponents were estimated to quantify the local dynamic stability of human walking kinematics. Local scaling exponents, defined as the local slopes of the correlation sum curves, were also calculated to quantify the local scaling structure of each embedded time series. Comparisons were made between overground and motorized treadmill walking in young healthy subjects and between diabetic neuropathic (NP) patients and healthy controls (CO) during overground walking. A modification of the method of surrogate data was developed to examine the stochastic nature of the fluctuations overlying the nominally periodic patterns in these data sets. Results demonstrated that having subjects walk on a motorized treadmill artificially stabilized their natural locomotor kinematics by small but statistically significant amounts. Furthermore, a paradox previously present in the biomechanical literature that resulted from mistakenly equating variability with dynamic stability was resolved. By slowing their self-selected walking speeds, NP patients adopted more locally stable gait patterns, even though they simultaneously exhibited greater kinematic variability than CO subjects. Additionally, the loss of peripheral sensation in NP patients was associated with statistically significant differences in the local scaling structure of their walking kinematics at those length scales where it was anticipated that sensory feedback would play the greatest role. Lastly, stride-to-stride fluctuations in the walking patterns of all three subject groups were clearly distinguishable from linearly autocorrelated Gaussian noise. As a collateral benefit of the methodological approach taken in this study, some of the first steps at characterizing the underlying structure of human locomotor dynamics have been taken. Implications for understanding the neuromuscular control of locomotion are discussed.

The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models

PubMed Central

Grabowski, Mary K.; Lessler, Justin; Redd, Andrew D.; Kagaayi, Joseph; Laeyendecker, Oliver; Ndyanabo, Anthony; Nelson, Martha I.; Cummings, Derek A. T.; Bwanika, John Baptiste; Mueller, Amy C.; Reynolds, Steven J.; Munshaw, Supriya; Ray, Stuart C.; Lutalo, Tom; Manucci, Jordyn; Tobian, Aaron A. R.; Chang, Larry W.; Beyrer, Chris; Jennings, Jacky M.; Nalugoda, Fred; Serwadda, David; Wawer, Maria J.; Quinn, Thomas C.; Gray, Ronald H.

2014-01-01

Background It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities—home to two-thirds of the African population—is driven by intra-community sexual networks versus viral introductions from outside of communities. Methods and Findings We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7–3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%–42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%–70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai. Conclusions Our findings suggest that HIV introductions into communities are common and account for a significant proportion of new HIV infections acquired outside of households in rural Uganda, though the extent to which this is true elsewhere in Africa remains unknown. Our results also suggest that HIV prevention efforts should be implemented at spatial scales broader than the community and should target key populations likely responsible for introductions into communities. Please see later in the article for the Editors' Summary PMID:24595023

Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

PubMed Central

Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

2014-01-01

Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms. PMID:24723806

Decomposition-based multiobjective evolutionary algorithm for community detection in dynamic social networks.

PubMed

Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

2014-01-01

Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

Quantifying and Monetizing Potential Climate Change Policy Impacts on Terrestrial Ecosystem Carbon Storage and Wildfires in the United States

EPA Science Inventory

This paper quantifies and monetizes climate change impacts on carbon stored in terrestrial vegetation and wildfire incidence in the contiguous United States to assess the benefits of alternative mitigation policies. The MC-1 dynamic global vegetation model was used to develop int...

Biogeochemical Indicators in High- and Low-Arctic Marine and Terrestrial Avian Community Changes: Comparative Isotopic (13C, 15N, and 34S) Studies in Alaska and Greenland

NASA Astrophysics Data System (ADS)

Causey, D.; Bargmann, N. A.; Burnham, K. K.; Burnham, J. L.; Padula, V. M.; Johnson, J. A.; Welker, J. M.

2011-12-01

Understanding the complex dynamics of environmental change in northern latitudes is of paramount importance today, given documented rapid shifts in sea ice, plant phenology, temperatures, deglaciation, and habitat fidelity. This knowledge is particularly critical for Arctic avian communities, which are integral components by which biological teleconnections are maintained between the mid and northern latitudes. Furthermore, Arctic birds are fundamental to Native subsistence lifestyles and a focus for conservation activities. Avian communities of marine and terrestrial Arctic environments represent a broad spectrum of trophic levels, from herbivores (eg., geese Chen spp.), planktivores (eg., auklets Aethia spp.), and insectivores (eg., passerines: Wheatears Oenanthe spp., Longspurs Calcarius spp.), to predators of marine invertebrates (eg., eiders Somateria spp.), nearshore and offshore fish (eg., cormorants Phalacrocorax spp, puffins Fratercula spp.), even other bird species (eg., gulls Larus spp., falcons Peregrinus spp.). This diversity of trophic interconnections is an integral factor in the dynamics of Arctic ecosystem ecology, and they are key indicators for the strength and trajectories of change. We are especially interested in their feeding ecology, using stable isotope-diet relations to examine historical diets and to predict future feeding ecology by this range of species. Since 2009, we have been studying the foodweb ecology using stable isotopes (δ13C, δ15N, δ34S) of contemporaneous coastal and marine bird communities in High Arctic (Northwest Greenland) and Low Arctic (western Aleutian Islands, AK). We are quantifying the isotopic values of blood, organ tissues, and feathers, and have carried out comparisons between native and lipid-extracted samples. Although geographically distant, these communities comprise similar taxonomic and ecological congeners, including several species common to both (eg., Common Eider, Black-legged Kittiwake, Northern Fulmar). Generally, High Arctic species have tissues that are more enriched in δ15N compared to their Low Arctic counterparts, but δ13C values are similar in both regions. These patterns follow observed regional differences in Arctic isoscapes, and are probably related to isotopic variations in food rather than trophic level differentiation. Both Low- and High-Arctic bird communities show decadal-period shifts in stable isotope profiles, based on prior published results and previously collected specimens. For example, Aleutian birds feeding in upper trophic levels have tissues are more enriched in both δ13C and δ15N compared to specimens collected in 2000-2001. We anticipate broadening the time depth of this initial study using museum archival and archeological material, as well as continuing studies in 2013 and 2014.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

PubMed Central

2013-01-01

Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology. PMID:24238386

What Is a Pediatric Heart Surgeon?

MedlinePlus

... Life Family Life Family Life Medical Home Family Dynamics Media Work & Play Getting Involved in Your Community ... Life Medical Home Health Insurance Pediatric Specialists Family Dynamics Media Work & Play Getting Involved in Your Community ...

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE PAGES

Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...

2017-08-04

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justice, N. B.; Sczesnak, A.; Hazen, T. C.

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Modeling the effects of environmental disturbance on wildlife communities: Avian responses to prescribed fire

USGS Publications Warehouse

Russell, R.E.; Royle, J. Andrew; Saab, V.A.; Lehmkuhl, J.F.; Block, W.M.; Sauer, J.R.

2009-01-01

Prescribed fire is a management tool used to reduce fuel loads on public lands in forested areas in the western United States. Identifying the impacts of prescribed fire on bird communities in ponderosa pine (Pinus ponderosa) forests is necessary for providing land management agencies with information regarding the effects of fuel reduction on sensitive, threatened, and migratory bird species. Recent developments in occupancy modeling have established a framework for quantifying the impacts of management practices on wildlife community dynamics. We describe a Bayesian hierarchical model of multi-species occupancy accounting for detection probability, and we demonstrate the model's usefulness for identifying effects of habitat disturbances on wildlife communities. Advantages to using the model include the ability to estimate the effects of environmental impacts on rare or elusive species, the intuitive nature of the modeling, the incorporation of detection probability, the estimation of parameter uncertainty, the flexibility of the model to suit a variety of experimental designs, and the composite estimate of the response that applies to the collection of observed species as opposed to merely a small subset of common species. Our modeling of the impacts of prescribed fire on avian communities in a ponderosa pine forest in Washington indicate that prescribed fire treatments result in increased occupancy rates for several bark-insectivore, cavity-nesting species including a management species of interest, Black-backed Woodpeckers (Picoides arcticus). Three aerial insectivore species, and the ground insectivore, American Robin (Turdus migratorius), also responded positively to prescribed fire, whereas three foliage insectivores and two seed specialists, Clark's Nutcracker (Nucifraga columbiana) and the Pine Siskin (Carduelis pinus), declined following treatments. Land management agencies interested in determining the effects of habitat manipulations on wildlife communities can use these methods to provide guidance for future management activities. ?? 2009 by the Ecological Society of America.

Response of Sierra Nevada forests to projected climate-wildfire interactions.

PubMed

Liang, Shuang; Hurteau, Matthew D; Westerling, Anthony LeRoy

2017-05-01

Climate influences forests directly and indirectly through disturbance. The interaction of climate change and increasing area burned has the potential to alter forest composition and community assembly. However, the overall forest response is likely to be influenced by species-specific responses to environmental change and the scale of change in overstory species cover. In this study, we sought to quantify how projected changes in climate and large wildfire size would alter forest communities and carbon (C) dynamics, irrespective of competition from nontree species and potential changes in other fire regimes, across the Sierra Nevada, USA. We used a species-specific, spatially explicit forest landscape model (LANDIS-II) to evaluate forest response to climate-wildfire interactions under historical (baseline) climate and climate projections from three climate models (GFDL, CCSM3, and CNRM) forced by a medium-high emission scenario (A2) in combination with corresponding climate-specific large wildfire projections. By late century, we found modest changes in the spatial distribution of dominant species by biomass relative to baseline, but extensive changes in recruitment distribution. Although forest recruitment declined across much of the Sierra, we found that projected climate and wildfire favored the recruitment of more drought-tolerant species over less drought-tolerant species relative to baseline, and this change was greatest at mid-elevations. We also found that projected climate and wildfire decreased tree species richness across a large proportion of the study area and transitioned more area to a C source, which reduced landscape-level C sequestration potential. Our study, although a conservative estimate, suggests that by late century, forest community distributions may not change as intact units as predicted by biome-based modeling, but are likely to trend toward simplified community composition as communities gradually disaggregate and the least tolerant species are no longer able to establish. The potential exists for substantial community composition change and forest simplification beyond this century. © 2016 John Wiley & Sons Ltd.

Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

USGS Publications Warehouse

Harris, Theodore D.; Graham, Jennifer L.

2015-01-01

The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

A novel dynamical community detection algorithm based on weighting scheme

NASA Astrophysics Data System (ADS)

Li, Ju; Yu, Kai; Hu, Ke

2015-12-01

Network dynamics plays an important role in analyzing the correlation between the function properties and the topological structure. In this paper, we propose a novel dynamical iteration (DI) algorithm, which incorporates the iterative process of membership vector with weighting scheme, i.e. weighting W and tightness T. These new elements can be used to adjust the link strength and the node compactness for improving the speed and accuracy of community structure detection. To estimate the optimal stop time of iteration, we utilize a new stability measure which is defined as the Markov random walk auto-covariance. We do not need to specify the number of communities in advance. It naturally supports the overlapping communities by associating each node with a membership vector describing the node's involvement in each community. Theoretical analysis and experiments show that the algorithm can uncover communities effectively and efficiently.

The Upper Mississippi River floodscape: spatial patterns of flood inundation and associated plant community distributions

USGS Publications Warehouse

DeJager, Nathan R.; Rohweder, Jason J.; Yin, Yao; Hoy, Erin E.

2016-01-01

Questions How is the distribution of different plant communities associated with patterns of flood inundation across a large floodplain landscape? Location Thirty-eight thousand nine hundred and seventy hectare of floodplain, spanning 320 km of the Upper Mississippi River (UMR). Methods High-resolution elevation data (Lidar) and 30 yr of daily river stage data were integrated to produce a ‘floodscape’ map of growing season flood inundation duration. The distributions of 16 different remotely sensed plant communities were quantified along the gradient of flood duration. Results Models fitted to the cumulative frequency of occurrence of different vegetation types as a function of flood duration showed that most types exist along a continuum of flood-related occurrence. The diversity of community types was greatest at high elevations (0–10 d of flooding), where both upland and lowland community types were found, as well as at very low elevations (70–180 d of flooding), where a variety of lowland herbaceous communities were found. Intermediate elevations (20–60 d of flooding) tended to be dominated by floodplain forest and had the lowest diversity of community types. Conclusions Although variation in flood inundation is often considered to be the main driver of spatial patterns in floodplain plant communities, few studies have quantified flood–vegetation relationships at broad scales. Our results can be used to identify targets for restoration of historical hydrological regimes or better anticipate hydro-ecological effects of climate change at broad scales.

Architectural design influences the diversity and structure of the built environment microbiome

PubMed Central

Kembel, Steven W; Jones, Evan; Kline, Jeff; Northcutt, Dale; Stenson, Jason; Womack, Ann M; Bohannan, Brendan JM; Brown, G Z; Green, Jessica L

2012-01-01

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors. PMID:22278670

Analysis of Fragmentation During Dynamic Loading: Investigations in the Ries Impact Crater, Germany

NASA Astrophysics Data System (ADS)

Weimer, D.; Hergarten, S.; Kenkmann, T.

2015-09-01

We tested three methods to quantify fragmentation of rocks during dynamic loading and found a trend of decreasing fracture density with increasing distance from crater center. Fragmentation attenuation rates in the near- and far-field are different.

CARBON DYNAMICS OF THE CONSERVATION AND WETLAND RESERVE PROGRAMS

EPA Science Inventory

Data from the Conservation (CRP) and Wetland (WRP) Reserve Programs were analyzed to quantify the carbon (C) dynamics of associated cropland converted to grassland or forestland. Land-area enrollments were multiplied by grassland- and forestland-C densities to calculate C pools a...

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

A phylogenetic perspective on the individual species-area relationship in temperate and tropical tree communities.

PubMed

Yang, Jie; Swenson, Nathan G; Cao, Min; Chuyong, George B; Ewango, Corneille E N; Howe, Robert; Kenfack, David; Thomas, Duncan; Wolf, Amy; Lin, Luxiang

2013-01-01

Ecologists have historically used species-area relationships (SARs) as a tool to understand the spatial distribution of species. Recent work has extended SARs to focus on individual-level distributions to generate individual species area relationships (ISARs). The ISAR approach quantifies whether individuals of a species tend have more or less species richness surrounding them than expected by chance. By identifying richness 'accumulators' and 'repellers', respectively, the ISAR approach has been used to infer the relative importance of abiotic and biotic interactions and neutrality. A clear limitation of the SAR and ISAR approaches is that all species are treated as evolutionarily independent and that a large amount of work has now shown that local tree neighborhoods exhibit non-random phylogenetic structure given the species richness. Here, we use nine tropical and temperate forest dynamics plots to ask: (i) do ISARs change predictably across latitude?; (ii) is the phylogenetic diversity in the neighborhood of species accumulators and repellers higher or lower than that expected given the observed species richness?; and (iii) do species accumulators, repellers distributed non-randomly on the community phylogenetic tree? The results indicate no clear trend in ISARs from the temperate zone to the tropics and that the phylogenetic diversity surrounding the individuals of species is generally only non-random on very local scales. Interestingly the distribution of species accumulators and repellers was non-random on the community phylogenies suggesting the presence of phylogenetic signal in the ISAR across latitude.

A System Dynamics Approach to Understanding Cost and Revenue Interactions in the Community College Financial System.

ERIC Educational Resources Information Center

Howard, James E.

After identifying the components of a community college financial system as enrollment, costs, revenues and tuition, this paper addresses the need for a system dynamics analysis of a California community college district. This systems approach would assess the possible effects of alternative policies on the characteristic behavior modes of the…

Economic Impact of Loyola University Chicago. Fiscal Year 1994.

ERIC Educational Resources Information Center

Loyola Univ., Chicago, IL.

This report describes and quantifies the magnitude of Loyola University's operations and how they affect the economy of Chicago (Illinois), analyzing the impact on the local community and on various segments of the metropolitan area. It first describes the university's four campuses, the university's role in the community, and the size of its…

Inequality in Preschool Quality? Community-Level Disparities in Access to High-Quality Learning Environments

ERIC Educational Resources Information Center

Bassok, Daphna; Galdo, Eva

2016-01-01

In recent years, unequal access to high-quality preschool has emerged as a growing public policy concern. Because of data limitations, it is notoriously difficult to measure disparities in access to early learning opportunities across communities and particularly challenging to quantify gaps in access to "high-quality" programs. Research…

Litter chemistry, community shift, and non-additive effects drive litter decomposition changes following invasion by a generalist pathogen

Treesearch

Richard C. Cobb; David M. Rizzo

2016-01-01

Forest pathogens have strong potential to shape ecosystem function by altering litterfall, microclimate, and changing community structure. We quantified changes in litter decomposition from a set of distinct diseases caused by Phytophthora ramorum, an exotic generalist pathogen. Phytophthora ramorum causes leaf blight and...

Assessing wildland fire risk transmission to communities in northern Spain

Treesearch

Fermín J. Alcasena; Michele Salis; Alan A. Ager; Rafael Castell; Cristina Vega-García

2017-01-01

We assessed potential economic losses and transmission to residential houses from wildland fires in a rural area of central Navarra (Spain). Expected losses were quantified at the individual structure level (n = 306) in 14 rural communities by combining fire model predictions of burn probability and fire intensity with susceptibility functions derived from expert...

The Use of Field and Mesocosm Experiments to Quantify Effects of Physical and Chemical Stressors in Mining-Contaminated Streams.

PubMed

Cadmus, Pete; Clements, William H; Williamson, Jacob L; Ranville, James F; Meyer, Joseph S; Gutiérrez Ginés, María Jesús

2016-07-19

Identifying causal relationships between acid mine drainage (AMD) and ecological responses in the field is challenging. In addition to the direct toxicological effects of elevated metals and reduced pH, mining activities influence aquatic organisms indirectly through physical alterations of habitat. The primary goal of this research was to quantify the relative importance of physical (metal-oxide deposition) and chemical (elevated metal concentrations) stressors on benthic macroinvertebrate communities. Mesocosm experiments conducted with natural assemblages of benthic macroinvertebrates established concentration-response relationships between metals and community structure. Field experiments quantified effects of metal-oxide contaminated substrate and showed significant differences in sensitivity among taxa. To predict the recovery of dominant taxa in the field, we integrated our measures of metal tolerance and substrate tolerance with estimates of drift propensity obtained from the literature. Our estimates of recovery were consistent with patterns observed at downstream recovery sites in the NFCC, which were dominated by caddisflies and baetid mayflies. We conclude that mesocosm and small-scale field experiments, particularly those conducted with natural communities, provide an ecologically realistic complement to laboratory toxicity tests. These experiments also control for the confounding variables associated with field-based approaches, thereby supporting causal relationships between AMD stressors and responses.

Hydrodynamic and Longitudinal Impedance Analysis of Cerebrospinal Fluid Dynamics at the Craniovertebral Junction in Type I Chiari Malformation

PubMed Central

Martin, Bryn A.; Kalata, Wojciech; Shaffer, Nicholas; Fischer, Paul; Luciano, Mark; Loth, Francis

2013-01-01

Elevated or reduced velocity of cerebrospinal fluid (CSF) at the craniovertebral junction (CVJ) has been associated with type I Chiari malformation (CMI). Thus, quantification of hydrodynamic parameters that describe the CSF dynamics could help assess disease severity and surgical outcome. In this study, we describe the methodology to quantify CSF hydrodynamic parameters near the CVJ and upper cervical spine utilizing subject-specific computational fluid dynamics (CFD) simulations based on in vivo MRI measurements of flow and geometry. Hydrodynamic parameters were computed for a healthy subject and two CMI patients both pre- and post-decompression surgery to determine the differences between cases. For the first time, we present the methods to quantify longitudinal impedance (LI) to CSF motion, a subject-specific hydrodynamic parameter that may have value to help quantify the CSF flow blockage severity in CMI. In addition, the following hydrodynamic parameters were quantified for each case: maximum velocity in systole and diastole, Reynolds and Womersley number, and peak pressure drop during the CSF cardiac flow cycle. The following geometric parameters were quantified: cross-sectional area and hydraulic diameter of the spinal subarachnoid space (SAS). The mean values of the geometric parameters increased post-surgically for the CMI models, but remained smaller than the healthy volunteer. All hydrodynamic parameters, except pressure drop, decreased post-surgically for the CMI patients, but remained greater than in the healthy case. Peak pressure drop alterations were mixed. To our knowledge this study represents the first subject-specific CFD simulation of CMI decompression surgery and quantification of LI in the CSF space. Further study in a larger patient and control group is needed to determine if the presented geometric and/or hydrodynamic parameters are helpful for surgical planning. PMID:24130704

Symbiont dynamics during ecosystem succession: co-occurring plant and arbuscular mycorrhizal fungal communities.

PubMed

García de León, David; Moora, Mari; Öpik, Maarja; Neuenkamp, Lena; Gerz, Maret; Jairus, Teele; Vasar, Martti; Bueno, C Guillermo; Davison, John; Zobel, Martin

2016-07-01

Although mycorrhizas are expected to play a key role in community assembly during ecological succession, little is known about the dynamics of the symbiotic partners in natural systems. For instance, it is unclear how efficiently plants and arbuscular mycorrhizal (AM) fungi disperse into early successional ecosystems, and which, if either, symbiotic partner drives successional dynamics. This study describes the dynamics of plant and AM fungal communities, assesses correlation in the composition of plant and AM fungal communities and compares dispersal limitation of plants and AM fungi during succession. We studied gravel pits 20 and 50 years post abandonment and undisturbed grasslands in Western Estonia. The composition of plant and AM fungal communities was strongly correlated, and the strength of the correlation remained unchanged as succession progressed, indicating a stable dependence among mycorrhizal plants and AM fungi. A relatively high proportion of the AM fungal taxon pool was present in early successional sites, in comparison with the respective fraction of plants. These results suggest that AM fungi arrived faster than plants and may thus drive vegetation dynamics along secondary vegetation succession. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Unravel the submesoscale dynamics of the phytoplanktonic community in the NW Mediterranean Sea by in situ observations: the 2015 OSCAHR cruise

NASA Astrophysics Data System (ADS)

Marrec, Pierre; Doglioli, Andrea M.; Grégori, Gérald; Della Penna, Alice; Wagener, Thibaut; Rougier, Gille; Bhairy, Nagib; Dugenne, Mathilde; Lahbib, Soumaya; Thyssen, Melilotus

2017-04-01

Submesoscale phenomena have been recently recognized as a key factor in physical-biological-biogeochemical interactions, even if it remains unclear how these processes affect the global state of the ocean. Significant large-scale impacts of submesoscale structures on primary production and influence on the phytoplankton community structure and diversity have also been reported. In the past decade submesoscale dynamics have been predominately studied through the analysis of numerical simulations. Observing the coupled physical and biogeochemical variability at this scale remains challenging due to the ephemeral nature of submesoscale structures. The in-situ study of such structures necessitates multidisciplinary approaches involving in situ observations, remote sensing and modeling. Last progresses in biogeochemical sensor development and advanced methodology including Lagrangian real-time adaptative strategies represent outstanding opportunities. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted thanks to a multidisciplinary approach in order to improve the understanding of submesoscale processes. An ephemeral submesoscale structure was first identified in the Ligurian Sea in fall 2015 using both satellite and numerical modeling data before the campaign. Afterwards, advanced observing systems for the physical, biological and biogeochemical characterization of the sea surface layer at a high spatial and temporal frequency were deployed during a 10-days cruise. A MVP (Moving Vessel Profiler) was used to obtain high resolution CTD profiles associated to a new pumping system with 1-m vertical resolution. Moreover, along the ship track, in addition to the standard measurements of seawater surface samples (Chl-a, nutrients, O2, SST, SSS …), we deployed an automated flow cytometer for near real-time characterization of phytoplankton functional groups (from micro-phytoplankton down to cyanobacteria). The observed submesoscale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Six phytoplankton groups were identified across the structure with an unprecedented spatial and temporal resolution. According to our observations, we could quantify the influence of the fast established physical structure on the spatial distribution of the phytoplankton functional groups, giving coherence to the observed community structuration. Moreover, the high resolution of our observations allows us to estimate the growth rate of the main phytoplankton groups. Our innovative adaptative strategy with a multidisciplinary and transversal approach provides a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.

Coupling of WRF and Building-resolved CFD Simulations for Greenhouse Gas Transport and Dispersion

NASA Astrophysics Data System (ADS)

Prasad, K.; Hu, H.; McDermott, R.; Lopez-Coto, I.; Davis, K. J.; Whetstone, J. R.; Lauvaux, T.

2014-12-01

The Indianapolis Flux Experiment (INFLUX) aims to use a top-down inversion methodology to quantify sources of Greenhouse Gas (GHG) emissions over an urban domain with high spatial and temporal resolution. Atmospheric transport of tracer gases from an emission source to a tower mounted receptor are usually conducted using the Weather Research and Forecasting (WRF) model. WRF is used extensively in the atmospheric community to simulate mesoscale atmospheric transport. For such simulations, WRF employs a parameterized turbulence model and does not resolve the fine scale dynamics that are generated by the flow around buildings and communities that are part of a large city. Since the model domain includes the city of Indianapolis, much of the flow of interest is over an urban topography. The NIST Fire Dynamics Simulator (FDS) is a computational fluid dynamics model to perform large eddy simulations of flow around buildings, but it has not been nested within a larger-scale atmospheric transport model such as WRF. FDS has the potential to evaluate the impact of complex urban topography on near-field dispersion and mixing that cannot be simulated with a mesoscale atmospheric model, and which may be important to determining urban GHG emissions using atmospheric measurements. A methodology has been developed to run FDS as a sub-grid scale model within a WRF simulation. The coupling is based on nudging the FDS flow field towards the one computed by WRF, and is currently limited to one way coupling performed in an off-line mode. Using the coupled WRF / FDS model, NIST will investigate the effects of the urban canopy at horizontal resolutions of 2-10 m. The coupled WRF-FDS simulations will be used to calculate the dispersion of tracer gases in an urban domain and to evaluate the upwind areas that contribute to tower observations, referred to in the inversion community as influence functions. Predicted mixing ratios will be compared with tower measurements and WRF simulations, and FDS influence functions will be compared with those generated from WRF and the Lagrangian Particle Dispersion Model. Results of this study will provide guidance regarding the importance of explicit simulations of urban atmospheric turbulence in obtaining accurate estimates of greenhouse gas emissions.

A bacterial pioneer produces cellulase complexes that persist through community succession

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession

DOE PAGES

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; ...

2017-11-06

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession.

PubMed

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; Denzel, Evelyn; Hiras, Jennifer; Gabriel, Raphael; Bäcker, Nora; Chan, Leanne Jade G; Eichorst, Stephanie A; Frey, Dario; Chen, Qiushi; Azadi, Parastoo; Adams, Paul D; Pray, Todd R; Tanjore, Deepti; Petzold, Christopher J; Gladden, John M; Simmons, Blake A; Singer, Steven W

2018-01-01

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.

[Fungal community structure in phase II composting of Volvariella volvacea].

PubMed

Chen, Changqing; Li, Tong; Jiang, Yun; Li, Yu

2014-12-04

To understand the fungal community succession during the phase II of Volvariella volvacea compost and clarify the predominant fungi in different fermentation stages, to monitor the dynamic compost at the molecular level accurately and quickly, and reveal the mechanism. The 18S rDNA-denaturing gradient gel electrophoresis (DGGE) and sequencing methods were used to analyze the fungal community structure during the course of compost. The DGGE profile shows that there were differences in the diversity of fungal community with the fermentation progress. The diversity was higher in the stages of high temperature. And the dynamic changes of predominant community and relative intensity was observed. Among the 20 predominant clone strains, 9 were unknown eukaryote and fungi, the others were Eurotiales, Aspergillus sp., Melanocarpus albomyces, Colletotrichum sp., Rhizomucor sp., Verticillium sp., Penicillium commune, Microascus trigonosporus and Trichosporon lactis. The 14 clone strains were detected in the stages of high and durative temperature. The fungal community structure and predominant community have taken dynamic succession during the phase II of Volvariella volvacea compost.

Modeling the spread of tuberculosis in semiclosed communities.

PubMed

Herrera, Mauricio; Bosch, Paul; Nájera, Manuel; Aguilera, Ximena

2013-01-01

We address the problem of long-term dynamics of tuberculosis (TB) and latent tuberculosis (LTB) in semiclosed communities. These communities are congregate settings with the potential for sustained daily contact for weeks, months, and even years between their members. Basic examples of these communities are prisons, but certain urban/rural communities, some schools, among others could possibly fit well into this definition. These communities present a sort of ideal conditions for TB spread. In order to describe key relevant dynamics of the disease in these communities, we consider a five compartments SEIR model with five possible routes toward TB infection: primary infection after a contact with infected and infectious individuals (fast TB), endogenous reactivation after a period of latency (slow TB), relapse by natural causes after a cure, exogenous reinfection of latently infected, and exogenous reinfection of recovered individuals. We discuss the possible existence of multiple endemic equilibrium states and the role that the two types of exogenous reinfections in the long-term dynamics of the disease could play.

Strong seasonality and interannual recurrence in marine myovirus communities.

PubMed

Pagarete, A; Chow, C-E T; Johannessen, T; Fuhrman, J A; Thingstad, T F; Sandaa, R A

2013-10-01

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

Modeling the Spread of Tuberculosis in Semiclosed Communities

PubMed Central

Herrera, Mauricio; Bosch, Paul; Nájera, Manuel; Aguilera, Ximena

2013-01-01

We address the problem of long-term dynamics of tuberculosis (TB) and latent tuberculosis (LTB) in semiclosed communities. These communities are congregate settings with the potential for sustained daily contact for weeks, months, and even years between their members. Basic examples of these communities are prisons, but certain urban/rural communities, some schools, among others could possibly fit well into this definition. These communities present a sort of ideal conditions for TB spread. In order to describe key relevant dynamics of the disease in these communities, we consider a five compartments SEIR model with five possible routes toward TB infection: primary infection after a contact with infected and infectious individuals (fast TB), endogenous reactivation after a period of latency (slow TB), relapse by natural causes after a cure, exogenous reinfection of latently infected, and exogenous reinfection of recovered individuals. We discuss the possible existence of multiple endemic equilibrium states and the role that the two types of exogenous reinfections in the long-term dynamics of the disease could play. PMID:23762194

Using nonlinear methods to quantify changes in infant limb movements and vocalizations.

PubMed

Abney, Drew H; Warlaumont, Anne S; Haussman, Anna; Ross, Jessica M; Wallot, Sebastian

2014-01-01

The pairing of dynamical systems theory and complexity science brings novel concepts and methods to the study of infant motor development. Accordingly, this longitudinal case study presents a new approach to characterizing the dynamics of infant limb and vocalization behaviors. A single infant's vocalizations and limb movements were recorded from 51-days to 305-days of age. On each recording day, accelerometers were placed on all four of the infant's limbs and an audio recorder was worn on the child's chest. Using nonlinear time series analysis methods, such as recurrence quantification analysis and Allan factor, we quantified changes in the stability and multiscale properties of the infant's behaviors across age as well as how these dynamics relate across modalities and effectors. We observed that particular changes in these dynamics preceded or coincided with the onset of various developmental milestones. For example, the largest changes in vocalization dynamics preceded the onset of canonical babbling. The results show that nonlinear analyses can help to understand the functional co-development of different aspects of infant behavior.

Risk assessment by dynamic representation of vulnerability, exploitation, and impact

NASA Astrophysics Data System (ADS)

Cam, Hasan

2015-05-01

Assessing and quantifying cyber risk accurately in real-time is essential to providing security and mission assurance in any system and network. This paper presents a modeling and dynamic analysis approach to assessing cyber risk of a network in real-time by representing dynamically its vulnerabilities, exploitations, and impact using integrated Bayesian network and Markov models. Given the set of vulnerabilities detected by a vulnerability scanner in a network, this paper addresses how its risk can be assessed by estimating in real-time the exploit likelihood and impact of vulnerability exploitation on the network, based on real-time observations and measurements over the network. The dynamic representation of the network in terms of its vulnerabilities, sensor measurements, and observations is constructed dynamically using the integrated Bayesian network and Markov models. The transition rates of outgoing and incoming links of states in hidden Markov models are used in determining exploit likelihood and impact of attacks, whereas emission rates help quantify the attack states of vulnerabilities. Simulation results show the quantification and evolving risk scores over time for individual and aggregated vulnerabilities of a network.

Using nonlinear methods to quantify changes in infant limb movements and vocalizations

PubMed Central

Abney, Drew H.; Warlaumont, Anne S.; Haussman, Anna; Ross, Jessica M.; Wallot, Sebastian

2014-01-01

The pairing of dynamical systems theory and complexity science brings novel concepts and methods to the study of infant motor development. Accordingly, this longitudinal case study presents a new approach to characterizing the dynamics of infant limb and vocalization behaviors. A single infant's vocalizations and limb movements were recorded from 51-days to 305-days of age. On each recording day, accelerometers were placed on all four of the infant's limbs and an audio recorder was worn on the child's chest. Using nonlinear time series analysis methods, such as recurrence quantification analysis and Allan factor, we quantified changes in the stability and multiscale properties of the infant's behaviors across age as well as how these dynamics relate across modalities and effectors. We observed that particular changes in these dynamics preceded or coincided with the onset of various developmental milestones. For example, the largest changes in vocalization dynamics preceded the onset of canonical babbling. The results show that nonlinear analyses can help to understand the functional co-development of different aspects of infant behavior. PMID:25161629

The Importance of Hydrological Signature and Its Recurring Dynamics

NASA Astrophysics Data System (ADS)

Wendi, D.; Marwan, N.; Merz, B.

2017-12-01

Temporal changes in hydrology are known to be challenging to detect and attribute due to multiple drivers that include complex processes that are non-stationary and highly variable. These drivers, such as human-induced climate change, natural climate variability, implementation of flood defense, river training, and land use change, could impact variably on space-time scales and influence or mask each other. Besides, data depicting these drivers are often not available. One conventional approach of analyzing the change is based on discrete points of magnitude (e.g. the frequency of recurring extreme discharge) and often linearly quantified and hence do not reveal the potential change in the hydrological process. Moreover, discharge series are often subject to measurement errors, such as rating curve error especially in the case of flood peaks where observation are derived through extrapolation. In this study, the system dynamics inferred from the hydrological signature (i.e. the shape of hydrograph) is being emphasized. One example is to see if certain flood dynamics (instead of flood peak) in the recent years, had also occurred in the past (or rather extraordinary), and if so what is its recurring rate and if there had been a shift in its occurrence in time or seasonality (e.g. earlier snow melt dominant flood). The utilization of hydrological signature here is extended beyond those of classical hydrology such as base flow index, recession and rising limb slope, and time to peak. It is in fact all these characteristics combined i.e. from the start until the end of the hydrograph. Recurrence plot is used as a method to quantify and visualize the recurring hydrological signature through its phase space trajectories, and usually in the order of dimension above 2. Such phase space trajectories are constructed by embedding the time series into a series of variables (i.e. number of dimension) corresponding to the time delay. Since the method is rather novel in hydrological community, the study presents an overview and a guideline to the method with an application example on analyzing the change of hydrological signature and discussion of its benefits and flaws.

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil.

PubMed

Ke, Xiubin; Angel, Roey; Lu, Yahai; Conrad, Ralf

2013-08-01

The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differences in the distribution of bacterial and archaeal ammonia oxidizers, and of Nitrobacter-like and Nitrospira-like nitrite oxidizers were found in the different compartments of planted paddy soil indicating niche differentiation. In bulk soil, ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) were at low abundance and displayed no activity, but in surface soil their activity and abundance was high. Nitrite oxidation in surface soil was dominated by Nitrospira spp. By contrast, ammonia-oxidizing Thaumarchaeota and Nitrobacter spp. seemed to dominate nitrification in rhizospheric soil and on rice roots. In contrast to soil compartment, the level of N fertilization and the time point of sampling had only little effect on the abundance, composition and activity of the nitrifying communities. The results of our study show that in rice fields population dynamics and activity of nitrifiers is mainly differentiated by the soil compartments rather than by nitrogen amendment or season. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Temporal carbon dynamics of forests in Washington, US: implications for ecological theory and carbon management

Treesearch

Crystal L. Raymond; Donald McKenzie

2014-01-01

We quantified carbon (C) dynamics of forests in Washington, US using theoretical models of C dynamics as a function of forest age. We fit empirical models to chronosequences of forest inventory data at two scales: a coarse-scale ecosystem classification (ecosections) and forest types (potential vegetation) within ecosections. We hypothesized that analysis at the finer...

Introducing Co-Activation Pattern Metrics to Quantify Spontaneous Brain Network Dynamics

PubMed Central

Chen, Jingyuan E.; Chang, Catie; Greicius, Michael D.; Glover, Gary H.

2015-01-01

Recently, fMRI researchers have begun to realize that the brain's intrinsic network patterns may undergo substantial changes during a single resting state (RS) scan. However, despite the growing interest in brain dynamics, metrics that can quantify the variability of network patterns are still quite limited. Here, we first introduce various quantification metrics based on the extension of co-activation pattern (CAP) analysis, a recently proposed point-process analysis that tracks state alternations at each individual time frame and relies on very few assumptions; then apply these proposed metrics to quantify changes of brain dynamics during a sustained 2-back working memory (WM) task compared to rest. We focus on the functional connectivity of two prominent RS networks, the default-mode network (DMN) and executive control network (ECN). We first demonstrate less variability of global Pearson correlations with respect to the two chosen networks using a sliding-window approach during WM task compared to rest; then we show that the macroscopic decrease in variations in correlations during a WM task is also well characterized by the combined effect of a reduced number of dominant CAPs, increased spatial consistency across CAPs, and increased fractional contributions of a few dominant CAPs. These CAP metrics may provide alternative and more straightforward quantitative means of characterizing brain network dynamics than time-windowed correlation analyses. PMID:25662866

Modular interdependency in complex dynamical systems.

PubMed

Watson, Richard A; Pollack, Jordan B

2005-01-01

Herbert A. Simon's characterization of modularity in dynamical systems describes subsystems as having dynamics that are approximately independent of those of other subsystems (in the short term). This fits with the general intuition that modules must, by definition, be approximately independent. In the evolution of complex systems, such modularity may enable subsystems to be modified and adapted independently of other subsystems, whereas in a nonmodular system, modifications to one part of the system may result in deleterious side effects elsewhere in the system. But this notion of modularity and its effect on evolvability is not well quantified and is rather simplistic. In particular, modularity need not imply that intermodule dependences are weak or unimportant. In dynamical systems this is acknowledged by Simon's suggestion that, in the long term, the dynamical behaviors of subsystems do interact with one another, albeit in an "aggregate" manner--but this kind of intermodule interaction is omitted in models of modularity for evolvability. In this brief discussion we seek to unify notions of modularity in dynamical systems with notions of how modularity affects evolvability. This leads to a quantifiable measure of modularity and a different understanding of its effect on evolvability.

Land-Use History and Contemporary Management Inform an Ecological Reference Model for Longleaf Pine Woodland Understory Plant Communities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brudvig, Lars A.; Orrock, John L.; Damschen, Ellen I.

Ecological restoration is frequently guided by reference conditions describing a successfully restored ecosystem; however, the causes and magnitude of ecosystem degradation vary, making simple knowledge of reference conditions insufficient for prioritizing and guiding restoration. Ecological reference models provide further guidance by quantifying reference conditions, as well as conditions at degraded states that deviate from reference conditions. Many reference models remain qualitative, however, limiting their utility. We quantified and evaluated a reference model for southeastern U.S. longleaf pine woodland understory plant communities. We used regression trees to classify 232 longleaf pine woodland sites at three locations along the Atlantic coastal plainmore » based on relationships between understory plant community composition, soils lol(which broadly structure these communities), and factors associated with understory degradation, including fire frequency, agricultural history, and tree basal area. To understand the spatial generality of this model, we classified all sites together. and for each of three study locations separately. Both the regional and location-specific models produced quantifiable degradation gradients–i.e., progressive deviation from conditions at 38 reference sites, based on understory species composition, diversity and total cover, litter depth, and other attributes. Regionally, fire suppression was the most important degrading factor, followed by agricultural history, but at individual locations, agricultural history or tree basal area was most important. At one location, the influence of a degrading factor depended on soil attributes. We suggest that our regional model can help prioritize longleaf pine woodland restoration across our study region; however, due to substantial landscape-to-landscape variation, local management decisions should take into account additional factors (e.g., soil attributes). Our study demonstrates the utility of quantifying degraded states and provides a series of hypotheses for future experimental restoration work. More broadly, our work provides a framework for developing and evaluating reference models that incorporate multiple, interactive anthropogenic drivers of ecosystem degradation.« less

A Lagrangian cylindrical coordinate system for characterizing dynamic surface geometry of tubular anatomic structures.

PubMed

Lundh, Torbjörn; Suh, Ga-Young; DiGiacomo, Phillip; Cheng, Christopher

2018-03-03

Vascular morphology characterization is useful for disease diagnosis, risk stratification, treatment planning, and prediction of treatment durability. To quantify the dynamic surface geometry of tubular-shaped anatomic structures, we propose a simple, rigorous Lagrangian cylindrical coordinate system to monitor well-defined surface points. Specifically, the proposed system enables quantification of surface curvature and cross-sectional eccentricity. Using idealized software phantom examples, we validate the method's ability to accurately quantify longitudinal and circumferential surface curvature, as well as eccentricity and orientation of eccentricity. We then apply the method to several medical imaging data sets of human vascular structures to exemplify the utility of this coordinate system for analyzing morphology and dynamic geometric changes in blood vessels throughout the body. Graphical abstract Pointwise longitudinal curvature of a thoracic aortic endograft surface for systole and diastole, with their absolute difference.

Detectability Thresholds and Optimal Algorithms for Community Structure in Dynamic Networks

NASA Astrophysics Data System (ADS)

Ghasemian, Amir; Zhang, Pan; Clauset, Aaron; Moore, Cristopher; Peel, Leto

2016-07-01

The detection of communities within a dynamic network is a common means for obtaining a coarse-grained view of a complex system and for investigating its underlying processes. While a number of methods have been proposed in the machine learning and physics literature, we lack a theoretical analysis of their strengths and weaknesses, or of the ultimate limits on when communities can be detected. Here, we study the fundamental limits of detecting community structure in dynamic networks. Specifically, we analyze the limits of detectability for a dynamic stochastic block model where nodes change their community memberships over time, but where edges are generated independently at each time step. Using the cavity method, we derive a precise detectability threshold as a function of the rate of change and the strength of the communities. Below this sharp threshold, we claim that no efficient algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this threshold. The first uses belief propagation, which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the belief propagation equations. These results extend our understanding of the limits of community detection in an important direction, and introduce new mathematical tools for similar extensions to networks with other types of auxiliary information.

Reserve size and fragmentation alter community assembly, diversity, and dynamics.

PubMed

Lasky, Jesse R; Keitt, Timothy H

2013-11-01

Researchers have disputed whether a single large habitat reserve will support more species than many small reserves. However, relatively little is known from a theoretical perspective about how reserve size affects competitive communities structured by spatial abiotic gradients. We investigate how reserve size affects theoretical communities whose assembly is governed by dispersal limitation, abiotic niche differentiation, and source-sink dynamics. Simulations were conducted with varying scales of dispersal across landscapes with variable environmental spatial autocorrelation. Landscapes were inhabited by simulated trees with seedling and adult stages. For a fixed total area in reserves, we found that small reserve systems increased the distance between environments dominated by different species, diminishing the effects of source-sink dynamics. As reserve size decreased, environmental limitations to community assembly became stronger, α species richness decreased, and γ richness increased. When dispersal occurred across short distances, a large reserve strategy caused greater stochastic community variation, greater α richness, and lower γ richness than in small reserve systems. We found that reserve size variation trades off between preserving different aspects of natural communities, including α diversity versus γ diversity. Optimal reserve size will depend on the importance of source-sink dynamics and the value placed on different characteristics of natural communities. Anthropogenic changes to the size and separation of remnant habitats can have far-reaching effects on community structure and assembly.

STABLE ISOTOPES AS INDICATORS OF SOIL WATER DYNAMICS IN WATERSHEDS

EPA Science Inventory

Stream water quality and quantity depend on discharge rates of water and nutrients from soils. However, soil-water storage is very dynamic and strongly influenced by plants. We analyzed stable isotopes of oxygen and hydrogen to quantify spatial and temporal changes in evaporati...

Quantifying the role of forested lands in providing surface drinking water supply for Puerto Rico

Treesearch

Erika Cohen; Ge Sun; Liangxia Zhang; Peter Caldwell; Suzanne Krieger

2017-01-01

The Forest Service, U.S. Department of Agriculture published a General Technical Report (GTR-SRS-197) in 2014 that quantified the role that water originating on National Forest System lands contributed to the drinking water supply and determined what population and communities were being served in the 13 Southern States of Region 8 of the Forest Service. The...

Moving Uphill: Microbial Facilitation at the Leading Edge of Plant Species Distributional Shifts

NASA Astrophysics Data System (ADS)

Suding, K.; Farrer, E.; Spasojevic, M.; Porazinska, D.; Bueno de Mesquita, C.; Schmidt, S. K.

2016-12-01

Climate change is expected to influence species distributions and reshuffle patterns of biodiversity. A key challenge to our understanding of these effects is that biotic interactions - new species to compete with, new stressors that increase dependence on facilitation, new prey or predators - will likely affect the ability of species to track climate at the leading edges of their distributional range. While it is well established that soil biota strongly influence plant abundance and diversity, it has been difficult to quantify the key belowground dynamics. This presentation will investigate the influence of one key biotic interaction, between plants and soil microbiota, on the ability of plant species to track climate change and expand their range uphill in a high montane system in the Front Range of Colorado. High-resolution photography from 1972 and 2008 indicate colonization of tundra vegetation in formerly unvegetated areas. Observational work on the distributions patterns of both plants and soil microbiota (bacteria, fungi and nematodes) in a spatially-explicit grid at the upper edge of plant distributions indicate strong, mostly positive, associations between plant species and soil taxa. Abiotic factors, while important, consistently underpredicted the occurrence of plant species and, in nine of the 12 most common tundra plants, co-occurring microbial taxa were important predictors of plant occurrence. Comparison of plant and microbial distributional patterns in 2007 and 2015 indicate the influence of microbial community composition on assembly and beta-diversity of the plant community over time. Plant colonization patterns in this region previously devoid of vegetation will likely influence carbon, nitrogen and phosphorus dynamics, with downstream consequences on nutrient limitation and phytoplankton composition in alpine lakes.

Annual variation in seedfall, postdispersal predation, and recruitment of a neotropical tree

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schupp, E.W.

1990-04-01

Knowledge of the dynamics of seed production and seedling recruitment of individual tree species is crucial for a complete understanding of tropical forest dynamics, yet multiyear studies on the seed and young seedling stages of tropical trees are virtually nonexistent. In a 4-yr study of the understory tree Faramea occidentalis on Barro Colorado Island, Panama, the author quantified natural levels of viable seedfall, seedling emergence, and seedling establishment, and experimentally estimated postdispersal seed predation. The levels of viable seedfall, seed predation, seedling emergence, early seedling survival, and seedling recruitment all differed significantly among years. The proportion of fallen seeds destroyedmore » by predators before germination was not related to the quantity of F. occidentalis seedfall. Within a year, however, F. occidentalis seed predation appeared to be influenced by community-wide seedfall, with high predation rates during times of low seed abundance and very low predation during the late dry season peak in seedfall by the community. Most of the annual variation in recruitment can be explained by the combination of seedfall and seed predation; in 3 of the 4 yr seedling emergence could be predicted from a knowledge of viable seedfall and the probability of a seed surviving until the peak of germination. The 4th yr, however, demonstrated that environmental conditions provide a sporadic, though important, limitation to recruitment. In comparison to many tree species, early seedling survival was relatively high, as was the ratio of seedlings recruited per seed falling. The highly successful recruitment of F. occidentalis is associated with a high population density of both saplings and adults in the study area.« less

Exposure-driven macroalgal phase shift following catastrophic disturbance on coral reefs

NASA Astrophysics Data System (ADS)

Roff, George; Chollett, Iliana; Doropoulos, Christopher; Golbuu, Yimnang; Steneck, Robert S.; Isechal, Adelle L.; van Woesik, Robert; Mumby, Peter J.

2015-09-01

Environmental conditions play an important role in post-disturbance dynamics of ecosystems by modulating recovery of surviving communities and influencing patterns of succession. Here, we document the effects of wave exposure following a catastrophic disturbance on coral reefs in driving a phase shift to macroalgal dominance. In December 2012, a Category 5 super typhoon (`Typhoon Bopha') passed 50 km to the south of Palau (Micronesia), causing a major loss of reef corals. Immediately post-disturbance, a rapid and extensive phase shift of the macroalgae Liagora sp. (Rhodophyta) was observed at sites exposed to chronic wave exposure. To quantify the influence of biotic and abiotic drivers in modulating the extent of post-disturbance Liagora blooms, we compared benthic substrates and herbivore assemblages at sites surveyed pre- and post-disturbance across a gradient of wave exposure. Relative changes in herbivore biomass and coral cover before and after disturbance did not significantly predict the extent of Liagora cover, indicating that changes in herbivore biomass or reductions in grazing pressure were not directly responsible for driving the Liagora blooms. By contrast, the degree of wave exposure experienced at sites post-disturbance explained >90 % of model variance ( p < 0.001, R 2 = 0.69), in that Liagora was absent at low exposure sites, while most extensive blooms were observed at highly exposed sites. At regional scales, spatial maps of wave exposure accurately predicted the presence of Liagora at impacted sites throughout the Palau archipelago (>150 km distance), highlighting the predictive capacity of wave exposure as an explanatory variable and the deterministic nature of post-disturbance macroalgal blooms. Understanding how physical conditions modulate recovery of ecosystems after disturbance allows insight into post-disturbance dynamics and succession of communities, ultimately allowing management strategies to prioritise restoration efforts in regions that are most effective.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

Seasonal sediment dynamics shape temperate bedrock reef communities

USGS Publications Warehouse

Figurski, Jared D.; Freiwald, Jan; Lonhart, Steve I.; Storlazzi, Curt

2016-01-01

Mobilized seafloor sediment can impact benthic reef communities through burial, scour, and turbidity. These processes are ubiquitous in coastal oceans and, through their influence on the survival, fitness, and interactions of species, can alter the structure and function of benthic communities. In northern Monterey Bay, California, USA, as much as 30% of the seafloor is buried or exposed seasonally, making this an ideal location to test how subtidal temperate rocky reef communities vary in the presence and absence of chronic sediment-based disturbances. Designated dynamic plots were naturally inundated by sediment in summer (50 to 100% cover) and swept clean in winter, whereas designated stable plots remained free of sediment during our study. Multivariate analyses indicated significant differences in the structure of sessile and mobile communities between dynamic and stable reef habitats. For sessile species, community structure in disturbed plots was less variable in space and time than in stable plots due to the maintenance of an early successional state. In contrast, community structure of mobile species varied more in disturbed plots than in stable plots, reflecting how mobile species distribute in response to sediment dynamics. Some species were found only in these disturbed areas, suggesting that the spatial mosaic of disturbance could increase regional diversity. We discuss how the relative ability of species to tolerate disturbance at different life history stages and their ability to colonize habitat translate into community-level differences among habitats, and how this response varies between mobile and sessile communities.

Quantifying carbon stores and decomposition in dead wood: A review

Treesearch

Matthew B. Russell; Shawn Fraver; Tuomas Aakala; Jeffrey H. Gove; Christopher W. Woodall; Anthony W. D’Amato; Mark J. Ducey

2015-01-01

The amount and dynamics of forest dead wood (both standing and downed) has been quantified by a variety of approaches throughout the forest science and ecology literature. Differences in the sampling and quantification of dead wood can lead to differences in our understanding of forests and their role in the sequestration and emissions of CO2, as...

Classifying and quantifying basins of attraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sprott, J. C.; Xiong, Anda

2015-08-15

A scheme is proposed to classify the basins for attractors of dynamical systems in arbitrary dimensions. There are four basic classes depending on their size and extent, and each class can be further quantified to facilitate comparisons. The calculation uses a Monte Carlo method and is applied to numerous common dissipative chaotic maps and flows in various dimensions.

Cyanobacterial blooms in stratified and destratified eutrophic reservoirs in semi-arid region of Brazil.

PubMed

Dantas, Enio W; Moura, Ariadne N; Bittencourt-Oliveira, Maria do Carmo

2011-12-01

This study investigated the dynamics of cyanobacteria in two deep, eutrophic reservoirs in a semi-arid region of Brazil during periods of stratification and destratification. Four collections were carried out at each reservoir at two depths at three-month intervals. The following abiotic variables were analyzed: water temperature, dissolved oxygen, pH, turbidity, water transparency, total phosphorus, total dissolved phosphorus, orthophosphate and total nitrogen. Phytoplankton density was quantified for the determination of the biomass of cyanobacteria. The data were analyzed using CCA. Higher mean phytoplankton biomass values (29.8 mm(3).L(-1)) occurred in the period of thermal stratification. A greater similarity in the phytoplankton communities also occurred in this period and was related to the development of cyanobacteria, mainly Cylindrospermopsis raciborskii (>3.9 mm(3).L(-1)). During the period of thermal destratification, this species co-dominated the environment with Planktothrix agardhii, Geitlerinema amphibium, Microcystis aeruginosa and Merismopedia tenuissima, as well as with diatoms and phytoflagellates. Environmental instability and competition among algae hindered the establishment of blooms more during the mixture period than during the stratification period. Thermal changes in the water column caused by climatologic events altered other physiochemical conditions of the water, leading to changes in the composition and biomass of the cyanobacterial community in tropical reservoirs.

Patterns of precipitation and soil moisture extremes in Texas, US: A complex network analysis

NASA Astrophysics Data System (ADS)

Sun, Alexander Y.; Xia, Youlong; Caldwell, Todd G.; Hao, Zengchao

2018-02-01

Understanding of the spatial and temporal dynamics of extreme precipitation not only improves prediction skills, but also helps to prioritize hazard mitigation efforts. This study seeks to enhance the understanding of spatiotemporal covariation patterns embedded in precipitation (P) and soil moisture (SM) by using an event-based, complex-network-theoretic approach. Events concurrences are quantified using a nonparametric event synchronization measure, and spatial patterns of hydroclimate variables are analyzed by using several network measures and a community detection algorithm. SM-P coupling is examined using a directional event coincidence analysis measure that takes the order of event occurrences into account. The complex network approach is demonstrated for Texas, US, a region possessing a rich set of hydroclimate features and is frequented by catastrophic flooding. Gridded daily observed P data and simulated SM data are used to create complex networks of P and SM extremes. The uncovered high degree centrality regions and community structures are qualitatively in agreement with the overall existing knowledge of hydroclimate extremes in the study region. Our analyses provide new visual insights on the propagation, connectivity, and synchronicity of P extremes, as well as the SM-P coupling, in this flood-prone region, and can be readily used as a basis for event-driven predictive analytics for other regions.

Dynamic graphs, community detection, and Riemannian geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakker, Craig; Halappanavar, Mahantesh; Visweswara Sathanur, Arun

A community is a subset of a wider network where the members of that subset are more strongly connected to each other than they are to the rest of the network. In this paper, we consider the problem of identifying and tracking communities in graphs that change over time {dynamic community detection} and present a framework based on Riemannian geometry to aid in this task. Our framework currently supports several important operations such as interpolating between and averaging over graph snapshots. We compare these Riemannian methods with entry-wise linear interpolation and that the Riemannian methods are generally better suited tomore » dynamic community detection. Next steps with the Riemannian framework include developing higher-order interpolation methods (e.g. the analogues of polynomial and spline interpolation) and a Riemannian least-squares regression method for working with noisy data.« less

Synchrony, compensatory dynamics, and the functional trait basis of phenological diversity in a tropical dry forest tree community: effects of rainfall seasonality

NASA Astrophysics Data System (ADS)

Lasky, Jesse R.; Uriarte, María; Muscarella, Robert

2016-11-01

Interspecific variation in phenology is a key axis of functional diversity, potentially mediating how communities respond to climate change. The diverse drivers of phenology act across multiple temporal scales. For example, abiotic constraints favor synchronous reproduction (positive covariance among species), while biotic interactions can favor synchrony or compensatory dynamics (negative covariance). We used wavelet analyses to examine phenology of community flower and seed production for 45 tree species across multiple temporal scales in a tropical dry forest in Puerto Rico with marked rainfall seasonality. We asked three questions: (1) do species exhibit synchronous or compensatory temporal dynamics in reproduction, (2) do interspecific differences in phenology reflect variable responses to rainfall, and (3) is interspecific variation in phenology and response to a major drought associated with functional traits that mediate responses to moisture? Community-level flowering was synchronized at seasonal scales (˜5-6 mo) and at short scales (˜1 mo, following rainfall). However, seed rain exhibited significant compensatory dynamics at intraseasonal scales (˜3 mo), suggesting interspecific variation in temporal niches. Species with large leaves (associated with sensitivity to water deficit) peaked in reproduction synchronously with the peak of seasonal rainfall (˜5 mo scale). By contrast, species with high wood specific gravity (associated with drought resistance) tended to flower in drier periods. Flowering of tall species and those with large leaves was most tightly linked to intraseasonal (˜2 mo scale) rainfall fluctuations. Although the 2015 drought dramatically reduced community-wide reproduction, functional traits were not associated with the magnitude of species-specific declines. Our results suggest opposing drivers of synchronous versus compensatory dynamics at different temporal scales. Phenology associations with functional traits indicated that distinct strategies for coping with seasonality underlie phenological diversity. Observed drought responses highlight the importance of non-linear community responses to climate. Community phenology exhibits scale-specific patterns highlighting the need for multi-scale approaches to community dynamics.

Isolation by Time During an Arctic Phytoplankton Spring Bloom.

PubMed

Tammilehto, Anna; Watts, Phillip C; Lundholm, Nina

2017-03-01

The arctic phytoplankton spring bloom, which is often diatom-dominated, is a key event that provides the high latitude communities with a fundamental flux of organic carbon. During a bloom, phytoplankton may increase its biomass by orders of magnitude within days. Yet, very little is known about phytoplankton bloom dynamics, including for example how blooming affects genetic composition and diversity of a population. Here, we quantified the genetic composition and temporal changes of the diatom Fragilariopsis cylindrus, which is one of the most important primary producers in the Arctic, during the spring bloom in western Greenland, using 13 novel microsatellite markers developed for this study. We found that genetic differentiation (quantified using sample-specific F ST ) decreased between time points as the bloom progressed, with the most drastic changes in F ST occurring at the start of the bloom; thus the genetic structure of the bloom is characterized by isolation by time. There was little temporal variation in genetic diversity throughout the bloom (mean H E  = 0.57), despite marked fluctuations in F. cylindrus cell concentrations and the temporal change in sample-specific F ST . On the basis of this novel pattern of genetic differentiation, we suggest that blooming behavior may promote genetic diversity of a phytoplankton population. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Fish Assemblage Response to a Small Dam Removal in the Eightmile River System, Connecticut, USA

NASA Astrophysics Data System (ADS)

Poulos, Helen M.; Miller, Kate E.; Kraczkowski, Michelle L.; Welchel, Adam W.; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Fish assemblage response to a small dam removal in the Eightmile River system, Connecticut, USA.

PubMed

Poulos, Helen M; Miller, Kate E; Kraczkowski, Michelle L; Welchel, Adam W; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Food Quality and Phytoplankton Community Composition in San Francisco Bay using Imaging Spectroscopy Data from the California HyspIRI Airborne Campaign

NASA Astrophysics Data System (ADS)

Palacios, S. L.; Peacock, M. B.; Golini, A. N.; Cloern, J. E.; Senn, D. B.; Guild, L. S.; Kudela, R. M.

2016-12-01

The San Francisco Bay (SFB) is the largest estuary on the west coast of the United States. It is an important transition zone between marine, freshwater, and inland terrestrial watersheds. The SFB is an important region for the cycling of nutrients and pollutants and it supports nurseries of ecologically and commercially important fisheries, including some threatened species. Phytoplankton community structure influences food web dynamics, and the taxonomy of the phytoplankton may be more important in determining primary "food quality" than environmental factors. As such, estimating food quality from phytoplankton community composition can be a robust tool to understand trophic transfer of energy. Recent work explores phytoplankton "food quality" in SFB through the use of microscopy and phytoplankton chemotaxonomy to evaluate how changes in phytoplankton composition may have influenced the recent trophic collapse of pelagic fishes in the northern part of the SFB. The objective of this study is to determine if the approach can also be applied to imaging spectroscopy data in order to quantify phytoplankton "food quality" from space. Imaging spectroscopy data of SFB from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) was collected during the Hyperspectral Infrared (HyspIRI) Airborne Campaign in California (2013 - 2015) and used in this study. Estimates of ocean chlorophyll and phytoplankton community structure were determined using standard ocean chlorophyll algorithms and the PHYtoplankton Detection with Optics (PHYDOTax) algorithms. These were validated using in situ observations of phytoplankton composition using microscopic cell counts and phytoplankton chemotaxonomy from the US Geological Survey's ship surveys of the SFB. The findings from this study may inform the use of future high spectral resolution satellite sensors with the spatial resolution appropriate for coastal systems (e.g., HyspIRI) to assess "food quality" from space.

Beyond Currents: The Next Phase in GOCE Oceanographic Research

NASA Astrophysics Data System (ADS)

Bingham, Rory J.; Haines, Keith; Hughes, Chris W.

2015-03-01

GOCE has mapped the surface currents of the world’s oceans in unprecedented detail. What is now required is a concerted effort by the oceanographic community to go beyond currents and exploit these measurements for societal benefit. The aim of this review paper is to explore the ways in which this may be achieved, particularly in relation to ocean modelling. With the final gravity models now released, we begin by reviewing the progress GOCE has in made in measuring the ocean’s mean dynamic topography and associated ocean currents. In the light of this progress, we then examine the important oceanographic questions and technical challenges of societal relevance that can potentially be addressed with the help of the observations GOCE has delivered and outline the benefits their solution could deliver. Benefits may either be direct, through, for example, improved ocean modelling and operational forecasting, or indirect through improved understanding of particular oceanographic processes, such as heat transport by the Atlantic meridional overturning circulation or sea level change. Next we consider the technical challenges that must be overcome in bringing GOCE to bear on these problems. In particular we examine how best to use GOCE error information, this being an especially uncertain, underdeveloped and challenging area of investigation, due largely to the fact that such information has not been previously available to the user community. Finally, we consider measures of success; that is, metrics that can be used to quantify any GOCE-enabled progress that the community makes towards answering these questions. Such metrics are essential for demonstrating progress. Ultimately, with this review paper, we aim to paint a road map that will act as an impetus to the oceanography community to exploit the yet untapped potential of GOCE for scientific understanding and societal benefit.

Soil microbial responses to climate warming in Northern Andean alpine ecosystems

NASA Astrophysics Data System (ADS)

Gallery, R. E.; Lasso, E.

2017-12-01

The historically cooler temperatures and waterlogged soils of tropical alpine grasslands (páramo) have resulted in low decomposition rates and a large buildup of organic matter, making páramo one of the most important carbon sinks in tropical biomes. The climatic factors that favored the carbon accumulation are changing, and as a result páramo could play a disproportionate role in driving climate feedbacks through increased carbon released from these large soil carbon stores. Open top chamber warming experiments were established in the Colombian Andes in 2016 to quantify the magnitude of climate change on carbon balance and identify microbial and plant traits that regulate these impacts. Two focal sites differ in mean annual temperature, precipitation, and plant community richness. Heterotrophic respiration (RH,) was measured from soil cores incubated at temperatures representing current and projected warming. The warming effect on RH was sensitive to soil moisture, which could reflect shifts in microbial community composition and/or extracellular enzyme production or efficiency as soils dry. Bacterial, archaeal, and fungal communities in ambient and warmed plots were measured through high-throughput amplicon sequencing of the 16S rRNA and ITS1 rRNA gene regions. Communities showed strong spatial structuring both within and among páramo, reflecting the topographic heterogeneity of these ecosystems. Significant differences in relative abundance of dominant microbial taxa between páramo could be largely explained by soil bulk density, water holding capacity, and non-vascular plant cover. Phototrophs common to anoxic soils (e.g., Rhodospirillaceae, Hyphomicrobiaceae) were abundant. Taxa within Euryarchaeota were recovered, suggesting methanogenesis potential. Exploration of the magnitude and temperature sensitivity of methane flux is needed in these seasonally anoxic soils whose dynamics could have significant implications for the global climate system.

Global changes alter soil fungal communities and alter rates of organic matter decomposition

NASA Astrophysics Data System (ADS)

Moore, J.; Frey, S. D.

2016-12-01

Global changes - such as warming, more frequent and severe droughts, increasing atmospheric CO2, and increasing nitrogen (N) deposition rates - are altering ecosystem processes. The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of detrital organisms, namely soil fungi, and yet their sensitivity to global changes remains unresolved. We present results from a meta-analysis of 200+ studies spanning manipulative and observational field experiments to quantify fungal responses to global change and expected consequences for ecosystem C dynamics. Warming altered the functional soil microbial community by reducing the ratio of fungi to bacteria (f:b) total fungal biomass. Additionally, warming reduced lignolytic enzyme activity generally by one-third. Simulated N deposition affected f:b differently than warming, but the effect on fungal biomass and activity was similar. The effect of N-enrichment on f:b was contingent upon ecosystem type; f:b increased in alpine meadows and heathlands but decreased in temperate forests following N-enrichment. Across ecosystems, fungal biomass marginally declined by 8% in N-enriched soils. In general, N-enrichment reduced fungal lignolytic enzyme activity, which could explain why soil C accumulates in some ecosystems following warming and N-enrichment. Several global change experiments have reported the surprising result that soil C builds up following increases in temperature and N deposition rates. While site-specific studies have examined the role of soil fungi in ecosystem responses to global change, we present the first meta-analysis documenting general patterns of global change impacts on soil fungal communities, biomass, and activity. In sum, we provide evidence that soil microbial community shifts and activity plays a large part in ecosystem responses to global changes, and have the potential to alter the magnitude of the C-climate feedback.

Propagation of a finite-amplitude elastic pulse in a bar of Berea sandstone: A detailed look at the mechanisms of classical nonlinearity, hysteresis, and nonequilibrium dynamics: Nonlinear propagation of elastic pulse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remillieux, Marcel C.; Ulrich, T. J.; Goodman, Harvey E.

Here, we study the propagation of a finite-amplitude elastic pulse in a long thin bar of Berea sandstone. In previous work, this type of experiment has been conducted to quantify classical nonlinearity, based on the amplitude growth of the second harmonic as a function of propagation distance. To greatly expand on that early work, a non-contact scanning 3D laser Doppler vibrometer was used to track the evolution of the axial component of the particle velocity over the entire surface of the bar as functions of the propagation distance and source amplitude. With these new measurements, the combined effects of classicalmore » nonlinearity, hysteresis, and nonequilibrium dynamics have all been measured simultaneously. We then show that the numerical resolution of the 1D wave equation with terms for classical nonlinearity and attenuation accurately captures the spectral features of the waves up to the second harmonic. But, for higher harmonics the spectral content is shown to be strongly influenced by hysteresis. This work also shows data which not only quantifies classical nonlinearity but also the nonequilibrium dynamics based on the relative change in the arrival time of the elastic pulse as a function of strain and distance from the source. Finally, a comparison is made to a resonant bar measurement, a reference experiment used to quantify nonequilibrium dynamics, based on the relative shift of the resonance frequencies as a function of the maximum dynamic strain in the sample.« less

The "Chaos Theory" and nonlinear dynamics in heart rate variability analysis: does it work in short-time series in patients with coronary heart disease?

PubMed

Krstacic, Goran; Krstacic, Antonija; Smalcelj, Anton; Milicic, Davor; Jembrek-Gostovic, Mirjana

2007-04-01

Dynamic analysis techniques may quantify abnormalities in heart rate variability (HRV) based on nonlinear and fractal analysis (chaos theory). The article emphasizes clinical and prognostic significance of dynamic changes in short-time series applied on patients with coronary heart disease (CHD) during the exercise electrocardiograph (ECG) test. The subjects were included in the series after complete cardiovascular diagnostic data. Series of R-R and ST-T intervals were obtained from exercise ECG data after sampling digitally. The range rescaled analysis method determined the fractal dimension of the intervals. To quantify fractal long-range correlation's properties of heart rate variability, the detrended fluctuation analysis technique was used. Approximate entropy (ApEn) was applied to quantify the regularity and complexity of time series, as well as unpredictability of fluctuations in time series. It was found that the short-term fractal scaling exponent (alpha(1)) is significantly lower in patients with CHD (0.93 +/- 0.07 vs 1.09 +/- 0.04; P < 0.001). The patients with CHD had higher fractal dimension in each exercise test program separately, as well as in exercise program at all. ApEn was significant lower in CHD group in both RR and ST-T ECG intervals (P < 0.001). The nonlinear dynamic methods could have clinical and prognostic applicability also in short-time ECG series. Dynamic analysis based on chaos theory during the exercise ECG test point out the multifractal time series in CHD patients who loss normal fractal characteristics and regularity in HRV. Nonlinear analysis technique may complement traditional ECG analysis.

Propagation of a finite-amplitude elastic pulse in a bar of Berea sandstone: A detailed look at the mechanisms of classical nonlinearity, hysteresis, and nonequilibrium dynamics: Nonlinear propagation of elastic pulse

DOE PAGES

Remillieux, Marcel C.; Ulrich, T. J.; Goodman, Harvey E.; ...

2017-10-18

Here, we study the propagation of a finite-amplitude elastic pulse in a long thin bar of Berea sandstone. In previous work, this type of experiment has been conducted to quantify classical nonlinearity, based on the amplitude growth of the second harmonic as a function of propagation distance. To greatly expand on that early work, a non-contact scanning 3D laser Doppler vibrometer was used to track the evolution of the axial component of the particle velocity over the entire surface of the bar as functions of the propagation distance and source amplitude. With these new measurements, the combined effects of classicalmore » nonlinearity, hysteresis, and nonequilibrium dynamics have all been measured simultaneously. We then show that the numerical resolution of the 1D wave equation with terms for classical nonlinearity and attenuation accurately captures the spectral features of the waves up to the second harmonic. But, for higher harmonics the spectral content is shown to be strongly influenced by hysteresis. This work also shows data which not only quantifies classical nonlinearity but also the nonequilibrium dynamics based on the relative change in the arrival time of the elastic pulse as a function of strain and distance from the source. Finally, a comparison is made to a resonant bar measurement, a reference experiment used to quantify nonequilibrium dynamics, based on the relative shift of the resonance frequencies as a function of the maximum dynamic strain in the sample.« less

Short‐term time step convergence in a climate model

PubMed Central

Rasch, Philip J.; Taylor, Mark A.; Jablonowski, Christiane

2015-01-01

Abstract This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities. PMID:27660669

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms.

PubMed

Kadowaki, Kohmei; Inouye, Brian D; Miller, Thomas E

2012-01-01

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly. We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition. A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the "ingredients" (species) in ecological communities but their "recipes" as well.

Dynamics of microbial communities in untreated and autoclaved food waste anaerobic digesters.

PubMed

Blasco, Lucia; Kahala, Minna; Tampio, Elina; Ervasti, Satu; Paavola, Teija; Rintala, Jukka; Joutsjoki, Vesa

2014-10-01

This study describes the microbial community richness and dynamics of two semi-continuously stirred biogas reactors during a time-course study of 120 days. The reactors were fed with untreated and autoclaved (160 °C, 6.2 bar) food waste. The microbial community was analysed using a bacteria- and archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism (T-RFLP) approach. Compared with the archaeal community, the structures and functions of the bacterial community were found to be more complex and diverse. With the principal coordinates analysis it was possible to separate both microbial communities with 75 and 50% difference for bacteria and archaea, respectively, in the two reactors fed with the same waste but with different pretreatment. Despite the use of the same feeding material, anaerobic reactors showed a distinct community profile which could explain the differences in methane yield (2-17%). The community composition was highly dynamic for bacteria and archaea during the entire studied period. This study illustrates that microbial communities are dependent on feeding material and that correlations among specific bacterial and archaeal T-RFs can be established. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dynamic social community detection and its applications.

PubMed

Nguyen, Nam P; Dinh, Thang N; Shen, Yilin; Thai, My T

2014-01-01

Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods.

Dynamic Social Community Detection and Its Applications

PubMed Central

Nguyen, Nam P.; Dinh, Thang N.; Shen, Yilin; Thai, My T.

2014-01-01

Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods. PMID:24722164

Using Eddy Covariance to Quantify Methane Emissions from a Dynamic Heterogeneous Area

EPA Science Inventory

Measuring emissions of CH4, CO2, H2O, and other greenhouse gases from heterogeneous land area sources is challenging. Dynamic changes within the source area as well as changing environmental conditions make individual point measurements less informative than desired, especially w...

Using Eddy Covariance to Quantify Methane Emission from a Dynamic Heterogeneous Area

EPA Science Inventory

Measuring emissions of CH4, CO2, H2O, and other greenhouse gases from heterogeneous land area sources is challenging. Dynamic changes within the source area as well as changing environmental conditions make individual point measurements less informative than desired, especially w...

Geographic variation in mycangial communities of Xyleborus glabratus

Treesearch

Alina S. Campbell; Randy C. Ploetz; Tyler J. Dreaden; Paul E. Kendra; Wayne S. Montgomery

2016-01-01

Factors that influence fungal communities in ambrosia beetle mycangia are poorly understood. The beetle that is responsible for spreading laurel wilt in SE USA, Xyleborus glabratrus, was examined at three sites along a 500 km N-S transect in Florida, each populated by host trees in the Lauraceae. Fungal phenotypes were quantified in mycangia of individual females that...